diff -ruN ccp4srs-old/Makefile.am ccp4srs/Makefile.am
--- ccp4srs-old/Makefile.am	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/Makefile.am	2014-09-09 21:34:12.000000000 -0700
@@ -13,7 +13,7 @@
 	ccp4srs/ccp4srs_chicenter.cpp  ccp4srs/ccp4srs_types.cpp   \
 	ccp4srs/ccp4srs_container.cpp  ccp4srs/memio_.cpp          \
 	ccp4srs/ccp4srs_entry.cpp      ccp4srs/mpfile_.cpp         \
-	ccp4srs/ccp4srs_index.cpp
+	ccp4srs/ccp4srs_index.cpp      ccp4srs/ccp4srs_smiles.cpp
 
 pkginclude_HEADERS = \
 	ccp4srs/ccp4srs_angle.h        ccp4srs/ccp4srs_index.h    \
@@ -24,15 +24,16 @@
 	ccp4srs/ccp4srs_chicenter.h    ccp4srs/ccp4srs_tree.h     \
 	ccp4srs/ccp4srs_container.h    ccp4srs/ccp4srs_types.h    \
 	ccp4srs/ccp4srs_defs.h         ccp4srs/memio_.h           \
-	ccp4srs/ccp4srs_entry.h        ccp4srs/mpfile_.h
+	ccp4srs/ccp4srs_entry.h        ccp4srs/mpfile_.h          \
+        ccp4srs/ccp4srs_smiles.h
 
-ccp4srs_libccp4srs_la_LIBADD = -lmmdb -lz
+ccp4srs_libccp4srs_la_LIBADD = -lmmdb2 -lz
 ccp4srs_libccp4srs_la_LDFLAGS = -no-undefined
 
 srsgen_SOURCES = srsgen.cpp
-srsgen_LDADD = ccp4srs/libccp4srs.la -lmmdb
+srsgen_LDADD = ccp4srs/libccp4srs.la -lmmdb2
 pdb2to3_SOURCES = srsrem.cpp
-pdb2to3_LDADD = ccp4srs/libccp4srs.la -lmmdb
+pdb2to3_LDADD = ccp4srs/libccp4srs.la -lmmdb2
 srsview_SOURCES = srsview.cpp
-srsview_LDADD = ccp4srs/libccp4srs.la -lmmdb
+srsview_LDADD = ccp4srs/libccp4srs.la -lmmdb2
 
diff -ruN ccp4srs-old/Makefile.in ccp4srs/Makefile.in
--- ccp4srs-old/Makefile.in	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/Makefile.in	2014-09-09 21:34:12.000000000 -0700
@@ -1,9 +1,8 @@
-# Makefile.in generated by automake 1.11.3 from Makefile.am.
+# Makefile.in generated by automake 1.13.4 from Makefile.am.
 # @configure_input@
 
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+
 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
@@ -18,6 +17,51 @@
 
 
 VPATH = @srcdir@
+am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__make_running_with_option = \
+  case $${target_option-} in \
+      ?) ;; \
+      *) echo "am__make_running_with_option: internal error: invalid" \
+              "target option '$${target_option-}' specified" >&2; \
+         exit 1;; \
+  esac; \
+  has_opt=no; \
+  sane_makeflags=$$MAKEFLAGS; \
+  if $(am__is_gnu_make); then \
+    sane_makeflags=$$MFLAGS; \
+  else \
+    case $$MAKEFLAGS in \
+      *\\[\ \	]*) \
+        bs=\\; \
+        sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
+          | sed "s/$$bs$$bs[$$bs $$bs	]*//g"`;; \
+    esac; \
+  fi; \
+  skip_next=no; \
+  strip_trailopt () \
+  { \
+    flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
+  }; \
+  for flg in $$sane_makeflags; do \
+    test $$skip_next = yes && { skip_next=no; continue; }; \
+    case $$flg in \
+      *=*|--*) continue;; \
+        -*I) strip_trailopt 'I'; skip_next=yes;; \
+      -*I?*) strip_trailopt 'I';; \
+        -*O) strip_trailopt 'O'; skip_next=yes;; \
+      -*O?*) strip_trailopt 'O';; \
+        -*l) strip_trailopt 'l'; skip_next=yes;; \
+      -*l?*) strip_trailopt 'l';; \
+      -[dEDm]) skip_next=yes;; \
+      -[JT]) skip_next=yes;; \
+    esac; \
+    case $$flg in \
+      *$$target_option*) has_opt=yes; break;; \
+    esac; \
+  done; \
+  test $$has_opt = yes
+am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
 pkgdatadir = $(datadir)/@PACKAGE@
 pkgincludedir = $(includedir)/@PACKAGE@
 pkglibdir = $(libdir)/@PACKAGE@
@@ -39,11 +83,18 @@
 bin_PROGRAMS = pdb2to3$(EXEEXT)
 noinst_PROGRAMS = srsgen$(EXEEXT) srsview$(EXEEXT)
 subdir = .
-DIST_COMMON = $(am__configure_deps) $(pkginclude_HEADERS) \
-	$(srcdir)/Makefile.am $(srcdir)/Makefile.in \
-	$(srcdir)/config.h.in $(top_srcdir)/configure \
-	build-aux/config.guess build-aux/config.sub build-aux/depcomp \
-	build-aux/install-sh build-aux/ltmain.sh build-aux/missing
+DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
+	$(top_srcdir)/configure $(am__configure_deps) \
+	$(srcdir)/config.h.in $(top_srcdir)/build-aux/depcomp \
+	$(pkginclude_HEADERS) build-aux/ar-lib build-aux/config.guess \
+	build-aux/config.sub build-aux/depcomp build-aux/install-sh \
+	build-aux/missing build-aux/ltmain.sh \
+	$(top_srcdir)/build-aux/ar-lib \
+	$(top_srcdir)/build-aux/config.guess \
+	$(top_srcdir)/build-aux/config.sub \
+	$(top_srcdir)/build-aux/install-sh \
+	$(top_srcdir)/build-aux/ltmain.sh \
+	$(top_srcdir)/build-aux/missing
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
 am__aclocal_m4_deps = $(top_srcdir)/m4/libtool.m4 \
 	$(top_srcdir)/m4/ltoptions.m4 $(top_srcdir)/m4/ltsugar.m4 \
@@ -96,12 +147,14 @@
 	ccp4srs/ccp4srs_torsion.lo ccp4srs/ccp4srs_chem.lo \
 	ccp4srs/ccp4srs_tree.lo ccp4srs/ccp4srs_chicenter.lo \
 	ccp4srs/ccp4srs_types.lo ccp4srs/ccp4srs_container.lo \
+        ccp4srs/ccp4srs_smiles.lo \
 	ccp4srs/memio_.lo ccp4srs/ccp4srs_entry.lo ccp4srs/mpfile_.lo \
 	ccp4srs/ccp4srs_index.lo
 ccp4srs_libccp4srs_la_OBJECTS = $(am_ccp4srs_libccp4srs_la_OBJECTS)
 AM_V_lt = $(am__v_lt_@AM_V@)
 am__v_lt_ = $(am__v_lt_@AM_DEFAULT_V@)
 am__v_lt_0 = --silent
+am__v_lt_1 = 
 ccp4srs_libccp4srs_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CXX \
 	$(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CXXLD) \
 	$(AM_CXXFLAGS) $(CXXFLAGS) $(ccp4srs_libccp4srs_la_LDFLAGS) \
@@ -116,6 +169,18 @@
 am_srsview_OBJECTS = srsview.$(OBJEXT)
 srsview_OBJECTS = $(am_srsview_OBJECTS)
 srsview_DEPENDENCIES = ccp4srs/libccp4srs.la
+AM_V_P = $(am__v_P_@AM_V@)
+am__v_P_ = $(am__v_P_@AM_DEFAULT_V@)
+am__v_P_0 = false
+am__v_P_1 = :
+AM_V_GEN = $(am__v_GEN_@AM_V@)
+am__v_GEN_ = $(am__v_GEN_@AM_DEFAULT_V@)
+am__v_GEN_0 = @echo "  GEN     " $@;
+am__v_GEN_1 = 
+AM_V_at = $(am__v_at_@AM_V@)
+am__v_at_ = $(am__v_at_@AM_DEFAULT_V@)
+am__v_at_0 = @
+am__v_at_1 = 
 DEFAULT_INCLUDES = -I.@am__isrc@
 depcomp = $(SHELL) $(top_srcdir)/build-aux/depcomp
 am__depfiles_maybe = depfiles
@@ -128,27 +193,48 @@
 	$(AM_CXXFLAGS) $(CXXFLAGS)
 AM_V_CXX = $(am__v_CXX_@AM_V@)
 am__v_CXX_ = $(am__v_CXX_@AM_DEFAULT_V@)
-am__v_CXX_0 = @echo "  CXX   " $@;
-AM_V_at = $(am__v_at_@AM_V@)
-am__v_at_ = $(am__v_at_@AM_DEFAULT_V@)
-am__v_at_0 = @
+am__v_CXX_0 = @echo "  CXX     " $@;
+am__v_CXX_1 = 
 CXXLD = $(CXX)
 CXXLINK = $(LIBTOOL) $(AM_V_lt) --tag=CXX $(AM_LIBTOOLFLAGS) \
 	$(LIBTOOLFLAGS) --mode=link $(CXXLD) $(AM_CXXFLAGS) \
 	$(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
 AM_V_CXXLD = $(am__v_CXXLD_@AM_V@)
 am__v_CXXLD_ = $(am__v_CXXLD_@AM_DEFAULT_V@)
-am__v_CXXLD_0 = @echo "  CXXLD " $@;
-AM_V_GEN = $(am__v_GEN_@AM_V@)
-am__v_GEN_ = $(am__v_GEN_@AM_DEFAULT_V@)
-am__v_GEN_0 = @echo "  GEN   " $@;
+am__v_CXXLD_0 = @echo "  CXXLD   " $@;
+am__v_CXXLD_1 = 
 SOURCES = $(ccp4srs_libccp4srs_la_SOURCES) $(pdb2to3_SOURCES) \
 	$(srsgen_SOURCES) $(srsview_SOURCES)
 DIST_SOURCES = $(ccp4srs_libccp4srs_la_SOURCES) $(pdb2to3_SOURCES) \
 	$(srsgen_SOURCES) $(srsview_SOURCES)
+am__can_run_installinfo = \
+  case $$AM_UPDATE_INFO_DIR in \
+    n|no|NO) false;; \
+    *) (install-info --version) >/dev/null 2>&1;; \
+  esac
 HEADERS = $(pkginclude_HEADERS)
+am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) \
+	$(LISP)config.h.in
+# Read a list of newline-separated strings from the standard input,
+# and print each of them once, without duplicates.  Input order is
+# *not* preserved.
+am__uniquify_input = $(AWK) '\
+  BEGIN { nonempty = 0; } \
+  { items[$$0] = 1; nonempty = 1; } \
+  END { if (nonempty) { for (i in items) print i; }; } \
+'
+# Make sure the list of sources is unique.  This is necessary because,
+# e.g., the same source file might be shared among _SOURCES variables
+# for different programs/libraries.
+am__define_uniq_tagged_files = \
+  list='$(am__tagged_files)'; \
+  unique=`for i in $$list; do \
+    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+  done | $(am__uniquify_input)`
 ETAGS = etags
 CTAGS = ctags
+CSCOPE = cscope
+AM_RECURSIVE_TARGETS = cscope
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 distdir = $(PACKAGE)-$(VERSION)
 top_distdir = $(distdir)
@@ -158,8 +244,10 @@
       && rm -rf "$(distdir)" \
       || { sleep 5 && rm -rf "$(distdir)"; }; \
   else :; fi
+am__post_remove_distdir = $(am__remove_distdir)
 DIST_ARCHIVES = $(distdir).tar.gz
 GZIP_ENV = --best
+DIST_TARGETS = dist-gzip
 distuninstallcheck_listfiles = find . -type f -print
 am__distuninstallcheck_listfiles = $(distuninstallcheck_listfiles) \
   | sed 's|^\./|$(prefix)/|' | grep -v '$(infodir)/dir$$'
@@ -296,7 +384,7 @@
 	ccp4srs/ccp4srs_chicenter.cpp  ccp4srs/ccp4srs_types.cpp   \
 	ccp4srs/ccp4srs_container.cpp  ccp4srs/memio_.cpp          \
 	ccp4srs/ccp4srs_entry.cpp      ccp4srs/mpfile_.cpp         \
-	ccp4srs/ccp4srs_index.cpp
+	ccp4srs/ccp4srs_index.cpp      ccp4srs/ccp4srs_smiles.cpp
 
 pkginclude_HEADERS = \
 	ccp4srs/ccp4srs_angle.h        ccp4srs/ccp4srs_index.h    \
@@ -307,16 +395,17 @@
 	ccp4srs/ccp4srs_chicenter.h    ccp4srs/ccp4srs_tree.h     \
 	ccp4srs/ccp4srs_container.h    ccp4srs/ccp4srs_types.h    \
 	ccp4srs/ccp4srs_defs.h         ccp4srs/memio_.h           \
-	ccp4srs/ccp4srs_entry.h        ccp4srs/mpfile_.h
+	ccp4srs/ccp4srs_entry.h        ccp4srs/mpfile_.h          \
+        ccp4srs/ccp4srs_smiles.h
 
-ccp4srs_libccp4srs_la_LIBADD = -lmmdb -lz
+ccp4srs_libccp4srs_la_LIBADD = -lmmdb2 -lz
 ccp4srs_libccp4srs_la_LDFLAGS = -no-undefined
 srsgen_SOURCES = srsgen.cpp
-srsgen_LDADD = ccp4srs/libccp4srs.la -lmmdb
+srsgen_LDADD = ccp4srs/libccp4srs.la -lmmdb2
 pdb2to3_SOURCES = srsrem.cpp
-pdb2to3_LDADD = ccp4srs/libccp4srs.la -lmmdb
+pdb2to3_LDADD = ccp4srs/libccp4srs.la -lmmdb2
 srsview_SOURCES = srsview.cpp
-srsview_LDADD = ccp4srs/libccp4srs.la -lmmdb
+srsview_LDADD = ccp4srs/libccp4srs.la -lmmdb2
 all: config.h
 	$(MAKE) $(AM_MAKEFLAGS) all-am
 
@@ -371,9 +460,9 @@
 
 distclean-hdr:
 	-rm -f config.h stamp-h1
+
 install-libLTLIBRARIES: $(lib_LTLIBRARIES)
 	@$(NORMAL_INSTALL)
-	test -z "$(libdir)" || $(MKDIR_P) "$(DESTDIR)$(libdir)"
 	@list='$(lib_LTLIBRARIES)'; test -n "$(libdir)" || list=; \
 	list2=; for p in $$list; do \
 	  if test -f $$p; then \
@@ -381,6 +470,8 @@
 	  else :; fi; \
 	done; \
 	test -z "$$list2" || { \
+	  echo " $(MKDIR_P) '$(DESTDIR)$(libdir)'"; \
+	  $(MKDIR_P) "$(DESTDIR)$(libdir)" || exit 1; \
 	  echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 '$(DESTDIR)$(libdir)'"; \
 	  $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 "$(DESTDIR)$(libdir)"; \
 	}
@@ -396,12 +487,14 @@
 
 clean-libLTLIBRARIES:
 	-test -z "$(lib_LTLIBRARIES)" || rm -f $(lib_LTLIBRARIES)
-	@list='$(lib_LTLIBRARIES)'; for p in $$list; do \
-	  dir="`echo $$p | sed -e 's|/[^/]*$$||'`"; \
-	  test "$$dir" != "$$p" || dir=.; \
-	  echo "rm -f \"$${dir}/so_locations\""; \
-	  rm -f "$${dir}/so_locations"; \
-	done
+	@list='$(lib_LTLIBRARIES)'; \
+	locs=`for p in $$list; do echo $$p; done | \
+	      sed 's|^[^/]*$$|.|; s|/[^/]*$$||; s|$$|/so_locations|' | \
+	      sort -u`; \
+	test -z "$$locs" || { \
+	  echo rm -f $${locs}; \
+	  rm -f $${locs}; \
+	}
 ccp4srs/$(am__dirstamp):
 	@$(MKDIR_P) ccp4srs
 	@: > ccp4srs/$(am__dirstamp)
@@ -442,18 +535,26 @@
 	ccp4srs/$(DEPDIR)/$(am__dirstamp)
 ccp4srs/ccp4srs_index.lo: ccp4srs/$(am__dirstamp) \
 	ccp4srs/$(DEPDIR)/$(am__dirstamp)
+ccp4srs/ccp4srs_smiles.lo: ccp4srs/$(am__dirstamp) \
+        ccp4srs/$(DEPDIR)/$(am__dirstamp)
+
 ccp4srs/libccp4srs.la: $(ccp4srs_libccp4srs_la_OBJECTS) $(ccp4srs_libccp4srs_la_DEPENDENCIES) $(EXTRA_ccp4srs_libccp4srs_la_DEPENDENCIES) ccp4srs/$(am__dirstamp)
 	$(AM_V_CXXLD)$(ccp4srs_libccp4srs_la_LINK) -rpath $(libdir) $(ccp4srs_libccp4srs_la_OBJECTS) $(ccp4srs_libccp4srs_la_LIBADD) $(LIBS)
 install-binPROGRAMS: $(bin_PROGRAMS)
 	@$(NORMAL_INSTALL)
-	test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
 	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
+	if test -n "$$list"; then \
+	  echo " $(MKDIR_P) '$(DESTDIR)$(bindir)'"; \
+	  $(MKDIR_P) "$(DESTDIR)$(bindir)" || exit 1; \
+	fi; \
 	for p in $$list; do echo "$$p $$p"; done | \
 	sed 's/$(EXEEXT)$$//' | \
-	while read p p1; do if test -f $$p || test -f $$p1; \
-	  then echo "$$p"; echo "$$p"; else :; fi; \
+	while read p p1; do if test -f $$p \
+	 || test -f $$p1 \
+	  ; then echo "$$p"; echo "$$p"; else :; fi; \
 	done | \
-	sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+	sed -e 'p;s,.*/,,;n;h' \
+	    -e 's|.*|.|' \
 	    -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
 	sed 'N;N;N;s,\n, ,g' | \
 	$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
@@ -474,7 +575,8 @@
 	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
 	files=`for p in $$list; do echo "$$p"; done | \
 	  sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
-	      -e 's/$$/$(EXEEXT)/' `; \
+	      -e 's/$$/$(EXEEXT)/' \
+	`; \
 	test -n "$$list" || exit 0; \
 	echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
 	cd "$(DESTDIR)$(bindir)" && rm -f $$files
@@ -496,52 +598,23 @@
 	list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
 	echo " rm -f" $$list; \
 	rm -f $$list
+
 pdb2to3$(EXEEXT): $(pdb2to3_OBJECTS) $(pdb2to3_DEPENDENCIES) $(EXTRA_pdb2to3_DEPENDENCIES) 
 	@rm -f pdb2to3$(EXEEXT)
 	$(AM_V_CXXLD)$(CXXLINK) $(pdb2to3_OBJECTS) $(pdb2to3_LDADD) $(LIBS)
+
 srsgen$(EXEEXT): $(srsgen_OBJECTS) $(srsgen_DEPENDENCIES) $(EXTRA_srsgen_DEPENDENCIES) 
 	@rm -f srsgen$(EXEEXT)
 	$(AM_V_CXXLD)$(CXXLINK) $(srsgen_OBJECTS) $(srsgen_LDADD) $(LIBS)
+
 srsview$(EXEEXT): $(srsview_OBJECTS) $(srsview_DEPENDENCIES) $(EXTRA_srsview_DEPENDENCIES) 
 	@rm -f srsview$(EXEEXT)
 	$(AM_V_CXXLD)$(CXXLINK) $(srsview_OBJECTS) $(srsview_LDADD) $(LIBS)
 
 mostlyclean-compile:
 	-rm -f *.$(OBJEXT)
-	-rm -f ccp4srs/ccp4srs_angle.$(OBJEXT)
-	-rm -f ccp4srs/ccp4srs_angle.lo
-	-rm -f ccp4srs/ccp4srs_atom.$(OBJEXT)
-	-rm -f ccp4srs/ccp4srs_atom.lo
-	-rm -f ccp4srs/ccp4srs_base.$(OBJEXT)
-	-rm -f ccp4srs/ccp4srs_base.lo
-	-rm -f ccp4srs/ccp4srs_bond.$(OBJEXT)
-	-rm -f ccp4srs/ccp4srs_bond.lo
-	-rm -f ccp4srs/ccp4srs_chem.$(OBJEXT)
-	-rm -f ccp4srs/ccp4srs_chem.lo
-	-rm -f ccp4srs/ccp4srs_chicenter.$(OBJEXT)
-	-rm -f ccp4srs/ccp4srs_chicenter.lo
-	-rm -f ccp4srs/ccp4srs_container.$(OBJEXT)
-	-rm -f ccp4srs/ccp4srs_container.lo
-	-rm -f ccp4srs/ccp4srs_entry.$(OBJEXT)
-	-rm -f ccp4srs/ccp4srs_entry.lo
-	-rm -f ccp4srs/ccp4srs_index.$(OBJEXT)
-	-rm -f ccp4srs/ccp4srs_index.lo
-	-rm -f ccp4srs/ccp4srs_manager.$(OBJEXT)
-	-rm -f ccp4srs/ccp4srs_manager.lo
-	-rm -f ccp4srs/ccp4srs_monomer.$(OBJEXT)
-	-rm -f ccp4srs/ccp4srs_monomer.lo
-	-rm -f ccp4srs/ccp4srs_plane.$(OBJEXT)
-	-rm -f ccp4srs/ccp4srs_plane.lo
-	-rm -f ccp4srs/ccp4srs_torsion.$(OBJEXT)
-	-rm -f ccp4srs/ccp4srs_torsion.lo
-	-rm -f ccp4srs/ccp4srs_tree.$(OBJEXT)
-	-rm -f ccp4srs/ccp4srs_tree.lo
-	-rm -f ccp4srs/ccp4srs_types.$(OBJEXT)
-	-rm -f ccp4srs/ccp4srs_types.lo
-	-rm -f ccp4srs/memio_.$(OBJEXT)
-	-rm -f ccp4srs/memio_.lo
-	-rm -f ccp4srs/mpfile_.$(OBJEXT)
-	-rm -f ccp4srs/mpfile_.lo
+	-rm -f ccp4srs/*.$(OBJEXT)
+	-rm -f ccp4srs/*.lo
 
 distclean-compile:
 	-rm -f *.tab.c
@@ -558,6 +631,7 @@
 @AMDEP_TRUE@@am__include@ @am__quote@ccp4srs/$(DEPDIR)/ccp4srs_container.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@ccp4srs/$(DEPDIR)/ccp4srs_entry.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@ccp4srs/$(DEPDIR)/ccp4srs_index.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@ccp4srs/$(DEPDIR)/ccp4srs_smiles.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@ccp4srs/$(DEPDIR)/ccp4srs_manager.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@ccp4srs/$(DEPDIR)/ccp4srs_monomer.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@ccp4srs/$(DEPDIR)/ccp4srs_plane.Plo@am__quote@
@@ -602,8 +676,11 @@
 	-rm -f libtool config.lt
 install-pkgincludeHEADERS: $(pkginclude_HEADERS)
 	@$(NORMAL_INSTALL)
-	test -z "$(pkgincludedir)" || $(MKDIR_P) "$(DESTDIR)$(pkgincludedir)"
 	@list='$(pkginclude_HEADERS)'; test -n "$(pkgincludedir)" || list=; \
+	if test -n "$$list"; then \
+	  echo " $(MKDIR_P) '$(DESTDIR)$(pkgincludedir)'"; \
+	  $(MKDIR_P) "$(DESTDIR)$(pkgincludedir)" || exit 1; \
+	fi; \
 	for p in $$list; do \
 	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
 	  echo "$$d$$p"; \
@@ -619,26 +696,15 @@
 	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
 	dir='$(DESTDIR)$(pkgincludedir)'; $(am__uninstall_files_from_dir)
 
-ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-	list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
-	mkid -fID $$unique
-tags: TAGS
+ID: $(am__tagged_files)
+	$(am__define_uniq_tagged_files); mkid -fID $$unique
+tags: tags-am
+TAGS: tags
 
-TAGS:  $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \
-		$(TAGS_FILES) $(LISP)
+tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
 	set x; \
 	here=`pwd`; \
-	list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	$(am__define_uniq_tagged_files); \
 	shift; \
 	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
 	  test -n "$$unique" || unique=$$empty_fix; \
@@ -650,15 +716,11 @@
 	      $$unique; \
 	  fi; \
 	fi
-ctags: CTAGS
-CTAGS:  $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \
-		$(TAGS_FILES) $(LISP)
-	list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \
-	unique=`for i in $$list; do \
-	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-	  done | \
-	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+ctags: ctags-am
+
+CTAGS: ctags
+ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+	$(am__define_uniq_tagged_files); \
 	test -z "$(CTAGS_ARGS)$$unique" \
 	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
 	     $$unique
@@ -667,9 +729,31 @@
 	here=`$(am__cd) $(top_builddir) && pwd` \
 	  && $(am__cd) $(top_srcdir) \
 	  && gtags -i $(GTAGS_ARGS) "$$here"
+cscope: cscope.files
+	test ! -s cscope.files \
+	  || $(CSCOPE) -b -q $(AM_CSCOPEFLAGS) $(CSCOPEFLAGS) -i cscope.files $(CSCOPE_ARGS)
+clean-cscope:
+	-rm -f cscope.files
+cscope.files: clean-cscope cscopelist
+cscopelist: cscopelist-am
+
+cscopelist-am: $(am__tagged_files)
+	list='$(am__tagged_files)'; \
+	case "$(srcdir)" in \
+	  [\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
+	  *) sdir=$(subdir)/$(srcdir) ;; \
+	esac; \
+	for i in $$list; do \
+	  if test -f "$$i"; then \
+	    echo "$(subdir)/$$i"; \
+	  else \
+	    echo "$$sdir/$$i"; \
+	  fi; \
+	done >> $(top_builddir)/cscope.files
 
 distclean-tags:
 	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
+	-rm -f cscope.out cscope.in.out cscope.po.out cscope.files
 
 distdir: $(DISTFILES)
 	$(am__remove_distdir)
@@ -712,40 +796,36 @@
 	|| chmod -R a+r "$(distdir)"
 dist-gzip: distdir
 	tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
-	$(am__remove_distdir)
+	$(am__post_remove_distdir)
 
 dist-bzip2: distdir
 	tardir=$(distdir) && $(am__tar) | BZIP2=$${BZIP2--9} bzip2 -c >$(distdir).tar.bz2
-	$(am__remove_distdir)
+	$(am__post_remove_distdir)
 
 dist-lzip: distdir
 	tardir=$(distdir) && $(am__tar) | lzip -c $${LZIP_OPT--9} >$(distdir).tar.lz
-	$(am__remove_distdir)
-
-dist-lzma: distdir
-	tardir=$(distdir) && $(am__tar) | lzma -9 -c >$(distdir).tar.lzma
-	$(am__remove_distdir)
+	$(am__post_remove_distdir)
 
 dist-xz: distdir
 	tardir=$(distdir) && $(am__tar) | XZ_OPT=$${XZ_OPT--e} xz -c >$(distdir).tar.xz
-	$(am__remove_distdir)
+	$(am__post_remove_distdir)
 
 dist-tarZ: distdir
 	tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
-	$(am__remove_distdir)
+	$(am__post_remove_distdir)
 
 dist-shar: distdir
 	shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
-	$(am__remove_distdir)
+	$(am__post_remove_distdir)
 
 dist-zip: distdir
 	-rm -f $(distdir).zip
 	zip -rq $(distdir).zip $(distdir)
-	$(am__remove_distdir)
+	$(am__post_remove_distdir)
 
-dist dist-all: distdir
-	tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
-	$(am__remove_distdir)
+dist dist-all:
+	$(MAKE) $(AM_MAKEFLAGS) $(DIST_TARGETS) am__post_remove_distdir='@:'
+	$(am__post_remove_distdir)
 
 # This target untars the dist file and tries a VPATH configuration.  Then
 # it guarantees that the distribution is self-contained by making another
@@ -756,8 +836,6 @@
 	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\
 	*.tar.bz2*) \
 	  bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\
-	*.tar.lzma*) \
-	  lzma -dc $(distdir).tar.lzma | $(am__untar) ;;\
 	*.tar.lz*) \
 	  lzip -dc $(distdir).tar.lz | $(am__untar) ;;\
 	*.tar.xz*) \
@@ -769,9 +847,9 @@
 	*.zip*) \
 	  unzip $(distdir).zip ;;\
 	esac
-	chmod -R a-w $(distdir); chmod a+w $(distdir)
-	mkdir $(distdir)/_build
-	mkdir $(distdir)/_inst
+	chmod -R a-w $(distdir)
+	chmod u+w $(distdir)
+	mkdir $(distdir)/_build $(distdir)/_inst
 	chmod a-w $(distdir)
 	test -d $(distdir)/_build || exit 0; \
 	dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
@@ -803,7 +881,7 @@
 	  && $(MAKE) $(AM_MAKEFLAGS) distcleancheck \
 	  && cd "$$am__cwd" \
 	  || exit 1
-	$(am__remove_distdir)
+	$(am__post_remove_distdir)
 	@(echo "$(distdir) archives ready for distribution: "; \
 	  list='$(DIST_ARCHIVES)'; for i in $$list; do echo $$i; done) | \
 	  sed -e 1h -e 1s/./=/g -e 1p -e 1x -e '$$p' -e '$$x'
@@ -951,24 +1029,24 @@
 
 .MAKE: all install-am install-strip
 
-.PHONY: CTAGS GTAGS all all-am am--refresh check check-am clean \
-	clean-binPROGRAMS clean-generic clean-libLTLIBRARIES \
-	clean-libtool clean-noinstPROGRAMS ctags dist dist-all \
-	dist-bzip2 dist-gzip dist-lzip dist-lzma dist-shar dist-tarZ \
-	dist-xz dist-zip distcheck distclean distclean-compile \
-	distclean-generic distclean-hdr distclean-libtool \
-	distclean-tags distcleancheck distdir distuninstallcheck dvi \
-	dvi-am html html-am info info-am install install-am \
-	install-binPROGRAMS install-data install-data-am install-dvi \
-	install-dvi-am install-exec install-exec-am install-html \
-	install-html-am install-info install-info-am \
-	install-libLTLIBRARIES install-man install-pdf install-pdf-am \
-	install-pkgincludeHEADERS install-ps install-ps-am \
-	install-strip installcheck installcheck-am installdirs \
-	maintainer-clean maintainer-clean-generic mostlyclean \
-	mostlyclean-compile mostlyclean-generic mostlyclean-libtool \
-	pdf pdf-am ps ps-am tags uninstall uninstall-am \
-	uninstall-binPROGRAMS uninstall-libLTLIBRARIES \
+.PHONY: CTAGS GTAGS TAGS all all-am am--refresh check check-am clean \
+	clean-binPROGRAMS clean-cscope clean-generic \
+	clean-libLTLIBRARIES clean-libtool clean-noinstPROGRAMS cscope \
+	cscopelist-am ctags ctags-am dist dist-all dist-bzip2 \
+	dist-gzip dist-lzip dist-shar dist-tarZ dist-xz dist-zip \
+	distcheck distclean distclean-compile distclean-generic \
+	distclean-hdr distclean-libtool distclean-tags distcleancheck \
+	distdir distuninstallcheck dvi dvi-am html html-am info \
+	info-am install install-am install-binPROGRAMS install-data \
+	install-data-am install-dvi install-dvi-am install-exec \
+	install-exec-am install-html install-html-am install-info \
+	install-info-am install-libLTLIBRARIES install-man install-pdf \
+	install-pdf-am install-pkgincludeHEADERS install-ps \
+	install-ps-am install-strip installcheck installcheck-am \
+	installdirs maintainer-clean maintainer-clean-generic \
+	mostlyclean mostlyclean-compile mostlyclean-generic \
+	mostlyclean-libtool pdf pdf-am ps ps-am tags tags-am uninstall \
+	uninstall-am uninstall-binPROGRAMS uninstall-libLTLIBRARIES \
 	uninstall-pkgincludeHEADERS
 
 
diff -ruN ccp4srs-old/aclocal.m4 ccp4srs/aclocal.m4
--- ccp4srs-old/aclocal.m4	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/aclocal.m4	2014-09-09 21:34:12.000000000 -0700
@@ -1,8 +1,7 @@
-# generated automatically by aclocal 1.11.3 -*- Autoconf -*-
+# generated automatically by aclocal 1.13.4 -*- Autoconf -*-
+
+# Copyright (C) 1996-2013 Free Software Foundation, Inc.
 
-# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
-# 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software Foundation,
-# Inc.
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
@@ -12,33 +11,31 @@
 # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
 # PARTICULAR PURPOSE.
 
+m4_ifndef([AC_CONFIG_MACRO_DIRS], [m4_defun([_AM_CONFIG_MACRO_DIRS], [])m4_defun([AC_CONFIG_MACRO_DIRS], [_AM_CONFIG_MACRO_DIRS($@)])])
 m4_ifndef([AC_AUTOCONF_VERSION],
   [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
-m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.68],,
-[m4_warning([this file was generated for autoconf 2.68.
+m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.69],,
+[m4_warning([this file was generated for autoconf 2.69.
 You have another version of autoconf.  It may work, but is not guaranteed to.
 If you have problems, you may need to regenerate the build system entirely.
-To do so, use the procedure documented by the package, typically `autoreconf'.])])
+To do so, use the procedure documented by the package, typically 'autoreconf'.])])
 
-# Copyright (C) 2002, 2003, 2005, 2006, 2007, 2008, 2011 Free Software
-# Foundation, Inc.
+# Copyright (C) 2002-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 1
-
 # AM_AUTOMAKE_VERSION(VERSION)
 # ----------------------------
 # Automake X.Y traces this macro to ensure aclocal.m4 has been
 # generated from the m4 files accompanying Automake X.Y.
 # (This private macro should not be called outside this file.)
 AC_DEFUN([AM_AUTOMAKE_VERSION],
-[am__api_version='1.11'
+[am__api_version='1.13'
 dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
 dnl require some minimum version.  Point them to the right macro.
-m4_if([$1], [1.11.3], [],
+m4_if([$1], [1.13.4], [],
       [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
 ])
 
@@ -54,24 +51,81 @@
 # Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
 # This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
 AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
-[AM_AUTOMAKE_VERSION([1.11.3])dnl
+[AM_AUTOMAKE_VERSION([1.13.4])dnl
 m4_ifndef([AC_AUTOCONF_VERSION],
   [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
 _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
 
+# Copyright (C) 2011-2013 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# AM_PROG_AR([ACT-IF-FAIL])
+# -------------------------
+# Try to determine the archiver interface, and trigger the ar-lib wrapper
+# if it is needed.  If the detection of archiver interface fails, run
+# ACT-IF-FAIL (default is to abort configure with a proper error message).
+AC_DEFUN([AM_PROG_AR],
+[AC_BEFORE([$0], [LT_INIT])dnl
+AC_BEFORE([$0], [AC_PROG_LIBTOOL])dnl
+AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
+AC_REQUIRE_AUX_FILE([ar-lib])dnl
+AC_CHECK_TOOLS([AR], [ar lib "link -lib"], [false])
+: ${AR=ar}
+
+AC_CACHE_CHECK([the archiver ($AR) interface], [am_cv_ar_interface],
+  [am_cv_ar_interface=ar
+   AC_COMPILE_IFELSE([AC_LANG_SOURCE([[int some_variable = 0;]])],
+     [am_ar_try='$AR cru libconftest.a conftest.$ac_objext >&AS_MESSAGE_LOG_FD'
+      AC_TRY_EVAL([am_ar_try])
+      if test "$ac_status" -eq 0; then
+        am_cv_ar_interface=ar
+      else
+        am_ar_try='$AR -NOLOGO -OUT:conftest.lib conftest.$ac_objext >&AS_MESSAGE_LOG_FD'
+        AC_TRY_EVAL([am_ar_try])
+        if test "$ac_status" -eq 0; then
+          am_cv_ar_interface=lib
+        else
+          am_cv_ar_interface=unknown
+        fi
+      fi
+      rm -f conftest.lib libconftest.a
+     ])
+   ])
+
+case $am_cv_ar_interface in
+ar)
+  ;;
+lib)
+  # Microsoft lib, so override with the ar-lib wrapper script.
+  # FIXME: It is wrong to rewrite AR.
+  # But if we don't then we get into trouble of one sort or another.
+  # A longer-term fix would be to have automake use am__AR in this case,
+  # and then we could set am__AR="$am_aux_dir/ar-lib \$(AR)" or something
+  # similar.
+  AR="$am_aux_dir/ar-lib $AR"
+  ;;
+unknown)
+  m4_default([$1],
+             [AC_MSG_ERROR([could not determine $AR interface])])
+  ;;
+esac
+AC_SUBST([AR])dnl
+])
+
 # AM_AUX_DIR_EXPAND                                         -*- Autoconf -*-
 
-# Copyright (C) 2001, 2003, 2005, 2011 Free Software Foundation, Inc.
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 1
-
 # For projects using AC_CONFIG_AUX_DIR([foo]), Autoconf sets
-# $ac_aux_dir to `$srcdir/foo'.  In other projects, it is set to
-# `$srcdir', `$srcdir/..', or `$srcdir/../..'.
+# $ac_aux_dir to '$srcdir/foo'.  In other projects, it is set to
+# '$srcdir', '$srcdir/..', or '$srcdir/../..'.
 #
 # Of course, Automake must honor this variable whenever it calls a
 # tool from the auxiliary directory.  The problem is that $srcdir (and
@@ -90,7 +144,7 @@
 #
 # The reason of the latter failure is that $top_srcdir and $ac_aux_dir
 # are both prefixed by $srcdir.  In an in-source build this is usually
-# harmless because $srcdir is `.', but things will broke when you
+# harmless because $srcdir is '.', but things will broke when you
 # start a VPATH build or use an absolute $srcdir.
 #
 # So we could use something similar to $top_srcdir/$ac_aux_dir/missing,
@@ -116,22 +170,19 @@
 
 # AM_CONDITIONAL                                            -*- Autoconf -*-
 
-# Copyright (C) 1997, 2000, 2001, 2003, 2004, 2005, 2006, 2008
-# Free Software Foundation, Inc.
+# Copyright (C) 1997-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 9
-
 # AM_CONDITIONAL(NAME, SHELL-CONDITION)
 # -------------------------------------
 # Define a conditional.
 AC_DEFUN([AM_CONDITIONAL],
-[AC_PREREQ(2.52)dnl
- ifelse([$1], [TRUE],  [AC_FATAL([$0: invalid condition: $1])],
-	[$1], [FALSE], [AC_FATAL([$0: invalid condition: $1])])dnl
+[AC_PREREQ([2.52])dnl
+ m4_if([$1], [TRUE],  [AC_FATAL([$0: invalid condition: $1])],
+       [$1], [FALSE], [AC_FATAL([$0: invalid condition: $1])])dnl
 AC_SUBST([$1_TRUE])dnl
 AC_SUBST([$1_FALSE])dnl
 _AM_SUBST_NOTMAKE([$1_TRUE])dnl
@@ -150,16 +201,14 @@
 Usually this means the macro was only invoked conditionally.]])
 fi])])
 
-# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2009,
-# 2010, 2011 Free Software Foundation, Inc.
+# Copyright (C) 1999-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 12
 
-# There are a few dirty hacks below to avoid letting `AC_PROG_CC' be
+# There are a few dirty hacks below to avoid letting 'AC_PROG_CC' be
 # written in clear, in which case automake, when reading aclocal.m4,
 # will think it sees a *use*, and therefore will trigger all it's
 # C support machinery.  Also note that it means that autoscan, seeing
@@ -169,7 +218,7 @@
 # _AM_DEPENDENCIES(NAME)
 # ----------------------
 # See how the compiler implements dependency checking.
-# NAME is "CC", "CXX", "GCJ", or "OBJC".
+# NAME is "CC", "CXX", "OBJC", "OBJCXX", "UPC", or "GJC".
 # We try a few techniques and use that to set a single cache variable.
 #
 # We don't AC_REQUIRE the corresponding AC_PROG_CC since the latter was
@@ -182,12 +231,13 @@
 AC_REQUIRE([AM_MAKE_INCLUDE])dnl
 AC_REQUIRE([AM_DEP_TRACK])dnl
 
-ifelse([$1], CC,   [depcc="$CC"   am_compiler_list=],
-       [$1], CXX,  [depcc="$CXX"  am_compiler_list=],
-       [$1], OBJC, [depcc="$OBJC" am_compiler_list='gcc3 gcc'],
-       [$1], UPC,  [depcc="$UPC"  am_compiler_list=],
-       [$1], GCJ,  [depcc="$GCJ"  am_compiler_list='gcc3 gcc'],
-                   [depcc="$$1"   am_compiler_list=])
+m4_if([$1], [CC],   [depcc="$CC"   am_compiler_list=],
+      [$1], [CXX],  [depcc="$CXX"  am_compiler_list=],
+      [$1], [OBJC], [depcc="$OBJC" am_compiler_list='gcc3 gcc'],
+      [$1], [OBJCXX], [depcc="$OBJCXX" am_compiler_list='gcc3 gcc'],
+      [$1], [UPC],  [depcc="$UPC"  am_compiler_list=],
+      [$1], [GCJ],  [depcc="$GCJ"  am_compiler_list='gcc3 gcc'],
+                    [depcc="$$1"   am_compiler_list=])
 
 AC_CACHE_CHECK([dependency style of $depcc],
                [am_cv_$1_dependencies_compiler_type],
@@ -195,8 +245,8 @@
   # We make a subdir and do the tests there.  Otherwise we can end up
   # making bogus files that we don't know about and never remove.  For
   # instance it was reported that on HP-UX the gcc test will end up
-  # making a dummy file named `D' -- because `-MD' means `put the output
-  # in D'.
+  # making a dummy file named 'D' -- because '-MD' means "put the output
+  # in D".
   rm -rf conftest.dir
   mkdir conftest.dir
   # Copy depcomp to subdir because otherwise we won't find it if we're
@@ -236,16 +286,16 @@
     : > sub/conftest.c
     for i in 1 2 3 4 5 6; do
       echo '#include "conftst'$i'.h"' >> sub/conftest.c
-      # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
-      # Solaris 8's {/usr,}/bin/sh.
-      touch sub/conftst$i.h
+      # Using ": > sub/conftst$i.h" creates only sub/conftst1.h with
+      # Solaris 10 /bin/sh.
+      echo '/* dummy */' > sub/conftst$i.h
     done
     echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
 
-    # We check with `-c' and `-o' for the sake of the "dashmstdout"
+    # We check with '-c' and '-o' for the sake of the "dashmstdout"
     # mode.  It turns out that the SunPro C++ compiler does not properly
-    # handle `-M -o', and we need to detect this.  Also, some Intel
-    # versions had trouble with output in subdirs
+    # handle '-M -o', and we need to detect this.  Also, some Intel
+    # versions had trouble with output in subdirs.
     am__obj=sub/conftest.${OBJEXT-o}
     am__minus_obj="-o $am__obj"
     case $depmode in
@@ -254,8 +304,8 @@
       test "$am__universal" = false || continue
       ;;
     nosideeffect)
-      # after this tag, mechanisms are not by side-effect, so they'll
-      # only be used when explicitly requested
+      # After this tag, mechanisms are not by side-effect, so they'll
+      # only be used when explicitly requested.
       if test "x$enable_dependency_tracking" = xyes; then
 	continue
       else
@@ -263,7 +313,7 @@
       fi
       ;;
     msvc7 | msvc7msys | msvisualcpp | msvcmsys)
-      # This compiler won't grok `-c -o', but also, the minuso test has
+      # This compiler won't grok '-c -o', but also, the minuso test has
       # not run yet.  These depmodes are late enough in the game, and
       # so weak that their functioning should not be impacted.
       am__obj=conftest.${OBJEXT-o}
@@ -311,7 +361,7 @@
 # AM_SET_DEPDIR
 # -------------
 # Choose a directory name for dependency files.
-# This macro is AC_REQUIREd in _AM_DEPENDENCIES
+# This macro is AC_REQUIREd in _AM_DEPENDENCIES.
 AC_DEFUN([AM_SET_DEPDIR],
 [AC_REQUIRE([AM_SET_LEADING_DOT])dnl
 AC_SUBST([DEPDIR], ["${am__leading_dot}deps"])dnl
@@ -321,9 +371,13 @@
 # AM_DEP_TRACK
 # ------------
 AC_DEFUN([AM_DEP_TRACK],
-[AC_ARG_ENABLE(dependency-tracking,
-[  --disable-dependency-tracking  speeds up one-time build
-  --enable-dependency-tracking   do not reject slow dependency extractors])
+[AC_ARG_ENABLE([dependency-tracking], [dnl
+AS_HELP_STRING(
+  [--enable-dependency-tracking],
+  [do not reject slow dependency extractors])
+AS_HELP_STRING(
+  [--disable-dependency-tracking],
+  [speeds up one-time build])])
 if test "x$enable_dependency_tracking" != xno; then
   am_depcomp="$ac_aux_dir/depcomp"
   AMDEPBACKSLASH='\'
@@ -338,20 +392,18 @@
 
 # Generate code to set up dependency tracking.              -*- Autoconf -*-
 
-# Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2008
-# Free Software Foundation, Inc.
+# Copyright (C) 1999-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-#serial 5
 
 # _AM_OUTPUT_DEPENDENCY_COMMANDS
 # ------------------------------
 AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
 [{
-  # Autoconf 2.62 quotes --file arguments for eval, but not when files
+  # Older Autoconf quotes --file arguments for eval, but not when files
   # are listed without --file.  Let's play safe and only enable the eval
   # if we detect the quoting.
   case $CONFIG_FILES in
@@ -364,7 +416,7 @@
     # Strip MF so we end up with the name of the file.
     mf=`echo "$mf" | sed -e 's/:.*$//'`
     # Check whether this is an Automake generated Makefile or not.
-    # We used to match only the files named `Makefile.in', but
+    # We used to match only the files named 'Makefile.in', but
     # some people rename them; so instead we look at the file content.
     # Grep'ing the first line is not enough: some people post-process
     # each Makefile.in and add a new line on top of each file to say so.
@@ -376,21 +428,19 @@
       continue
     fi
     # Extract the definition of DEPDIR, am__include, and am__quote
-    # from the Makefile without running `make'.
+    # from the Makefile without running 'make'.
     DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
     test -z "$DEPDIR" && continue
     am__include=`sed -n 's/^am__include = //p' < "$mf"`
-    test -z "am__include" && continue
+    test -z "$am__include" && continue
     am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
-    # When using ansi2knr, U may be empty or an underscore; expand it
-    U=`sed -n 's/^U = //p' < "$mf"`
     # Find all dependency output files, they are included files with
     # $(DEPDIR) in their names.  We invoke sed twice because it is the
     # simplest approach to changing $(DEPDIR) to its actual value in the
     # expansion.
     for file in `sed -n "
       s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
-	 sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
+	 sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g'`; do
       # Make sure the directory exists.
       test -f "$dirpart/$file" && continue
       fdir=`AS_DIRNAME(["$file"])`
@@ -408,7 +458,7 @@
 # This macro should only be invoked once -- use via AC_REQUIRE.
 #
 # This code is only required when automatic dependency tracking
-# is enabled.  FIXME.  This creates each `.P' file that we will
+# is enabled.  FIXME.  This creates each '.P' file that we will
 # need in order to bootstrap the dependency handling code.
 AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
 [AC_CONFIG_COMMANDS([depfiles],
@@ -418,15 +468,12 @@
 
 # Do all the work for Automake.                             -*- Autoconf -*-
 
-# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
-# 2005, 2006, 2008, 2009 Free Software Foundation, Inc.
+# Copyright (C) 1996-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 16
-
 # This macro actually does too much.  Some checks are only needed if
 # your package does certain things.  But this isn't really a big deal.
 
@@ -442,7 +489,7 @@
 # arguments mandatory, and then we can depend on a new Autoconf
 # release and drop the old call support.
 AC_DEFUN([AM_INIT_AUTOMAKE],
-[AC_PREREQ([2.62])dnl
+[AC_PREREQ([2.65])dnl
 dnl Autoconf wants to disallow AM_ names.  We explicitly allow
 dnl the ones we care about.
 m4_pattern_allow([^AM_[A-Z]+FLAGS$])dnl
@@ -471,31 +518,40 @@
 # Define the identity of the package.
 dnl Distinguish between old-style and new-style calls.
 m4_ifval([$2],
-[m4_ifval([$3], [_AM_SET_OPTION([no-define])])dnl
+[AC_DIAGNOSE([obsolete],
+             [$0: two- and three-arguments forms are deprecated.])
+m4_ifval([$3], [_AM_SET_OPTION([no-define])])dnl
  AC_SUBST([PACKAGE], [$1])dnl
  AC_SUBST([VERSION], [$2])],
 [_AM_SET_OPTIONS([$1])dnl
 dnl Diagnose old-style AC_INIT with new-style AM_AUTOMAKE_INIT.
-m4_if(m4_ifdef([AC_PACKAGE_NAME], 1)m4_ifdef([AC_PACKAGE_VERSION], 1), 11,,
+m4_if(
+  m4_ifdef([AC_PACKAGE_NAME], [ok]):m4_ifdef([AC_PACKAGE_VERSION], [ok]),
+  [ok:ok],,
   [m4_fatal([AC_INIT should be called with package and version arguments])])dnl
  AC_SUBST([PACKAGE], ['AC_PACKAGE_TARNAME'])dnl
  AC_SUBST([VERSION], ['AC_PACKAGE_VERSION'])])dnl
 
 _AM_IF_OPTION([no-define],,
-[AC_DEFINE_UNQUOTED(PACKAGE, "$PACKAGE", [Name of package])
- AC_DEFINE_UNQUOTED(VERSION, "$VERSION", [Version number of package])])dnl
+[AC_DEFINE_UNQUOTED([PACKAGE], ["$PACKAGE"], [Name of package])
+ AC_DEFINE_UNQUOTED([VERSION], ["$VERSION"], [Version number of package])])dnl
 
 # Some tools Automake needs.
 AC_REQUIRE([AM_SANITY_CHECK])dnl
 AC_REQUIRE([AC_ARG_PROGRAM])dnl
-AM_MISSING_PROG(ACLOCAL, aclocal-${am__api_version})
-AM_MISSING_PROG(AUTOCONF, autoconf)
-AM_MISSING_PROG(AUTOMAKE, automake-${am__api_version})
-AM_MISSING_PROG(AUTOHEADER, autoheader)
-AM_MISSING_PROG(MAKEINFO, makeinfo)
+AM_MISSING_PROG([ACLOCAL], [aclocal-${am__api_version}])
+AM_MISSING_PROG([AUTOCONF], [autoconf])
+AM_MISSING_PROG([AUTOMAKE], [automake-${am__api_version}])
+AM_MISSING_PROG([AUTOHEADER], [autoheader])
+AM_MISSING_PROG([MAKEINFO], [makeinfo])
 AC_REQUIRE([AM_PROG_INSTALL_SH])dnl
 AC_REQUIRE([AM_PROG_INSTALL_STRIP])dnl
-AC_REQUIRE([AM_PROG_MKDIR_P])dnl
+AC_REQUIRE([AC_PROG_MKDIR_P])dnl
+# For better backward compatibility.  To be removed once Automake 1.9.x
+# dies out for good.  For more background, see:
+# <http://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
+# <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
+AC_SUBST([mkdir_p], ['$(MKDIR_P)'])
 # We need awk for the "check" target.  The system "awk" is bad on
 # some platforms.
 AC_REQUIRE([AC_PROG_AWK])dnl
@@ -506,28 +562,32 @@
 			     [_AM_PROG_TAR([v7])])])
 _AM_IF_OPTION([no-dependencies],,
 [AC_PROVIDE_IFELSE([AC_PROG_CC],
-		  [_AM_DEPENDENCIES(CC)],
-		  [define([AC_PROG_CC],
-			  defn([AC_PROG_CC])[_AM_DEPENDENCIES(CC)])])dnl
+		  [_AM_DEPENDENCIES([CC])],
+		  [m4_define([AC_PROG_CC],
+			     m4_defn([AC_PROG_CC])[_AM_DEPENDENCIES([CC])])])dnl
 AC_PROVIDE_IFELSE([AC_PROG_CXX],
-		  [_AM_DEPENDENCIES(CXX)],
-		  [define([AC_PROG_CXX],
-			  defn([AC_PROG_CXX])[_AM_DEPENDENCIES(CXX)])])dnl
+		  [_AM_DEPENDENCIES([CXX])],
+		  [m4_define([AC_PROG_CXX],
+			     m4_defn([AC_PROG_CXX])[_AM_DEPENDENCIES([CXX])])])dnl
 AC_PROVIDE_IFELSE([AC_PROG_OBJC],
-		  [_AM_DEPENDENCIES(OBJC)],
-		  [define([AC_PROG_OBJC],
-			  defn([AC_PROG_OBJC])[_AM_DEPENDENCIES(OBJC)])])dnl
+		  [_AM_DEPENDENCIES([OBJC])],
+		  [m4_define([AC_PROG_OBJC],
+			     m4_defn([AC_PROG_OBJC])[_AM_DEPENDENCIES([OBJC])])])dnl
+AC_PROVIDE_IFELSE([AC_PROG_OBJCXX],
+		  [_AM_DEPENDENCIES([OBJCXX])],
+		  [m4_define([AC_PROG_OBJCXX],
+			     m4_defn([AC_PROG_OBJCXX])[_AM_DEPENDENCIES([OBJCXX])])])dnl
 ])
-_AM_IF_OPTION([silent-rules], [AC_REQUIRE([AM_SILENT_RULES])])dnl
-dnl The `parallel-tests' driver may need to know about EXEEXT, so add the
-dnl `am__EXEEXT' conditional if _AM_COMPILER_EXEEXT was seen.  This macro
-dnl is hooked onto _AC_COMPILER_EXEEXT early, see below.
+AC_REQUIRE([AM_SILENT_RULES])dnl
+dnl The testsuite driver may need to know about EXEEXT, so add the
+dnl 'am__EXEEXT' conditional if _AM_COMPILER_EXEEXT was seen.  This
+dnl macro is hooked onto _AC_COMPILER_EXEEXT early, see below.
 AC_CONFIG_COMMANDS_PRE(dnl
 [m4_provide_if([_AM_COMPILER_EXEEXT],
   [AM_CONDITIONAL([am__EXEEXT], [test -n "$EXEEXT"])])])dnl
 ])
 
-dnl Hook into `_AC_COMPILER_EXEEXT' early to learn its expansion.  Do not
+dnl Hook into '_AC_COMPILER_EXEEXT' early to learn its expansion.  Do not
 dnl add the conditional right here, as _AC_COMPILER_EXEEXT may be further
 dnl mangled by Autoconf and run in a shell conditional statement.
 m4_define([_AC_COMPILER_EXEEXT],
@@ -555,15 +615,12 @@
 done
 echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])
 
-# Copyright (C) 2001, 2003, 2005, 2008, 2011 Free Software Foundation,
-# Inc.
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 1
-
 # AM_PROG_INSTALL_SH
 # ------------------
 # Define $install_sh.
@@ -577,16 +634,14 @@
     install_sh="\${SHELL} $am_aux_dir/install-sh"
   esac
 fi
-AC_SUBST(install_sh)])
+AC_SUBST([install_sh])])
 
-# Copyright (C) 2003, 2005  Free Software Foundation, Inc.
+# Copyright (C) 2003-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 2
-
 # Check whether the underlying file-system supports filenames
 # with a leading dot.  For instance MS-DOS doesn't.
 AC_DEFUN([AM_SET_LEADING_DOT],
@@ -603,20 +658,17 @@
 # Add --enable-maintainer-mode option to configure.         -*- Autoconf -*-
 # From Jim Meyering
 
-# Copyright (C) 1996, 1998, 2000, 2001, 2002, 2003, 2004, 2005, 2008,
-# 2011 Free Software Foundation, Inc.
+# Copyright (C) 1996-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 5
-
 # AM_MAINTAINER_MODE([DEFAULT-MODE])
 # ----------------------------------
 # Control maintainer-specific portions of Makefiles.
-# Default is to disable them, unless `enable' is passed literally.
-# For symmetry, `disable' may be passed as well.  Anyway, the user
+# Default is to disable them, unless 'enable' is passed literally.
+# For symmetry, 'disable' may be passed as well.  Anyway, the user
 # can override the default with the --enable/--disable switch.
 AC_DEFUN([AM_MAINTAINER_MODE],
 [m4_case(m4_default([$1], [disable]),
@@ -627,10 +679,11 @@
 AC_MSG_CHECKING([whether to enable maintainer-specific portions of Makefiles])
   dnl maintainer-mode's default is 'disable' unless 'enable' is passed
   AC_ARG_ENABLE([maintainer-mode],
-[  --][am_maintainer_other][-maintainer-mode  am_maintainer_other make rules and dependencies not useful
-			  (and sometimes confusing) to the casual installer],
-      [USE_MAINTAINER_MODE=$enableval],
-      [USE_MAINTAINER_MODE=]m4_if(am_maintainer_other, [enable], [no], [yes]))
+    [AS_HELP_STRING([--]am_maintainer_other[-maintainer-mode],
+      am_maintainer_other[ make rules and dependencies not useful
+      (and sometimes confusing) to the casual installer])],
+    [USE_MAINTAINER_MODE=$enableval],
+    [USE_MAINTAINER_MODE=]m4_if(am_maintainer_other, [enable], [no], [yes]))
   AC_MSG_RESULT([$USE_MAINTAINER_MODE])
   AM_CONDITIONAL([MAINTAINER_MODE], [test $USE_MAINTAINER_MODE = yes])
   MAINT=$MAINTAINER_MODE_TRUE
@@ -638,18 +691,14 @@
 ]
 )
 
-AU_DEFUN([jm_MAINTAINER_MODE], [AM_MAINTAINER_MODE])
-
 # Check to see how 'make' treats includes.	            -*- Autoconf -*-
 
-# Copyright (C) 2001, 2002, 2003, 2005, 2009  Free Software Foundation, Inc.
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 4
-
 # AM_MAKE_INCLUDE()
 # -----------------
 # Check to see how make treats includes.
@@ -667,7 +716,7 @@
 _am_result=none
 # First try GNU make style include.
 echo "include confinc" > confmf
-# Ignore all kinds of additional output from `make'.
+# Ignore all kinds of additional output from 'make'.
 case `$am_make -s -f confmf 2> /dev/null` in #(
 *the\ am__doit\ target*)
   am__include=include
@@ -694,15 +743,12 @@
 
 # Fake the existence of programs that GNU maintainers use.  -*- Autoconf -*-
 
-# Copyright (C) 1997, 1999, 2000, 2001, 2003, 2004, 2005, 2008
-# Free Software Foundation, Inc.
+# Copyright (C) 1997-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 6
-
 # AM_MISSING_PROG(NAME, PROGRAM)
 # ------------------------------
 AC_DEFUN([AM_MISSING_PROG],
@@ -710,11 +756,10 @@
 $1=${$1-"${am_missing_run}$2"}
 AC_SUBST($1)])
 
-
 # AM_MISSING_HAS_RUN
 # ------------------
-# Define MISSING if not defined so far and test if it supports --run.
-# If it does, set am_missing_run to use it, otherwise, to nothing.
+# Define MISSING if not defined so far and test if it is modern enough.
+# If it is, set am_missing_run to use it, otherwise, to nothing.
 AC_DEFUN([AM_MISSING_HAS_RUN],
 [AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
 AC_REQUIRE_AUX_FILE([missing])dnl
@@ -727,54 +772,22 @@
   esac
 fi
 # Use eval to expand $SHELL
-if eval "$MISSING --run true"; then
-  am_missing_run="$MISSING --run "
+if eval "$MISSING --is-lightweight"; then
+  am_missing_run="$MISSING "
 else
   am_missing_run=
-  AC_MSG_WARN([`missing' script is too old or missing])
+  AC_MSG_WARN(['missing' script is too old or missing])
 fi
 ])
 
-# Copyright (C) 2003, 2004, 2005, 2006, 2011 Free Software Foundation,
-# Inc.
-#
-# This file is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# serial 1
-
-# AM_PROG_MKDIR_P
-# ---------------
-# Check for `mkdir -p'.
-AC_DEFUN([AM_PROG_MKDIR_P],
-[AC_PREREQ([2.60])dnl
-AC_REQUIRE([AC_PROG_MKDIR_P])dnl
-dnl Automake 1.8 to 1.9.6 used to define mkdir_p.  We now use MKDIR_P,
-dnl while keeping a definition of mkdir_p for backward compatibility.
-dnl @MKDIR_P@ is magic: AC_OUTPUT adjusts its value for each Makefile.
-dnl However we cannot define mkdir_p as $(MKDIR_P) for the sake of
-dnl Makefile.ins that do not define MKDIR_P, so we do our own
-dnl adjustment using top_builddir (which is defined more often than
-dnl MKDIR_P).
-AC_SUBST([mkdir_p], ["$MKDIR_P"])dnl
-case $mkdir_p in
-  [[\\/$]]* | ?:[[\\/]]*) ;;
-  */*) mkdir_p="\$(top_builddir)/$mkdir_p" ;;
-esac
-])
-
 # Helper functions for option handling.                     -*- Autoconf -*-
 
-# Copyright (C) 2001, 2002, 2003, 2005, 2008, 2010 Free Software
-# Foundation, Inc.
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 5
-
 # _AM_MANGLE_OPTION(NAME)
 # -----------------------
 AC_DEFUN([_AM_MANGLE_OPTION],
@@ -784,7 +797,7 @@
 # --------------------
 # Set option NAME.  Presently that only means defining a flag for this option.
 AC_DEFUN([_AM_SET_OPTION],
-[m4_define(_AM_MANGLE_OPTION([$1]), 1)])
+[m4_define(_AM_MANGLE_OPTION([$1]), [1])])
 
 # _AM_SET_OPTIONS(OPTIONS)
 # ------------------------
@@ -800,22 +813,16 @@
 
 # Check to make sure that the build environment is sane.    -*- Autoconf -*-
 
-# Copyright (C) 1996, 1997, 2000, 2001, 2003, 2005, 2008
-# Free Software Foundation, Inc.
+# Copyright (C) 1996-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 5
-
 # AM_SANITY_CHECK
 # ---------------
 AC_DEFUN([AM_SANITY_CHECK],
 [AC_MSG_CHECKING([whether build environment is sane])
-# Just in case
-sleep 1
-echo timestamp > conftest.file
 # Reject unsafe characters in $srcdir or the absolute working directory
 # name.  Accept space and tab only in the latter.
 am_lf='
@@ -826,32 +833,40 @@
 esac
 case $srcdir in
   *[[\\\"\#\$\&\'\`$am_lf\ \	]]*)
-    AC_MSG_ERROR([unsafe srcdir value: `$srcdir']);;
+    AC_MSG_ERROR([unsafe srcdir value: '$srcdir']);;
 esac
 
-# Do `set' in a subshell so we don't clobber the current shell's
+# Do 'set' in a subshell so we don't clobber the current shell's
 # arguments.  Must try -L first in case configure is actually a
 # symlink; some systems play weird games with the mod time of symlinks
 # (eg FreeBSD returns the mod time of the symlink's containing
 # directory).
 if (
-   set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
-   if test "$[*]" = "X"; then
-      # -L didn't work.
-      set X `ls -t "$srcdir/configure" conftest.file`
-   fi
-   rm -f conftest.file
-   if test "$[*]" != "X $srcdir/configure conftest.file" \
-      && test "$[*]" != "X conftest.file $srcdir/configure"; then
-
-      # If neither matched, then we have a broken ls.  This can happen
-      # if, for instance, CONFIG_SHELL is bash and it inherits a
-      # broken ls alias from the environment.  This has actually
-      # happened.  Such a system could not be considered "sane".
-      AC_MSG_ERROR([ls -t appears to fail.  Make sure there is not a broken
-alias in your environment])
-   fi
-
+   am_has_slept=no
+   for am_try in 1 2; do
+     echo "timestamp, slept: $am_has_slept" > conftest.file
+     set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
+     if test "$[*]" = "X"; then
+	# -L didn't work.
+	set X `ls -t "$srcdir/configure" conftest.file`
+     fi
+     if test "$[*]" != "X $srcdir/configure conftest.file" \
+	&& test "$[*]" != "X conftest.file $srcdir/configure"; then
+
+	# If neither matched, then we have a broken ls.  This can happen
+	# if, for instance, CONFIG_SHELL is bash and it inherits a
+	# broken ls alias from the environment.  This has actually
+	# happened.  Such a system could not be considered "sane".
+	AC_MSG_ERROR([ls -t appears to fail.  Make sure there is not a broken
+  alias in your environment])
+     fi
+     if test "$[2]" = conftest.file || test $am_try -eq 2; then
+       break
+     fi
+     # Just in case.
+     sleep 1
+     am_has_slept=yes
+   done
    test "$[2]" = conftest.file
    )
 then
@@ -861,31 +876,50 @@
    AC_MSG_ERROR([newly created file is older than distributed files!
 Check your system clock])
 fi
-AC_MSG_RESULT(yes)])
+AC_MSG_RESULT([yes])
+# If we didn't sleep, we still need to ensure time stamps of config.status and
+# generated files are strictly newer.
+am_sleep_pid=
+if grep 'slept: no' conftest.file >/dev/null 2>&1; then
+  ( sleep 1 ) &
+  am_sleep_pid=$!
+fi
+AC_CONFIG_COMMANDS_PRE(
+  [AC_MSG_CHECKING([that generated files are newer than configure])
+   if test -n "$am_sleep_pid"; then
+     # Hide warnings about reused PIDs.
+     wait $am_sleep_pid 2>/dev/null
+   fi
+   AC_MSG_RESULT([done])])
+rm -f conftest.file
+])
 
-# Copyright (C) 2009, 2011  Free Software Foundation, Inc.
+# Copyright (C) 2009-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 2
-
 # AM_SILENT_RULES([DEFAULT])
 # --------------------------
 # Enable less verbose build rules; with the default set to DEFAULT
-# (`yes' being less verbose, `no' or empty being verbose).
+# ("yes" being less verbose, "no" or empty being verbose).
 AC_DEFUN([AM_SILENT_RULES],
-[AC_ARG_ENABLE([silent-rules],
-[  --enable-silent-rules          less verbose build output (undo: `make V=1')
-  --disable-silent-rules         verbose build output (undo: `make V=0')])
-case $enable_silent_rules in
-yes) AM_DEFAULT_VERBOSITY=0;;
-no)  AM_DEFAULT_VERBOSITY=1;;
-*)   AM_DEFAULT_VERBOSITY=m4_if([$1], [yes], [0], [1]);;
+[AC_ARG_ENABLE([silent-rules], [dnl
+AS_HELP_STRING(
+  [--enable-silent-rules],
+  [less verbose build output (undo: "make V=1")])
+AS_HELP_STRING(
+  [--disable-silent-rules],
+  [verbose build output (undo: "make V=0")])dnl
+])
+case $enable_silent_rules in @%:@ (((
+  yes) AM_DEFAULT_VERBOSITY=0;;
+   no) AM_DEFAULT_VERBOSITY=1;;
+    *) AM_DEFAULT_VERBOSITY=m4_if([$1], [yes], [0], [1]);;
 esac
 dnl
-dnl A few `make' implementations (e.g., NonStop OS and NextStep)
+dnl A few 'make' implementations (e.g., NonStop OS and NextStep)
 dnl do not support nested variable expansions.
 dnl See automake bug#9928 and bug#10237.
 am_make=${MAKE-make}
@@ -903,7 +937,7 @@
   am_cv_make_support_nested_variables=no
 fi])
 if test $am_cv_make_support_nested_variables = yes; then
-  dnl Using `$V' instead of `$(V)' breaks IRIX make.
+  dnl Using '$V' instead of '$(V)' breaks IRIX make.
   AM_V='$(V)'
   AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
 else
@@ -920,44 +954,40 @@
 _AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl
 ])
 
-# Copyright (C) 2001, 2003, 2005, 2011 Free Software Foundation, Inc.
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 1
-
 # AM_PROG_INSTALL_STRIP
 # ---------------------
-# One issue with vendor `install' (even GNU) is that you can't
+# One issue with vendor 'install' (even GNU) is that you can't
 # specify the program used to strip binaries.  This is especially
 # annoying in cross-compiling environments, where the build's strip
 # is unlikely to handle the host's binaries.
 # Fortunately install-sh will honor a STRIPPROG variable, so we
-# always use install-sh in `make install-strip', and initialize
+# always use install-sh in "make install-strip", and initialize
 # STRIPPROG with the value of the STRIP variable (set by the user).
 AC_DEFUN([AM_PROG_INSTALL_STRIP],
 [AC_REQUIRE([AM_PROG_INSTALL_SH])dnl
-# Installed binaries are usually stripped using `strip' when the user
-# run `make install-strip'.  However `strip' might not be the right
+# Installed binaries are usually stripped using 'strip' when the user
+# run "make install-strip".  However 'strip' might not be the right
 # tool to use in cross-compilation environments, therefore Automake
-# will honor the `STRIP' environment variable to overrule this program.
-dnl Don't test for $cross_compiling = yes, because it might be `maybe'.
+# will honor the 'STRIP' environment variable to overrule this program.
+dnl Don't test for $cross_compiling = yes, because it might be 'maybe'.
 if test "$cross_compiling" != no; then
   AC_CHECK_TOOL([STRIP], [strip], :)
 fi
 INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
 AC_SUBST([INSTALL_STRIP_PROGRAM])])
 
-# Copyright (C) 2006, 2008, 2010 Free Software Foundation, Inc.
+# Copyright (C) 2006-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 3
-
 # _AM_SUBST_NOTMAKE(VARIABLE)
 # ---------------------------
 # Prevent Automake from outputting VARIABLE = @VARIABLE@ in Makefile.in.
@@ -971,18 +1001,16 @@
 
 # Check how to create a tarball.                            -*- Autoconf -*-
 
-# Copyright (C) 2004, 2005, 2012 Free Software Foundation, Inc.
+# Copyright (C) 2004-2013 Free Software Foundation, Inc.
 #
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
 
-# serial 2
-
 # _AM_PROG_TAR(FORMAT)
 # --------------------
 # Check how to create a tarball in format FORMAT.
-# FORMAT should be one of `v7', `ustar', or `pax'.
+# FORMAT should be one of 'v7', 'ustar', or 'pax'.
 #
 # Substitute a variable $(am__tar) that is a command
 # writing to stdout a FORMAT-tarball containing the directory
@@ -992,76 +1020,114 @@
 # Substitute a variable $(am__untar) that extract such
 # a tarball read from stdin.
 #     $(am__untar) < result.tar
+#
 AC_DEFUN([_AM_PROG_TAR],
 [# Always define AMTAR for backward compatibility.  Yes, it's still used
 # in the wild :-(  We should find a proper way to deprecate it ...
 AC_SUBST([AMTAR], ['$${TAR-tar}'])
-m4_if([$1], [v7],
-     [am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'],
-     [m4_case([$1], [ustar],, [pax],,
-              [m4_fatal([Unknown tar format])])
-AC_MSG_CHECKING([how to create a $1 tar archive])
-# Loop over all known methods to create a tar archive until one works.
+
+# We'll loop over all known methods to create a tar archive until one works.
 _am_tools='gnutar m4_if([$1], [ustar], [plaintar]) pax cpio none'
-_am_tools=${am_cv_prog_tar_$1-$_am_tools}
-# Do not fold the above two line into one, because Tru64 sh and
-# Solaris sh will not grok spaces in the rhs of `-'.
-for _am_tool in $_am_tools
-do
-  case $_am_tool in
-  gnutar)
-    for _am_tar in tar gnutar gtar;
-    do
-      AM_RUN_LOG([$_am_tar --version]) && break
-    done
-    am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
-    am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'
-    am__untar="$_am_tar -xf -"
-    ;;
-  plaintar)
-    # Must skip GNU tar: if it does not support --format= it doesn't create
-    # ustar tarball either.
-    (tar --version) >/dev/null 2>&1 && continue
-    am__tar='tar chf - "$$tardir"'
-    am__tar_='tar chf - "$tardir"'
-    am__untar='tar xf -'
-    ;;
-  pax)
-    am__tar='pax -L -x $1 -w "$$tardir"'
-    am__tar_='pax -L -x $1 -w "$tardir"'
-    am__untar='pax -r'
-    ;;
-  cpio)
-    am__tar='find "$$tardir" -print | cpio -o -H $1 -L'
-    am__tar_='find "$tardir" -print | cpio -o -H $1 -L'
-    am__untar='cpio -i -H $1 -d'
-    ;;
-  none)
-    am__tar=false
-    am__tar_=false
-    am__untar=false
-    ;;
-  esac
 
-  # If the value was cached, stop now.  We just wanted to have am__tar
-  # and am__untar set.
-  test -n "${am_cv_prog_tar_$1}" && break
+m4_if([$1], [v7],
+  [am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'],
 
-  # tar/untar a dummy directory, and stop if the command works
-  rm -rf conftest.dir
-  mkdir conftest.dir
-  echo GrepMe > conftest.dir/file
-  AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
+  [m4_case([$1],
+    [ustar],
+     [# The POSIX 1988 'ustar' format is defined with fixed-size fields.
+      # There is notably a 21 bits limit for the UID and the GID.  In fact,
+      # the 'pax' utility can hang on bigger UID/GID (see automake bug#8343
+      # and bug#13588).
+      am_max_uid=2097151 # 2^21 - 1
+      am_max_gid=$am_max_uid
+      # The $UID and $GID variables are not portable, so we need to resort
+      # to the POSIX-mandated id(1) utility.  Errors in the 'id' calls
+      # below are definitely unexpected, so allow the users to see them
+      # (that is, avoid stderr redirection).
+      am_uid=`id -u || echo unknown`
+      am_gid=`id -g || echo unknown`
+      AC_MSG_CHECKING([whether UID '$am_uid' is supported by ustar format])
+      if test $am_uid -le $am_max_uid; then
+         AC_MSG_RESULT([yes])
+      else
+         AC_MSG_RESULT([no])
+         _am_tools=none
+      fi
+      AC_MSG_CHECKING([whether GID '$am_gid' is supported by ustar format])
+      if test $am_gid -le $am_max_gid; then
+         AC_MSG_RESULT([yes])
+      else
+        AC_MSG_RESULT([no])
+        _am_tools=none
+      fi],
+
+  [pax],
+    [],
+
+  [m4_fatal([Unknown tar format])])
+
+  AC_MSG_CHECKING([how to create a $1 tar archive])
+
+  # Go ahead even if we have the value already cached.  We do so because we
+  # need to set the values for the 'am__tar' and 'am__untar' variables.
+  _am_tools=${am_cv_prog_tar_$1-$_am_tools}
+
+  for _am_tool in $_am_tools; do
+    case $_am_tool in
+    gnutar)
+      for _am_tar in tar gnutar gtar; do
+        AM_RUN_LOG([$_am_tar --version]) && break
+      done
+      am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
+      am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'
+      am__untar="$_am_tar -xf -"
+      ;;
+    plaintar)
+      # Must skip GNU tar: if it does not support --format= it doesn't create
+      # ustar tarball either.
+      (tar --version) >/dev/null 2>&1 && continue
+      am__tar='tar chf - "$$tardir"'
+      am__tar_='tar chf - "$tardir"'
+      am__untar='tar xf -'
+      ;;
+    pax)
+      am__tar='pax -L -x $1 -w "$$tardir"'
+      am__tar_='pax -L -x $1 -w "$tardir"'
+      am__untar='pax -r'
+      ;;
+    cpio)
+      am__tar='find "$$tardir" -print | cpio -o -H $1 -L'
+      am__tar_='find "$tardir" -print | cpio -o -H $1 -L'
+      am__untar='cpio -i -H $1 -d'
+      ;;
+    none)
+      am__tar=false
+      am__tar_=false
+      am__untar=false
+      ;;
+    esac
+
+    # If the value was cached, stop now.  We just wanted to have am__tar
+    # and am__untar set.
+    test -n "${am_cv_prog_tar_$1}" && break
+
+    # tar/untar a dummy directory, and stop if the command works.
+    rm -rf conftest.dir
+    mkdir conftest.dir
+    echo GrepMe > conftest.dir/file
+    AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
+    rm -rf conftest.dir
+    if test -s conftest.tar; then
+      AM_RUN_LOG([$am__untar <conftest.tar])
+      AM_RUN_LOG([cat conftest.dir/file])
+      grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
+    fi
+  done
   rm -rf conftest.dir
-  if test -s conftest.tar; then
-    AM_RUN_LOG([$am__untar <conftest.tar])
-    grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
-  fi
-done
-rm -rf conftest.dir
 
-AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
-AC_MSG_RESULT([$am_cv_prog_tar_$1])])
+  AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
+  AC_MSG_RESULT([$am_cv_prog_tar_$1])])
+
 AC_SUBST([am__tar])
 AC_SUBST([am__untar])
 ]) # _AM_PROG_TAR
diff -ruN ccp4srs-old/build-aux/config.guess ccp4srs/build-aux/config.guess
--- ccp4srs-old/build-aux/config.guess	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/build-aux/config.guess	2014-09-09 21:34:12.000000000 -0700
@@ -1,14 +1,12 @@
 #! /bin/sh
 # Attempt to guess a canonical system name.
-#   Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
-#   2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009
-#   Free Software Foundation, Inc.
+#   Copyright 1992-2013 Free Software Foundation, Inc.
 
-timestamp='2009-11-20'
+timestamp='2013-06-10'
 
 # This file is free software; you can redistribute it and/or modify it
 # under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2 of the License, or
+# the Free Software Foundation; either version 3 of the License, or
 # (at your option) any later version.
 #
 # This program is distributed in the hope that it will be useful, but
@@ -17,26 +15,22 @@
 # General Public License for more details.
 #
 # You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA
-# 02110-1301, USA.
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
 #
 # As a special exception to the GNU General Public License, if you
 # distribute this file as part of a program that contains a
 # configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-
-# Originally written by Per Bothner.  Please send patches (context
-# diff format) to <config-patches@gnu.org> and include a ChangeLog
-# entry.
+# the same distribution terms that you use for the rest of that
+# program.  This Exception is an additional permission under section 7
+# of the GNU General Public License, version 3 ("GPLv3").
 #
-# This script attempts to guess a canonical system name similar to
-# config.sub.  If it succeeds, it prints the system name on stdout, and
-# exits with 0.  Otherwise, it exits with 1.
+# Originally written by Per Bothner.
 #
 # You can get the latest version of this script from:
 # http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
+#
+# Please send patches with a ChangeLog entry to config-patches@gnu.org.
+
 
 me=`echo "$0" | sed -e 's,.*/,,'`
 
@@ -56,8 +50,7 @@
 GNU config.guess ($timestamp)
 
 Originally written by Per Bothner.
-Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001,
-2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+Copyright 1992-2013 Free Software Foundation, Inc.
 
 This is free software; see the source for copying conditions.  There is NO
 warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
@@ -139,12 +132,43 @@
 UNAME_SYSTEM=`(uname -s) 2>/dev/null`  || UNAME_SYSTEM=unknown
 UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown
 
+case "${UNAME_SYSTEM}" in
+Linux|GNU|GNU/*)
+	# If the system lacks a compiler, then just pick glibc.
+	# We could probably try harder.
+	LIBC=gnu
+
+	eval $set_cc_for_build
+	cat <<-EOF > $dummy.c
+	#include <features.h>
+	#if defined(__UCLIBC__)
+	LIBC=uclibc
+	#elif defined(__dietlibc__)
+	LIBC=dietlibc
+	#else
+	LIBC=gnu
+	#endif
+	EOF
+	eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC'`
+	;;
+esac
+
+case "${UNAME_MACHINE}" in
+  i?86)
+     test -z "$VENDOR" && VENDOR=pc
+     ;;
+  *)
+     test -z "$VENDOR" && VENDOR=unknown
+     ;;
+esac
+test -f /etc/SuSE-release -o -f /.buildenv && VENDOR=suse
+
 # Note: order is significant - the case branches are not exclusive.
 
 case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
     *:NetBSD:*:*)
 	# NetBSD (nbsd) targets should (where applicable) match one or
-	# more of the tupples: *-*-netbsdelf*, *-*-netbsdaout*,
+	# more of the tuples: *-*-netbsdelf*, *-*-netbsdaout*,
 	# *-*-netbsdecoff* and *-*-netbsd*.  For targets that recently
 	# switched to ELF, *-*-netbsd* would select the old
 	# object file format.  This provides both forward
@@ -180,7 +204,7 @@
 		fi
 		;;
 	    *)
-	        os=netbsd
+		os=netbsd
 		;;
 	esac
 	# The OS release
@@ -201,21 +225,25 @@
 	# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used.
 	echo "${machine}-${os}${release}"
 	exit ;;
+    *:Bitrig:*:*)
+	UNAME_MACHINE_ARCH=`arch | sed 's/Bitrig.//'`
+	echo ${UNAME_MACHINE_ARCH}-${VENDOR}-bitrig${UNAME_RELEASE}
+	exit ;;
     *:OpenBSD:*:*)
 	UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'`
-	echo ${UNAME_MACHINE_ARCH}-unknown-openbsd${UNAME_RELEASE}
+	echo ${UNAME_MACHINE_ARCH}-${VENDOR}-openbsd${UNAME_RELEASE}
 	exit ;;
     *:ekkoBSD:*:*)
-	echo ${UNAME_MACHINE}-unknown-ekkobsd${UNAME_RELEASE}
+	echo ${UNAME_MACHINE}-${VENDOR}-ekkobsd${UNAME_RELEASE}
 	exit ;;
     *:SolidBSD:*:*)
-	echo ${UNAME_MACHINE}-unknown-solidbsd${UNAME_RELEASE}
+	echo ${UNAME_MACHINE}-${VENDOR}-solidbsd${UNAME_RELEASE}
 	exit ;;
     macppc:MirBSD:*:*)
-	echo powerpc-unknown-mirbsd${UNAME_RELEASE}
+	echo powerpc-${VENDOR}-mirbsd${UNAME_RELEASE}
 	exit ;;
     *:MirBSD:*:*)
-	echo ${UNAME_MACHINE}-unknown-mirbsd${UNAME_RELEASE}
+	echo ${UNAME_MACHINE}-${VENDOR}-mirbsd${UNAME_RELEASE}
 	exit ;;
     alpha:OSF1:*:*)
 	case $UNAME_RELEASE in
@@ -223,7 +251,7 @@
 		UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'`
 		;;
 	*5.*)
-	        UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
+		UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
 		;;
 	esac
 	# According to Compaq, /usr/sbin/psrinfo has been available on
@@ -269,7 +297,10 @@
 	# A Xn.n version is an unreleased experimental baselevel.
 	# 1.2 uses "1.2" for uname -r.
 	echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
-	exit ;;
+	# Reset EXIT trap before exiting to avoid spurious non-zero exit code.
+	exitcode=$?
+	trap '' 0
+	exit $exitcode ;;
     Alpha\ *:Windows_NT*:*)
 	# How do we know it's Interix rather than the generic POSIX subsystem?
 	# Should we change UNAME_MACHINE based on the output of uname instead
@@ -280,13 +311,13 @@
 	echo alpha-dec-winnt3.5
 	exit ;;
     Amiga*:UNIX_System_V:4.0:*)
-	echo m68k-unknown-sysv4
+	echo m68k-${VENDOR}-sysv4
 	exit ;;
     *:[Aa]miga[Oo][Ss]:*:*)
-	echo ${UNAME_MACHINE}-unknown-amigaos
+	echo ${UNAME_MACHINE}-${VENDOR}-amigaos
 	exit ;;
     *:[Mm]orph[Oo][Ss]:*:*)
-	echo ${UNAME_MACHINE}-unknown-morphos
+	echo ${UNAME_MACHINE}-${VENDOR}-morphos
 	exit ;;
     *:OS/390:*:*)
 	echo i370-ibm-openedition
@@ -295,13 +326,13 @@
 	echo s390-ibm-zvmoe
 	exit ;;
     *:OS400:*:*)
-        echo powerpc-ibm-os400
+	echo powerpc-ibm-os400
 	exit ;;
     arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*)
 	echo arm-acorn-riscix${UNAME_RELEASE}
 	exit ;;
-    arm:riscos:*:*|arm:RISCOS:*:*)
-	echo arm-unknown-riscos
+    arm*:riscos:*:*|arm*:RISCOS:*:*)
+	echo arm-${VENDOR}-riscos
 	exit ;;
     SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*)
 	echo hppa1.1-hitachi-hiuxmpp
@@ -394,23 +425,23 @@
     # MiNT.  But MiNT is downward compatible to TOS, so this should
     # be no problem.
     atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*)
-        echo m68k-atari-mint${UNAME_RELEASE}
+	echo m68k-atari-mint${UNAME_RELEASE}
 	exit ;;
     atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*)
 	echo m68k-atari-mint${UNAME_RELEASE}
-        exit ;;
+	exit ;;
     *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*)
-        echo m68k-atari-mint${UNAME_RELEASE}
+	echo m68k-atari-mint${UNAME_RELEASE}
 	exit ;;
     milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*)
-        echo m68k-milan-mint${UNAME_RELEASE}
-        exit ;;
+	echo m68k-milan-mint${UNAME_RELEASE}
+	exit ;;
     hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*)
-        echo m68k-hades-mint${UNAME_RELEASE}
-        exit ;;
+	echo m68k-hades-mint${UNAME_RELEASE}
+	exit ;;
     *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*)
-        echo m68k-unknown-mint${UNAME_RELEASE}
-        exit ;;
+	echo m68k-${VENDOR}-mint${UNAME_RELEASE}
+	exit ;;
     m68k:machten:*:*)
 	echo m68k-apple-machten${UNAME_RELEASE}
 	exit ;;
@@ -480,8 +511,8 @@
 	echo m88k-motorola-sysv3
 	exit ;;
     AViiON:dgux:*:*)
-        # DG/UX returns AViiON for all architectures
-        UNAME_PROCESSOR=`/usr/bin/uname -p`
+	# DG/UX returns AViiON for all architectures
+	UNAME_PROCESSOR=`/usr/bin/uname -p`
 	if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ]
 	then
 	    if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \
@@ -494,7 +525,7 @@
 	else
 	    echo i586-dg-dgux${UNAME_RELEASE}
 	fi
- 	exit ;;
+	exit ;;
     M88*:DolphinOS:*:*)	# DolphinOS (SVR3)
 	echo m88k-dolphin-sysv3
 	exit ;;
@@ -551,7 +582,7 @@
 		echo rs6000-ibm-aix3.2
 	fi
 	exit ;;
-    *:AIX:*:[456])
+    *:AIX:*:[4567])
 	IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'`
 	if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then
 		IBM_ARCH=rs6000
@@ -594,52 +625,52 @@
 	    9000/[678][0-9][0-9])
 		if [ -x /usr/bin/getconf ]; then
 		    sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null`
-                    sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null`
-                    case "${sc_cpu_version}" in
-                      523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0
-                      528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1
-                      532)                      # CPU_PA_RISC2_0
-                        case "${sc_kernel_bits}" in
-                          32) HP_ARCH="hppa2.0n" ;;
-                          64) HP_ARCH="hppa2.0w" ;;
+		    sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null`
+		    case "${sc_cpu_version}" in
+		      523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0
+		      528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1
+		      532)                      # CPU_PA_RISC2_0
+			case "${sc_kernel_bits}" in
+			  32) HP_ARCH="hppa2.0n" ;;
+			  64) HP_ARCH="hppa2.0w" ;;
 			  '') HP_ARCH="hppa2.0" ;;   # HP-UX 10.20
-                        esac ;;
-                    esac
+			esac ;;
+		    esac
 		fi
 		if [ "${HP_ARCH}" = "" ]; then
 		    eval $set_cc_for_build
-		    sed 's/^              //' << EOF >$dummy.c
+		    sed 's/^		//' << EOF >$dummy.c
+
+		#define _HPUX_SOURCE
+		#include <stdlib.h>
+		#include <unistd.h>
 
-              #define _HPUX_SOURCE
-              #include <stdlib.h>
-              #include <unistd.h>
-
-              int main ()
-              {
-              #if defined(_SC_KERNEL_BITS)
-                  long bits = sysconf(_SC_KERNEL_BITS);
-              #endif
-                  long cpu  = sysconf (_SC_CPU_VERSION);
-
-                  switch (cpu)
-              	{
-              	case CPU_PA_RISC1_0: puts ("hppa1.0"); break;
-              	case CPU_PA_RISC1_1: puts ("hppa1.1"); break;
-              	case CPU_PA_RISC2_0:
-              #if defined(_SC_KERNEL_BITS)
-              	    switch (bits)
-              		{
-              		case 64: puts ("hppa2.0w"); break;
-              		case 32: puts ("hppa2.0n"); break;
-              		default: puts ("hppa2.0"); break;
-              		} break;
-              #else  /* !defined(_SC_KERNEL_BITS) */
-              	    puts ("hppa2.0"); break;
-              #endif
-              	default: puts ("hppa1.0"); break;
-              	}
-                  exit (0);
-              }
+		int main ()
+		{
+		#if defined(_SC_KERNEL_BITS)
+		    long bits = sysconf(_SC_KERNEL_BITS);
+		#endif
+		    long cpu  = sysconf (_SC_CPU_VERSION);
+
+		    switch (cpu)
+			{
+			case CPU_PA_RISC1_0: puts ("hppa1.0"); break;
+			case CPU_PA_RISC1_1: puts ("hppa1.1"); break;
+			case CPU_PA_RISC2_0:
+		#if defined(_SC_KERNEL_BITS)
+			    switch (bits)
+				{
+				case 64: puts ("hppa2.0w"); break;
+				case 32: puts ("hppa2.0n"); break;
+				default: puts ("hppa2.0"); break;
+				} break;
+		#else  /* !defined(_SC_KERNEL_BITS) */
+			    puts ("hppa2.0"); break;
+		#endif
+			default: puts ("hppa1.0"); break;
+			}
+		    exit (0);
+		}
 EOF
 		    (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy`
 		    test -z "$HP_ARCH" && HP_ARCH=hppa
@@ -720,9 +751,9 @@
 	exit ;;
     i*86:OSF1:*:*)
 	if [ -x /usr/sbin/sysversion ] ; then
-	    echo ${UNAME_MACHINE}-unknown-osf1mk
+	    echo ${UNAME_MACHINE}-${VENDOR}-osf1mk
 	else
-	    echo ${UNAME_MACHINE}-unknown-osf1
+	    echo ${UNAME_MACHINE}-${VENDOR}-osf1
 	fi
 	exit ;;
     parisc*:Lites*:*:*)
@@ -730,22 +761,22 @@
 	exit ;;
     C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*)
 	echo c1-convex-bsd
-        exit ;;
+	exit ;;
     C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*)
 	if getsysinfo -f scalar_acc
 	then echo c32-convex-bsd
 	else echo c2-convex-bsd
 	fi
-        exit ;;
+	exit ;;
     C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*)
 	echo c34-convex-bsd
-        exit ;;
+	exit ;;
     C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*)
 	echo c38-convex-bsd
-        exit ;;
+	exit ;;
     C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*)
 	echo c4-convex-bsd
-        exit ;;
+	exit ;;
     CRAY*Y-MP:*:*:*)
 	echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
 	exit ;;
@@ -769,57 +800,62 @@
 	exit ;;
     F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*)
 	FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
-        FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
-        FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
-        echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
-        exit ;;
+	FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
+	FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
+	echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+	exit ;;
     5000:UNIX_System_V:4.*:*)
-        FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
-        FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'`
-        echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+	FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
+	FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'`
+	echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
 	exit ;;
     i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*)
 	echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE}
 	exit ;;
     sparc*:BSD/OS:*:*)
-	echo sparc-unknown-bsdi${UNAME_RELEASE}
+	echo sparc-${VENDOR}-bsdi${UNAME_RELEASE}
 	exit ;;
     *:BSD/OS:*:*)
-	echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE}
+	echo ${UNAME_MACHINE}-${VENDOR}-bsdi${UNAME_RELEASE}
 	exit ;;
     *:FreeBSD:*:*)
-	case ${UNAME_MACHINE} in
-	    pc98)
-		echo i386-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
+	UNAME_PROCESSOR=`/usr/bin/uname -p`
+	case ${UNAME_PROCESSOR} in
 	    amd64)
-		echo x86_64-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
+		echo x86_64-${VENDOR}-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
 	    *)
-		echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
+		echo ${UNAME_PROCESSOR}-${VENDOR}-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
 	esac
 	exit ;;
     i*:CYGWIN*:*)
 	echo ${UNAME_MACHINE}-pc-cygwin
 	exit ;;
+    *:MINGW64*:*)
+	echo ${UNAME_MACHINE}-pc-mingw64
+	exit ;;
     *:MINGW*:*)
 	echo ${UNAME_MACHINE}-pc-mingw32
 	exit ;;
+    i*:MSYS*:*)
+	echo ${UNAME_MACHINE}-pc-msys
+	exit ;;
     i*:windows32*:*)
-    	# uname -m includes "-pc" on this system.
-    	echo ${UNAME_MACHINE}-mingw32
+	# uname -m includes "-pc" on this system.
+	echo ${UNAME_MACHINE}-mingw32
 	exit ;;
     i*:PW*:*)
 	echo ${UNAME_MACHINE}-pc-pw32
 	exit ;;
     *:Interix*:*)
-    	case ${UNAME_MACHINE} in
+	case ${UNAME_MACHINE} in
 	    x86)
 		echo i586-pc-interix${UNAME_RELEASE}
 		exit ;;
 	    authenticamd | genuineintel | EM64T)
-		echo x86_64-unknown-interix${UNAME_RELEASE}
+		echo x86_64-${VENDOR}-interix${UNAME_RELEASE}
 		exit ;;
 	    IA64)
-		echo ia64-unknown-interix${UNAME_RELEASE}
+		echo ia64-${VENDOR}-interix${UNAME_RELEASE}
 		exit ;;
 	esac ;;
     [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*)
@@ -838,25 +874,32 @@
 	echo ${UNAME_MACHINE}-pc-uwin
 	exit ;;
     amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*)
-	echo x86_64-unknown-cygwin
+	echo x86_64-${VENDOR}-cygwin
 	exit ;;
     p*:CYGWIN*:*)
-	echo powerpcle-unknown-cygwin
+	echo powerpcle-${VENDOR}-cygwin
 	exit ;;
     prep*:SunOS:5.*:*)
-	echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+	echo powerpcle-${VENDOR}-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
 	exit ;;
     *:GNU:*:*)
 	# the GNU system
-	echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'`
+	echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-${VENDOR}-${LIBC}`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'`
 	exit ;;
     *:GNU/*:*:*)
 	# other systems with GNU libc and userland
-	echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu
+	echo ${UNAME_MACHINE}-${VENDOR}-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-${LIBC}
 	exit ;;
     i*86:Minix:*:*)
 	echo ${UNAME_MACHINE}-pc-minix
 	exit ;;
+    aarch64:Linux:*:*)
+	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
+	exit ;;
+    aarch64_be:Linux:*:*)
+	UNAME_MACHINE=aarch64_be
+	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
+	exit ;;
     alpha:Linux:*:*)
 	case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in
 	  EV5)   UNAME_MACHINE=alphaev5 ;;
@@ -866,52 +909,56 @@
 	  EV6)   UNAME_MACHINE=alphaev6 ;;
 	  EV67)  UNAME_MACHINE=alphaev67 ;;
 	  EV68*) UNAME_MACHINE=alphaev68 ;;
-        esac
+	esac
 	objdump --private-headers /bin/sh | grep -q ld.so.1
-	if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi
-	echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC}
+	if test "$?" = 0 ; then LIBC="gnulibc1" ; fi
+	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
+	exit ;;
+    arc:Linux:*:* | arceb:Linux:*:*)
+	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
 	exit ;;
     arm*:Linux:*:*)
 	eval $set_cc_for_build
 	if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \
 	    | grep -q __ARM_EABI__
 	then
-	    echo ${UNAME_MACHINE}-unknown-linux-gnu
+	    echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
 	else
-	    echo ${UNAME_MACHINE}-unknown-linux-gnueabi
+	    if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \
+		| grep -q __ARM_PCS_VFP
+	    then
+		echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}eabi
+	    else
+		echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}eabihf
+	    fi
 	fi
 	exit ;;
     avr32*:Linux:*:*)
-	echo ${UNAME_MACHINE}-unknown-linux-gnu
+	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
 	exit ;;
     cris:Linux:*:*)
-	echo cris-axis-linux-gnu
+	echo ${UNAME_MACHINE}-axis-linux-${LIBC}
 	exit ;;
     crisv32:Linux:*:*)
-	echo crisv32-axis-linux-gnu
+	echo ${UNAME_MACHINE}-axis-linux-${LIBC}
 	exit ;;
     frv:Linux:*:*)
-    	echo frv-unknown-linux-gnu
+	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
+	exit ;;
+    hexagon:Linux:*:*)
+	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
 	exit ;;
     i*86:Linux:*:*)
-	LIBC=gnu
-	eval $set_cc_for_build
-	sed 's/^	//' << EOF >$dummy.c
-	#ifdef __dietlibc__
-	LIBC=dietlibc
-	#endif
-EOF
-	eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC'`
-	echo "${UNAME_MACHINE}-pc-linux-${LIBC}"
+	echo ${UNAME_MACHINE}-pc-linux-${LIBC}
 	exit ;;
     ia64:Linux:*:*)
-	echo ${UNAME_MACHINE}-unknown-linux-gnu
+	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
 	exit ;;
     m32r*:Linux:*:*)
-	echo ${UNAME_MACHINE}-unknown-linux-gnu
+	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
 	exit ;;
     m68*:Linux:*:*)
-	echo ${UNAME_MACHINE}-unknown-linux-gnu
+	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
 	exit ;;
     mips:Linux:*:* | mips64:Linux:*:*)
 	eval $set_cc_for_build
@@ -930,51 +977,63 @@
 	#endif
 EOF
 	eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^CPU'`
-	test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; }
+	test x"${CPU}" != x && { echo "${CPU}-${VENDOR}-linux-${LIBC}"; exit; }
 	;;
+    or1k:Linux:*:*)
+	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
+	exit ;;
     or32:Linux:*:*)
-	echo or32-unknown-linux-gnu
+	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
 	exit ;;
     padre:Linux:*:*)
-	echo sparc-unknown-linux-gnu
+	echo sparc-${VENDOR}-linux-${LIBC}
 	exit ;;
     parisc64:Linux:*:* | hppa64:Linux:*:*)
-	echo hppa64-unknown-linux-gnu
+	echo hppa64-${VENDOR}-linux-${LIBC}
 	exit ;;
     parisc:Linux:*:* | hppa:Linux:*:*)
 	# Look for CPU level
 	case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in
-	  PA7*) echo hppa1.1-unknown-linux-gnu ;;
-	  PA8*) echo hppa2.0-unknown-linux-gnu ;;
-	  *)    echo hppa-unknown-linux-gnu ;;
+	  PA7*) echo hppa1.1-${VENDOR}-linux-${LIBC} ;;
+	  PA8*) echo hppa2.0-${VENDOR}-linux-${LIBC} ;;
+	  *)    echo hppa-${VENDOR}-linux-${LIBC} ;;
 	esac
 	exit ;;
     ppc64:Linux:*:*)
-	echo powerpc64-unknown-linux-gnu
+	echo powerpc64-${VENDOR}-linux-${LIBC}
 	exit ;;
     ppc:Linux:*:*)
-	echo powerpc-unknown-linux-gnu
+	echo powerpc-${VENDOR}-linux-${LIBC}
+	exit ;;
+    ppc64le:Linux:*:*)
+	echo powerpc64le-${VENDOR}-linux-${LIBC}
+	exit ;;
+    ppcle:Linux:*:*)
+	echo powerpcle-${VENDOR}-linux-${LIBC}
 	exit ;;
     s390:Linux:*:* | s390x:Linux:*:*)
-	echo ${UNAME_MACHINE}-ibm-linux
+	echo ${UNAME_MACHINE}-ibm-linux-${LIBC}
 	exit ;;
     sh64*:Linux:*:*)
-    	echo ${UNAME_MACHINE}-unknown-linux-gnu
+	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
 	exit ;;
     sh*:Linux:*:*)
-	echo ${UNAME_MACHINE}-unknown-linux-gnu
+	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
 	exit ;;
     sparc:Linux:*:* | sparc64:Linux:*:*)
-	echo ${UNAME_MACHINE}-unknown-linux-gnu
+	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
+	exit ;;
+    tile*:Linux:*:*)
+	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
 	exit ;;
     vax:Linux:*:*)
-	echo ${UNAME_MACHINE}-dec-linux-gnu
+	echo ${UNAME_MACHINE}-dec-linux-${LIBC}
 	exit ;;
     x86_64:Linux:*:*)
-	echo x86_64-unknown-linux-gnu
+	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
 	exit ;;
     xtensa*:Linux:*:*)
-    	echo ${UNAME_MACHINE}-unknown-linux-gnu
+	echo ${UNAME_MACHINE}-${VENDOR}-linux-${LIBC}
 	exit ;;
     i*86:DYNIX/ptx:4*:*)
 	# ptx 4.0 does uname -s correctly, with DYNIX/ptx in there.
@@ -983,11 +1042,11 @@
 	echo i386-sequent-sysv4
 	exit ;;
     i*86:UNIX_SV:4.2MP:2.*)
-        # Unixware is an offshoot of SVR4, but it has its own version
-        # number series starting with 2...
-        # I am not positive that other SVR4 systems won't match this,
+	# Unixware is an offshoot of SVR4, but it has its own version
+	# number series starting with 2...
+	# I am not positive that other SVR4 systems won't match this,
 	# I just have to hope.  -- rms.
-        # Use sysv4.2uw... so that sysv4* matches it.
+	# Use sysv4.2uw... so that sysv4* matches it.
 	echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION}
 	exit ;;
     i*86:OS/2:*:*)
@@ -996,16 +1055,16 @@
 	echo ${UNAME_MACHINE}-pc-os2-emx
 	exit ;;
     i*86:XTS-300:*:STOP)
-	echo ${UNAME_MACHINE}-unknown-stop
+	echo ${UNAME_MACHINE}-${VENDOR}-stop
 	exit ;;
     i*86:atheos:*:*)
-	echo ${UNAME_MACHINE}-unknown-atheos
+	echo ${UNAME_MACHINE}-${VENDOR}-atheos
 	exit ;;
     i*86:syllable:*:*)
 	echo ${UNAME_MACHINE}-pc-syllable
 	exit ;;
     i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*)
-	echo i386-unknown-lynxos${UNAME_RELEASE}
+	echo i386-${VENODR}-lynxos${UNAME_RELEASE}
 	exit ;;
     i*86:*DOS:*:*)
 	echo ${UNAME_MACHINE}-pc-msdosdjgpp
@@ -1019,13 +1078,13 @@
 	fi
 	exit ;;
     i*86:*:5:[678]*)
-    	# UnixWare 7.x, OpenUNIX and OpenServer 6.
+	# UnixWare 7.x, OpenUNIX and OpenServer 6.
 	case `/bin/uname -X | grep "^Machine"` in
 	    *486*)	     UNAME_MACHINE=i486 ;;
 	    *Pentium)	     UNAME_MACHINE=i586 ;;
 	    *Pent*|*Celeron) UNAME_MACHINE=i686 ;;
 	esac
-	echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION}
+	echo ${UNAME_MACHINE}-${VENDOR}-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION}
 	exit ;;
     i*86:*:3.2:*)
 	if test -f /usr/options/cb.name; then
@@ -1047,13 +1106,13 @@
 	exit ;;
     pc:*:*:*)
 	# Left here for compatibility:
-        # uname -m prints for DJGPP always 'pc', but it prints nothing about
-        # the processor, so we play safe by assuming i586.
+	# uname -m prints for DJGPP always 'pc', but it prints nothing about
+	# the processor, so we play safe by assuming i586.
 	# Note: whatever this is, it MUST be the same as what config.sub
 	# prints for the "djgpp" host, or else GDB configury will decide that
 	# this is a cross-build.
 	echo i586-pc-msdosdjgpp
-        exit ;;
+	exit ;;
     Intel:Mach:3*:*)
 	echo i386-pc-mach3
 	exit ;;
@@ -1064,7 +1123,7 @@
 	if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then
 	  echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4
 	else # Add other i860-SVR4 vendors below as they are discovered.
-	  echo i860-unknown-sysv${UNAME_RELEASE}  # Unknown i860-SVR4
+	  echo i860-${VENODR}-sysv${UNAME_RELEASE}  # Unknown i860-SVR4
 	fi
 	exit ;;
     mini*:CTIX:SYS*5:*)
@@ -1088,8 +1147,8 @@
 	/bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
 	  && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;;
     3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*)
-        /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
-          && { echo i486-ncr-sysv4; exit; } ;;
+	/bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+	  && { echo i486-ncr-sysv4; exit; } ;;
     NCR*:*:4.2:* | MPRAS*:*:4.2:*)
 	OS_REL='.3'
 	test -r /etc/.relid \
@@ -1101,19 +1160,19 @@
 	/bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \
 	    && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;;
     m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*)
-	echo m68k-unknown-lynxos${UNAME_RELEASE}
+	echo m68k-${VENDOR}-lynxos${UNAME_RELEASE}
 	exit ;;
     mc68030:UNIX_System_V:4.*:*)
 	echo m68k-atari-sysv4
 	exit ;;
     TSUNAMI:LynxOS:2.*:*)
-	echo sparc-unknown-lynxos${UNAME_RELEASE}
+	echo sparc-${VENDOR}-lynxos${UNAME_RELEASE}
 	exit ;;
     rs6000:LynxOS:2.*:*)
-	echo rs6000-unknown-lynxos${UNAME_RELEASE}
+	echo rs6000-${VENDOR}-lynxos${UNAME_RELEASE}
 	exit ;;
     PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*)
-	echo powerpc-unknown-lynxos${UNAME_RELEASE}
+	echo powerpc-${VENDOR}-lynxos${UNAME_RELEASE}
 	exit ;;
     SM[BE]S:UNIX_SV:*:*)
 	echo mips-dde-sysv${UNAME_RELEASE}
@@ -1132,10 +1191,10 @@
 		echo ns32k-sni-sysv
 	fi
 	exit ;;
-    PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort
-                      # says <Richard.M.Bartel@ccMail.Census.GOV>
-        echo i586-unisys-sysv4
-        exit ;;
+    PENTIUM:*:4.0*:*)	# Unisys `ClearPath HMP IX 4000' SVR4/MP effort
+			# says <Richard.M.Bartel@ccMail.Census.GOV>
+	echo i586-unisys-sysv4
+	exit ;;
     *:UNIX_System_V:4*:FTX*)
 	# From Gerald Hewes <hewes@openmarket.com>.
 	# How about differentiating between stratus architectures? -djm
@@ -1161,11 +1220,11 @@
 	exit ;;
     R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*)
 	if [ -d /usr/nec ]; then
-	        echo mips-nec-sysv${UNAME_RELEASE}
+		echo mips-nec-sysv${UNAME_RELEASE}
 	else
-	        echo mips-unknown-sysv${UNAME_RELEASE}
+		echo mips-${VENDOR}-sysv${UNAME_RELEASE}
 	fi
-        exit ;;
+	exit ;;
     BeBox:BeOS:*:*)	# BeOS running on hardware made by Be, PPC only.
 	echo powerpc-be-beos
 	exit ;;
@@ -1178,6 +1237,9 @@
     BePC:Haiku:*:*)	# Haiku running on Intel PC compatible.
 	echo i586-pc-haiku
 	exit ;;
+    x86_64:Haiku:*:*)
+	echo x86_64-${VENDOR}-haiku
+	exit ;;
     SX-4:SUPER-UX:*:*)
 	echo sx4-nec-superux${UNAME_RELEASE}
 	exit ;;
@@ -1204,19 +1266,21 @@
 	exit ;;
     *:Darwin:*:*)
 	UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown
-	case $UNAME_PROCESSOR in
-	    i386)
-		eval $set_cc_for_build
-		if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then
-		  if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \
-		      (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \
-		      grep IS_64BIT_ARCH >/dev/null
-		  then
-		      UNAME_PROCESSOR="x86_64"
-		  fi
-		fi ;;
-	    unknown) UNAME_PROCESSOR=powerpc ;;
-	esac
+	eval $set_cc_for_build
+	if test "$UNAME_PROCESSOR" = unknown ; then
+	    UNAME_PROCESSOR=powerpc
+	fi
+	if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then
+	    if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \
+		(CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \
+		grep IS_64BIT_ARCH >/dev/null
+	    then
+		case $UNAME_PROCESSOR in
+		    i386) UNAME_PROCESSOR=x86_64 ;;
+		    powerpc) UNAME_PROCESSOR=powerpc64 ;;
+		esac
+	    fi
+	fi
 	echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE}
 	exit ;;
     *:procnto*:*:* | *:QNX:[0123456789]*:*)
@@ -1230,7 +1294,10 @@
     *:QNX:*:4*)
 	echo i386-pc-qnx
 	exit ;;
-    NSE-?:NONSTOP_KERNEL:*:*)
+    NEO-?:NONSTOP_KERNEL:*:*)
+	echo neo-tandem-nsk${UNAME_RELEASE}
+	exit ;;
+    NSE-*:NONSTOP_KERNEL:*:*)
 	echo nse-tandem-nsk${UNAME_RELEASE}
 	exit ;;
     NSR-?:NONSTOP_KERNEL:*:*)
@@ -1254,13 +1321,13 @@
 	else
 	    UNAME_MACHINE="$cputype"
 	fi
-	echo ${UNAME_MACHINE}-unknown-plan9
+	echo ${UNAME_MACHINE}-${VENDOR}-plan9
 	exit ;;
     *:TOPS-10:*:*)
-	echo pdp10-unknown-tops10
+	echo pdp10-${VENDOR}-tops10
 	exit ;;
     *:TENEX:*:*)
-	echo pdp10-unknown-tenex
+	echo pdp10-${VENDOR}-tenex
 	exit ;;
     KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*)
 	echo pdp10-dec-tops20
@@ -1269,19 +1336,19 @@
 	echo pdp10-xkl-tops20
 	exit ;;
     *:TOPS-20:*:*)
-	echo pdp10-unknown-tops20
+	echo pdp10-${VENDOR}-tops20
 	exit ;;
     *:ITS:*:*)
-	echo pdp10-unknown-its
+	echo pdp10-${VENDOR}-its
 	exit ;;
     SEI:*:*:SEIUX)
-        echo mips-sei-seiux${UNAME_RELEASE}
+	echo mips-sei-seiux${UNAME_RELEASE}
 	exit ;;
     *:DragonFly:*:*)
-	echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
+	echo ${UNAME_MACHINE}-${VENDOR}-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
 	exit ;;
     *:*VMS:*:*)
-    	UNAME_MACHINE=`(uname -p) 2>/dev/null`
+	UNAME_MACHINE=`(uname -p) 2>/dev/null`
 	case "${UNAME_MACHINE}" in
 	    A*) echo alpha-dec-vms ; exit ;;
 	    I*) echo ia64-dec-vms ; exit ;;
@@ -1299,11 +1366,11 @@
     i*86:AROS:*:*)
 	echo ${UNAME_MACHINE}-pc-aros
 	exit ;;
+    x86_64:VMkernel:*:*)
+	echo ${UNAME_MACHINE}-${VENDOR}-esx
+	exit ;;
 esac
 
-#echo '(No uname command or uname output not recognized.)' 1>&2
-#echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2
-
 eval $set_cc_for_build
 cat >$dummy.c <<EOF
 #ifdef _SEQUENT_
@@ -1321,11 +1388,11 @@
 #include <sys/param.h>
   printf ("m68k-sony-newsos%s\n",
 #ifdef NEWSOS4
-          "4"
+	"4"
 #else
-	  ""
+	""
 #endif
-         ); exit (0);
+	); exit (0);
 #endif
 #endif
 
diff -ruN ccp4srs-old/build-aux/config.sub ccp4srs/build-aux/config.sub
--- ccp4srs-old/build-aux/config.sub	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/build-aux/config.sub	2014-09-09 21:34:12.000000000 -0700
@@ -1,38 +1,31 @@
 #! /bin/sh
 # Configuration validation subroutine script.
-#   Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
-#   2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009
-#   Free Software Foundation, Inc.
-
-timestamp='2009-11-20'
-
-# This file is (in principle) common to ALL GNU software.
-# The presence of a machine in this file suggests that SOME GNU software
-# can handle that machine.  It does not imply ALL GNU software can.
-#
-# This file is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2 of the License, or
+#   Copyright 1992-2013 Free Software Foundation, Inc.
+
+timestamp='2013-04-24'
+
+# This file is free software; you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 3 of the License, or
 # (at your option) any later version.
 #
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# General Public License for more details.
 #
 # You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA
-# 02110-1301, USA.
+# along with this program; if not, see <http://www.gnu.org/licenses/>.
 #
 # As a special exception to the GNU General Public License, if you
 # distribute this file as part of a program that contains a
 # configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
+# the same distribution terms that you use for the rest of that
+# program.  This Exception is an additional permission under section 7
+# of the GNU General Public License, version 3 ("GPLv3").
 
 
-# Please send patches to <config-patches@gnu.org>.  Submit a context
-# diff and a properly formatted GNU ChangeLog entry.
+# Please send patches with a ChangeLog entry to config-patches@gnu.org.
 #
 # Configuration subroutine to validate and canonicalize a configuration type.
 # Supply the specified configuration type as an argument.
@@ -75,8 +68,7 @@
 version="\
 GNU config.sub ($timestamp)
 
-Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001,
-2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+Copyright 1992-2013 Free Software Foundation, Inc.
 
 This is free software; see the source for copying conditions.  There is NO
 warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
@@ -123,13 +115,18 @@
 # Here we must recognize all the valid KERNEL-OS combinations.
 maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'`
 case $maybe_os in
-  nto-qnx* | linux-gnu* | linux-dietlibc | linux-newlib* | linux-uclibc* | \
-  uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | \
+  nto-qnx* | linux-gnu* | linux-android* | linux-dietlibc | linux-newlib* | \
+  linux-musl* | linux-uclibc* | uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | \
+  knetbsd*-gnu* | netbsd*-gnu* | \
   kopensolaris*-gnu* | \
   storm-chaos* | os2-emx* | rtmk-nova*)
     os=-$maybe_os
     basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
     ;;
+  android-linux)
+    os=-linux-android
+    basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`-unknown
+    ;;
   *)
     basic_machine=`echo $1 | sed 's/-[^-]*$//'`
     if [ $basic_machine != $1 ]
@@ -152,12 +149,12 @@
 	-convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\
 	-c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \
 	-harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \
-	-apple | -axis | -knuth | -cray | -microblaze)
+	-apple | -axis | -knuth | -cray | -microblaze*)
 		os=
 		basic_machine=$1
 		;;
-        -bluegene*)
-	        os=-cnk
+	-bluegene*)
+		os=-cnk
 		;;
 	-sim | -cisco | -oki | -wec | -winbond)
 		os=
@@ -173,10 +170,10 @@
 		os=-chorusos
 		basic_machine=$1
 		;;
- 	-chorusrdb)
- 		os=-chorusrdb
+	-chorusrdb)
+		os=-chorusrdb
 		basic_machine=$1
- 		;;
+		;;
 	-hiux*)
 		os=-hiuxwe2
 		;;
@@ -221,6 +218,12 @@
 	-isc*)
 		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
 		;;
+	-lynx*178)
+		os=-lynxos178
+		;;
+	-lynx*5)
+		os=-lynxos5
+		;;
 	-lynx*)
 		os=-lynxos
 		;;
@@ -245,20 +248,27 @@
 	# Some are omitted here because they have special meanings below.
 	1750a | 580 \
 	| a29k \
+	| aarch64 | aarch64_be \
 	| alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \
 	| alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \
 	| am33_2.0 \
-	| arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr | avr32 \
+	| arc | arceb \
+	| arm | arm[bl]e | arme[lb] | armv[2-8] | armv[3-8][lb] | armv7[arm] \
+	| avr | avr32 \
+	| be32 | be64 \
 	| bfin \
 	| c4x | clipper \
 	| d10v | d30v | dlx | dsp16xx \
+	| epiphany \
 	| fido | fr30 | frv \
 	| h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \
+	| hexagon \
 	| i370 | i860 | i960 | ia64 \
 	| ip2k | iq2000 \
+	| le32 | le64 \
 	| lm32 \
 	| m32c | m32r | m32rle | m68000 | m68k | m88k \
-	| maxq | mb | microblaze | mcore | mep | metag \
+	| maxq | mb | microblaze | microblazeel | mcore | mep | metag \
 	| mips | mipsbe | mipseb | mipsel | mipsle \
 	| mips16 \
 	| mips64 | mips64el \
@@ -276,34 +286,45 @@
 	| mipsisa64r2 | mipsisa64r2el \
 	| mipsisa64sb1 | mipsisa64sb1el \
 	| mipsisa64sr71k | mipsisa64sr71kel \
+	| mipsr5900 | mipsr5900el \
 	| mipstx39 | mipstx39el \
 	| mn10200 | mn10300 \
 	| moxie \
 	| mt \
 	| msp430 \
-	| nios | nios2 \
+	| nds32 | nds32le | nds32be \
+	| nios | nios2 | nios2eb | nios2el \
 	| ns16k | ns32k \
-	| or32 \
+	| open8 \
+	| or1k | or32 \
 	| pdp10 | pdp11 | pj | pjl \
-	| powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \
+	| powerpc | powerpc64 | powerpc64le | powerpcle \
 	| pyramid \
-	| rx \
+	| rl78 | rx \
 	| score \
 	| sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \
 	| sh64 | sh64le \
 	| sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \
 	| sparcv8 | sparcv9 | sparcv9b | sparcv9v \
-	| spu | strongarm \
-	| tahoe | thumb | tic4x | tic80 | tron \
+	| spu \
+	| tahoe | tic4x | tic54x | tic55x | tic6x | tic80 | tron \
 	| ubicom32 \
-	| v850 | v850e \
+	| v850 | v850e | v850e1 | v850e2 | v850es | v850e2v3 \
 	| we32k \
-	| x86 | xc16x | xscale | xscalee[bl] | xstormy16 | xtensa \
+	| x86 | xc16x | xstormy16 | xtensa \
 	| z8k | z80)
 		basic_machine=$basic_machine-unknown
 		;;
-	m6811 | m68hc11 | m6812 | m68hc12 | picochip)
-		# Motorola 68HC11/12.
+	c54x)
+		basic_machine=tic54x-unknown
+		;;
+	c55x)
+		basic_machine=tic55x-unknown
+		;;
+	c6x)
+		basic_machine=tic6x-unknown
+		;;
+	m6811 | m68hc11 | m6812 | m68hc12 | m68hcs12x | picochip)
 		basic_machine=$basic_machine-unknown
 		os=-none
 		;;
@@ -313,6 +334,21 @@
 		basic_machine=mt-unknown
 		;;
 
+	strongarm | thumb | xscale)
+		basic_machine=arm-unknown
+		;;
+	xgate)
+		basic_machine=$basic_machine-unknown
+		os=-none
+		;;
+	xscaleeb)
+		basic_machine=armeb-unknown
+		;;
+
+	xscaleel)
+		basic_machine=armel-unknown
+		;;
+
 	# We use `pc' rather than `unknown'
 	# because (1) that's what they normally are, and
 	# (2) the word "unknown" tends to confuse beginning users.
@@ -327,25 +363,30 @@
 	# Recognize the basic CPU types with company name.
 	580-* \
 	| a29k-* \
+	| aarch64-* | aarch64_be-* \
 	| alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \
 	| alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \
-	| alphapca5[67]-* | alpha64pca5[67]-* | arc-* \
+	| alphapca5[67]-* | alpha64pca5[67]-* | arc-* | arceb-* \
 	| arm-*  | armbe-* | armle-* | armeb-* | armv*-* \
 	| avr-* | avr32-* \
+	| be32-* | be64-* \
 	| bfin-* | bs2000-* \
-	| c[123]* | c30-* | [cjt]90-* | c4x-* | c54x-* | c55x-* | c6x-* \
+	| c[123]* | c30-* | [cjt]90-* | c4x-* \
 	| clipper-* | craynv-* | cydra-* \
 	| d10v-* | d30v-* | dlx-* \
 	| elxsi-* \
 	| f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \
 	| h8300-* | h8500-* \
 	| hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \
+	| hexagon-* \
 	| i*86-* | i860-* | i960-* | ia64-* \
 	| ip2k-* | iq2000-* \
+	| le32-* | le64-* \
 	| lm32-* \
 	| m32c-* | m32r-* | m32rle-* \
 	| m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \
-	| m88110-* | m88k-* | maxq-* | mcore-* | metag-* | microblaze-* \
+	| m88110-* | m88k-* | maxq-* | mcore-* | metag-* \
+	| microblaze-* | microblazeel-* \
 	| mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \
 	| mips16-* \
 	| mips64-* | mips64el-* \
@@ -363,29 +404,34 @@
 	| mipsisa64r2-* | mipsisa64r2el-* \
 	| mipsisa64sb1-* | mipsisa64sb1el-* \
 	| mipsisa64sr71k-* | mipsisa64sr71kel-* \
+	| mipsr5900-* | mipsr5900el-* \
 	| mipstx39-* | mipstx39el-* \
 	| mmix-* \
 	| mt-* \
 	| msp430-* \
-	| nios-* | nios2-* \
+	| nds32-* | nds32le-* | nds32be-* \
+	| nios-* | nios2-* | nios2eb-* | nios2el-* \
 	| none-* | np1-* | ns16k-* | ns32k-* \
+	| open8-* \
 	| orion-* \
 	| pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \
-	| powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \
+	| powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* \
 	| pyramid-* \
-	| romp-* | rs6000-* | rx-* \
+	| rl78-* | romp-* | rs6000-* | rx-* \
 	| sh-* | sh[1234]-* | sh[24]a-* | sh[24]aeb-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \
 	| shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \
 	| sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \
 	| sparclite-* \
-	| sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | strongarm-* | sv1-* | sx?-* \
-	| tahoe-* | thumb-* \
-	| tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* | tile-* \
+	| sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | sv1-* | sx?-* \
+	| tahoe-* \
+	| tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \
+	| tile*-* \
 	| tron-* \
 	| ubicom32-* \
-	| v850-* | v850e-* | vax-* \
+	| v850-* | v850e-* | v850e1-* | v850es-* | v850e2-* | v850e2v3-* \
+	| vax-* \
 	| we32k-* \
-	| x86-* | x86_64-* | xc16x-* | xps100-* | xscale-* | xscalee[bl]-* \
+	| x86-* | x86_64-* | xc16x-* | xps100-* \
 	| xstormy16-* | xtensa*-* \
 	| ymp-* \
 	| z8k-* | z80-*)
@@ -410,7 +456,7 @@
 		basic_machine=a29k-amd
 		os=-udi
 		;;
-    	abacus)
+	abacus)
 		basic_machine=abacus-unknown
 		;;
 	adobe68k)
@@ -480,11 +526,20 @@
 		basic_machine=powerpc-ibm
 		os=-cnk
 		;;
+	c54x-*)
+		basic_machine=tic54x-`echo $basic_machine | sed 's/^[^-]*-//'`
+		;;
+	c55x-*)
+		basic_machine=tic55x-`echo $basic_machine | sed 's/^[^-]*-//'`
+		;;
+	c6x-*)
+		basic_machine=tic6x-`echo $basic_machine | sed 's/^[^-]*-//'`
+		;;
 	c90)
 		basic_machine=c90-cray
 		os=-unicos
 		;;
-        cegcc)
+	cegcc)
 		basic_machine=arm-unknown
 		os=-cegcc
 		;;
@@ -516,7 +571,7 @@
 		basic_machine=craynv-cray
 		os=-unicosmp
 		;;
-	cr16)
+	cr16 | cr16-*)
 		basic_machine=cr16-unknown
 		os=-elf
 		;;
@@ -674,7 +729,6 @@
 	i370-ibm* | ibm*)
 		basic_machine=i370-ibm
 		;;
-# I'm not sure what "Sysv32" means.  Should this be sysv3.2?
 	i*86v32)
 		basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
 		os=-sysv32
@@ -732,9 +786,13 @@
 		basic_machine=ns32k-utek
 		os=-sysv
 		;;
-        microblaze)
+	microblaze*)
 		basic_machine=microblaze-xilinx
 		;;
+	mingw64)
+		basic_machine=x86_64-pc
+		os=-mingw64
+		;;
 	mingw32)
 		basic_machine=i386-pc
 		os=-mingw32
@@ -771,10 +829,18 @@
 	ms1-*)
 		basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'`
 		;;
+	msys)
+		basic_machine=i386-pc
+		os=-msys
+		;;
 	mvs)
 		basic_machine=i370-ibm
 		os=-mvs
 		;;
+	nacl)
+		basic_machine=le32-unknown
+		os=-nacl
+		;;
 	ncr3000)
 		basic_machine=i486-ncr
 		os=-sysv4
@@ -839,6 +905,12 @@
 	np1)
 		basic_machine=np1-gould
 		;;
+	neo-tandem)
+		basic_machine=neo-tandem
+		;;
+	nse-tandem)
+		basic_machine=nse-tandem
+		;;
 	nsr-tandem)
 		basic_machine=nsr-tandem
 		;;
@@ -921,9 +993,10 @@
 		;;
 	power)	basic_machine=power-ibm
 		;;
-	ppc)	basic_machine=powerpc-unknown
+	ppc | ppcbe)	basic_machine=powerpc-unknown
 		;;
-	ppc-*)	basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'`
+	ppc-* | ppcbe-*)
+		basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'`
 		;;
 	ppcle | powerpclittle | ppc-le | powerpc-little)
 		basic_machine=powerpcle-unknown
@@ -948,7 +1021,11 @@
 		basic_machine=i586-unknown
 		os=-pw32
 		;;
-	rdos)
+	rdos | rdos64)
+		basic_machine=x86_64-pc
+		os=-rdos
+		;;
+	rdos32)
 		basic_machine=i386-pc
 		os=-rdos
 		;;
@@ -1017,6 +1094,9 @@
 		basic_machine=i860-stratus
 		os=-sysv4
 		;;
+	strongarm-* | thumb-*)
+		basic_machine=arm-`echo $basic_machine | sed 's/^[^-]*-//'`
+		;;
 	sun2)
 		basic_machine=m68000-sun
 		;;
@@ -1073,20 +1153,8 @@
 		basic_machine=t90-cray
 		os=-unicos
 		;;
-	tic54x | c54x*)
-		basic_machine=tic54x-unknown
-		os=-coff
-		;;
-	tic55x | c55x*)
-		basic_machine=tic55x-unknown
-		os=-coff
-		;;
-	tic6x | c6x*)
-		basic_machine=tic6x-unknown
-		os=-coff
-		;;
 	tile*)
-		basic_machine=tile-unknown
+		basic_machine=$basic_machine-unknown
 		os=-linux-gnu
 		;;
 	tx39)
@@ -1156,6 +1224,9 @@
 	xps | xps100)
 		basic_machine=xps100-honeywell
 		;;
+	xscale-* | xscalee[bl]-*)
+		basic_machine=`echo $basic_machine | sed 's/^xscale/arm/'`
+		;;
 	ymp)
 		basic_machine=ymp-cray
 		os=-unicos
@@ -1253,11 +1324,11 @@
 if [ x"$os" != x"" ]
 then
 case $os in
-        # First match some system type aliases
-        # that might get confused with valid system types.
+	# First match some system type aliases
+	# that might get confused with valid system types.
 	# -solaris* is a basic system type, with this one exception.
-        -auroraux)
-	        os=-auroraux
+	-auroraux)
+		os=-auroraux
 		;;
 	-solaris1 | -solaris1.*)
 		os=`echo $os | sed -e 's|solaris1|sunos4|'`
@@ -1281,20 +1352,21 @@
 	-gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \
 	      | -*vms* | -sco* | -esix* | -isc* | -aix* | -cnk* | -sunos | -sunos[34]*\
 	      | -hpux* | -unos* | -osf* | -luna* | -dgux* | -auroraux* | -solaris* \
-	      | -sym* | -kopensolaris* \
+	      | -sym* | -kopensolaris* | -plan9* \
 	      | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \
 	      | -aos* | -aros* \
 	      | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \
 	      | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \
 	      | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \
-	      | -openbsd* | -solidbsd* \
+	      | -bitrig* | -openbsd* | -solidbsd* \
 	      | -ekkobsd* | -kfreebsd* | -freebsd* | -riscix* | -lynxos* \
 	      | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \
 	      | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \
 	      | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \
 	      | -chorusos* | -chorusrdb* | -cegcc* \
-	      | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
-	      | -mingw32* | -linux-gnu* | -linux-newlib* | -linux-uclibc* \
+	      | -cygwin* | -msys* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
+	      | -mingw32* | -mingw64* | -linux-gnu* | -linux-android* \
+	      | -linux-newlib* | -linux-musl* | -linux-uclibc* \
 	      | -uxpv* | -beos* | -mpeix* | -udk* \
 	      | -interix* | -uwin* | -mks* | -rhapsody* | -darwin* | -opened* \
 	      | -openstep* | -oskit* | -conix* | -pw32* | -nonstopux* \
@@ -1341,7 +1413,7 @@
 	-opened*)
 		os=-openedition
 		;;
-        -os400*)
+	-os400*)
 		os=-os400
 		;;
 	-wince*)
@@ -1390,7 +1462,7 @@
 	-sinix*)
 		os=-sysv4
 		;;
-        -tpf*)
+	-tpf*)
 		os=-tpf
 		;;
 	-triton*)
@@ -1426,15 +1498,14 @@
 	-aros*)
 		os=-aros
 		;;
-	-kaos*)
-		os=-kaos
-		;;
 	-zvmoe)
 		os=-zvmoe
 		;;
 	-dicos*)
 		os=-dicos
 		;;
+	-nacl*)
+		;;
 	-none)
 		;;
 	*)
@@ -1457,10 +1528,10 @@
 # system, and we'll never get to this point.
 
 case $basic_machine in
-        score-*)
+	score-*)
 		os=-elf
 		;;
-        spu-*)
+	spu-*)
 		os=-elf
 		;;
 	*-acorn)
@@ -1472,8 +1543,20 @@
 	arm*-semi)
 		os=-aout
 		;;
-        c4x-* | tic4x-*)
-        	os=-coff
+	c4x-* | tic4x-*)
+		os=-coff
+		;;
+	hexagon-*)
+		os=-elf
+		;;
+	tic54x-*)
+		os=-coff
+		;;
+	tic55x-*)
+		os=-coff
+		;;
+	tic6x-*)
+		os=-coff
 		;;
 	# This must come before the *-dec entry.
 	pdp10-*)
@@ -1493,14 +1576,11 @@
 		;;
 	m68000-sun)
 		os=-sunos3
-		# This also exists in the configure program, but was not the
-		# default.
-		# os=-sunos4
 		;;
 	m68*-cisco)
 		os=-aout
 		;;
-        mep-*)
+	mep-*)
 		os=-elf
 		;;
 	mips*-cisco)
@@ -1509,6 +1589,9 @@
 	mips*-*)
 		os=-elf
 		;;
+	or1k-*)
+		os=-elf
+		;;
 	or32-*)
 		os=-coff
 		;;
@@ -1527,7 +1610,7 @@
 	*-ibm)
 		os=-aix
 		;;
-    	*-knuth)
+	*-knuth)
 		os=-mmixware
 		;;
 	*-wec)
diff -ruN ccp4srs-old/build-aux/depcomp ccp4srs/build-aux/depcomp
--- ccp4srs-old/build-aux/depcomp	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/build-aux/depcomp	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,9 @@
 #! /bin/sh
 # depcomp - compile a program generating dependencies as side-effects
 
-scriptversion=2009-04-28.21; # UTC
+scriptversion=2013-05-30.07; # UTC
 
-# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 Free
-# Software Foundation, Inc.
+# Copyright (C) 1999-2013 Free Software Foundation, Inc.
 
 # This program is free software; you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -28,9 +27,9 @@
 
 case $1 in
   '')
-     echo "$0: No command.  Try \`$0 --help' for more information." 1>&2
-     exit 1;
-     ;;
+    echo "$0: No command.  Try '$0 --help' for more information." 1>&2
+    exit 1;
+    ;;
   -h | --h*)
     cat <<\EOF
 Usage: depcomp [--help] [--version] PROGRAM [ARGS]
@@ -40,11 +39,11 @@
 
 Environment variables:
   depmode     Dependency tracking mode.
-  source      Source file read by `PROGRAMS ARGS'.
-  object      Object file output by `PROGRAMS ARGS'.
+  source      Source file read by 'PROGRAMS ARGS'.
+  object      Object file output by 'PROGRAMS ARGS'.
   DEPDIR      directory where to store dependencies.
   depfile     Dependency file to output.
-  tmpdepfile  Temporary file to use when outputing dependencies.
+  tmpdepfile  Temporary file to use when outputting dependencies.
   libtool     Whether libtool is used (yes/no).
 
 Report bugs to <bug-automake@gnu.org>.
@@ -57,6 +56,66 @@
     ;;
 esac
 
+# Get the directory component of the given path, and save it in the
+# global variables '$dir'.  Note that this directory component will
+# be either empty or ending with a '/' character.  This is deliberate.
+set_dir_from ()
+{
+  case $1 in
+    */*) dir=`echo "$1" | sed -e 's|/[^/]*$|/|'`;;
+      *) dir=;;
+  esac
+}
+
+# Get the suffix-stripped basename of the given path, and save it the
+# global variable '$base'.
+set_base_from ()
+{
+  base=`echo "$1" | sed -e 's|^.*/||' -e 's/\.[^.]*$//'`
+}
+
+# If no dependency file was actually created by the compiler invocation,
+# we still have to create a dummy depfile, to avoid errors with the
+# Makefile "include basename.Plo" scheme.
+make_dummy_depfile ()
+{
+  echo "#dummy" > "$depfile"
+}
+
+# Factor out some common post-processing of the generated depfile.
+# Requires the auxiliary global variable '$tmpdepfile' to be set.
+aix_post_process_depfile ()
+{
+  # If the compiler actually managed to produce a dependency file,
+  # post-process it.
+  if test -f "$tmpdepfile"; then
+    # Each line is of the form 'foo.o: dependency.h'.
+    # Do two passes, one to just change these to
+    #   $object: dependency.h
+    # and one to simply output
+    #   dependency.h:
+    # which is needed to avoid the deleted-header problem.
+    { sed -e "s,^.*\.[$lower]*:,$object:," < "$tmpdepfile"
+      sed -e "s,^.*\.[$lower]*:[$tab ]*,," -e 's,$,:,' < "$tmpdepfile"
+    } > "$depfile"
+    rm -f "$tmpdepfile"
+  else
+    make_dummy_depfile
+  fi
+}
+
+# A tabulation character.
+tab='	'
+# A newline character.
+nl='
+'
+# Character ranges might be problematic outside the C locale.
+# These definitions help.
+upper=ABCDEFGHIJKLMNOPQRSTUVWXYZ
+lower=abcdefghijklmnopqrstuvwxyz
+digits=0123456789
+alpha=${upper}${lower}
+
 if test -z "$depmode" || test -z "$source" || test -z "$object"; then
   echo "depcomp: Variables source, object and depmode must be set" 1>&2
   exit 1
@@ -69,6 +128,9 @@
 
 rm -f "$tmpdepfile"
 
+# Avoid interferences from the environment.
+gccflag= dashmflag=
+
 # Some modes work just like other modes, but use different flags.  We
 # parameterize here, but still list the modes in the big case below,
 # to make depend.m4 easier to write.  Note that we *cannot* use a case
@@ -80,18 +142,32 @@
 fi
 
 if test "$depmode" = dashXmstdout; then
-   # This is just like dashmstdout with a different argument.
-   dashmflag=-xM
-   depmode=dashmstdout
+  # This is just like dashmstdout with a different argument.
+  dashmflag=-xM
+  depmode=dashmstdout
 fi
 
 cygpath_u="cygpath -u -f -"
 if test "$depmode" = msvcmsys; then
-   # This is just like msvisualcpp but w/o cygpath translation.
-   # Just convert the backslash-escaped backslashes to single forward
-   # slashes to satisfy depend.m4
-   cygpath_u="sed s,\\\\\\\\,/,g"
-   depmode=msvisualcpp
+  # This is just like msvisualcpp but w/o cygpath translation.
+  # Just convert the backslash-escaped backslashes to single forward
+  # slashes to satisfy depend.m4
+  cygpath_u='sed s,\\\\,/,g'
+  depmode=msvisualcpp
+fi
+
+if test "$depmode" = msvc7msys; then
+  # This is just like msvc7 but w/o cygpath translation.
+  # Just convert the backslash-escaped backslashes to single forward
+  # slashes to satisfy depend.m4
+  cygpath_u='sed s,\\\\,/,g'
+  depmode=msvc7
+fi
+
+if test "$depmode" = xlc; then
+  # IBM C/C++ Compilers xlc/xlC can output gcc-like dependency information.
+  gccflag=-qmakedep=gcc,-MF
+  depmode=gcc
 fi
 
 case "$depmode" in
@@ -114,8 +190,7 @@
   done
   "$@"
   stat=$?
-  if test $stat -eq 0; then :
-  else
+  if test $stat -ne 0; then
     rm -f "$tmpdepfile"
     exit $stat
   fi
@@ -123,13 +198,17 @@
   ;;
 
 gcc)
+## Note that this doesn't just cater to obsosete pre-3.x GCC compilers.
+## but also to in-use compilers like IMB xlc/xlC and the HP C compiler.
+## (see the conditional assignment to $gccflag above).
 ## There are various ways to get dependency output from gcc.  Here's
 ## why we pick this rather obscure method:
 ## - Don't want to use -MD because we'd like the dependencies to end
 ##   up in a subdir.  Having to rename by hand is ugly.
 ##   (We might end up doing this anyway to support other compilers.)
 ## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
-##   -MM, not -M (despite what the docs say).
+##   -MM, not -M (despite what the docs say).  Also, it might not be
+##   supported by the other compilers which use the 'gcc' depmode.
 ## - Using -M directly means running the compiler twice (even worse
 ##   than renaming).
   if test -z "$gccflag"; then
@@ -137,31 +216,31 @@
   fi
   "$@" -Wp,"$gccflag$tmpdepfile"
   stat=$?
-  if test $stat -eq 0; then :
-  else
+  if test $stat -ne 0; then
     rm -f "$tmpdepfile"
     exit $stat
   fi
   rm -f "$depfile"
   echo "$object : \\" > "$depfile"
-  alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
-## The second -e expression handles DOS-style file names with drive letters.
+  # The second -e expression handles DOS-style file names with drive
+  # letters.
   sed -e 's/^[^:]*: / /' \
       -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
-## This next piece of magic avoids the `deleted header file' problem.
+## This next piece of magic avoids the "deleted header file" problem.
 ## The problem is that when a header file which appears in a .P file
 ## is deleted, the dependency causes make to die (because there is
 ## typically no way to rebuild the header).  We avoid this by adding
 ## dummy dependencies for each header file.  Too bad gcc doesn't do
 ## this for us directly.
-  tr ' ' '
-' < "$tmpdepfile" |
-## Some versions of gcc put a space before the `:'.  On the theory
+## Some versions of gcc put a space before the ':'.  On the theory
 ## that the space means something, we add a space to the output as
-## well.
+## well.  hp depmode also adds that space, but also prefixes the VPATH
+## to the object.  Take care to not repeat it in the output.
 ## Some versions of the HPUX 10.20 sed can't process this invocation
 ## correctly.  Breaking it into two sed invocations is a workaround.
-    sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+  tr ' ' "$nl" < "$tmpdepfile" \
+    | sed -e 's/^\\$//' -e '/^$/d' -e "s|.*$object$||" -e '/:$/d' \
+    | sed -e 's/$/ :/' >> "$depfile"
   rm -f "$tmpdepfile"
   ;;
 
@@ -179,8 +258,7 @@
     "$@" -MDupdate "$tmpdepfile"
   fi
   stat=$?
-  if test $stat -eq 0; then :
-  else
+  if test $stat -ne 0; then
     rm -f "$tmpdepfile"
     exit $stat
   fi
@@ -188,43 +266,41 @@
 
   if test -f "$tmpdepfile"; then  # yes, the sourcefile depend on other files
     echo "$object : \\" > "$depfile"
-
     # Clip off the initial element (the dependent).  Don't try to be
     # clever and replace this with sed code, as IRIX sed won't handle
     # lines with more than a fixed number of characters (4096 in
     # IRIX 6.2 sed, 8192 in IRIX 6.5).  We also remove comment lines;
-    # the IRIX cc adds comments like `#:fec' to the end of the
+    # the IRIX cc adds comments like '#:fec' to the end of the
     # dependency line.
-    tr ' ' '
-' < "$tmpdepfile" \
-    | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
-    tr '
-' ' ' >> "$depfile"
+    tr ' ' "$nl" < "$tmpdepfile" \
+      | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' \
+      | tr "$nl" ' ' >> "$depfile"
     echo >> "$depfile"
-
     # The second pass generates a dummy entry for each header file.
-    tr ' ' '
-' < "$tmpdepfile" \
-   | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
-   >> "$depfile"
+    tr ' ' "$nl" < "$tmpdepfile" \
+      | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
+      >> "$depfile"
   else
-    # The sourcefile does not contain any dependencies, so just
-    # store a dummy comment line, to avoid errors with the Makefile
-    # "include basename.Plo" scheme.
-    echo "#dummy" > "$depfile"
+    make_dummy_depfile
   fi
   rm -f "$tmpdepfile"
   ;;
 
+xlc)
+  # This case exists only to let depend.m4 do its work.  It works by
+  # looking at the text of this script.  This case will never be run,
+  # since it is checked for above.
+  exit 1
+  ;;
+
 aix)
   # The C for AIX Compiler uses -M and outputs the dependencies
   # in a .u file.  In older versions, this file always lives in the
-  # current directory.  Also, the AIX compiler puts `$object:' at the
+  # current directory.  Also, the AIX compiler puts '$object:' at the
   # start of each line; $object doesn't have directory information.
   # Version 6 uses the directory in both cases.
-  dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
-  test "x$dir" = "x$object" && dir=
-  base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+  set_dir_from "$object"
+  set_base_from "$object"
   if test "$libtool" = yes; then
     tmpdepfile1=$dir$base.u
     tmpdepfile2=$base.u
@@ -237,9 +313,7 @@
     "$@" -M
   fi
   stat=$?
-
-  if test $stat -eq 0; then :
-  else
+  if test $stat -ne 0; then
     rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
     exit $stat
   fi
@@ -248,44 +322,100 @@
   do
     test -f "$tmpdepfile" && break
   done
-  if test -f "$tmpdepfile"; then
-    # Each line is of the form `foo.o: dependent.h'.
-    # Do two passes, one to just change these to
-    # `$object: dependent.h' and one to simply `dependent.h:'.
-    sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
-    # That's a tab and a space in the [].
-    sed -e 's,^.*\.[a-z]*:[	 ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
-  else
-    # The sourcefile does not contain any dependencies, so just
-    # store a dummy comment line, to avoid errors with the Makefile
-    # "include basename.Plo" scheme.
-    echo "#dummy" > "$depfile"
+  aix_post_process_depfile
+  ;;
+
+tcc)
+  # tcc (Tiny C Compiler) understand '-MD -MF file' since version 0.9.26
+  # FIXME: That version still under development at the moment of writing.
+  #        Make that this statement remains true also for stable, released
+  #        versions.
+  # It will wrap lines (doesn't matter whether long or short) with a
+  # trailing '\', as in:
+  #
+  #   foo.o : \
+  #    foo.c \
+  #    foo.h \
+  #
+  # It will put a trailing '\' even on the last line, and will use leading
+  # spaces rather than leading tabs (at least since its commit 0394caf7
+  # "Emit spaces for -MD").
+  "$@" -MD -MF "$tmpdepfile"
+  stat=$?
+  if test $stat -ne 0; then
+    rm -f "$tmpdepfile"
+    exit $stat
   fi
+  rm -f "$depfile"
+  # Each non-empty line is of the form 'foo.o : \' or ' dep.h \'.
+  # We have to change lines of the first kind to '$object: \'.
+  sed -e "s|.*:|$object :|" < "$tmpdepfile" > "$depfile"
+  # And for each line of the second kind, we have to emit a 'dep.h:'
+  # dummy dependency, to avoid the deleted-header problem.
+  sed -n -e 's|^  *\(.*\) *\\$|\1:|p' < "$tmpdepfile" >> "$depfile"
   rm -f "$tmpdepfile"
   ;;
 
-icc)
-  # Intel's C compiler understands `-MD -MF file'.  However on
-  #    icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
-  # ICC 7.0 will fill foo.d with something like
-  #    foo.o: sub/foo.c
-  #    foo.o: sub/foo.h
-  # which is wrong.  We want:
-  #    sub/foo.o: sub/foo.c
-  #    sub/foo.o: sub/foo.h
-  #    sub/foo.c:
-  #    sub/foo.h:
-  # ICC 7.1 will output
+## The order of this option in the case statement is important, since the
+## shell code in configure will try each of these formats in the order
+## listed in this file.  A plain '-MD' option would be understood by many
+## compilers, so we must ensure this comes after the gcc and icc options.
+pgcc)
+  # Portland's C compiler understands '-MD'.
+  # Will always output deps to 'file.d' where file is the root name of the
+  # source file under compilation, even if file resides in a subdirectory.
+  # The object file name does not affect the name of the '.d' file.
+  # pgcc 10.2 will output
   #    foo.o: sub/foo.c sub/foo.h
-  # and will wrap long lines using \ :
+  # and will wrap long lines using '\' :
   #    foo.o: sub/foo.c ... \
   #     sub/foo.h ... \
   #     ...
+  set_dir_from "$object"
+  # Use the source, not the object, to determine the base name, since
+  # that's sadly what pgcc will do too.
+  set_base_from "$source"
+  tmpdepfile=$base.d
+
+  # For projects that build the same source file twice into different object
+  # files, the pgcc approach of using the *source* file root name can cause
+  # problems in parallel builds.  Use a locking strategy to avoid stomping on
+  # the same $tmpdepfile.
+  lockdir=$base.d-lock
+  trap "
+    echo '$0: caught signal, cleaning up...' >&2
+    rmdir '$lockdir'
+    exit 1
+  " 1 2 13 15
+  numtries=100
+  i=$numtries
+  while test $i -gt 0; do
+    # mkdir is a portable test-and-set.
+    if mkdir "$lockdir" 2>/dev/null; then
+      # This process acquired the lock.
+      "$@" -MD
+      stat=$?
+      # Release the lock.
+      rmdir "$lockdir"
+      break
+    else
+      # If the lock is being held by a different process, wait
+      # until the winning process is done or we timeout.
+      while test -d "$lockdir" && test $i -gt 0; do
+        sleep 1
+        i=`expr $i - 1`
+      done
+    fi
+    i=`expr $i - 1`
+  done
+  trap - 1 2 13 15
+  if test $i -le 0; then
+    echo "$0: failed to acquire lock after $numtries attempts" >&2
+    echo "$0: check lockdir '$lockdir'" >&2
+    exit 1
+  fi
 
-  "$@" -MD -MF "$tmpdepfile"
-  stat=$?
-  if test $stat -eq 0; then :
-  else
+  if test $stat -ne 0; then
     rm -f "$tmpdepfile"
     exit $stat
   fi
@@ -297,8 +427,8 @@
   sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
   # Some versions of the HPUX 10.20 sed can't process this invocation
   # correctly.  Breaking it into two sed invocations is a workaround.
-  sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
-    sed -e 's/$/ :/' >> "$depfile"
+  sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" \
+    | sed -e 's/$/ :/' >> "$depfile"
   rm -f "$tmpdepfile"
   ;;
 
@@ -309,9 +439,8 @@
   # 'foo.d', which lands next to the object file, wherever that
   # happens to be.
   # Much of this is similar to the tru64 case; see comments there.
-  dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
-  test "x$dir" = "x$object" && dir=
-  base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+  set_dir_from  "$object"
+  set_base_from "$object"
   if test "$libtool" = yes; then
     tmpdepfile1=$dir$base.d
     tmpdepfile2=$dir.libs/$base.d
@@ -322,8 +451,7 @@
     "$@" +Maked
   fi
   stat=$?
-  if test $stat -eq 0; then :
-  else
+  if test $stat -ne 0; then
      rm -f "$tmpdepfile1" "$tmpdepfile2"
      exit $stat
   fi
@@ -333,77 +461,107 @@
     test -f "$tmpdepfile" && break
   done
   if test -f "$tmpdepfile"; then
-    sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile"
-    # Add `dependent.h:' lines.
+    sed -e "s,^.*\.[$lower]*:,$object:," "$tmpdepfile" > "$depfile"
+    # Add 'dependent.h:' lines.
     sed -ne '2,${
-	       s/^ *//
-	       s/ \\*$//
-	       s/$/:/
-	       p
-	     }' "$tmpdepfile" >> "$depfile"
+               s/^ *//
+               s/ \\*$//
+               s/$/:/
+               p
+             }' "$tmpdepfile" >> "$depfile"
   else
-    echo "#dummy" > "$depfile"
+    make_dummy_depfile
   fi
   rm -f "$tmpdepfile" "$tmpdepfile2"
   ;;
 
 tru64)
-   # The Tru64 compiler uses -MD to generate dependencies as a side
-   # effect.  `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
-   # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
-   # dependencies in `foo.d' instead, so we check for that too.
-   # Subdirectories are respected.
-   dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
-   test "x$dir" = "x$object" && dir=
-   base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
-
-   if test "$libtool" = yes; then
-      # With Tru64 cc, shared objects can also be used to make a
-      # static library.  This mechanism is used in libtool 1.4 series to
-      # handle both shared and static libraries in a single compilation.
-      # With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
-      #
-      # With libtool 1.5 this exception was removed, and libtool now
-      # generates 2 separate objects for the 2 libraries.  These two
-      # compilations output dependencies in $dir.libs/$base.o.d and
-      # in $dir$base.o.d.  We have to check for both files, because
-      # one of the two compilations can be disabled.  We should prefer
-      # $dir$base.o.d over $dir.libs/$base.o.d because the latter is
-      # automatically cleaned when .libs/ is deleted, while ignoring
-      # the former would cause a distcleancheck panic.
-      tmpdepfile1=$dir.libs/$base.lo.d   # libtool 1.4
-      tmpdepfile2=$dir$base.o.d          # libtool 1.5
-      tmpdepfile3=$dir.libs/$base.o.d    # libtool 1.5
-      tmpdepfile4=$dir.libs/$base.d      # Compaq CCC V6.2-504
-      "$@" -Wc,-MD
-   else
-      tmpdepfile1=$dir$base.o.d
-      tmpdepfile2=$dir$base.d
-      tmpdepfile3=$dir$base.d
-      tmpdepfile4=$dir$base.d
-      "$@" -MD
-   fi
+  # The Tru64 compiler uses -MD to generate dependencies as a side
+  # effect.  'cc -MD -o foo.o ...' puts the dependencies into 'foo.o.d'.
+  # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
+  # dependencies in 'foo.d' instead, so we check for that too.
+  # Subdirectories are respected.
+  set_dir_from  "$object"
+  set_base_from "$object"
+
+  if test "$libtool" = yes; then
+    # Libtool generates 2 separate objects for the 2 libraries.  These
+    # two compilations output dependencies in $dir.libs/$base.o.d and
+    # in $dir$base.o.d.  We have to check for both files, because
+    # one of the two compilations can be disabled.  We should prefer
+    # $dir$base.o.d over $dir.libs/$base.o.d because the latter is
+    # automatically cleaned when .libs/ is deleted, while ignoring
+    # the former would cause a distcleancheck panic.
+    tmpdepfile1=$dir$base.o.d          # libtool 1.5
+    tmpdepfile2=$dir.libs/$base.o.d    # Likewise.
+    tmpdepfile3=$dir.libs/$base.d      # Compaq CCC V6.2-504
+    "$@" -Wc,-MD
+  else
+    tmpdepfile1=$dir$base.d
+    tmpdepfile2=$dir$base.d
+    tmpdepfile3=$dir$base.d
+    "$@" -MD
+  fi
+
+  stat=$?
+  if test $stat -ne 0; then
+    rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
+    exit $stat
+  fi
 
-   stat=$?
-   if test $stat -eq 0; then :
-   else
-      rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
-      exit $stat
-   fi
-
-   for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
-   do
-     test -f "$tmpdepfile" && break
-   done
-   if test -f "$tmpdepfile"; then
-      sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
-      # That's a tab and a space in the [].
-      sed -e 's,^.*\.[a-z]*:[	 ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
-   else
-      echo "#dummy" > "$depfile"
-   fi
-   rm -f "$tmpdepfile"
-   ;;
+  for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
+  do
+    test -f "$tmpdepfile" && break
+  done
+  # Same post-processing that is required for AIX mode.
+  aix_post_process_depfile
+  ;;
+
+msvc7)
+  if test "$libtool" = yes; then
+    showIncludes=-Wc,-showIncludes
+  else
+    showIncludes=-showIncludes
+  fi
+  "$@" $showIncludes > "$tmpdepfile"
+  stat=$?
+  grep -v '^Note: including file: ' "$tmpdepfile"
+  if test $stat -ne 0; then
+    rm -f "$tmpdepfile"
+    exit $stat
+  fi
+  rm -f "$depfile"
+  echo "$object : \\" > "$depfile"
+  # The first sed program below extracts the file names and escapes
+  # backslashes for cygpath.  The second sed program outputs the file
+  # name when reading, but also accumulates all include files in the
+  # hold buffer in order to output them again at the end.  This only
+  # works with sed implementations that can handle large buffers.
+  sed < "$tmpdepfile" -n '
+/^Note: including file:  *\(.*\)/ {
+  s//\1/
+  s/\\/\\\\/g
+  p
+}' | $cygpath_u | sort -u | sed -n '
+s/ /\\ /g
+s/\(.*\)/'"$tab"'\1 \\/p
+s/.\(.*\) \\/\1:/
+H
+$ {
+  s/.*/'"$tab"'/
+  G
+  p
+}' >> "$depfile"
+  echo >> "$depfile" # make sure the fragment doesn't end with a backslash
+  rm -f "$tmpdepfile"
+  ;;
+
+msvc7msys)
+  # This case exists only to let depend.m4 do its work.  It works by
+  # looking at the text of this script.  This case will never be run,
+  # since it is checked for above.
+  exit 1
+  ;;
 
 #nosideeffect)
   # This comment above is used by automake to tell side-effect
@@ -422,7 +580,7 @@
     shift
   fi
 
-  # Remove `-o $object'.
+  # Remove '-o $object'.
   IFS=" "
   for arg
   do
@@ -442,18 +600,18 @@
   done
 
   test -z "$dashmflag" && dashmflag=-M
-  # Require at least two characters before searching for `:'
+  # Require at least two characters before searching for ':'
   # in the target name.  This is to cope with DOS-style filenames:
-  # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.
+  # a dependency such as 'c:/foo/bar' could be seen as target 'c' otherwise.
   "$@" $dashmflag |
-    sed 's:^[  ]*[^: ][^:][^:]*\:[    ]*:'"$object"'\: :' > "$tmpdepfile"
+    sed "s|^[$tab ]*[^:$tab ][^:][^:]*:[$tab ]*|$object: |" > "$tmpdepfile"
   rm -f "$depfile"
   cat < "$tmpdepfile" > "$depfile"
-  tr ' ' '
-' < "$tmpdepfile" | \
-## Some versions of the HPUX 10.20 sed can't process this invocation
-## correctly.  Breaking it into two sed invocations is a workaround.
-    sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+  # Some versions of the HPUX 10.20 sed can't process this sed invocation
+  # correctly.  Breaking it into two sed invocations is a workaround.
+  tr ' ' "$nl" < "$tmpdepfile" \
+    | sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' \
+    | sed -e 's/$/ :/' >> "$depfile"
   rm -f "$tmpdepfile"
   ;;
 
@@ -503,12 +661,15 @@
   touch "$tmpdepfile"
   ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
   rm -f "$depfile"
-  cat < "$tmpdepfile" > "$depfile"
-  sed '1,2d' "$tmpdepfile" | tr ' ' '
-' | \
-## Some versions of the HPUX 10.20 sed can't process this invocation
-## correctly.  Breaking it into two sed invocations is a workaround.
-    sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+  # makedepend may prepend the VPATH from the source file name to the object.
+  # No need to regex-escape $object, excess matching of '.' is harmless.
+  sed "s|^.*\($object *:\)|\1|" "$tmpdepfile" > "$depfile"
+  # Some versions of the HPUX 10.20 sed can't process the last invocation
+  # correctly.  Breaking it into two sed invocations is a workaround.
+  sed '1,2d' "$tmpdepfile" \
+    | tr ' ' "$nl" \
+    | sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' \
+    | sed -e 's/$/ :/' >> "$depfile"
   rm -f "$tmpdepfile" "$tmpdepfile".bak
   ;;
 
@@ -525,7 +686,7 @@
     shift
   fi
 
-  # Remove `-o $object'.
+  # Remove '-o $object'.
   IFS=" "
   for arg
   do
@@ -544,10 +705,10 @@
     esac
   done
 
-  "$@" -E |
-    sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
-       -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
-    sed '$ s: \\$::' > "$tmpdepfile"
+  "$@" -E \
+    | sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
+             -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
+    | sed '$ s: \\$::' > "$tmpdepfile"
   rm -f "$depfile"
   echo "$object : \\" > "$depfile"
   cat < "$tmpdepfile" >> "$depfile"
@@ -579,23 +740,23 @@
       shift
       ;;
     "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
-	set fnord "$@"
-	shift
-	shift
-	;;
+        set fnord "$@"
+        shift
+        shift
+        ;;
     *)
-	set fnord "$@" "$arg"
-	shift
-	shift
-	;;
+        set fnord "$@" "$arg"
+        shift
+        shift
+        ;;
     esac
   done
   "$@" -E 2>/dev/null |
   sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile"
   rm -f "$depfile"
   echo "$object : \\" > "$depfile"
-  sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::	\1 \\:p' >> "$depfile"
-  echo "	" >> "$depfile"
+  sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::'"$tab"'\1 \\:p' >> "$depfile"
+  echo "$tab" >> "$depfile"
   sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile"
   rm -f "$tmpdepfile"
   ;;
diff -ruN ccp4srs-old/build-aux/install-sh ccp4srs/build-aux/install-sh
--- ccp4srs-old/build-aux/install-sh	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/build-aux/install-sh	2014-09-09 21:34:12.000000000 -0700
@@ -1,7 +1,7 @@
 #!/bin/sh
 # install - install a program, script, or datafile
 
-scriptversion=2009-04-28.21; # UTC
+scriptversion=2011-11-20.07; # UTC
 
 # This originates from X11R5 (mit/util/scripts/install.sh), which was
 # later released in X11R6 (xc/config/util/install.sh) with the
@@ -35,7 +35,7 @@
 # FSF changes to this file are in the public domain.
 #
 # Calling this script install-sh is preferred over install.sh, to prevent
-# `make' implicit rules from creating a file called install from it
+# 'make' implicit rules from creating a file called install from it
 # when there is no Makefile.
 #
 # This script is compatible with the BSD install script, but was written
@@ -156,6 +156,10 @@
     -s) stripcmd=$stripprog;;
 
     -t) dst_arg=$2
+	# Protect names problematic for 'test' and other utilities.
+	case $dst_arg in
+	  -* | [=\(\)!]) dst_arg=./$dst_arg;;
+	esac
 	shift;;
 
     -T) no_target_directory=true;;
@@ -186,6 +190,10 @@
     fi
     shift # arg
     dst_arg=$arg
+    # Protect names problematic for 'test' and other utilities.
+    case $dst_arg in
+      -* | [=\(\)!]) dst_arg=./$dst_arg;;
+    esac
   done
 fi
 
@@ -194,13 +202,17 @@
     echo "$0: no input file specified." >&2
     exit 1
   fi
-  # It's OK to call `install-sh -d' without argument.
+  # It's OK to call 'install-sh -d' without argument.
   # This can happen when creating conditional directories.
   exit 0
 fi
 
 if test -z "$dir_arg"; then
-  trap '(exit $?); exit' 1 2 13 15
+  do_exit='(exit $ret); exit $ret'
+  trap "ret=129; $do_exit" 1
+  trap "ret=130; $do_exit" 2
+  trap "ret=141; $do_exit" 13
+  trap "ret=143; $do_exit" 15
 
   # Set umask so as not to create temps with too-generous modes.
   # However, 'strip' requires both read and write access to temps.
@@ -228,9 +240,9 @@
 
 for src
 do
-  # Protect names starting with `-'.
+  # Protect names problematic for 'test' and other utilities.
   case $src in
-    -*) src=./$src;;
+    -* | [=\(\)!]) src=./$src;;
   esac
 
   if test -n "$dir_arg"; then
@@ -252,12 +264,7 @@
       echo "$0: no destination specified." >&2
       exit 1
     fi
-
     dst=$dst_arg
-    # Protect names starting with `-'.
-    case $dst in
-      -*) dst=./$dst;;
-    esac
 
     # If destination is a directory, append the input filename; won't work
     # if double slashes aren't ignored.
@@ -347,7 +354,7 @@
 	      if test -z "$dir_arg" || {
 		   # Check for POSIX incompatibilities with -m.
 		   # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
-		   # other-writeable bit of parent directory when it shouldn't.
+		   # other-writable bit of parent directory when it shouldn't.
 		   # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
 		   ls_ld_tmpdir=`ls -ld "$tmpdir"`
 		   case $ls_ld_tmpdir in
@@ -385,7 +392,7 @@
 
       case $dstdir in
 	/*) prefix='/';;
-	-*) prefix='./';;
+	[-=\(\)!]*) prefix='./';;
 	*)  prefix='';;
       esac
 
@@ -403,7 +410,7 @@
 
       for d
       do
-	test -z "$d" && continue
+	test X"$d" = X && continue
 
 	prefix=$prefix$d
 	if test -d "$prefix"; then
diff -ruN ccp4srs-old/build-aux/missing ccp4srs/build-aux/missing
--- ccp4srs-old/build-aux/missing	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/build-aux/missing	2014-09-09 21:34:12.000000000 -0700
@@ -1,11 +1,10 @@
 #! /bin/sh
-# Common stub for a few missing GNU programs while installing.
+# Common wrapper for a few potentially missing GNU programs.
 
-scriptversion=2009-04-28.21; # UTC
+scriptversion=2012-06-26.16; # UTC
 
-# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006,
-# 2008, 2009 Free Software Foundation, Inc.
-# Originally by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
+# Copyright (C) 1996-2013 Free Software Foundation, Inc.
+# Originally written by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
 
 # This program is free software; you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -26,69 +25,40 @@
 # the same distribution terms that you use for the rest of that program.
 
 if test $# -eq 0; then
-  echo 1>&2 "Try \`$0 --help' for more information"
+  echo 1>&2 "Try '$0 --help' for more information"
   exit 1
 fi
 
-run=:
-sed_output='s/.* --output[ =]\([^ ]*\).*/\1/p'
-sed_minuso='s/.* -o \([^ ]*\).*/\1/p'
-
-# In the cases where this matters, `missing' is being run in the
-# srcdir already.
-if test -f configure.ac; then
-  configure_ac=configure.ac
-else
-  configure_ac=configure.in
-fi
+case $1 in
 
-msg="missing on your system"
+  --is-lightweight)
+    # Used by our autoconf macros to check whether the available missing
+    # script is modern enough.
+    exit 0
+    ;;
 
-case $1 in
---run)
-  # Try to run requested program, and just exit if it succeeds.
-  run=
-  shift
-  "$@" && exit 0
-  # Exit code 63 means version mismatch.  This often happens
-  # when the user try to use an ancient version of a tool on
-  # a file that requires a minimum version.  In this case we
-  # we should proceed has if the program had been absent, or
-  # if --run hadn't been passed.
-  if test $? = 63; then
-    run=:
-    msg="probably too old"
-  fi
-  ;;
+  --run)
+    # Back-compat with the calling convention used by older automake.
+    shift
+    ;;
 
   -h|--h|--he|--hel|--help)
     echo "\
 $0 [OPTION]... PROGRAM [ARGUMENT]...
 
-Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
-error status if there is no known handling for PROGRAM.
+Run 'PROGRAM [ARGUMENT]...', returning a proper advice when this fails due
+to PROGRAM being missing or too old.
 
 Options:
   -h, --help      display this help and exit
   -v, --version   output version information and exit
-  --run           try to run the given command, and emulate it if it fails
 
 Supported PROGRAM values:
-  aclocal      touch file \`aclocal.m4'
-  autoconf     touch file \`configure'
-  autoheader   touch file \`config.h.in'
-  autom4te     touch the output file, or create a stub one
-  automake     touch all \`Makefile.in' files
-  bison        create \`y.tab.[ch]', if possible, from existing .[ch]
-  flex         create \`lex.yy.c', if possible, from existing .c
-  help2man     touch the output file
-  lex          create \`lex.yy.c', if possible, from existing .c
-  makeinfo     touch the output file
-  tar          try tar, gnutar, gtar, then tar without non-portable flags
-  yacc         create \`y.tab.[ch]', if possible, from existing .[ch]
+  aclocal   autoconf  autoheader   autom4te  automake  makeinfo
+  bison     yacc      flex         lex       help2man
 
-Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and
-\`g' are ignored when checking the name.
+Version suffixes to PROGRAM as well as the prefixes 'gnu-', 'gnu', and
+'g' are ignored when checking the name.
 
 Send bug reports to <bug-automake@gnu.org>."
     exit $?
@@ -100,272 +70,141 @@
     ;;
 
   -*)
-    echo 1>&2 "$0: Unknown \`$1' option"
-    echo 1>&2 "Try \`$0 --help' for more information"
+    echo 1>&2 "$0: unknown '$1' option"
+    echo 1>&2 "Try '$0 --help' for more information"
     exit 1
     ;;
 
 esac
 
-# normalize program name to check for.
-program=`echo "$1" | sed '
-  s/^gnu-//; t
-  s/^gnu//; t
-  s/^g//; t'`
-
-# Now exit if we have it, but it failed.  Also exit now if we
-# don't have it and --version was passed (most likely to detect
-# the program).  This is about non-GNU programs, so use $1 not
-# $program.
-case $1 in
-  lex*|yacc*)
-    # Not GNU programs, they don't have --version.
-    ;;
-
-  tar*)
-    if test -n "$run"; then
-       echo 1>&2 "ERROR: \`tar' requires --run"
-       exit 1
-    elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
-       exit 1
-    fi
-    ;;
+# Run the given program, remember its exit status.
+"$@"; st=$?
 
-  *)
-    if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
-       # We have it, but it failed.
-       exit 1
-    elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
-       # Could not run --version or --help.  This is probably someone
-       # running `$TOOL --version' or `$TOOL --help' to check whether
-       # $TOOL exists and not knowing $TOOL uses missing.
-       exit 1
-    fi
-    ;;
-esac
-
-# If it does not exist, or fails to run (possibly an outdated version),
-# try to emulate it.
-case $program in
-  aclocal*)
-    echo 1>&2 "\
-WARNING: \`$1' is $msg.  You should only need it if
-         you modified \`acinclude.m4' or \`${configure_ac}'.  You might want
-         to install the \`Automake' and \`Perl' packages.  Grab them from
-         any GNU archive site."
-    touch aclocal.m4
-    ;;
-
-  autoconf*)
-    echo 1>&2 "\
-WARNING: \`$1' is $msg.  You should only need it if
-         you modified \`${configure_ac}'.  You might want to install the
-         \`Autoconf' and \`GNU m4' packages.  Grab them from any GNU
-         archive site."
-    touch configure
-    ;;
-
-  autoheader*)
-    echo 1>&2 "\
-WARNING: \`$1' is $msg.  You should only need it if
-         you modified \`acconfig.h' or \`${configure_ac}'.  You might want
-         to install the \`Autoconf' and \`GNU m4' packages.  Grab them
-         from any GNU archive site."
-    files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
-    test -z "$files" && files="config.h"
-    touch_files=
-    for f in $files; do
-      case $f in
-      *:*) touch_files="$touch_files "`echo "$f" |
-				       sed -e 's/^[^:]*://' -e 's/:.*//'`;;
-      *) touch_files="$touch_files $f.in";;
-      esac
-    done
-    touch $touch_files
-    ;;
-
-  automake*)
-    echo 1>&2 "\
-WARNING: \`$1' is $msg.  You should only need it if
-         you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'.
-         You might want to install the \`Automake' and \`Perl' packages.
-         Grab them from any GNU archive site."
-    find . -type f -name Makefile.am -print |
-	   sed 's/\.am$/.in/' |
-	   while read f; do touch "$f"; done
-    ;;
+# If it succeeded, we are done.
+test $st -eq 0 && exit 0
 
-  autom4te*)
-    echo 1>&2 "\
-WARNING: \`$1' is needed, but is $msg.
-         You might have modified some files without having the
-         proper tools for further handling them.
-         You can get \`$1' as part of \`Autoconf' from any GNU
-         archive site."
-
-    file=`echo "$*" | sed -n "$sed_output"`
-    test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
-    if test -f "$file"; then
-	touch $file
-    else
-	test -z "$file" || exec >$file
-	echo "#! /bin/sh"
-	echo "# Created by GNU Automake missing as a replacement of"
-	echo "#  $ $@"
-	echo "exit 0"
-	chmod +x $file
-	exit 1
-    fi
-    ;;
-
-  bison*|yacc*)
-    echo 1>&2 "\
-WARNING: \`$1' $msg.  You should only need it if
-         you modified a \`.y' file.  You may need the \`Bison' package
-         in order for those modifications to take effect.  You can get
-         \`Bison' from any GNU archive site."
-    rm -f y.tab.c y.tab.h
-    if test $# -ne 1; then
-        eval LASTARG="\${$#}"
-	case $LASTARG in
-	*.y)
-	    SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
-	    if test -f "$SRCFILE"; then
-	         cp "$SRCFILE" y.tab.c
-	    fi
-	    SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
-	    if test -f "$SRCFILE"; then
-	         cp "$SRCFILE" y.tab.h
-	    fi
-	  ;;
-	esac
-    fi
-    if test ! -f y.tab.h; then
-	echo >y.tab.h
-    fi
-    if test ! -f y.tab.c; then
-	echo 'main() { return 0; }' >y.tab.c
-    fi
-    ;;
-
-  lex*|flex*)
-    echo 1>&2 "\
-WARNING: \`$1' is $msg.  You should only need it if
-         you modified a \`.l' file.  You may need the \`Flex' package
-         in order for those modifications to take effect.  You can get
-         \`Flex' from any GNU archive site."
-    rm -f lex.yy.c
-    if test $# -ne 1; then
-        eval LASTARG="\${$#}"
-	case $LASTARG in
-	*.l)
-	    SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
-	    if test -f "$SRCFILE"; then
-	         cp "$SRCFILE" lex.yy.c
-	    fi
-	  ;;
-	esac
-    fi
-    if test ! -f lex.yy.c; then
-	echo 'main() { return 0; }' >lex.yy.c
-    fi
-    ;;
-
-  help2man*)
-    echo 1>&2 "\
-WARNING: \`$1' is $msg.  You should only need it if
-	 you modified a dependency of a manual page.  You may need the
-	 \`Help2man' package in order for those modifications to take
-	 effect.  You can get \`Help2man' from any GNU archive site."
-
-    file=`echo "$*" | sed -n "$sed_output"`
-    test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
-    if test -f "$file"; then
-	touch $file
-    else
-	test -z "$file" || exec >$file
-	echo ".ab help2man is required to generate this page"
-	exit $?
-    fi
-    ;;
-
-  makeinfo*)
-    echo 1>&2 "\
-WARNING: \`$1' is $msg.  You should only need it if
-         you modified a \`.texi' or \`.texinfo' file, or any other file
-         indirectly affecting the aspect of the manual.  The spurious
-         call might also be the consequence of using a buggy \`make' (AIX,
-         DU, IRIX).  You might want to install the \`Texinfo' package or
-         the \`GNU make' package.  Grab either from any GNU archive site."
-    # The file to touch is that specified with -o ...
-    file=`echo "$*" | sed -n "$sed_output"`
-    test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
-    if test -z "$file"; then
-      # ... or it is the one specified with @setfilename ...
-      infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
-      file=`sed -n '
-	/^@setfilename/{
-	  s/.* \([^ ]*\) *$/\1/
-	  p
-	  q
-	}' $infile`
-      # ... or it is derived from the source name (dir/f.texi becomes f.info)
-      test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info
-    fi
-    # If the file does not exist, the user really needs makeinfo;
-    # let's fail without touching anything.
-    test -f $file || exit 1
-    touch $file
-    ;;
-
-  tar*)
-    shift
-
-    # We have already tried tar in the generic part.
-    # Look for gnutar/gtar before invocation to avoid ugly error
-    # messages.
-    if (gnutar --version > /dev/null 2>&1); then
-       gnutar "$@" && exit 0
-    fi
-    if (gtar --version > /dev/null 2>&1); then
-       gtar "$@" && exit 0
-    fi
-    firstarg="$1"
-    if shift; then
-	case $firstarg in
-	*o*)
-	    firstarg=`echo "$firstarg" | sed s/o//`
-	    tar "$firstarg" "$@" && exit 0
-	    ;;
-	esac
-	case $firstarg in
-	*h*)
-	    firstarg=`echo "$firstarg" | sed s/h//`
-	    tar "$firstarg" "$@" && exit 0
-	    ;;
-	esac
-    fi
-
-    echo 1>&2 "\
-WARNING: I can't seem to be able to run \`tar' with the given arguments.
-         You may want to install GNU tar or Free paxutils, or check the
-         command line arguments."
-    exit 1
-    ;;
-
-  *)
-    echo 1>&2 "\
-WARNING: \`$1' is needed, and is $msg.
-         You might have modified some files without having the
-         proper tools for further handling them.  Check the \`README' file,
-         it often tells you about the needed prerequisites for installing
-         this package.  You may also peek at any GNU archive site, in case
-         some other package would contain this missing \`$1' program."
-    exit 1
-    ;;
-esac
+# Also exit now if we it failed (or wasn't found), and '--version' was
+# passed; such an option is passed most likely to detect whether the
+# program is present and works.
+case $2 in --version|--help) exit $st;; esac
+
+# Exit code 63 means version mismatch.  This often happens when the user
+# tries to use an ancient version of a tool on a file that requires a
+# minimum version.
+if test $st -eq 63; then
+  msg="probably too old"
+elif test $st -eq 127; then
+  # Program was missing.
+  msg="missing on your system"
+else
+  # Program was found and executed, but failed.  Give up.
+  exit $st
+fi
 
-exit 0
+perl_URL=http://www.perl.org/
+flex_URL=http://flex.sourceforge.net/
+gnu_software_URL=http://www.gnu.org/software
+
+program_details ()
+{
+  case $1 in
+    aclocal|automake)
+      echo "The '$1' program is part of the GNU Automake package:"
+      echo "<$gnu_software_URL/automake>"
+      echo "It also requires GNU Autoconf, GNU m4 and Perl in order to run:"
+      echo "<$gnu_software_URL/autoconf>"
+      echo "<$gnu_software_URL/m4/>"
+      echo "<$perl_URL>"
+      ;;
+    autoconf|autom4te|autoheader)
+      echo "The '$1' program is part of the GNU Autoconf package:"
+      echo "<$gnu_software_URL/autoconf/>"
+      echo "It also requires GNU m4 and Perl in order to run:"
+      echo "<$gnu_software_URL/m4/>"
+      echo "<$perl_URL>"
+      ;;
+  esac
+}
+
+give_advice ()
+{
+  # Normalize program name to check for.
+  normalized_program=`echo "$1" | sed '
+    s/^gnu-//; t
+    s/^gnu//; t
+    s/^g//; t'`
+
+  printf '%s\n' "'$1' is $msg."
+
+  configure_deps="'configure.ac' or m4 files included by 'configure.ac'"
+  case $normalized_program in
+    autoconf*)
+      echo "You should only need it if you modified 'configure.ac',"
+      echo "or m4 files included by it."
+      program_details 'autoconf'
+      ;;
+    autoheader*)
+      echo "You should only need it if you modified 'acconfig.h' or"
+      echo "$configure_deps."
+      program_details 'autoheader'
+      ;;
+    automake*)
+      echo "You should only need it if you modified 'Makefile.am' or"
+      echo "$configure_deps."
+      program_details 'automake'
+      ;;
+    aclocal*)
+      echo "You should only need it if you modified 'acinclude.m4' or"
+      echo "$configure_deps."
+      program_details 'aclocal'
+      ;;
+   autom4te*)
+      echo "You might have modified some maintainer files that require"
+      echo "the 'automa4te' program to be rebuilt."
+      program_details 'autom4te'
+      ;;
+    bison*|yacc*)
+      echo "You should only need it if you modified a '.y' file."
+      echo "You may want to install the GNU Bison package:"
+      echo "<$gnu_software_URL/bison/>"
+      ;;
+    lex*|flex*)
+      echo "You should only need it if you modified a '.l' file."
+      echo "You may want to install the Fast Lexical Analyzer package:"
+      echo "<$flex_URL>"
+      ;;
+    help2man*)
+      echo "You should only need it if you modified a dependency" \
+           "of a man page."
+      echo "You may want to install the GNU Help2man package:"
+      echo "<$gnu_software_URL/help2man/>"
+    ;;
+    makeinfo*)
+      echo "You should only need it if you modified a '.texi' file, or"
+      echo "any other file indirectly affecting the aspect of the manual."
+      echo "You might want to install the Texinfo package:"
+      echo "<$gnu_software_URL/texinfo/>"
+      echo "The spurious makeinfo call might also be the consequence of"
+      echo "using a buggy 'make' (AIX, DU, IRIX), in which case you might"
+      echo "want to install GNU make:"
+      echo "<$gnu_software_URL/make/>"
+      ;;
+    *)
+      echo "You might have modified some files without having the proper"
+      echo "tools for further handling them.  Check the 'README' file, it"
+      echo "often tells you about the needed prerequisites for installing"
+      echo "this package.  You may also peek at any GNU archive site, in"
+      echo "case some other package contains this missing '$1' program."
+      ;;
+  esac
+}
+
+give_advice "$1" | sed -e '1s/^/WARNING: /' \
+                       -e '2,$s/^/         /' >&2
+
+# Propagate the correct exit status (expected to be 127 for a program
+# not found, 63 for a program that failed due to version mismatch).
+exit $st
 
 # Local variables:
 # eval: (add-hook 'write-file-hooks 'time-stamp)
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_angle.cpp ccp4srs/ccp4srs/ccp4srs_angle.cpp
--- ccp4srs-old/ccp4srs/ccp4srs_angle.cpp	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_angle.cpp	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_angle.cpp, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_angle.cpp $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,16 +22,16 @@
 //
 //  =================================================================
 //
-//    11.03.10   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_angle  <implementation>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSAngle  - angle restraint class
+//  **** Classes :  ccp4srs::Angle  - angle restraint class
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010
+//  (C) E. Krissinel 2010-2013
 //
 //  =================================================================
 //
@@ -39,105 +39,107 @@
 #include "ccp4srs_angle.h"
 #include "ccp4srs_defs.h"
 
-CCP4SRSAngle::CCP4SRSAngle()  {
-  atom_1    = -1;
-  atom_2    = -1;
-  atom_3    = -1;
-  angle     = 0.0;
-  angle_esd = 0.0;
-}
-
-CCP4SRSAngle::~CCP4SRSAngle()  {
-}
-
-
-int CCP4SRSAngle::readFromCIF ( PCMMCIFLoop mmCIFLoop, int angleNo,
-                            CCP4SRSContainer<CCP4SRSAtom> & atoms )  {
-int rc;
-
-  rc = 0;
-
-  get_atom_from_cif ( atom_1,mmCIFLoop,MMCIF_TAG_ATOM_ID_1,
-                      angleNo,atoms,rc );
-  get_atom_from_cif ( atom_2,mmCIFLoop,MMCIF_TAG_ATOM_ID_2,
-                      angleNo,atoms,rc );
-  get_atom_from_cif ( atom_3,mmCIFLoop,MMCIF_TAG_ATOM_ID_3,
-                      angleNo,atoms,rc );
-
-  mmCIFLoop->CopyReal(angle    ,MMCIF_TAG_VALUE_ANGLE    ,angleNo,rc);
-  mmCIFLoop->CopyReal(angle_esd,MMCIF_TAG_VALUE_ANGLE_ESD,angleNo,rc);
-
-  return rc;
-
-}
-
-/*
-loop_
-_chem_comp_angle.comp_id
-_chem_comp_angle.atom_id_1
-_chem_comp_angle.atom_id_2
-_chem_comp_angle.atom_id_3
-_chem_comp_angle.value_angle
-_chem_comp_angle.value_angle_esd
- ATP      O2A    PA     O1A     119.900    3.000
-*/
-
-
-void CCP4SRSAngle::makeCIFTags ( PCMMCIFLoop mmCIFLoop )  {
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_COMP_ID         );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_1       );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_2       );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_3       );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_VALUE_ANGLE     );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_VALUE_ANGLE_ESD );
-}
-
-void CCP4SRSAngle::writeToCIF ( PCMMCIFLoop mmCIFLoop, cpstr monID,
-                            CCP4SRSContainer<CCP4SRSAtom> & atoms )  {
-  mmCIFLoop->AddString ( monID,False );
-  add_atom_to_cif ( mmCIFLoop,atom_1,atoms );
-  add_atom_to_cif ( mmCIFLoop,atom_2,atoms );
-  add_atom_to_cif ( mmCIFLoop,atom_3,atoms );
-  mmCIFLoop->AddReal ( angle    ,"%10.3f" );
-  mmCIFLoop->AddReal ( angle_esd,"%10.3f" );
-}
-
-void  CCP4SRSAngle::copy ( PCCP4SRSAngle ang, ivector anmatch )  {
-  if (anmatch)  {
-    atom_1 = anmatch[ang->atom1()];
-    atom_2 = anmatch[ang->atom2()];
-    atom_3 = anmatch[ang->atom3()];
-  } else  {
-    atom_1 = ang->atom1();
-    atom_2 = ang->atom2();
-    atom_3 = ang->atom3();
-  }
-  angle     = ang->value();
-  angle_esd = ang->esd  ();
-}
-
-
-void  CCP4SRSAngle::write_mem ( PCMemIO memIO, int version )  {
-UNUSED_ARGUMENT(version);
-  memIO->put_integer ( atom_1    );
-  memIO->put_integer ( atom_2    );
-  memIO->put_integer ( atom_3    );
-  memIO->put_float   ( angle     );
-  memIO->put_float   ( angle_esd );
-}
-
-Boolean CCP4SRSAngle::read_mem ( PCMemIO memIO, int version,
-                                 Boolean * Ok )  {
-UNUSED_ARGUMENT(version);
-Boolean success;
-  if (Ok)  success = *Ok;
-     else  success = True;
-  memIO->get_integer ( atom_1   ,&success );
-  memIO->get_integer ( atom_2   ,&success );
-  memIO->get_integer ( atom_3   ,&success );
-  memIO->get_float   ( angle    ,&success );
-  memIO->get_float   ( angle_esd,&success );
-  if (Ok)  *Ok = success;
-  return success;
-}
+namespace ccp4srs  {
 
+  Angle::Angle()  {
+    atom_1    = -1;
+    atom_2    = -1;
+    atom_3    = -1;
+    angle     = 0.0;
+    angle_esd = 0.0;
+  }
+
+  Angle::~Angle()  {
+  }
+
+
+  int Angle::readFromCIF ( mmdb::mmcif::PLoop mmCIFLoop, int angleNo,
+                           Container<Atom> & atoms )  {
+  int rc;
+
+    rc = 0;
+
+    get_atom_from_cif ( atom_1,mmCIFLoop,MMCIF_TAG_ATOM_ID_1,
+                        angleNo,atoms,rc );
+    get_atom_from_cif ( atom_2,mmCIFLoop,MMCIF_TAG_ATOM_ID_2,
+                        angleNo,atoms,rc );
+    get_atom_from_cif ( atom_3,mmCIFLoop,MMCIF_TAG_ATOM_ID_3,
+                        angleNo,atoms,rc );
+
+    mmCIFLoop->CopyReal(angle    ,MMCIF_TAG_VALUE_ANGLE    ,angleNo,rc);
+    mmCIFLoop->CopyReal(angle_esd,MMCIF_TAG_VALUE_ANGLE_ESD,angleNo,rc);
+
+    return rc;
+
+  }
+
+  /*
+  loop_
+  _chem_comp_angle.comp_id
+  _chem_comp_angle.atom_id_1
+  _chem_comp_angle.atom_id_2
+  _chem_comp_angle.atom_id_3
+  _chem_comp_angle.value_angle
+  _chem_comp_angle.value_angle_esd
+   ATP      O2A    PA     O1A     119.900    3.000
+  */
+
+
+  void Angle::makeCIFTags ( mmdb::mmcif::PLoop mmCIFLoop )  {
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_COMP_ID         );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_1       );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_2       );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_3       );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_VALUE_ANGLE     );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_VALUE_ANGLE_ESD );
+  }
+
+  void Angle::writeToCIF ( mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID,
+                              Container<Atom> & atoms )  {
+    mmCIFLoop->AddString ( monID,false );
+    add_atom_to_cif ( mmCIFLoop,atom_1,atoms );
+    add_atom_to_cif ( mmCIFLoop,atom_2,atoms );
+    add_atom_to_cif ( mmCIFLoop,atom_3,atoms );
+    mmCIFLoop->AddReal ( angle    ,"%10.3f" );
+    mmCIFLoop->AddReal ( angle_esd,"%10.3f" );
+  }
+
+  void  Angle::copy ( PAngle ang, mmdb::ivector anmatch )  {
+    if (anmatch)  {
+      atom_1 = anmatch[ang->atom1()];
+      atom_2 = anmatch[ang->atom2()];
+      atom_3 = anmatch[ang->atom3()];
+    } else  {
+      atom_1 = ang->atom1();
+      atom_2 = ang->atom2();
+      atom_3 = ang->atom3();
+    }
+    angle     = ang->value();
+    angle_esd = ang->esd  ();
+  }
+
+
+  void  Angle::write_mem ( PMemIO memIO, int version )  {
+  UNUSED_ARGUMENT(version);
+    memIO->put_integer ( atom_1    );
+    memIO->put_integer ( atom_2    );
+    memIO->put_integer ( atom_3    );
+    memIO->put_float   ( angle     );
+    memIO->put_float   ( angle_esd );
+  }
+
+  bool Angle::read_mem ( PMemIO memIO, int version, bool * Ok ) {
+  UNUSED_ARGUMENT(version);
+  bool success;
+    if (Ok)  success = *Ok;
+       else  success = true;
+    memIO->get_integer ( atom_1   ,&success );
+    memIO->get_integer ( atom_2   ,&success );
+    memIO->get_integer ( atom_3   ,&success );
+    memIO->get_float   ( angle    ,&success );
+    memIO->get_float   ( angle_esd,&success );
+    if (Ok)  *Ok = success;
+    return success;
+  }
+
+}  // namespace ccp4srs
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_angle.h ccp4srs/ccp4srs/ccp4srs_angle.h
--- ccp4srs-old/ccp4srs/ccp4srs_angle.h	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_angle.h	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_angle.h, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_angle.h $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,16 +22,16 @@
 //
 //  =================================================================
 //
-//    11.03.10   <--  Date of Last Modification.
+//    03.02.14   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_angle  <interface>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSAngle  - angle restraint class
+//  **** Classes :  ccp4srs::Angle  - angle restraint class
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010
+//  (C) E. Krissinel 2010-2014
 //
 //  =================================================================
 //
@@ -41,39 +41,43 @@
 
 #include "ccp4srs_atom.h"
 
-DefineClass(CCP4SRSAngle)
+namespace ccp4srs  {
 
-class CCP4SRSAngle  {
+  DefineClass(Angle);
 
-  public:
-    CCP4SRSAngle();
-    virtual ~CCP4SRSAngle();
-
-    inline int      atom1() { return atom_1;    }
-    inline int      atom2() { return atom_2;    }
-    inline int      atom3() { return atom_3;    }
-    inline realtype value() { return angle;     }
-    inline realtype esd  () { return angle_esd; }
-
-    static void makeCIFTags ( PCMMCIFLoop mmCIFLoop );
-    int  readFromCIF ( PCMMCIFLoop mmCIFLoop, int angleNo,
-                       CCP4SRSContainer<CCP4SRSAtom> & atoms );
-    void writeToCIF  ( PCMMCIFLoop mmCIFLoop, cpstr monID,
-                       CCP4SRSContainer<CCP4SRSAtom> & atoms );
-
-    void    write_mem ( PCMemIO memIO, int version );
-    Boolean read_mem  ( PCMemIO memIO, int version,
-                        Boolean * Ok = NULL );
-
-    void copy ( PCCP4SRSAngle ang, ivector anmatch=NULL );
-
-  protected:
-    int      atom_1,atom_2,atom_3; // ordinal numbers of of atoms
-                                   //   that form the angle [0,1,...]
-    realtype angle;                // angle in degrees
-    realtype angle_esd;            // angle esd in degrees; set to 0.0
-                                   // if not provided
+  class Angle  {
 
-};
+    public:
+      Angle();
+      virtual ~Angle();
+
+      inline int            atom1() { return atom_1;    }
+      inline int            atom2() { return atom_2;    }
+      inline int            atom3() { return atom_3;    }
+      inline mmdb::realtype value() { return angle;     }
+      inline mmdb::realtype esd  () { return angle_esd; }
+
+      static void makeCIFTags ( mmdb::mmcif::PLoop mmCIFLoop );
+      int  readFromCIF ( mmdb::mmcif::PLoop mmCIFLoop, int angleNo,
+                         Container<Atom> & atoms );
+      void writeToCIF  ( mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID,
+                         Container<Atom> & atoms );
+
+      void write_mem ( PMemIO memIO, int version );
+      bool read_mem  ( PMemIO memIO, int version,
+                          bool * Ok = NULL );
+
+      void copy ( PAngle ang, mmdb::ivector anmatch=NULL );
+
+    protected:
+      int  atom_1,atom_2,atom_3; // ordinal numbers of of atoms
+                                 //   that form the angle [0,1,...]
+      mmdb::realtype angle;      // angle in degrees
+      mmdb::realtype angle_esd;  // angle esd in degrees; set to 0.0
+                                 // if not provided
+
+  };
+
+}  // namespace ccp4srs
 
 #endif // CCP4SRS_ANGLE_H
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_atom.cpp ccp4srs/ccp4srs/ccp4srs_atom.cpp
--- ccp4srs-old/ccp4srs/ccp4srs_atom.cpp	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_atom.cpp	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_atom.cpp, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_atom.cpp $
 //  =================================================================
 //
-//   CCP4 SRS Library: Storage, Retrievak and Search support for
+//   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,502 +22,506 @@
 //
 //  =================================================================
 //
-//    26.02.13   <--  Date of Last Modification.
+//    03.02.14   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_atom  <implementation>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSAtom  - atom description class
+//  **** Classes :  ccp4srs::Atom  - atom description class
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010-2013
+//  (C) E. Krissinel 2010-2014
 //
 //  =================================================================
 //
 
-
-#ifndef  __STRING_H
 #include <string.h>
-#endif
-
-#include "mmdb/mmdb_tables.h"
 
+#include "mmdb2/mmdb_tables.h"
 #include "ccp4srs_atom.h"
+#include "ccp4srs_types.h"
 #include "ccp4srs_defs.h"
 
+namespace ccp4srs  {
+
+  Atom::Atom()  {
+    Init();
+  }
+
+  Atom::~Atom()  {}
+
+  void Atom::Init()  {
+
+    atomName    [0] = char(0);       // atom name
+    rcsbAtomName[0] = char(0);       // alternative atom name
+    oldAtomName [0] = char(0);       // old atom name
+    chemElement [0] = char(0);       // chemical element name
+    energyType  [0] = char(0);       // energy type
+    pdb_x           = -mmdb::MaxShortReal/2.0; // cartesian coordinates
+    pdb_y           = pdb_x;
+    pdb_z           = pdb_x;
+    pdbx_x          = pdb_x;         // idealized coordinates
+    pdbx_y          = pdb_x;
+    pdbx_z          = pdb_x;
+    mlib_x          = pdb_x;         // monomer library coordinates
+    mlib_y          = pdb_x;
+    mlib_z          = pdb_x;
+    atomCharge      = 0.0;           // partial charge
+    atomWeight      = 0.0;           // atomic weight (in a.u.)
+    vdwRadius       = 0.0;           // Van-Der-Waals radius
+    vdwhRadius      = 0.0;           // Van-Der-Waals radius with hydrogen
+    ionRadius       = 0.0;           // ion radius
+    atomValency     = 0;             // valency
+    atomSP          = 0;             // sp-hybridization
+    property[0]     = '-';           // RCSB chirality : 'R', 'S' or 'N'
+    property[1]     = '-';           // MLib chirality : 'R', 'S' or 'N'
+    property[2]     = '-';           // leaving atom: 'Y' or 'N'
+    property[3]     = '-';           // hydrogen bond type:
+                                     //           'D' donor
+                                     //           'A' acceptor
+                                     //           'B' both
+                                     //           'H' hydrogen candidate
+                                     //           'N' neither
+
+  }
+
+
+  mmdb::cpstr Atom::name_pdb ( mmdb::pstr aname )  {
+  int  l;
+
+    l = strlen(atomName);
+    if (l>=4)
+      return atomName;
+
+    strcpy ( aname,"    " );
+
+    if (mmdb::isMetal(chemElement))
+          strncpy ( aname,atomName,l );
+    else  strncpy ( &(aname[1]),atomName,l );
+
+    return aname;
+
+  }
+
+  mmdb::cpstr Atom::rcsb_name_pdb ( mmdb::pstr aname )  {
+  int  l;
+
+    l = strlen(rcsbAtomName);
+    if (l>=4)
+      return rcsbAtomName;
+
+    strcpy ( aname,"    " );
+
+    if (mmdb::isMetal(chemElement))
+          strncpy ( aname,rcsbAtomName,l       );
+    else  strncpy ( &(aname[1]),rcsbAtomName,l );
+
+    return aname;
 
-CCP4SRSAtom::CCP4SRSAtom()  {
-  Init();
-}
-
-CCP4SRSAtom::~CCP4SRSAtom()  {}
-
-void CCP4SRSAtom::Init()  {
-
-  atomName    [0] = char(0);       // atom name
-  rcsbAtomName[0] = char(0);       // alternative atom name
-  oldAtomName [0] = char(0);       // old atom name
-  chemElement [0] = char(0);       // chemical element name
-  energyType  [0] = char(0);       // energy type
-  pdb_x           = -MaxShortReal/2.0; // cartesian coordinates
-  pdb_y           = pdb_x;
-  pdb_z           = pdb_x;
-  pdbx_x          = pdb_x;         // idealized coordinates
-  pdbx_y          = pdb_x;
-  pdbx_z          = pdb_x;
-  mlib_x          = pdb_x;         // monomer library coordinates
-  mlib_y          = pdb_x;
-  mlib_z          = pdb_x;
-  atomCharge      = 0.0;           // partial charge
-  atomWeight      = 0.0;           // atomic weight (in a.u.)
-  vdwRadius       = 0.0;           // Van-Der-Waals radius
-  vdwhRadius      = 0.0;           // Van-Der-Waals radius with hydrogen
-  ionRadius       = 0.0;           // ion radius
-  atomValency     = 0;             // valency
-  atomSP          = 0;             // sp-hybridization
-  property[0]     = '-';           // RCSB chirality : 'R', 'S' or 'N'
-  property[1]     = '-';           // MLib chirality : 'R', 'S' or 'N'
-  property[2]     = '-';           // leaving atom: 'Y' or 'N'
-  property[3]     = '-';           // hydrogen bond type:
-                                   //           'D' donor
-                                   //           'A' acceptor
-                                   //           'B' both
-                                   //           'H' hydrogen candidate
-                                   //           'N' neither
-
-}
-
-
-cpstr CCP4SRSAtom::name_pdb ( pstr aname )  {
-int  l;
-
-  l = strlen(atomName);
-  if (l>=4)
-    return atomName;
-
-  strcpy ( aname,"    " );
-
-  if (isMetal(chemElement))  strncpy ( aname,atomName,l );
-                       else  strncpy ( &(aname[1]),atomName,l );
-
-  return aname;
-
-}
-
-cpstr CCP4SRSAtom::rcsb_name_pdb ( pstr aname )  {
-int  l;
-
-  l = strlen(rcsbAtomName);
-  if (l>=4)
-    return rcsbAtomName;
-
-  strcpy ( aname,"    " );
-
-  if (isMetal(chemElement))  strncpy ( aname,rcsbAtomName,l       );
-                       else  strncpy ( &(aname[1]),rcsbAtomName,l );
-
-  return aname;
-
-}
-
-cpstr CCP4SRSAtom::old_name_pdb ( pstr aname )  {
-int  l;
-
-  l = strlen(oldAtomName);
-  if (l>=4)
-    return oldAtomName;
-
-  strcpy ( aname,"    " );
-
-  if (isMetal(chemElement))  strncpy ( aname,oldAtomName,l       );
-                       else  strncpy ( &(aname[1]),oldAtomName,l );
-
-  return aname;
-
-}
-
-cpstr CCP4SRSAtom::element_pdb ( pstr elem )  {
-
-  if (!chemElement[0])  {
-    elem[0] = ' ';
-    elem[1] = ' ';
-  } else if (!chemElement[1])  {
-    elem[0] = ' ';
-    elem[1] = chemElement[0];
-  } else  {
-    elem[0] = chemElement[0];
-    elem[1] = chemElement[1];
-  }
-  elem[2] = char(0);
-
-  return elem;
-
-}
-
-void CCP4SRSAtom::set_energy_type ( cpstr etype )  {
-  strcpy ( energyType,etype );
-}
-
-void CCP4SRSAtom::set_old_name ( cpstr name )  {
-  strcpy ( oldAtomName,name );
-}
-
-char CCP4SRSAtom::chirality() const  {
-// ccp4's; if not set then rcsb's
-  if (property[1]!='-')  return property[1];
-  return property[0];
-}
-
-void CCP4SRSAtom::makeCAtom ( RPCAtom a )  {
-AtomName aname;
-Element  elem;
-  if (!a)  a = newCAtom();
-  a->SetAtomName    ( 0,0,name_pdb(aname),"","",element_pdb(elem) );
-  a->SetCharge      ( RMax(0.0,atomCharge) );
-  a->SetCoordinates ( pdb_x,pdb_y,pdb_z,1.0,0.0  );
-  strcpy ( a->energyType,energyType  );
-  a->sigOcc = -1.0;  // signal that atom was added from SBase
-}
-
-PCAtom CCP4SRSAtom::makeCAtom()  {
-PCAtom   a;
-AtomName aname;
-Element  elem;
-  a = newCAtom();
-  a->SetAtomName    ( 0,0,name_pdb(aname),"","",element_pdb(elem) );
-  a->SetCharge      ( RMax(0.0,atomCharge) );
-  a->SetCoordinates ( pdb_x,pdb_y,pdb_z,1.0,0.0 );
-  strcpy ( a->energyType,energyType );
-  a->sigOcc = -1.0;  // signal that atom was added from SBase
-  return a;
-}
-
-
-void CCP4SRSAtom::makeCIFTags ( PCMMCIFLoop mmCIFLoop )  {
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_COMP_ID        );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID        );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_TYPE_SYMBOL    );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_TYPE_ENERGY    );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_PARTIAL_CHARGE );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_X              );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_Y              );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_Z              );
-}
-
-int CCP4SRSAtom::readFromCIF_ccp4 ( PCMMCIFLoop mmCIFLoop,
-                                    int atomNo )  {
-int  rc;
-
-  rc = 0;
-  mmCIFLoop->CopyString ( atomName,sizeof(AtomName)-1,
-                          MMCIF_TAG_ATOM_ID,atomNo,rc );
-  mmCIFLoop->CopyString ( chemElement,sizeof(Element)-1,
-                          MMCIF_TAG_TYPE_SYMBOL,atomNo,rc );
-  mmCIFLoop->CopyString ( energyType,sizeof(EnergyType)-1,
-                          MMCIF_TAG_TYPE_ENERGY,atomNo,rc );
-
-  mmCIFLoop->CopyReal   ( atomCharge,MMCIF_TAG_PARTIAL_CHARGE,
-                          atomNo,rc );
-
-  if (mmCIFLoop->GetTagNo(MMCIF_TAG_X)>=0)  {
-    mmCIFLoop->CopyReal ( mlib_x,MMCIF_TAG_X,atomNo,rc );
-    mmCIFLoop->CopyReal ( mlib_y,MMCIF_TAG_Y,atomNo,rc );
-    mmCIFLoop->CopyReal ( mlib_z,MMCIF_TAG_Y,atomNo,rc );
-  } else if (mmCIFLoop->GetTagNo(MMCIF_TAG_MODEL_CARTN_X)>=0)  {
-    mmCIFLoop->CopyReal ( mlib_x,MMCIF_TAG_MODEL_CARTN_X,atomNo,rc );
-    mmCIFLoop->CopyReal ( mlib_y,MMCIF_TAG_MODEL_CARTN_Y,atomNo,rc );
-    mmCIFLoop->CopyReal ( mlib_z,MMCIF_TAG_MODEL_CARTN_Z,atomNo,rc );
-  }
-  /*else  {
-    mlib_x = 0.0;
-    mlib_y = 0.0;
-    mlib_z = 0.0;
   }
-  */
 
-  return rc;
+  mmdb::cpstr Atom::old_name_pdb ( mmdb::pstr aname )  {
+  int  l;
 
-}
+    l = strlen(oldAtomName);
+    if (l>=4)
+      return oldAtomName;
 
-int CCP4SRSAtom::readFromCIF_rcsb ( PCMMCIFLoop mmCIFLoop,
-                                    int atomNo )  {
-pstr p;
-int  rc;
-
-  rc = 0;
-  mmCIFLoop->CopyString  ( atomName,sizeof(AtomName)-1,
-                           MMCIF_TAG_ATOM_ID,atomNo,rc );
-  mmCIFLoop->CopyString  ( rcsbAtomName,sizeof(AtomName)-1,
-                           MMCIF_TAG_ALT_ATOM_ID,atomNo,rc );
-  mmCIFLoop->CopyString  ( chemElement,sizeof(Element)-1,
-                           MMCIF_TAG_TYPE_SYMBOL,atomNo,rc );
-
-  if (mmCIFLoop->GetTagNo(MMCIF_TAG_MODEL_CARTN_X)>=0)  {
-    mmCIFLoop->CopyReal ( pdb_x,MMCIF_TAG_MODEL_CARTN_X,atomNo,rc );
-    mmCIFLoop->CopyReal ( pdb_y,MMCIF_TAG_MODEL_CARTN_Y,atomNo,rc );
-    mmCIFLoop->CopyReal ( pdb_z,MMCIF_TAG_MODEL_CARTN_Z,atomNo,rc );
-  }
-  if (mmCIFLoop->GetTagNo(MMCIF_TAG_PDBX_MODEL_CARTN_X)>=0)  {
-    mmCIFLoop->CopyReal ( pdbx_x,MMCIF_TAG_PDBX_MODEL_CARTN_X,atomNo,rc );
-    mmCIFLoop->CopyReal ( pdbx_y,MMCIF_TAG_PDBX_MODEL_CARTN_Y,atomNo,rc );
-    mmCIFLoop->CopyReal ( pdbx_z,MMCIF_TAG_PDBX_MODEL_CARTN_Z,atomNo,rc );
-  }
-
-  p = mmCIFLoop->GetString ( MMCIF_TAG_PDBX_STEREO_CONFIG,
-                             atomNo,rc );
-  if (!p)  property[0] = '-';
-     else  property[0] = p[0];
-
-
-  p = mmCIFLoop->GetString ( MMCIF_TAG_PDBX_LEAVING_ATOM_FLAG,
-                             atomNo,rc );
-  if (!p)              property[2] = 'N';
-  else if (p[0]=='Y')  property[2] = 'Y';
-                 else  property[2] = 'N';
-
-  return rc;
-
-}
-
-int CCP4SRSAtom::readFromCIF ( PCMMCIFStruct mmCIFStruct )  {
-pstr p;
-int  rc;
-
-  rc = 0;
-  p = mmCIFStruct->GetString ( MMCIF_TAG_ATOM_ID,rc );
-  if (p) strcpy ( atomName,p );
-  p = mmCIFStruct->GetString ( MMCIF_TAG_ALT_ATOM_ID,rc );
-  if (p) strcpy ( rcsbAtomName,p );
-  p = mmCIFStruct->GetString ( MMCIF_TAG_TYPE_SYMBOL,rc );
-  if (p) strcpy ( chemElement,p );
-  p = mmCIFStruct->GetString ( MMCIF_TAG_TYPE_ENERGY,rc );
-  if (p) strcpy ( energyType,p );
-
-  rc = mmCIFStruct->GetReal ( atomCharge,MMCIF_TAG_PARTIAL_CHARGE );
-
-  if (mmCIFStruct->GetTagNo(MMCIF_TAG_X)>=0)  {
-    rc = mmCIFStruct->GetReal ( mlib_x,MMCIF_TAG_X );
-    rc = mmCIFStruct->GetReal ( mlib_y,MMCIF_TAG_Y );
-    rc = mmCIFStruct->GetReal ( mlib_z,MMCIF_TAG_Y );
-  } else if (mmCIFStruct->GetTagNo(MMCIF_TAG_MODEL_CARTN_X)>=0)  {
-    rc = mmCIFStruct->GetReal ( pdb_x,MMCIF_TAG_MODEL_CARTN_X );
-    rc = mmCIFStruct->GetReal ( pdb_y,MMCIF_TAG_MODEL_CARTN_Y );
-    rc = mmCIFStruct->GetReal ( pdb_z,MMCIF_TAG_MODEL_CARTN_Y );
-    rc = mmCIFStruct->GetReal ( pdbx_x,MMCIF_TAG_PDBX_MODEL_CARTN_X );
-    rc = mmCIFStruct->GetReal ( pdbx_y,MMCIF_TAG_PDBX_MODEL_CARTN_Y );
-    rc = mmCIFStruct->GetReal ( pdbx_z,MMCIF_TAG_PDBX_MODEL_CARTN_Y );
-    p  = mmCIFStruct->GetString ( MMCIF_TAG_PDBX_LEAVING_ATOM_FLAG,rc );
+    strcpy ( aname,"    " );
+
+    if (mmdb::isMetal(chemElement))
+          strncpy ( aname,oldAtomName,l       );
+    else  strncpy ( &(aname[1]),oldAtomName,l );
+
+    return aname;
+
+  }
+
+  mmdb::cpstr Atom::element_pdb ( mmdb::pstr elem )  {
+
+    if (!chemElement[0])  {
+      elem[0] = ' ';
+      elem[1] = ' ';
+    } else if (!chemElement[1])  {
+      elem[0] = ' ';
+      elem[1] = chemElement[0];
+    } else  {
+      elem[0] = chemElement[0];
+      elem[1] = chemElement[1];
+    }
+    elem[2] = char(0);
+
+    return elem;
+
+  }
+
+  void Atom::set_energy_type ( mmdb::cpstr etype )  {
+    strcpy ( energyType,etype );
+  }
+
+  void Atom::set_old_name ( mmdb::cpstr name )  {
+    strcpy ( oldAtomName,name );
+  }
+
+  char Atom::chirality() const  {
+  // ccp4's; if not set then rcsb's
+    if (property[1]!='-')  return property[1];
+    return property[0];
+  }
+
+  void Atom::makeAtom ( mmdb::RPAtom a )  {
+  mmdb::AtomName aname;
+  mmdb::Element  elem;
+    if (!a)  a = mmdb::newAtom();
+    a->SetAtomName    ( 0,0,name_pdb(aname),"","",element_pdb(elem) );
+    a->SetCharge      ( mmdb::RMax(0.0,atomCharge) );
+    a->SetCoordinates ( pdb_x,pdb_y,pdb_z,1.0,0.0  );
+    strcpy ( a->energyType,energyType  );
+    a->sigOcc = -1.0;  // signal that atom was added from SBase
+  }
+
+  mmdb::PAtom Atom::makeAtom()  {
+  mmdb::PAtom   a;
+  mmdb::AtomName aname;
+  mmdb::Element  elem;
+    a = mmdb::newAtom();
+    a->SetAtomName    ( 0,0,name_pdb(aname),"","",element_pdb(elem) );
+    a->SetCharge      ( mmdb::RMax(0.0,atomCharge) );
+    a->SetCoordinates ( pdb_x,pdb_y,pdb_z,1.0,0.0 );
+    strcpy ( a->energyType,energyType );
+    a->sigOcc = -1.0;  // signal that atom was added from SBase
+    return a;
+  }
+
+
+  void Atom::makeCIFTags ( mmdb::mmcif::PLoop mmCIFLoop )  {
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_COMP_ID        );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID        );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_TYPE_SYMBOL    );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_TYPE_ENERGY    );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_PARTIAL_CHARGE );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_X              );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_Y              );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_Z              );
+  }
+
+  int Atom::readFromCIF_ccp4 ( mmdb::mmcif::PLoop mmCIFLoop,
+                                      int atomNo )  {
+  int  rc;
+
+    rc = 0;
+    mmCIFLoop->CopyString ( atomName,sizeof(mmdb::AtomName)-1,
+                            MMCIF_TAG_ATOM_ID,atomNo,rc );
+    mmCIFLoop->CopyString ( chemElement,sizeof(mmdb::Element)-1,
+                            MMCIF_TAG_TYPE_SYMBOL,atomNo,rc );
+    mmCIFLoop->CopyString ( energyType,sizeof(mmdb::EnergyType)-1,
+                            MMCIF_TAG_TYPE_ENERGY,atomNo,rc );
+
+    mmCIFLoop->CopyReal   ( atomCharge,MMCIF_TAG_PARTIAL_CHARGE,
+                            atomNo,rc );
+
+    if (mmCIFLoop->GetTagNo(MMCIF_TAG_X)>=0)  {
+      mmCIFLoop->CopyReal ( mlib_x,MMCIF_TAG_X,atomNo,rc );
+      mmCIFLoop->CopyReal ( mlib_y,MMCIF_TAG_Y,atomNo,rc );
+      mmCIFLoop->CopyReal ( mlib_z,MMCIF_TAG_Y,atomNo,rc );
+    } else if (mmCIFLoop->GetTagNo(MMCIF_TAG_MODEL_CARTN_X)>=0)  {
+      mmCIFLoop->CopyReal ( mlib_x,MMCIF_TAG_MODEL_CARTN_X,atomNo,rc );
+      mmCIFLoop->CopyReal ( mlib_y,MMCIF_TAG_MODEL_CARTN_Y,atomNo,rc );
+      mmCIFLoop->CopyReal ( mlib_z,MMCIF_TAG_MODEL_CARTN_Z,atomNo,rc );
+    }
+    /*else  {
+      mlib_x = 0.0;
+      mlib_y = 0.0;
+      mlib_z = 0.0;
+    }
+    */
+
+    return rc;
+
+  }
+
+  int Atom::readFromCIF_rcsb ( mmdb::mmcif::PLoop mmCIFLoop,
+                                      int atomNo )  {
+  mmdb::pstr p;
+  int        rc;
+
+    rc = 0;
+    mmCIFLoop->CopyString  ( atomName,sizeof(mmdb::AtomName)-1,
+                             MMCIF_TAG_ATOM_ID,atomNo,rc );
+    mmCIFLoop->CopyString  ( rcsbAtomName,sizeof(mmdb::AtomName)-1,
+                             MMCIF_TAG_ALT_ATOM_ID,atomNo,rc );
+    mmCIFLoop->CopyString  ( chemElement,sizeof(mmdb::Element)-1,
+                             MMCIF_TAG_TYPE_SYMBOL,atomNo,rc );
+
+    if (mmCIFLoop->GetTagNo(MMCIF_TAG_MODEL_CARTN_X)>=0)  {
+      mmCIFLoop->CopyReal ( pdb_x,MMCIF_TAG_MODEL_CARTN_X,atomNo,rc );
+      mmCIFLoop->CopyReal ( pdb_y,MMCIF_TAG_MODEL_CARTN_Y,atomNo,rc );
+      mmCIFLoop->CopyReal ( pdb_z,MMCIF_TAG_MODEL_CARTN_Z,atomNo,rc );
+    }
+    if (mmCIFLoop->GetTagNo(MMCIF_TAG_PDBX_MODEL_CARTN_X)>=0)  {
+      mmCIFLoop->CopyReal ( pdbx_x,MMCIF_TAG_PDBX_MODEL_CARTN_X,atomNo,rc );
+      mmCIFLoop->CopyReal ( pdbx_y,MMCIF_TAG_PDBX_MODEL_CARTN_Y,atomNo,rc );
+      mmCIFLoop->CopyReal ( pdbx_z,MMCIF_TAG_PDBX_MODEL_CARTN_Z,atomNo,rc );
+    }
+
+    p = mmCIFLoop->GetString ( MMCIF_TAG_PDBX_STEREO_CONFIG,
+                               atomNo,rc );
+    if (!p)  property[0] = '-';
+       else  property[0] = p[0];
+
+
+    p = mmCIFLoop->GetString ( MMCIF_TAG_PDBX_LEAVING_ATOM_FLAG,
+                               atomNo,rc );
     if (!p)              property[2] = 'N';
     else if (p[0]=='Y')  property[2] = 'Y';
                    else  property[2] = 'N';
+
+    return rc;
+
   }
-  /*
-  else  {
-    pdb_x  = 0.0;
-    pdb_y  = 0.0;
-    pdb_z  = 0.0;
-    pdbx_x = 0.0;
-    pdbx_y = 0.0;
-    pdbx_z = 0.0;
-  }
-  */
 
-  return rc;
+  int Atom::readFromCIF ( mmdb::mmcif::PStruct mmCIFStruct )  {
+  mmdb::pstr p;
+  int        rc;
+
+    rc = 0;
+    p = mmCIFStruct->GetString ( MMCIF_TAG_ATOM_ID,rc );
+    if (p) strcpy ( atomName,p );
+    p = mmCIFStruct->GetString ( MMCIF_TAG_ALT_ATOM_ID,rc );
+    if (p) strcpy ( rcsbAtomName,p );
+    p = mmCIFStruct->GetString ( MMCIF_TAG_TYPE_SYMBOL,rc );
+    if (p) strcpy ( chemElement,p );
+    p = mmCIFStruct->GetString ( MMCIF_TAG_TYPE_ENERGY,rc );
+    if (p) strcpy ( energyType,p );
+
+    rc = mmCIFStruct->GetReal ( atomCharge,MMCIF_TAG_PARTIAL_CHARGE );
+
+    if (mmCIFStruct->GetTagNo(MMCIF_TAG_X)>=0)  {
+      rc = mmCIFStruct->GetReal ( mlib_x,MMCIF_TAG_X );
+      rc = mmCIFStruct->GetReal ( mlib_y,MMCIF_TAG_Y );
+      rc = mmCIFStruct->GetReal ( mlib_z,MMCIF_TAG_Y );
+    } else if (mmCIFStruct->GetTagNo(MMCIF_TAG_MODEL_CARTN_X)>=0)  {
+      rc = mmCIFStruct->GetReal ( pdb_x,MMCIF_TAG_MODEL_CARTN_X );
+      rc = mmCIFStruct->GetReal ( pdb_y,MMCIF_TAG_MODEL_CARTN_Y );
+      rc = mmCIFStruct->GetReal ( pdb_z,MMCIF_TAG_MODEL_CARTN_Y );
+      rc = mmCIFStruct->GetReal ( pdbx_x,MMCIF_TAG_PDBX_MODEL_CARTN_X );
+      rc = mmCIFStruct->GetReal ( pdbx_y,MMCIF_TAG_PDBX_MODEL_CARTN_Y );
+      rc = mmCIFStruct->GetReal ( pdbx_z,MMCIF_TAG_PDBX_MODEL_CARTN_Y );
+      p  = mmCIFStruct->GetString ( MMCIF_TAG_PDBX_LEAVING_ATOM_FLAG,rc );
+      if (!p)              property[2] = 'N';
+      else if (p[0]=='Y')  property[2] = 'Y';
+                     else  property[2] = 'N';
+    }
+    /*
+    else  {
+      pdb_x  = 0.0;
+      pdb_y  = 0.0;
+      pdb_z  = 0.0;
+      pdbx_x = 0.0;
+      pdbx_y = 0.0;
+      pdbx_z = 0.0;
+    }
+    */
+
+    return rc;
+
+  }
 
-}
+  void Atom::writeToCIF  ( mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID )  {
 
-void CCP4SRSAtom::writeToCIF  ( PCMMCIFLoop mmCIFLoop, cpstr monID )  {
+    mmCIFLoop->AddString ( monID      ,false );
 
-  mmCIFLoop->AddString ( monID      ,False );
+    mmCIFLoop->AddString ( atomName   ,false );
+    mmCIFLoop->AddString ( chemElement,false );
+    mmCIFLoop->AddString ( energyType ,false );
+
+    mmCIFLoop->AddReal   ( atomCharge ,"%10.3f" );
+    mmCIFLoop->AddReal   ( mlib_x     ,"%10.3f" );
+    mmCIFLoop->AddReal   ( mlib_y     ,"%10.3f" );
+    mmCIFLoop->AddReal   ( mlib_z     ,"%10.3f" );
 
-  mmCIFLoop->AddString ( atomName   ,False );
-  mmCIFLoop->AddString ( chemElement,False );
-  mmCIFLoop->AddString ( energyType ,False );
-
-  mmCIFLoop->AddReal   ( atomCharge ,"%10.3f" );
-  mmCIFLoop->AddReal   ( mlib_x     ,"%10.3f" );
-  mmCIFLoop->AddReal   ( mlib_y     ,"%10.3f" );
-  mmCIFLoop->AddReal   ( mlib_z     ,"%10.3f" );
-
-}
-
-/*
-data_comp_ATP
-#
-loop_
-_chem_comp_atom.comp_id
-_chem_comp_atom.atom_id
-_chem_comp_atom.type_symbol
-_chem_comp_atom.type_energy
-_chem_comp_atom.partial_charge
-_chem_comp_atom.x
-_chem_comp_atom.y
-_chem_comp_atom.z
- ATP           O2A    O    OP       -0.500      0.000    0.000    0.000
-*/
-
-void CCP4SRSAtom::copy ( PCCP4SRSAtom atom )  {
-
-  strcpy ( atomName    ,atom->name       () );
-  strcpy ( rcsbAtomName,atom->rcsb_name  () );
-  strcpy ( oldAtomName ,atom->old_name   () );
-  strcpy ( chemElement ,atom->element    () );
-  strcpy ( energyType  ,atom->energy_type() );
-
-  pdb_x  = atom->x();
-  pdb_y  = atom->y();
-  pdb_z  = atom->z();
-  mlib_x = atom->x_mlib();
-  mlib_y = atom->y_mlib();
-  mlib_z = atom->z_mlib();
-  pdbx_x = atom->x_pdbx();
-  pdbx_y = atom->y_pdbx();
-  pdbx_z = atom->z_pdbx();
-
-  atomCharge  = atom->charge        ();
-  atomWeight  = atom->weight        ();
-  vdwRadius   = atom->vdw_radius    ();
-  vdwhRadius  = atom->vdwh_radius   ();
-  ionRadius   = atom->ion_radius    ();
-  atomValency = atom->valency       ();
-  atomSP      = atom->sp            ();
-  property[0] = atom->rcsb_chirality();
-  property[1] = atom->chirality     ();
-  property[2] = atom->leaving       ();
-  property[3] = atom->hb_type       ();
-
-}
-
-
-void CCP4SRSAtom::merge ( PCCP4SRSAtom atom )  {
-
-  if (!atomName    [0])  strcpy ( atomName    ,atom->name       () );
-  if (!rcsbAtomName[0])  strcpy ( rcsbAtomName,atom->rcsb_name  () );
-  if (!oldAtomName [0])  strcpy ( oldAtomName ,atom->old_name   () );
-  if (!chemElement [0])  strcpy ( chemElement ,atom->element    () );
-  if (!energyType  [0])  strcpy ( energyType  ,atom->energy_type() );
-
-  if (pdb_x==-MaxShortReal)  {
-    pdb_x = atom->x();
-    pdb_y = atom->y();
-    pdb_z = atom->z();
   }
-  if (pdbx_x==-MaxShortReal)  {
+
+  /*
+  data_comp_ATP
+  #
+  loop_
+  _chem_comp_atom.comp_id
+  _chem_comp_atom.atom_id
+  _chem_comp_atom.type_symbol
+  _chem_comp_atom.type_energy
+  _chem_comp_atom.partial_charge
+  _chem_comp_atom.x
+  _chem_comp_atom.y
+  _chem_comp_atom.z
+   ATP           O2A    O    OP       -0.500      0.000    0.000    0.000
+  */
+
+  void Atom::copy ( PAtom atom )  {
+
+    strcpy ( atomName    ,atom->name       () );
+    strcpy ( rcsbAtomName,atom->rcsb_name  () );
+    strcpy ( oldAtomName ,atom->old_name   () );
+    strcpy ( chemElement ,atom->element    () );
+    strcpy ( energyType  ,atom->energy_type() );
+
+    pdb_x  = atom->x();
+    pdb_y  = atom->y();
+    pdb_z  = atom->z();
+    mlib_x = atom->x_mlib();
+    mlib_y = atom->y_mlib();
+    mlib_z = atom->z_mlib();
     pdbx_x = atom->x_pdbx();
     pdbx_y = atom->y_pdbx();
     pdbx_z = atom->z_pdbx();
+
+    atomCharge  = atom->charge        ();
+    atomWeight  = atom->weight        ();
+    vdwRadius   = atom->vdw_radius    ();
+    vdwhRadius  = atom->vdwh_radius   ();
+    ionRadius   = atom->ion_radius    ();
+    atomValency = atom->valency       ();
+    atomSP      = atom->sp            ();
+    property[0] = atom->rcsb_chirality();
+    property[1] = atom->chirality     ();
+    property[2] = atom->leaving       ();
+    property[3] = atom->hb_type       ();
+
   }
-  if (mlib_x==-MaxShortReal)  {
-    mlib_x = atom->x_mlib();
-    mlib_y = atom->y_mlib();
-    mlib_z = atom->z_mlib();
+
+
+  void Atom::merge ( PAtom atom )  {
+
+    if (!atomName    [0])  strcpy ( atomName    ,atom->name       () );
+    if (!rcsbAtomName[0])  strcpy ( rcsbAtomName,atom->rcsb_name  () );
+    if (!oldAtomName [0])  strcpy ( oldAtomName ,atom->old_name   () );
+    if (!chemElement [0])  strcpy ( chemElement ,atom->element    () );
+    if (!energyType  [0])  strcpy ( energyType  ,atom->energy_type() );
+
+    if (pdb_x==-mmdb::MaxShortReal)  {
+      pdb_x = atom->x();
+      pdb_y = atom->y();
+      pdb_z = atom->z();
+    }
+    if (pdbx_x==-mmdb::MaxShortReal)  {
+      pdbx_x = atom->x_pdbx();
+      pdbx_y = atom->y_pdbx();
+      pdbx_z = atom->z_pdbx();
+    }
+    if (mlib_x==-mmdb::MaxShortReal)  {
+      mlib_x = atom->x_mlib();
+      mlib_y = atom->y_mlib();
+      mlib_z = atom->z_mlib();
+    }
+
+    if (atomCharge==0.0)  atomCharge  = atom->charge     ();
+    if (atomWeight==0.0)  atomWeight  = atom->weight     ();
+    if (vdwRadius ==0.0)  vdwRadius   = atom->vdw_radius ();
+    if (vdwhRadius==0.0)  vdwhRadius  = atom->vdwh_radius();
+    if (ionRadius ==0.0)  ionRadius   = atom->ion_radius ();
+    if (!atomValency)     atomValency = atom->valency    ();
+    if (!atomSP)          atomSP      = atom->sp         ();
+    if (property[0]=='-') property[0] = atom->rcsb_chirality();
+    if (property[1]=='-') property[1] = atom->chirality     ();
+    if (property[2]=='-') property[2] = atom->leaving       ();
+    if (property[3]=='-') property[3] = atom->hb_type       ();
+
+  }
+
+
+  void Atom::write_mem ( PMemIO memIO, int version )  {
+  UNUSED_ARGUMENT(version);
+    memIO->put_line     ( atomName     );
+    memIO->put_line     ( rcsbAtomName );
+    memIO->put_line     ( oldAtomName  );
+    memIO->put_line     ( chemElement  );
+    memIO->put_line     ( energyType   );
+    memIO->put_float    ( pdb_x        );
+    memIO->put_float    ( pdb_y        );
+    memIO->put_float    ( pdb_z        );
+    memIO->put_float    ( pdbx_x       );
+    memIO->put_float    ( pdbx_y       );
+    memIO->put_float    ( pdbx_z       );
+    memIO->put_float    ( mlib_x       );
+    memIO->put_float    ( mlib_y       );
+    memIO->put_float    ( mlib_z       );
+    memIO->put_float    ( atomCharge   );
+    memIO->put_float    ( atomWeight   );
+    memIO->put_float    ( vdwRadius    );
+    memIO->put_float    ( vdwhRadius   );
+    memIO->put_float    ( ionRadius    );
+    memIO->put_integer  ( atomValency  );
+    memIO->put_integer  ( atomSP       );
+    memIO->write_buffer ( property,sizeof(property) );
+  }
+
+  bool Atom::read_mem  ( PMemIO memIO, int version,
+                                bool * Ok )  {
+  UNUSED_ARGUMENT(version);
+  bool success;
+    if (Ok)  success = *Ok;
+       else  success = true;
+    memIO->get_line    ( atomName    ,&success );
+    memIO->get_line    ( rcsbAtomName,&success );
+    memIO->get_line    ( oldAtomName ,&success );
+    memIO->get_line    ( chemElement ,&success );
+    memIO->get_line    ( energyType  ,&success );
+    memIO->get_float   ( pdb_x       ,&success );
+    memIO->get_float   ( pdb_y       ,&success );
+    memIO->get_float   ( pdb_z       ,&success );
+    memIO->get_float   ( pdbx_x      ,&success );
+    memIO->get_float   ( pdbx_y      ,&success );
+    memIO->get_float   ( pdbx_z      ,&success );
+    memIO->get_float   ( mlib_x      ,&success );
+    memIO->get_float   ( mlib_y      ,&success );
+    memIO->get_float   ( mlib_z      ,&success );
+    memIO->get_float   ( atomCharge  ,&success );
+    memIO->get_float   ( atomWeight  ,&success );
+    memIO->get_float   ( vdwRadius   ,&success );
+    memIO->get_float   ( vdwhRadius  ,&success );
+    memIO->get_float   ( ionRadius   ,&success );
+    memIO->get_integer ( atomValency ,&success );
+    memIO->get_integer ( atomSP      ,&success );
+    if (version<2)  {
+      memIO->read_buffer ( &(property[1]),3,&success );
+      property[0] = property[1];
+    } else
+      memIO->read_buffer ( property,sizeof(property),&success );
+    if (Ok) *Ok = success;
+    return success;
+  }
+
+
+  void  get_atom_from_cif ( int & index, mmdb::mmcif::PLoop loop,
+                            mmdb::cpstr Tag,
+                            int row,Container<Atom> & atoms,
+                            int & rc )  {
+  mmdb::pstr p;
+     p = loop->GetString ( Tag,row,rc );
+     if (!p)                     index = -1;
+     else if (!strcmp(p,"n/a"))  index = AtomID_NA;
+                           else  index = atoms.index ( p );
+  }
+
+  void  get_atom_from_cif ( int & index, mmdb::mmcif::PStruct mmCIFStruct,
+                            mmdb::cpstr Tag,
+                            Container<Atom> & atoms,
+                            int & rc )  {
+  mmdb::pstr p;
+     p = mmCIFStruct->GetString ( Tag,rc );
+     if (!p)                     index = -1;
+     else if (!strcmp(p,"n/a"))  index = AtomID_NA;
+                           else  index = atoms.index ( p );
+  }
+
+  void add_atom_to_cif ( mmdb::mmcif::PLoop loop, int atom_no,
+                         Container<Atom> & atoms )  {
+    if ((atom_no>=0) && (atom_no<atoms.numberOf()))
+         loop->AddString ( atoms.at(atom_no)->name(),false );
+    else if (atom_no==AtomID_NA)
+         loop->AddString ( "n/a",false );
+    else loop->AddNoData ( mmdb::mmcif::CIF_NODATA_DOT );
   }
 
-  if (atomCharge==0.0)  atomCharge  = atom->charge     ();
-  if (atomWeight==0.0)  atomWeight  = atom->weight     ();
-  if (vdwRadius ==0.0)  vdwRadius   = atom->vdw_radius ();
-  if (vdwhRadius==0.0)  vdwhRadius  = atom->vdwh_radius();
-  if (ionRadius ==0.0)  ionRadius   = atom->ion_radius ();
-  if (!atomValency)     atomValency = atom->valency    ();
-  if (!atomSP)          atomSP      = atom->sp         ();
-  if (property[0]=='-') property[0] = atom->rcsb_chirality();
-  if (property[1]=='-') property[1] = atom->chirality     ();
-  if (property[2]=='-') property[2] = atom->leaving       ();
-  if (property[3]=='-') property[3] = atom->hb_type       ();
-
-}
-
-
-void CCP4SRSAtom::write_mem ( PCMemIO memIO, int version )  {
-UNUSED_ARGUMENT(version);
-  memIO->put_line     ( atomName     );
-  memIO->put_line     ( rcsbAtomName );
-  memIO->put_line     ( oldAtomName  );
-  memIO->put_line     ( chemElement  );
-  memIO->put_line     ( energyType   );
-  memIO->put_float    ( pdb_x        );
-  memIO->put_float    ( pdb_y        );
-  memIO->put_float    ( pdb_z        );
-  memIO->put_float    ( pdbx_x       );
-  memIO->put_float    ( pdbx_y       );
-  memIO->put_float    ( pdbx_z       );
-  memIO->put_float    ( mlib_x       );
-  memIO->put_float    ( mlib_y       );
-  memIO->put_float    ( mlib_z       );
-  memIO->put_float    ( atomCharge   );
-  memIO->put_float    ( atomWeight   );
-  memIO->put_float    ( vdwRadius    );
-  memIO->put_float    ( vdwhRadius   );
-  memIO->put_float    ( ionRadius    );
-  memIO->put_integer  ( atomValency  );
-  memIO->put_integer  ( atomSP       );
-  memIO->write_buffer ( property,sizeof(property) );
-}
-
-Boolean CCP4SRSAtom::read_mem  ( PCMemIO memIO, int version,
-                                 Boolean * Ok )  {
-UNUSED_ARGUMENT(version);
-Boolean success;
-  if (Ok)  success = *Ok;
-     else  success = True;
-  memIO->get_line    ( atomName    ,&success );
-  memIO->get_line    ( rcsbAtomName,&success );
-  memIO->get_line    ( oldAtomName ,&success );
-  memIO->get_line    ( chemElement ,&success );
-  memIO->get_line    ( energyType  ,&success );
-  memIO->get_float   ( pdb_x       ,&success );
-  memIO->get_float   ( pdb_y       ,&success );
-  memIO->get_float   ( pdb_z       ,&success );
-  memIO->get_float   ( pdbx_x      ,&success );
-  memIO->get_float   ( pdbx_y      ,&success );
-  memIO->get_float   ( pdbx_z      ,&success );
-  memIO->get_float   ( mlib_x      ,&success );
-  memIO->get_float   ( mlib_y      ,&success );
-  memIO->get_float   ( mlib_z      ,&success );
-  memIO->get_float   ( atomCharge  ,&success );
-  memIO->get_float   ( atomWeight  ,&success );
-  memIO->get_float   ( vdwRadius   ,&success );
-  memIO->get_float   ( vdwhRadius  ,&success );
-  memIO->get_float   ( ionRadius   ,&success );
-  memIO->get_integer ( atomValency ,&success );
-  memIO->get_integer ( atomSP      ,&success );
-  if (version<2)  {
-    memIO->read_buffer ( &(property[1]),3,&success );
-    property[0] = property[1];
-  } else
-    memIO->read_buffer ( property,sizeof(property),&success );
-  if (Ok) *Ok = success;
-  return success;
-}
-
-
-void  get_atom_from_cif ( int & index, PCMMCIFLoop loop, cpstr Tag,
-                          int row,CCP4SRSContainer<CCP4SRSAtom> & atoms,
-                          int & rc )  {
-pstr p;
-   p = loop->GetString ( Tag,row,rc );
-   if (!p)                     index = -1;
-   else if (!strcmp(p,"n/a"))  index = CCP4SRSAtomID_NA;
-                         else  index = atoms.index ( p );
-}
-
-void  get_atom_from_cif ( int & index, PCMMCIFStruct mmCIFStruct,
-                          cpstr Tag,
-                          CCP4SRSContainer<CCP4SRSAtom> & atoms,
-                          int & rc )  {
-pstr p;
-   p = mmCIFStruct->GetString ( Tag,rc );
-   if (!p)                     index = -1;
-   else if (!strcmp(p,"n/a"))  index = CCP4SRSAtomID_NA;
-                         else  index = atoms.index ( p );
-}
-
-void add_atom_to_cif ( PCMMCIFLoop loop, int atom_no,
-                       CCP4SRSContainer<CCP4SRSAtom> & atoms )  {
-  if ((atom_no>=0) && (atom_no<atoms.numberOf()))
-       loop->AddString ( atoms.at(atom_no)->name(),False );
-  else if (atom_no==CCP4SRSAtomID_NA)
-       loop->AddString ( "n/a",False );
-  else loop->AddNoData ( CIF_NODATA_DOT );
-}
+}  // namespace ccp4srs
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_atom.h ccp4srs/ccp4srs/ccp4srs_atom.h
--- ccp4srs-old/ccp4srs/ccp4srs_atom.h	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_atom.h	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_atom.h, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_atom.h $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,16 +22,16 @@
 //
 //  =================================================================
 //
-//    26.02.13   <--  Date of Last Modification.
+//    03.02.14   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_atom  <interface>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSAtom  - atom description class
+//  **** Classes :  ccp4srs::Atom  - atom description class
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010-2013
+//  (C) E. Krissinel 2010-2014
 //
 //  =================================================================
 //
@@ -39,131 +39,133 @@
 #ifndef CCP4SRS_ATOM_H
 #define CCP4SRS_ATOM_H
 
-
 #include "ccp4srs_container.h"
 #include "memio_.h"
 
-#include "mmdb/mmdb_atom.h"
-#include "mmdb/mmdb_mmcif.h"
-#include "mmdb/mmdb_defs.h"
-
-DefineClass(CCP4SRSAtom)
-
-class CCP4SRSAtom  {
-
-  public:
-    CCP4SRSAtom();
-    virtual ~CCP4SRSAtom();
-
-    // function for searches in containers
-    inline cpstr      id         () { return atomName;     }
-
-    inline cpstr      name       () { return atomName;     }
-    inline cpstr      rcsb_name  () { return rcsbAtomName; }
-    inline cpstr      old_name   () { return oldAtomName;  }
-    inline cpstr      element    () { return chemElement;  }
-    inline cpstr      energy_type() { return energyType;   }
-    inline realtype   x          () { return pdb_x;        }
-    inline realtype   y          () { return pdb_y;        }
-    inline realtype   z          () { return pdb_z;        }
-    inline realtype   x_pdbx     () { return pdbx_x;       }
-    inline realtype   y_pdbx     () { return pdbx_y;       }
-    inline realtype   z_pdbx     () { return pdbx_z;       }
-    inline realtype   x_mlib     () { return mlib_x;       }
-    inline realtype   y_mlib     () { return mlib_y;       }
-    inline realtype   z_mlib     () { return mlib_z;       }
-    inline realtype   charge     () { return atomCharge;   }
-    inline realtype   weight     () { return atomWeight;   }
-    inline realtype   vdw_radius () { return vdwRadius;    }
-    inline realtype   vdwh_radius() { return vdwhRadius;   }
-    inline realtype   ion_radius () { return ionRadius;    }
-    inline int        valency    () { return atomValency;  }
-    inline int        sp         () { return atomSP;       }
-
-    inline char rcsb_chirality() const { return property[0];  }
-    inline char ccp4_chirality() const { return property[1];  }
-    char chirality() const; // ccp4's; if not set then rcsb's
-    inline char leaving       () const { return property[2];  }
-    inline Boolean isLeaving  () const { return (property[2]=='Y'); }
-    inline char hb_type       () const { return property[3];  }
-
-
-    cpstr name_pdb      ( pstr aname );  // with significant spacing
-    cpstr rcsb_name_pdb ( pstr aname );  // with significant spacing
-    cpstr old_name_pdb  ( pstr aname );  // with significant spacing
-    cpstr element_pdb   ( pstr elem  );  // with significant spacing
-
-    void set_energy_type ( cpstr etype );
-    void set_old_name    ( cpstr name  );
-    inline void set_rcsb_chirality ( char c  )  { property[0] = c; }
-    inline void set_chirality      ( char c  )  { property[1] = c; }
-    inline void set_hb_type        ( char h  )  { property[3] = h; }
-
-    inline void set_vdw_radius  ( realtype r )  { vdwRadius   = r; }
-    inline void set_vdwh_radius ( realtype r )  { vdwhRadius  = r; }
-    inline void set_ion_radius  ( realtype r )  { ionRadius   = r; }
-    inline void set_valency     ( int v      )  { atomValency = v; }
-    inline void set_sp          ( int s      )  { atomSP      = s; }
-
-    void  makeCAtom ( RPCAtom a );
-    PCAtom makeCAtom();
-
-    static void makeCIFTags ( PCMMCIFLoop mmCIFLoop );
-    int  readFromCIF_ccp4 ( PCMMCIFLoop mmCIFLoop, int atomNo );
-    int  readFromCIF_rcsb ( PCMMCIFLoop mmCIFLoop, int atomNo );
-    int  readFromCIF      ( PCMMCIFStruct mmCIFStruct );
-    void writeToCIF       ( PCMMCIFLoop mmCIFLoop, cpstr monID );
-
-    void copy  ( PCCP4SRSAtom atom );
-    void merge ( PCCP4SRSAtom atom );
-
-    void    write_mem ( PCMemIO memIO, int version );
-    Boolean read_mem  ( PCMemIO memIO, int version,
-                        Boolean * Ok = NULL );
-
-  protected:
-    AtomName    atomName;     //!< atom name
-    AtomName    rcsbAtomName; //!< alternative atom name
-    AtomName    oldAtomName;  //!< old atom name
-    Element     chemElement;  //!< chemical element name
-    EnergyType  energyType;   //!< energy type
-    realtype    mlib_x,mlib_y,mlib_z; //!< m-lib cartesian coordinates
-    realtype    pdb_x ,pdb_y ,pdb_z ; //!< pdb cartesian coordinates
-    realtype    pdbx_x,pdbx_y,pdbx_z; //!< pdbx cartesian coordinates
-    realtype    atomCharge;   //!< partial charge
-    realtype    atomWeight;   //!< atomic weight (in a.u.)
-    realtype    vdwRadius;    //!< Van-Der-Waals radius
-    realtype    vdwhRadius;   //!< Van-Der-Waals radius with hydrogen
-    realtype    ionRadius;    //!< ion radius
-    int         atomValency;  //!< valency
-    int         atomSP;       //!< sp-hybridization
-    char        property[4];  //!< property vector:
-                              /// [0]: RCSB chirality : 'R', 'S' or 'N'
-                              /// [1]: MLib chirality : 'R', 'S' or 'N'
-                              /// [2]: leaving atom: 'Y' or 'N'
-                              /// [3]: hydrogen bond type:
-                              ///                 'D' donor
-                              ///                 'A' acceptor
-                              ///                 'B' both
-                              ///                 'H' hydrogen candidate
-                              ///                 'N' neither
-
-    void Init();
-
-};
-
-extern void get_atom_from_cif ( int & index, PCMMCIFLoop loop,
-                                cpstr Tag, int row,
-                                CCP4SRSContainer<CCP4SRSAtom> & atoms,
-                                int & rc );
-
-extern void get_atom_from_cif ( int & index, PCMMCIFStruct mmCIFStruct,
-                                cpstr Tag,
-                                CCP4SRSContainer<CCP4SRSAtom> & atoms,
-                                int & rc );
+#include "mmdb2/mmdb_atom.h"
+#include "mmdb2/mmdb_mmcif_.h"
+#include "mmdb2/mmdb_defs.h"
+
+namespace ccp4srs  {
+
+  DefineClass(Atom);
+
+  class Atom  {
+
+    public:
+      Atom();
+      virtual ~Atom();
+
+      // function for searches in containers
+      inline mmdb::cpstr      id         () { return atomName;     }
+
+      inline mmdb::cpstr      name       () { return atomName;     }
+      inline mmdb::cpstr      rcsb_name  () { return rcsbAtomName; }
+      inline mmdb::cpstr      old_name   () { return oldAtomName;  }
+      inline mmdb::cpstr      element    () { return chemElement;  }
+      inline mmdb::cpstr      energy_type() { return energyType;   }
+      inline mmdb::realtype   x          () { return pdb_x;        }
+      inline mmdb::realtype   y          () { return pdb_y;        }
+      inline mmdb::realtype   z          () { return pdb_z;        }
+      inline mmdb::realtype   x_pdbx     () { return pdbx_x;       }
+      inline mmdb::realtype   y_pdbx     () { return pdbx_y;       }
+      inline mmdb::realtype   z_pdbx     () { return pdbx_z;       }
+      inline mmdb::realtype   x_mlib     () { return mlib_x;       }
+      inline mmdb::realtype   y_mlib     () { return mlib_y;       }
+      inline mmdb::realtype   z_mlib     () { return mlib_z;       }
+      inline mmdb::realtype   charge     () { return atomCharge;   }
+      inline mmdb::realtype   weight     () { return atomWeight;   }
+      inline mmdb::realtype   vdw_radius () { return vdwRadius;    }
+      inline mmdb::realtype   vdwh_radius() { return vdwhRadius;   }
+      inline mmdb::realtype   ion_radius () { return ionRadius;    }
+      inline int              valency    () { return atomValency;  }
+      inline int              sp         () { return atomSP;       }
+
+      inline char rcsb_chirality() const { return property[0];  }
+      inline char ccp4_chirality() const { return property[1];  }
+      char chirality() const; // ccp4's; if not set then rcsb's
+      inline char leaving       () const { return property[2];  }
+      inline bool isLeaving     () const { return (property[2]=='Y'); }
+      inline char hb_type       () const { return property[3];  }
+
+
+      mmdb::cpstr name_pdb      ( mmdb::pstr aname );  // with significant spacing
+      mmdb::cpstr rcsb_name_pdb ( mmdb::pstr aname );  // with significant spacing
+      mmdb::cpstr old_name_pdb  ( mmdb::pstr aname );  // with significant spacing
+      mmdb::cpstr element_pdb   ( mmdb::pstr elem  );  // with significant spacing
+
+      void set_energy_type ( mmdb::cpstr etype );
+      void set_old_name    ( mmdb::cpstr name  );
+      inline void set_rcsb_chirality ( char c  )  { property[0] = c; }
+      inline void set_chirality      ( char c  )  { property[1] = c; }
+      inline void set_hb_type        ( char h  )  { property[3] = h; }
+
+      inline void set_vdw_radius  ( mmdb::realtype r )  { vdwRadius   = r; }
+      inline void set_vdwh_radius ( mmdb::realtype r )  { vdwhRadius  = r; }
+      inline void set_ion_radius  ( mmdb::realtype r )  { ionRadius   = r; }
+      inline void set_valency     ( int v      )  { atomValency = v; }
+      inline void set_sp          ( int s      )  { atomSP      = s; }
+
+      void  makeAtom ( mmdb::RPAtom a );
+      mmdb::PAtom makeAtom();
+
+      static void makeCIFTags ( mmdb::mmcif::PLoop mmCIFLoop );
+      int  readFromCIF_ccp4 ( mmdb::mmcif::PLoop mmCIFLoop, int atomNo );
+      int  readFromCIF_rcsb ( mmdb::mmcif::PLoop mmCIFLoop, int atomNo );
+      int  readFromCIF      ( mmdb::mmcif::PStruct mmCIFStruct );
+      void writeToCIF       ( mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID );
+
+      void copy  ( PAtom atom );
+      void merge ( PAtom atom );
+
+      void write_mem ( PMemIO memIO, int version );
+      bool read_mem  ( PMemIO memIO, int version, bool * Ok = NULL );
+
+    protected:
+      mmdb::AtomName    atomName;     //!< atom name
+      mmdb::AtomName    rcsbAtomName; //!< alternative atom name
+      mmdb::AtomName    oldAtomName;  //!< old atom name
+      mmdb::Element     chemElement;  //!< chemical element name
+      mmdb::EnergyType  energyType;   //!< energy type
+      mmdb::realtype    mlib_x,mlib_y,mlib_z; //!< m-lib cartesian coordinates
+      mmdb::realtype    pdb_x ,pdb_y ,pdb_z ; //!< pdb cartesian coordinates
+      mmdb::realtype    pdbx_x,pdbx_y,pdbx_z; //!< pdbx cartesian coordinates
+      mmdb::realtype    atomCharge;   //!< partial charge
+      mmdb::realtype    atomWeight;   //!< atomic weight (in a.u.)
+      mmdb::realtype    vdwRadius;    //!< Van-Der-Waals radius
+      mmdb::realtype    vdwhRadius;   //!< Van-Der-Waals radius with hydrogen
+      mmdb::realtype    ionRadius;    //!< ion radius
+      int               atomValency;  //!< valency
+      int               atomSP;       //!< sp-hybridization
+      char              property[4];  //!< property vector:
+                                /// [0]: RCSB chirality : 'R', 'S' or 'N'
+                                /// [1]: MLib chirality : 'R', 'S' or 'N'
+                                /// [2]: leaving atom: 'Y' or 'N'
+                                /// [3]: hydrogen bond type:
+                                ///                 'D' donor
+                                ///                 'A' acceptor
+                                ///                 'B' both
+                                ///                 'H' hydrogen candidate
+                                ///                 'N' neither
+
+      void Init();
+
+  };
+
+  extern void get_atom_from_cif ( int & index, mmdb::mmcif::PLoop loop,
+                                  mmdb::cpstr Tag, int row,
+                                  Container<Atom> & atoms,
+                                  int & rc );
+
+  extern void get_atom_from_cif ( int & index, mmdb::mmcif::PStruct mmCIFStruct,
+                                  mmdb::cpstr Tag,
+                                  Container<Atom> & atoms,
+                                  int & rc );
+
+  extern void add_atom_to_cif  ( mmdb::mmcif::PLoop loop, int atom_no,
+                                 Container<Atom> & atoms );
 
-extern void add_atom_to_cif  ( PCMMCIFLoop loop, int atom_no,
-                               CCP4SRSContainer<CCP4SRSAtom> & atoms );
+} // namespace ccp4srs
 
 
 #endif // CCP4SRS_ATOM_H
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_base.cpp ccp4srs/ccp4srs/ccp4srs_base.cpp
--- ccp4srs-old/ccp4srs/ccp4srs_base.cpp	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_base.cpp	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_base.cpp, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_base.cpp $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,882 +22,892 @@
 //
 //  =================================================================
 //
-//    26.02.13   <--  Date of Last Modification.
+//    03.02.14   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_base  <implementation>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSBase - SRS base manager class
+//  **** Classes :  ccp4srs::Base - SRS base manager class
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010-2013
+//  (C) E. Krissinel 2010-2014
 //
 //  =================================================================
 //
 
-
 #include <string.h>
 #include <stdlib.h>
 
 #include "ccp4srs_base.h"
 #include "ccp4srs_defs.h"
-#include "mmdb/mmdb_tables.h"
-
-CCP4SRSBase::CCP4SRSBase()  {
-  init_base();
-}
+#include "mmdb2/mmdb_tables.h"
 
-CCP4SRSBase::~CCP4SRSBase()  {
-  freeMemory();
-}
+namespace ccp4srs  {
 
-void CCP4SRSBase::init_base()  {
+  Base::Base()  {
+    init_base();
+  }
 
-  index       = NULL;
-  srsDir      = NULL;
-  srsVersion  = CCP4SRS_file_version;
-  nEntries    = 0;
-  index_alloc = 0;
+  Base::~Base()  {
+    freeMemory();
+  }
 
-}
+  void Base::init_base()  {
 
-void CCP4SRSBase::freeMemory()  {
-int i;
+    index       = NULL;
+    srsDir      = NULL;
+    srsVersion  = CCP4SRS_file_version;
+    nEntries    = 0;
+    index_alloc = 0;
 
-  if (index)  {
-    for (i=0;i<index_alloc;i++)
-      if (index[i])  delete index[i];
-    delete[] index;
-    index = NULL;
   }
-  nEntries    = 0;
-  index_alloc = 0;
 
-  if (srsDir)  delete[] srsDir;
-  srsDir = NULL;
+  void Base::freeMemory()  {
+  int i;
 
-}
+    if (index)  {
+      for (i=0;i<index_alloc;i++)
+        if (index[i])  delete index[i];
+      delete[] index;
+      index = NULL;
+    }
+    nEntries    = 0;
+    index_alloc = 0;
+
+    if (srsDir)  delete[] srsDir;
+    srsDir = NULL;
 
-int CCP4SRSBase::loadIndex ( cpstr srsPath )  {
-CFile   f;
-CMemIO  memIO;
-pstr    S;
-int     i;
+  }
 
-  freeMemory();
+  int Base::loadIndex ( mmdb::cpstr srsPath )  {
+  mmdb::io::File f;
+  MemIO          memIO;
+  mmdb::pstr     S;
+  int            i;
 
-  if (srsPath)  {
-    CreateCopy ( srsDir,srsPath );
-    if (srsPath[0])  {
-      if (srsPath[strlen(srsPath)-1]!=_dir_sep_c)
-        CreateConcat ( srsDir,_dir_sep );
+    freeMemory();
+
+    if (srsPath)  {
+      mmdb::CreateCopy ( srsDir,srsPath );
+      if (srsPath[0])  {
+        if (srsPath[strlen(srsPath)-1]!=mmdb::io::_dir_sep_c)
+          mmdb::CreateConcat ( srsDir,mmdb::io::_dir_sep );
+      }
     }
-  }
 
-  S = NULL;
-  f.assign ( getPath(S,srsIndexFile),False,True );
-  if (S)  delete[] S;
+    S = NULL;
+    f.assign ( getPath(S,srsIndexFile),false,true );
+    if (S)  delete[] S;
 
-  if (f.reset(True))  {
+    if (f.reset(true))  {
 
-    f.ReadInt ( &srsVersion  );
-    f.ReadInt ( &index_alloc );
+      f.ReadInt ( &srsVersion  );
+      f.ReadInt ( &index_alloc );
 
-    if (index_alloc>0)  {
+      if (index_alloc>0)  {
+
+        index = new PIndex[index_alloc];
+        for (i=0;(i<index_alloc) && (!f.FileEnd()) && f.Success();i++)  {
+          memIO.reset();
+          index[nEntries] = new Index();
+          if (index[i]->read(f,srsVersion,&memIO)!=CCP4SRS_Ok)
+                delete index[nEntries];
+          else  nEntries++;
+        }
+
+        for (i=nEntries;i<index_alloc;i++)
+          index[i] = NULL;
 
-      index = new PCCP4SRSIndex[index_alloc];
-      for (i=0;(i<index_alloc) && (!f.FileEnd()) && f.Success();i++)  {
-        memIO.reset();
-        index[nEntries] = new CCP4SRSIndex();
-        if (index[i]->read(f,srsVersion,&memIO)!=CCP4SRS_Ok)
-              delete index[nEntries];
-        else  nEntries++;
       }
 
-      for (i=nEntries;i<index_alloc;i++)
-        index[i] = NULL;
+      f.shut();
 
-    }
+      if (nEntries==index_alloc)  return CCP4SRS_Ok;
+      return CCP4SRS_IndexCorrupt;
+
+    } else
+      return CCP4SRS_FileNotFound;
 
-    f.shut();
+  }
 
-    if (nEntries==index_alloc)  return CCP4SRS_Ok;
-    return CCP4SRS_IndexCorrupt;
+  PIndex Base::getIndex ( mmdb::cpstr entryID )  {
+  int n = getEntryNo ( entryID );
+    if ((n>=0) && (n<nEntries))  return index[n];
+    return NULL;
+  }
 
-  } else
-    return CCP4SRS_FileNotFound;
+  PIndex Base::getIndex ( int n )  {
+    if ((n>=0) && (n<nEntries))  return index[n];
+    return NULL;
+  }
 
-}
 
-PCCP4SRSIndex CCP4SRSBase::getIndex ( cpstr entryID )  {
-int n = getEntryNo ( entryID );
-  if ((n>=0) && (n<nEntries))  return index[n];
-  return NULL;
-}
+  int  Base::loadStructure ( mmdb::cpstr entryID )  {
+  UNUSED_ARGUMENT(entryID);
+    return CCP4SRS_Ok;
+  }
 
-PCCP4SRSIndex CCP4SRSBase::getIndex ( int n )  {
-  if ((n>=0) && (n<nEntries))  return index[n];
-  return NULL;
-}
+  int  Base::unloadStructure ( mmdb::cpstr entryID )  {
+  UNUSED_ARGUMENT(entryID);
+    return CCP4SRS_Ok;
+  }
 
 
-int  CCP4SRSBase::loadStructure ( cpstr entryID )  {
-UNUSED_ARGUMENT(entryID);
-  return CCP4SRS_Ok;
-}
+  mmdb::pstr Base::getPath ( mmdb::pstr & S, mmdb::cpstr FName )  {
+    if (srsDir)  mmdb::CreateCopCat ( S,srsDir,FName );
+           else  mmdb::CreateCopy   ( S,FName );
+    return S;
+  }
 
-int  CCP4SRSBase::unloadStructure ( cpstr entryID )  {
-UNUSED_ARGUMENT(entryID);
-  return CCP4SRS_Ok;
-}
 
+  int Base::getEntryNo ( mmdb::cpstr entryID )  {
+  mmdb::ResName id;
+  int           l1,l2,l,k;
 
-pstr CCP4SRSBase::getPath ( pstr & S, cpstr FName )  {
-  if (srsDir)  CreateCopCat ( S,srsDir,FName );
-         else  CreateCopy   ( S,FName );
-  return S;
-}
+    mmdb::strcpy_css ( id,entryID );
 
+    k = -1;
 
-int CCP4SRSBase::getEntryNo ( cpstr entryID )  {
-int     l1,l2,l,k;
-ResName id;
+    if (nEntries<=3)  {
+      for (l=0;(l<nEntries) && (k<0);l++)
+        if (!strcmp(index[l]->entryID,id))
+          k = l;
+      if (k>=0)  return k;
+      return CCP4SRS_EntryNotFound;
+    }
 
-  strcpy_css ( id,entryID );
+    l  = 0;
+    l1 = 0;
+    l2 = nEntries-1;
+    while (l1<l2-1)  {
+      l = (l1+l2)/2;
+      k = strcmp ( index[l]->entryID,id );
+      if (k<0)       l1 = l;
+      else if (k>0)  l2 = l;
+      else {
+        l1 = l;
+        l2 = l;
+      }
+    }
 
-  k = -1;
+    if (k==0)  return l;
+    else if (l==l1)  {
+      if (!strcmp(index[l2]->entryID,id))  return l2;
+    } else if (l==l2)  {
+      if (!strcmp(index[l1]->entryID,id))  return l1;
+    }
 
-  if (nEntries<=3)  {
-    for (l=0;(l<nEntries) && (k<0);l++)
-      if (!strcmp(index[l]->entryID,id))
-        k = l;
-    if (k>=0)  return k;
     return CCP4SRS_EntryNotFound;
+
   }
 
-  l  = 0;
-  l1 = 0;
-  l2 = nEntries-1;
-  while (l1<l2-1)  {
-    l = (l1+l2)/2;
-    k = strcmp ( index[l]->entryID,id );
-    if (k<0)       l1 = l;
-    else if (k>0)  l2 = l;
-    else {
-      l1 = l;
-      l2 = l;
-    }
-  }
-
-  if (k==0)  return l;
-  else if (l==l1)  {
-    if (!strcmp(index[l2]->entryID,id))  return l2;
-  } else if (l==l2)  {
-    if (!strcmp(index[l1]->entryID,id))  return l1;
-  }
-
-  return CCP4SRS_EntryNotFound;
-
-}
-
-PCFile CCP4SRSBase::getStructFile()  {
-PCFile structFile;
-pstr   S;
-  structFile = new CFile();
-  S = NULL;
-  structFile->assign ( getPath(S,srsStructFile),False,True );
-  if (S)  delete[] S;
-  if (!structFile->reset(True))  {
-    delete structFile;
-    structFile = NULL;
-  }
-  return structFile;
-}
-
-PCFile CCP4SRSBase::getGraphFile()  {
-PCFile graphFile;
-pstr   S;
-  graphFile = new CFile();
-  S = NULL;
-  graphFile->assign ( getPath(S,srsGraphFile),False,True );
-  if (S)  delete[] S;
-  if (!graphFile->reset(True))  {
-    delete graphFile;
-    graphFile = NULL;
-  }
-  return graphFile;
-}
-
-
-PCCP4SRSMonomer CCP4SRSBase::getMonomer ( cpstr entryID )  {
-//   getMonomer returns pointer to the monomer structure
-// identified by 3-letter entryID. If such structure is not
-// found, the function returns NULL.
-//   The function returns a pointer to a private copy of the
-// structure. Modifying it will not change data in the structural
-// database. The application is responsible for deallocating
-// the structure after use (simply use delete).
-//   See description of CCP4SRSMonomer for the explanation of
-// its fields.
-PCFile          structFile;
-PCCP4SRSMonomer srsMonomer;
-int             entryNo;
-
-  srsMonomer = NULL;
-  entryNo    = getEntryNo ( entryID );
-  if (entryNo!=CCP4SRS_EntryNotFound)  {
-    structFile = getStructFile();
-    if (structFile)  {
-      structFile->seek ( index[entryNo]->fStructPos );
-      srsMonomer = new CCP4SRSMonomer();
-      memIO.reset();
-      if (srsMonomer->read(*structFile,srsVersion,&memIO)!=CCP4SRS_Ok) {
-        delete srsMonomer;
-        srsMonomer = NULL;
-      }
-      structFile->shut ();
+  mmdb::io::PFile Base::getStructFile()  {
+  mmdb::io::PFile structFile;
+  mmdb::pstr      S;
+    structFile = new mmdb::io::File();
+    S = NULL;
+    structFile->assign ( getPath(S,srsStructFile),false,true );
+    if (S)  delete[] S;
+    if (!structFile->reset(true))  {
       delete structFile;
+      structFile = NULL;
     }
+    return structFile;
   }
 
-  return srsMonomer;
-
-}
+  mmdb::io::PFile Base::getGraphFile()  {
+  mmdb::io::PFile graphFile;
+  mmdb::pstr      S;
+    graphFile = new mmdb::io::File();
+    S = NULL;
+    graphFile->assign ( getPath(S,srsGraphFile),false,true );
+    if (S)  delete[] S;
+    if (!graphFile->reset(true))  {
+      delete graphFile;
+      graphFile = NULL;
+    }
+    return graphFile;
+  }
 
-PCCP4SRSMonomer CCP4SRSBase::getMonomer ( int entryNo,
-                                          PCFile structFile )  {
-PCFile          sFile;
-PCCP4SRSMonomer srsMonomer;
 
-  srsMonomer = NULL;
-  if ((0<=entryNo) && (entryNo<nEntries))  {
-    if (!structFile)  sFile = getStructFile();
-                else  sFile = structFile;
-    if (sFile)  {
-      sFile->seek ( index[entryNo]->fStructPos );
-      srsMonomer = new CCP4SRSMonomer();
-      memIO.reset();
-      if (srsMonomer->read(*sFile,srsVersion,&memIO)!=CCP4SRS_Ok) {
-        delete srsMonomer;
-        srsMonomer = NULL;
+  PMonomer Base::getMonomer ( mmdb::cpstr entryID )  {
+  //   getMonomer returns pointer to the monomer structure
+  // identified by 3-letter entryID. If such structure is not
+  // found, the function returns NULL.
+  //   The function returns a pointer to a private copy of the
+  // structure. Modifying it will not change data in the structural
+  // database. The application is responsible for deallocating
+  // the structure after use (simply use delete).
+  //   See description of CCP4SRSMonomer for the explanation of
+  // its fields.
+  mmdb::io::PFile structFile;
+  PMonomer        srsMonomer;
+  int             entryNo;
+
+    srsMonomer = NULL;
+    entryNo    = getEntryNo ( entryID );
+    if (entryNo!=CCP4SRS_EntryNotFound)  {
+      structFile = getStructFile();
+      if (structFile)  {
+        structFile->seek ( index[entryNo]->fStructPos );
+        srsMonomer = new Monomer();
+        memIO.reset();
+        if (srsMonomer->read(*structFile,srsVersion,&memIO)!=CCP4SRS_Ok) {
+          delete srsMonomer;
+          srsMonomer = NULL;
+        }
+        structFile->shut ();
+        delete structFile;
       }
-      if (!structFile)  delete sFile;
     }
+
+    return srsMonomer;
+
   }
 
-  return srsMonomer;
+  PMonomer Base::getMonomer ( int entryNo, mmdb::io::PFile structFile ) {
+  mmdb::io::PFile sFile;
+  PMonomer        srsMonomer;
+
+    srsMonomer = NULL;
+    if ((0<=entryNo) && (entryNo<nEntries))  {
+      if (!structFile)  sFile = getStructFile();
+                  else  sFile = structFile;
+      if (sFile)  {
+        sFile->seek ( index[entryNo]->fStructPos );
+        srsMonomer = new Monomer();
+        memIO.reset();
+        if (srsMonomer->read(*sFile,srsVersion,&memIO)!=CCP4SRS_Ok) {
+          delete srsMonomer;
+          srsMonomer = NULL;
+        }
+        if (!structFile)  delete sFile;
+      }
+    }
+
+    return srsMonomer;
 
-}
+  }
 
-PCCP4SRSMonomer CCP4SRSBase::getMonomer ( cpstr entryID,
-                                              PCFile structFile )  {
-//   Another form of getMonomer(..) uses an open structure
-// file, which allows to save on opening/closing file if
-// multiple access to SRS structures is required.
-int entryNo;
+  PMonomer Base::getMonomer ( mmdb::cpstr entryID,
+                              mmdb::io::PFile structFile )  {
+  //   Another form of getMonomer(..) uses an open structure
+  // file, which allows to save on opening/closing file if
+  // multiple access to SRS structures is required.
+  int entryNo;
 
-  entryNo    = getEntryNo ( entryID );
-  if (entryNo!=CCP4SRS_EntryNotFound)
-        return getMonomer ( entryNo,structFile );
-  else  return NULL;
+    entryNo    = getEntryNo ( entryID );
+    if (entryNo!=CCP4SRS_EntryNotFound)
+          return getMonomer ( entryNo,structFile );
+    else  return NULL;
 
-}
+  }
 
-int  CCP4SRSBase::getGraph ( PCFile graphFile, RPCGraph G )  {
-pstr buffer;
-int  buffer_length,rc,n;
+  int  Base::getGraph ( mmdb::io::PFile graphFile,
+                        mmdb::math::RPGraph G )  {
+  mmdb::pstr buffer;
+  int        buffer_length,rc,n;
 
-  rc = CCP4SRS_Ok;
+    rc = CCP4SRS_Ok;
 
-  memIO.reset();
-  if (memIO.read(*graphFile)==CMemIO::Ok)  {
-    memIO.get_buffer ( &buffer,&buffer_length );
-    if (buffer_length<=0)  {
+    memIO.reset();
+    if (memIO.read(*graphFile)==MemIO::Ok)  {
+      memIO.get_buffer ( &buffer,&buffer_length );
+      if (buffer_length<=0)  {
+        if (G)  delete G;
+        G = NULL;
+      } else  {
+        if (!G)  G = new mmdb::math::Graph();
+        n = 0;
+        G->mem_read ( buffer,n );
+        if (n!=buffer_length)  {
+          delete G;
+          G  = NULL;
+          rc = CCP4SRS_ReadErrors;
+        }
+      }
+    } else  {
+      rc = CCP4SRS_ReadErrors;
       if (G)  delete G;
       G = NULL;
-    } else  {
-      if (!G)  G = new CGraph();
-      n = 0;
-      G->mem_read ( buffer,n );
-      if (n!=buffer_length)  {
-        delete G;
-        G  = NULL;
-        rc = CCP4SRS_ReadErrors;
-      }
     }
-  } else  {
-    rc = CCP4SRS_ReadErrors;
-    if (G)  delete G;
-    G = NULL;
-  }
 
-  return rc;
+    return rc;
 
-}
+  }
 
-int  CCP4SRSBase::getGraph ( PCFile graphFile, int entryNo,
-                             RPCGraph G, int Hflag )  {
-//   getGraph(..) retrieves data for chemical structure number
-// entryNo (as in Index) from graph file graphFile, then allocates
-// and builds the corresponding graph, which is returned in G.
-//   If Hflag is set to 1, all hydrogens are removed from the graph.
-//   If Hflag is set to 2, element types of atoms, to which hydrogens
-// are bonded, are modified with flag HYDROGEN_BOND and moved to
-// the end.
-//   Returns 0 in case of success.
-int rc,htype;
+  int  Base::getGraph ( mmdb::io::PFile graphFile, int entryNo,
+                               mmdb::math::RPGraph G, int Hflag )  {
+  //   getGraph(..) retrieves data for chemical structure number
+  // entryNo (as in Index) from graph file graphFile, then allocates
+  // and builds the corresponding graph, which is returned in G.
+  //   If Hflag is set to 1, all hydrogens are removed from the graph.
+  //   If Hflag is set to 2, element types of atoms, to which hydrogens
+  // are bonded, are modified with flag HYDROGEN_BOND and moved to
+  // the end.
+  //   Returns 0 in case of success.
+  int rc,htype;
 
-  if ((entryNo<0) || (entryNo>=nEntries))
-    return CCP4SRS_EntryNotFound;
+    if ((entryNo<0) || (entryNo>=nEntries))
+      return CCP4SRS_EntryNotFound;
 
-  rc = CCP4SRS_Ok;
+    rc = CCP4SRS_Ok;
 
-/*
-  if (Index[structNo]->loadPos>=0)  {
+  /*
+    if (Index[structNo]->loadPos>=0)  {
 
-    if (!G)  G = new CGraph();
-    G->Copy ( ldGraph[Index[structNo]->loadPos] );
+      if (!G)  G = new CGraph();
+      G->Copy ( ldGraph[Index[structNo]->loadPos] );
 
-  } else  {
-*/
-  graphFile->seek ( index[entryNo]->fGraphPos );
-  graphFile->SetSuccess();
-  rc = getGraph ( graphFile,G );
-/*
-  if (memIO.read(*graphFile)==CMemIO::Ok)  {
-//  StreamRead ( *graphFile,G );
-    pstr buffer;
-    int  buffer_length,n;
-    memIO.get_buffer ( &buffer,&buffer_length );
-    if (buffer_length<=0)  {
-      if (G)  delete G;
-      G = NULL;
     } else  {
-      if (!G)  G = new CGraph();
-      n = 0;
-      G->mem_read ( buffer,n );
-      if (n!=buffer_length)  {
-        delete G;
-        G  = NULL;
-        rc = CCP4SRS_ReadErrors;
+  */
+    graphFile->seek ( index[entryNo]->fGraphPos );
+    graphFile->SetSuccess();
+    rc = getGraph ( graphFile,G );
+  /*
+    if (memIO.read(*graphFile)==CMemIO::Ok)  {
+  //  StreamRead ( *graphFile,G );
+      pstr buffer;
+      int  buffer_length,n;
+      memIO.get_buffer ( &buffer,&buffer_length );
+      if (buffer_length<=0)  {
+        if (G)  delete G;
+        G = NULL;
+      } else  {
+        if (!G)  G = new CGraph();
+        n = 0;
+        G->mem_read ( buffer,n );
+        if (n!=buffer_length)  {
+          delete G;
+          G  = NULL;
+          rc = CCP4SRS_ReadErrors;
+        }
       }
+    } else  {
+  //  if (!graphFile->Success())  {
+      rc = CCP4SRS_ReadErrors;
+      if (G)  delete G;
+      G = NULL;
     }
-  } else  {
-//  if (!graphFile->Success())  {
-    rc = CCP4SRS_ReadErrors;
-    if (G)  delete G;
-    G = NULL;
-  }
-*/
+  */
 
-/*
-  }
-*/
+  /*
+    }
+  */
 
-  if (G)  {
-    G->MakeVertexIDs();
-    if (Hflag>=1)  {
-      htype = getElementNo(pstr("H"));
-      if (Hflag==2)  G->HideType    ( htype );
-               else  G->ExcludeType ( htype );
+    if (G)  {
+      G->MakeVertexIDs();
+      if (Hflag>=1)  {
+        htype = mmdb::getElementNo(mmdb::pstr("H"));
+        if (Hflag==2)  G->HideType    ( htype );
+                 else  G->ExcludeType ( htype );
+      }
+      G->Build ( false );
     }
-    G->Build ( False );
-  }
 
-  return rc;
+    return rc;
 
-}
+  }
 
-int  CCP4SRSBase::getGraph ( PCFile graphFile, RPCGraph G,
-                             int Hflag )  {
-//   getGraph(..) retrieves data for chemical structure, which is
-// next in the graph file, then allocates and builds the corresponding
-// graph, which is returned in G.
-//   If Hflag is set to 1, all hydrogens are removed from the graph.
-//   If Hflag is set to 2, element types of atoms, to which hydrogens
-// are bonded, are modified with flag HYDROGEN_BOND and moved to
-// the end.
-//   Returns 0 in case of success.
-int rc,htype;
+  int  Base::getGraph ( mmdb::io::PFile graphFile,
+                               mmdb::math::RPGraph G,
+                               int Hflag )  {
+  //   getGraph(..) retrieves data for chemical structure, which is
+  // next in the graph file, then allocates and builds the corresponding
+  // graph, which is returned in G.
+  //   If Hflag is set to 1, all hydrogens are removed from the graph.
+  //   If Hflag is set to 2, element types of atoms, to which hydrogens
+  // are bonded, are modified with flag HYDROGEN_BOND and moved to
+  // the end.
+  //   Returns 0 in case of success.
+  int rc,htype;
 
-//  rc = 0;
+  //  rc = 0;
 
-  graphFile->SetSuccess();
-  rc = getGraph ( graphFile,G );
-//  StreamRead ( *graphFile,G );
+    graphFile->SetSuccess();
+    rc = getGraph ( graphFile,G );
+  //  StreamRead ( *graphFile,G );
 
-  if (!graphFile->Success())  {
-    rc = CCP4SRS_ReadErrors;
-    if (G)  delete G;
-    G = NULL;
-  }
+    if (!graphFile->Success())  {
+      rc = CCP4SRS_ReadErrors;
+      if (G)  delete G;
+      G = NULL;
+    }
 
-  if (G)  {
-    G->MakeVertexIDs();
-    if (Hflag>=1)  {
-      htype = getElementNo(pstr("H"));
-      if (Hflag==2)  G->HideType    ( htype );
-               else  G->ExcludeType ( htype );
+    if (G)  {
+      G->MakeVertexIDs();
+      if (Hflag>=1)  {
+        htype = mmdb::getElementNo(mmdb::pstr("H"));
+        if (Hflag==2)  G->HideType    ( htype );
+                 else  G->ExcludeType ( htype );
+      }
+      G->Build ( false );
     }
-    G->Build ( False );
-  }
 
-  return rc;
+    return rc;
 
-}
+  }
 
-int  CCP4SRSBase::getGraph ( int entryNo, RPCGraph G, int Hflag ) {
-PCFile graphFile;
-int    rc,htype;
+  int  Base::getGraph ( int entryNo, mmdb::math::RPGraph G,
+                               int Hflag ) {
+  mmdb::io::PFile graphFile;
+  int             rc,htype;
 
-  if ((0<=entryNo) && (entryNo<nEntries))  {
-    /*
-    if (Index[structNo]->loadPos>=0)  {
-      if (!G) G = new CGraph();
-      G->Copy ( ldGraph[Index[structNo]->loadPos] );
-    } else  {
-    */
-    graphFile = getGraphFile();
-    if (graphFile)  {
-      graphFile->seek ( index[entryNo]->fGraphPos );
-      rc = getGraph ( graphFile,G );
-//      StreamRead  ( *graphFile,G );
-      graphFile->shut ();
-      delete graphFile;
-      if (rc!=CCP4SRS_Ok)
-        return rc;
+    if ((0<=entryNo) && (entryNo<nEntries))  {
+      /*
+      if (Index[structNo]->loadPos>=0)  {
+        if (!G) G = new CGraph();
+        G->Copy ( ldGraph[Index[structNo]->loadPos] );
+      } else  {
+      */
+      graphFile = getGraphFile();
+      if (graphFile)  {
+        graphFile->seek ( index[entryNo]->fGraphPos );
+        rc = getGraph ( graphFile,G );
+  //      StreamRead  ( *graphFile,G );
+        graphFile->shut ();
+        delete graphFile;
+        if (rc!=CCP4SRS_Ok)
+          return rc;
+      } else  {
+        if (G)  delete G;
+        G = NULL;
+        return CCP4SRS_FileNotFound;
+      }
+      /*
+      }
+      */
     } else  {
       if (G)  delete G;
       G = NULL;
-      return CCP4SRS_FileNotFound;
-    }
-    /*
+      return CCP4SRS_EntryNotFound;
     }
-    */
-  } else  {
-    if (G)  delete G;
-    G = NULL;
-    return CCP4SRS_EntryNotFound;
-  }
 
-  if (G)  {
-    G->MakeVertexIDs();
-    if (Hflag>=1)  {
-      htype = getElementNo(pstr("H"));
-      if (Hflag==2)  G->HideType    ( htype );
-               else  G->ExcludeType ( htype );
+    if (G)  {
+      G->MakeVertexIDs();
+      if (Hflag>=1)  {
+        htype = mmdb::getElementNo(mmdb::pstr("H"));
+        if (Hflag==2)  G->HideType    ( htype );
+                 else  G->ExcludeType ( htype );
+      }
+      G->Build ( false );
     }
-    G->Build ( False );
-  }
 
-  return CCP4SRS_Ok;
+    return CCP4SRS_Ok;
 
-}
+  }
 
-int  CCP4SRSBase::getGraph ( cpstr entryID, RPCGraph G, int Hflag ) {
-PCFile graphFile;
-int    rc,entryNo,htype;
+  int  Base::getGraph ( mmdb::cpstr entryID, mmdb::math::RPGraph G, int Hflag ) {
+  mmdb::io::PFile graphFile;
+  int    rc,entryNo,htype;
 
-  entryNo = getEntryNo ( entryID );
+    entryNo = getEntryNo ( entryID );
 
-  if (entryNo!=CCP4SRS_EntryNotFound)  {
-    /*
-    if (Index[structNo]->loadPos>=0)  {
-      if (!G )  G = new CGraph();
-      G->Copy ( ldGraph[Index[structNo]->loadPos] );
-    } else  {
-    */
-    graphFile = getGraphFile();
-    if (graphFile)  {
-      graphFile->seek ( index[entryNo]->fGraphPos );
-      rc = getGraph ( graphFile,G );
-//      StreamRead      ( *graphFile,G );
-      graphFile->shut ();
-      delete graphFile;
-      if (rc!=CCP4SRS_Ok)
+    if (entryNo!=CCP4SRS_EntryNotFound)  {
+      /*
+      if (Index[structNo]->loadPos>=0)  {
+        if (!G )  G = new CGraph();
+        G->Copy ( ldGraph[Index[structNo]->loadPos] );
+      } else  {
+      */
+      graphFile = getGraphFile();
+      if (graphFile)  {
+        graphFile->seek ( index[entryNo]->fGraphPos );
+        rc = getGraph ( graphFile,G );
+  //      StreamRead      ( *graphFile,G );
+        graphFile->shut ();
+        delete graphFile;
+        if (rc!=CCP4SRS_Ok)
+          entryNo = CCP4SRS_FileNotFound;
+      } else  {
         entryNo = CCP4SRS_FileNotFound;
+        if (G)  delete G;
+        G = NULL;
+      }
+      /*
+      }
+      */
     } else  {
-      entryNo = CCP4SRS_FileNotFound;
       if (G)  delete G;
       G = NULL;
     }
+
+    if (G)  {
+      G->MakeVertexIDs();
+      if (Hflag>=1)  {
+        htype = mmdb::getElementNo(mmdb::pstr("H"));
+        if (Hflag==2)  G->HideType    ( htype );
+                 else  G->ExcludeType ( htype );
+      }
+      G->Build ( false );
+    }
+
+    return  entryNo;
+
     /*
+    if (structNo!=SBASE_StructNotFound)  {
+      return  GetGraph ( structNo,G,Hflag );
+    } else  {
+      if (G)  delete G;
+      G = NULL;
+      return  structNo;
     }
     */
-  } else  {
-    if (G)  delete G;
-    G = NULL;
-  }
 
-  if (G)  {
-    G->MakeVertexIDs();
-    if (Hflag>=1)  {
-      htype = getElementNo(pstr("H"));
-      if (Hflag==2)  G->HideType    ( htype );
-               else  G->ExcludeType ( htype );
-    }
-    G->Build ( False );
   }
 
-  return  entryNo;
 
-  /*
-  if (structNo!=SBASE_StructNotFound)  {
-    return  GetGraph ( structNo,G,Hflag );
-  } else  {
-    if (G)  delete G;
-    G = NULL;
-    return  structNo;
+  int Base::getNofAtoms ( mmdb::cpstr entryID )  {
+  // Returns the number of atoms in the references monomer. 'entryID' is
+  // the 3-letter cif code. Non-negative return delivers the number of
+  // atoms, otherwise CCP4SRS_EntryNotFound indicates that the requested
+  // structure was not found in the database.
+  int entryNo;
+    entryNo = getEntryNo ( entryID );
+    if (entryNo>=0)
+      return index[entryNo]->nAtoms;
+    return entryNo;
+  }
+
+  int Base::getNofAtoms ( int entryNo )  {
+  // Returns the number of atoms in the references monomer. 'entryNo' is
+  // the entry number (0...n_entries()-1). Non-negative return delivers
+  // the number of atoms, otherwise CCP4SRS_EntryNotFound indicates that
+  // the requested structure was not found in the database
+    if ((0<=entryNo) && (entryNo<nEntries))
+      return index[entryNo]->nAtoms;
+    return CCP4SRS_EntryNotFound;
   }
-  */
 
-}
 
+  int Base::getNofAtoms ( int entryNo,  int & nNonHAtoms,
+                                 int & nHAtoms )  {
+  mmdb::pstr  p1,p2;
+
+    nNonHAtoms = 0;
+    nHAtoms    = 0;
+
+    if ((entryNo<0) || (entryNo>=nEntries))
+      return CCP4SRS_EntryNotFound;
+
+    nNonHAtoms = index[entryNo]->nAtoms;
+    nHAtoms    = 0;
+    if (index[entryNo]->Comp1)  {
+      p1 = strstr ( index[entryNo]->Comp1,"H(" );
+      if (p1)  {
+        p1 += 2;
+        p2  = p1;
+        while ((*p2) && (*p2!=')'))  p2++;
+        if (*p2==')')  {
+          *p2 = char(0);
+          nHAtoms = mmdb::mround(strtod(p1,NULL));
+          *p2 = ')';
+        }
+      }
+    }
 
-int CCP4SRSBase::getNofAtoms ( cpstr entryID )  {
-// Returns the number of atoms in the references monomer. 'entryID' is
-// the 3-letter cif code. Non-negative return delivers the number of
-// atoms, otherwise CCP4SRS_EntryNotFound indicates that the requested
-// structure was not found in the database.
-int entryNo;
-  entryNo = getEntryNo ( entryID );
-  if (entryNo>=0)
-    return index[entryNo]->nAtoms;
-  return entryNo;
-}
-
-int CCP4SRSBase::getNofAtoms ( int entryNo )  {
-// Returns the number of atoms in the references monomer. 'entryNo' is
-// the entry number (0...n_entries()-1). Non-negative return delivers
-// the number of atoms, otherwise CCP4SRS_EntryNotFound indicates that
-// the requested structure was not found in the database
-  if ((0<=entryNo) && (entryNo<nEntries))
-    return index[entryNo]->nAtoms;
-  return CCP4SRS_EntryNotFound;
-}
-
-
-int CCP4SRSBase::getNofAtoms ( int entryNo,  int & nNonHAtoms,
-                               int & nHAtoms )  {
-pstr  p1,p2;
+    nNonHAtoms -= nHAtoms;
 
-  nNonHAtoms = 0;
-  nHAtoms    = 0;
+    return CCP4SRS_Ok;
 
-  if ((entryNo<0) || (entryNo>=nEntries))
-    return CCP4SRS_EntryNotFound;
+  }
 
-  nNonHAtoms = index[entryNo]->nAtoms;
-  nHAtoms    = 0;
-  if (index[entryNo]->Comp1)  {
-    p1 = strstr ( index[entryNo]->Comp1,"H(" );
-    if (p1)  {
-      p1 += 2;
-      p2  = p1;
-      while ((*p2) && (*p2!=')'))  p2++;
-      if (*p2==')')  {
-        *p2 = char(0);
-        nHAtoms = mround(strtod(p1,NULL));
-        *p2 = ')';
-      }
-    }
+
+  int Base::getAtNames ( int  entryNo, mmdb::PAtomName AtName,
+                                int & nAtoms, int & nH )  {
+  mmdb::io::PFile structFile;
+  int             rc;
+    nAtoms = 0;
+    nH     = 0;
+    if ((entryNo<0) || (entryNo>=nEntries))
+      return CCP4SRS_EntryNotFound;
+    structFile = getStructFile();
+    if (structFile)  {
+      rc = getAtNames ( structFile,entryNo,AtName,nAtoms,nH );
+      structFile->shut();
+      delete structFile;
+    } else
+      return CCP4SRS_FileNotFound;
+    return rc;
   }
 
-  nNonHAtoms -= nHAtoms;
 
-  return CCP4SRS_Ok;
+  int Base::getAtNames ( mmdb::io::PFile structFile, int entryNo,
+                         mmdb::PAtomName AtName,
+                         int & nAtoms, int & nH )  {
+  PMonomer       monomer;
+  PAtom          atom;
+  mmdb::AtomName aname;
+  int            i,j;
+  mmdb::pstr     p1,p2;
+  bool           removeHydrogens;
+
+    if ((entryNo<0) || (entryNo>=nEntries))
+      return CCP4SRS_EntryNotFound;
+
+    removeHydrogens = (nH==-1);
+
+    monomer = getMonomer ( entryNo,structFile );
+    if (!monomer)
+      return CCP4SRS_ReadErrors;
+
+    nAtoms = index[entryNo]->nAtoms;
+    nH     = 0;
+    if (index[entryNo]->Comp1)  {
+      p1 = strstr ( index[entryNo]->Comp1,"H(" );
+      if (p1)  {
+        p1 += 2;
+        p2  = p1;
+        while ((*p2) && (*p2!=')'))  p2++;
+        if (*p2==')')  {
+          *p2 = char(0);
+          nH  = mmdb::mround(strtod(p1,NULL));
+          *p2 = ')';
+        }
+      }
+    }
 
-}
+    if (removeHydrogens)  {
+      j = 0;
+      for (i=0;i<nAtoms;i++)  {
+        atom = monomer->atom(i);
+        if (atom)  {
+          if ((atom->element()[0]!='H') || (atom->element()[1]))
+            strcpy ( AtName[j++],atom->name_pdb(aname) );
+        }
+      }
+    } else  {
+      for (i=0;i<nAtoms;i++)  {
+        atom = monomer->atom(i);
+        if (atom)
+          strcpy ( AtName[i],atom->name_pdb(aname) );
+      }
+    }
 
+    delete monomer;
 
-int CCP4SRSBase::getAtNames ( int  entryNo, PAtomName AtName,
-                              int & nAtoms, int & nH )  {
-int    rc;
-PCFile structFile;
-  nAtoms = 0;
-  nH     = 0;
-  if ((entryNo<0) || (entryNo>=nEntries))
-    return CCP4SRS_EntryNotFound;
-  structFile = getStructFile();
-  if (structFile)  {
-    rc = getAtNames ( structFile,entryNo,AtName,nAtoms,nH );
-    structFile->shut();
-    delete structFile;
-  } else
-    return CCP4SRS_FileNotFound;
-  return rc;
-}
-
-
-int CCP4SRSBase::getAtNames ( PCFile structFile, int entryNo,
-                              PAtomName AtName,
-                              int & nAtoms, int & nH )  {
-PCCP4SRSMonomer monomer;
-PCCP4SRSAtom    atom;
-AtomName        aname;
-int             i,j;
-pstr            p1,p2;
-Boolean         removeHydrogens;
+    return CCP4SRS_Ok;
 
-  if ((entryNo<0) || (entryNo>=nEntries))
-    return CCP4SRS_EntryNotFound;
+  }
 
-  removeHydrogens = (nH==-1);
 
-  monomer = getMonomer ( entryNo,structFile );
-  if (!monomer)
-    return CCP4SRS_ReadErrors;
-
-  nAtoms = index[entryNo]->nAtoms;
-  nH     = 0;
-  if (index[entryNo]->Comp1)  {
-    p1 = strstr ( index[entryNo]->Comp1,"H(" );
-    if (p1)  {
-      p1 += 2;
-      p2  = p1;
-      while ((*p2) && (*p2!=')'))  p2++;
-      if (*p2==')')  {
-        *p2 = char(0);
-        nH  = mround(strtod(p1,NULL));
-        *p2 = ')';
-      }
-    }
+  int _makeChirInd ( char chirality )  {
+    if (chirality=='S')  return -1;
+    if (chirality=='R')  return +1;
+    return 0;
   }
 
-  if (removeHydrogens)  {
-    j = 0;
-    for (i=0;i<nAtoms;i++)  {
-      atom = monomer->atom(i);
-      if (atom)  {
-        if ((atom->element()[0]!='H') || (atom->element()[1]))
-          strcpy ( AtName[j++],atom->name_pdb(aname) );
-      }
-    }
-  } else  {
-    for (i=0;i<nAtoms;i++)  {
-      atom = monomer->atom(i);
-      if (atom)
-        strcpy ( AtName[i],atom->name_pdb(aname) );
+  int _findName ( mmdb::PAtomName Nams, mmdb::cpstr N, int len )  {
+  mmdb::AtomName Nam;
+  int            i;
+    i = 0;
+    while (i<len)  {
+      strcpy ( Nam,Nams[i] );
+      if (!strcmp(N,Nam))  break;
+      i++;
     }
+    if (i>=len)  i = -1;
+    return i;
   }
 
-  delete monomer;
+  int Base::getAtoms ( mmdb::cpstr     entryID,
+                              int           & nNonHAtoms,
+                              mmdb::PAtomName NonHAtName,
+                              int           & nHAtoms,
+                              mmdb::PAtomName HAtName,
+                              mmdb::ivector   Hconnect,
+                              mmdb::ivector   Elem,
+                              mmdb::ivector   Chiral )  {
+  PMonomer       monomer;
+  PAtom          atom,atom2;
+  PBond          bond;
+  mmdb::AtomName aname;
+  int            i,j,entryNo,rc;
 
-  return CCP4SRS_Ok;
+    nNonHAtoms = 0;
+    nHAtoms    = 0;
 
-}
-
-
-int _makeChirInd ( char chirality )  {
-  if (chirality=='S')  return -1;
-  if (chirality=='R')  return +1;
-  return 0;
-}
-
-int _findName ( PAtomName Nams, cpstr N, int len )  {
-int      i;
-AtomName Nam;
-  i = 0;
-  while (i<len)  {
-    strcpy ( Nam,Nams[i] );
-    if (!strcmp(N,Nam))  break;
-    i++;
-  }
-  if (i>=len)  i = -1;
-  return i;
-}
-
-int CCP4SRSBase::getAtoms ( cpstr entryID,
-                            int & nNonHAtoms, PAtomName NonHAtName,
-                            int & nHAtoms,    PAtomName HAtName,
-                            ivector Hconnect, ivector Elem,
-                            ivector Chiral )  {
-PCCP4SRSMonomer monomer;
-PCCP4SRSAtom    atom,atom2;
-PCCP4SRSBond    bond;
-AtomName        aname;
-int             i,j,entryNo,rc;
-
-  nNonHAtoms = 0;
-  nHAtoms    = 0;
-
-  entryNo = getEntryNo ( entryID );
-  if (entryNo<0)  return CCP4SRS_EntryNotFound;
-
-  monomer = getMonomer ( entryNo,NULL );
-  if (!monomer)
-    return CCP4SRS_ReadErrors;
-
-  rc = CCP4SRS_Ok;
-
-  for (i=0;i<index[entryNo]->nAtoms;i++)  {
-    atom = monomer->atom(i);
-    if (atom)  {
-      Elem[i] = getElementNo ( atom->element() );
-      if ((atom->element()[0]=='H') && (!atom->element()[1]))  {
-        strcpy ( HAtName[nHAtoms],atom->name_pdb(aname) );
-        nHAtoms++;
-      } else  {
-        strcpy ( NonHAtName[nNonHAtoms],atom->name_pdb(aname) );
-        nNonHAtoms++;
+    entryNo = getEntryNo ( entryID );
+    if (entryNo<0)  return CCP4SRS_EntryNotFound;
+
+    monomer = getMonomer ( entryNo,NULL );
+    if (!monomer)
+      return CCP4SRS_ReadErrors;
+
+    rc = CCP4SRS_Ok;
+
+    for (i=0;i<index[entryNo]->nAtoms;i++)  {
+      atom = monomer->atom(i);
+      if (atom)  {
+        Elem[i] = mmdb::getElementNo ( atom->element() );
+        if ((atom->element()[0]=='H') && (!atom->element()[1]))  {
+          strcpy ( HAtName[nHAtoms],atom->name_pdb(aname) );
+          nHAtoms++;
+        } else  {
+          strcpy ( NonHAtName[nNonHAtoms],atom->name_pdb(aname) );
+          nNonHAtoms++;
+        }
+        Chiral[i] = _makeChirInd ( atom->chirality() );
       }
-      Chiral[i] = _makeChirInd ( atom->chirality() );
     }
-  }
 
-  if (nHAtoms>0)  {
-    for (j=0;j<nHAtoms;j++)
-      Hconnect[j] = -1;
-    for (i=0;i<index[entryNo]->nBonds;i++)  {
-      bond = monomer->bond(i);
-      if (bond)  {
-        atom  = monomer->atom(bond->atom1());
-        atom2 = monomer->atom(bond->atom2());
-        if (atom && atom2)  {
-          j = _findName ( HAtName,atom->name_pdb(aname),nHAtoms );
-          if (j>=0)
-            Hconnect[j] = _findName ( NonHAtName,
-                                      atom2->name_pdb(aname),
-                                      nNonHAtoms );
-          else  {
-            j = _findName ( HAtName,atom2->name_pdb(aname),nHAtoms );
+    if (nHAtoms>0)  {
+      for (j=0;j<nHAtoms;j++)
+        Hconnect[j] = -1;
+      for (i=0;i<index[entryNo]->nBonds;i++)  {
+        bond = monomer->bond(i);
+        if (bond)  {
+          atom  = monomer->atom(bond->atom1());
+          atom2 = monomer->atom(bond->atom2());
+          if (atom && atom2)  {
+            j = _findName ( HAtName,atom->name_pdb(aname),nHAtoms );
             if (j>=0)
               Hconnect[j] = _findName ( NonHAtName,
-                                        atom->name_pdb(aname),
+                                        atom2->name_pdb(aname),
                                         nNonHAtoms );
+            else  {
+              j = _findName ( HAtName,atom2->name_pdb(aname),nHAtoms );
+              if (j>=0)
+                Hconnect[j] = _findName ( NonHAtName,
+                                          atom->name_pdb(aname),
+                                          nNonHAtoms );
+            }
           }
         }
       }
+      j = 0;
+      while ((j<nHAtoms) && (Hconnect[j]>=0)) j++;
+      if (j<nHAtoms)
+        rc = CCP4SRS_BrokenBonds;
     }
-    j = 0;
-    while ((j<nHAtoms) && (Hconnect[j]>=0)) j++;
-    if (j<nHAtoms)
-      rc = CCP4SRS_BrokenBonds;
-  }
-
-  delete monomer;
-
-  return rc;
-
-}
-
-
-int  CCP4SRSBase::getBonds ( cpstr   entryID,
-                             ivector nBonds, imatrix bondPair,
-                             int &   nAtoms, int     maxNAtoms,
-                             int     maxNBonds )  {
-PCGraph G;
-PCEdge  edge;
-int     entryNo,i, a1,a2,a;
-
-  for (i=0;i<maxNAtoms;i++)
-    nBonds[i] = 0;
-
-  nAtoms = 0;
-
-  entryNo = getEntryNo ( entryID );
-  if (entryNo<0)  return CCP4SRS_EntryNotFound;
-
-  nAtoms = index[entryNo]->nAtoms;
-  if (nAtoms<=0)  return CCP4SRS_Ok;
-
-  G = NULL;
-  i = getGraph ( entryNo,G,0 );
-  if (i!=CCP4SRS_Ok)  return i;
-  if (!G)             return CCP4SRS_ReadErrors;
-
-  for (i=1;i<=G->GetNofEdges();i++) {
-    edge = G->GetEdge(i);
-    if (edge)  {
-      a1 = edge->GetVertex1() - 1;
-      a2 = edge->GetVertex2() - 1;
-      if (a1>a2)  {
-        a = a1;  a1 = a2;  a2 = a;
-      }
-      if (nBonds[a1]<maxNBonds)  {
-        bondPair[a1][nBonds[a1]] = a2;
-        nBonds[a1]++;
-      }
-    }
-  }
-
-  delete G;
-
-  return CCP4SRS_Ok;
-
-}
-
-
-int  CCP4SRSBase::getHetInfo ( cpstr       entryID,
-                               pstr        Formula,
-                               pstr        Hname,
-                               pstr        Hsynonym,
-                               pstr        Hcharge,
-                               PAtomName & ClinkAtom,
-                               PElement  & ClinkEle,
-                               PAtomName & SlinkAtom,
-                               PElement  & SlinkEle,
-                               int       & nLeavingAtoms )  {
-PCCP4SRSMonomer monomer;
-PCCP4SRSAtom    atom;
-AtomName        aname;
-Element         elem;
-ivector         leavingAtom;
-ivector         bondedAtom;
-int             i,entryNo;
-
-  Formula [0] = char(0);
-  Hname   [0] = char(0);
-  Hsynonym[0] = char(0);
-  Hcharge [0] = char(0);
-  ClinkAtom   = NULL;
-  ClinkEle    = NULL;
-  SlinkAtom   = NULL;
-  SlinkEle    = NULL;
-  nLeavingAtoms = 0;
-
-  entryNo = getEntryNo ( entryID );
-  if (entryNo<0)  return CCP4SRS_EntryNotFound;
-
-  monomer = getMonomer ( entryNo,NULL );
-  if (!monomer)
-    return CCP4SRS_ReadErrors;
-
-  if (monomer->chem_formula()) strcpy ( Formula ,monomer->chem_formula() );
-  if (monomer->chem_formula()) strcpy ( Hsynonym,monomer->chem_formula() );
-  if (monomer->chem_type   ()) strcpy ( Hsynonym,monomer->chem_type   () );
-  if (monomer->chem_name   ()) strcpy ( Hname   ,monomer->chem_name   () );
-//  if (monomer->Charge)  strcpy ( Hcharge ,monomer->Charge  );
-
-  leavingAtom = NULL;
-  bondedAtom  = NULL;
-  monomer->getLeavingAtoms ( nLeavingAtoms,leavingAtom,bondedAtom );
-
-  if (nLeavingAtoms>0)  {
-    SlinkAtom = new AtomName[nLeavingAtoms];
-    SlinkEle  = new Element [nLeavingAtoms];
-    ClinkAtom = new AtomName[nLeavingAtoms];
-    ClinkEle  = new Element [nLeavingAtoms];
-    for (i=0;i<nLeavingAtoms;i++)  {
-      atom = monomer->atom ( leavingAtom[i] );
-      strcpy (SlinkAtom[i],atom->name_pdb(aname) );
-      strcpy (SlinkEle [i],atom->element_pdb(elem) );
-      if (bondedAtom[i]>=0)  {
-        atom = monomer->atom ( bondedAtom[i] );
-        strcpy(ClinkAtom[i],atom->name_pdb(aname) );
-        strcpy(ClinkEle [i],atom->element_pdb(elem) );
-      } else  {
-        ClinkAtom[i][0] = char(0);
-        ClinkEle [i][0] = char(0);
+
+    delete monomer;
+
+    return rc;
+
+  }
+
+
+  int  Base::getBonds ( mmdb::cpstr   entryID,
+                               mmdb::ivector nBonds,
+                               mmdb::imatrix bondPair,
+                               int         & nAtoms,
+                               int           maxNAtoms,
+                               int           maxNBonds )  {
+  mmdb::math::PGraph G;
+  mmdb::math::PEdge  edge;
+  int                entryNo,i, a1,a2,a;
+
+    for (i=0;i<maxNAtoms;i++)
+      nBonds[i] = 0;
+
+    nAtoms = 0;
+
+    entryNo = getEntryNo ( entryID );
+    if (entryNo<0)  return CCP4SRS_EntryNotFound;
+
+    nAtoms = index[entryNo]->nAtoms;
+    if (nAtoms<=0)  return CCP4SRS_Ok;
+
+    G = NULL;
+    i = getGraph ( entryNo,G,0 );
+    if (i!=CCP4SRS_Ok)  return i;
+    if (!G)             return CCP4SRS_ReadErrors;
+
+    for (i=1;i<=G->GetNofEdges();i++) {
+      edge = G->GetEdge(i);
+      if (edge)  {
+        a1 = edge->GetVertex1() - 1;
+        a2 = edge->GetVertex2() - 1;
+        if (a1>a2)  {
+          a = a1;  a1 = a2;  a2 = a;
+        }
+        if (nBonds[a1]<maxNBonds)  {
+          bondPair[a1][nBonds[a1]] = a2;
+          nBonds[a1]++;
+        }
       }
     }
+
+    delete G;
+
+    return CCP4SRS_Ok;
+
   }
 
-  FreeVectorMemory ( leavingAtom,0 );
-  FreeVectorMemory ( bondedAtom ,0 );
-  delete monomer;
 
-  return CCP4SRS_Ok;
+  int  Base::getHetInfo ( mmdb::cpstr       entryID,
+                                 mmdb::pstr        Formula,
+                                 mmdb::pstr        Hname,
+                                 mmdb::pstr        Hsynonym,
+                                 mmdb::pstr        Hcharge,
+                                 mmdb::PAtomName & ClinkAtom,
+                                 mmdb::PElement  & ClinkEle,
+                                 mmdb::PAtomName & SlinkAtom,
+                                 mmdb::PElement  & SlinkEle,
+                                 int             & nLeavingAtoms )  {
+  PMonomer       monomer;
+  PAtom          atom;
+  mmdb::AtomName aname;
+  mmdb::Element  elem;
+  mmdb::ivector  leavingAtom;
+  mmdb::ivector  bondedAtom;
+  int            i,entryNo;
+
+    Formula [0] = char(0);
+    Hname   [0] = char(0);
+    Hsynonym[0] = char(0);
+    Hcharge [0] = char(0);
+    ClinkAtom   = NULL;
+    ClinkEle    = NULL;
+    SlinkAtom   = NULL;
+    SlinkEle    = NULL;
+    nLeavingAtoms = 0;
+
+    entryNo = getEntryNo ( entryID );
+    if (entryNo<0)  return CCP4SRS_EntryNotFound;
+
+    monomer = getMonomer ( entryNo,NULL );
+    if (!monomer)
+      return CCP4SRS_ReadErrors;
+
+    if (monomer->chem_formula()) strcpy ( Formula ,monomer->chem_formula() );
+    if (monomer->chem_formula()) strcpy ( Hsynonym,monomer->chem_formula() );
+    if (monomer->chem_type   ()) strcpy ( Hsynonym,monomer->chem_type   () );
+    if (monomer->chem_name   ()) strcpy ( Hname   ,monomer->chem_name   () );
+  //  if (monomer->Charge)  strcpy ( Hcharge ,monomer->Charge  );
+
+    leavingAtom = NULL;
+    bondedAtom  = NULL;
+    monomer->getLeavingAtoms ( nLeavingAtoms,leavingAtom,bondedAtom );
+
+    if (nLeavingAtoms>0)  {
+      SlinkAtom = new mmdb::AtomName[nLeavingAtoms];
+      SlinkEle  = new mmdb::Element [nLeavingAtoms];
+      ClinkAtom = new mmdb::AtomName[nLeavingAtoms];
+      ClinkEle  = new mmdb::Element [nLeavingAtoms];
+      for (i=0;i<nLeavingAtoms;i++)  {
+        atom = monomer->atom ( leavingAtom[i] );
+        strcpy (SlinkAtom[i],atom->name_pdb(aname) );
+        strcpy (SlinkEle [i],atom->element_pdb(elem) );
+        if (bondedAtom[i]>=0)  {
+          atom = monomer->atom ( bondedAtom[i] );
+          strcpy(ClinkAtom[i],atom->name_pdb(aname) );
+          strcpy(ClinkEle [i],atom->element_pdb(elem) );
+        } else  {
+          ClinkAtom[i][0] = char(0);
+          ClinkEle [i][0] = char(0);
+        }
+      }
+    }
+
+    mmdb::FreeVectorMemory ( leavingAtom,0 );
+    mmdb::FreeVectorMemory ( bondedAtom ,0 );
+    delete monomer;
+
+    return CCP4SRS_Ok;
+
+  }
 
-}
+}  // namespace ccp4srs
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_base.h ccp4srs/ccp4srs/ccp4srs_base.h
--- ccp4srs-old/ccp4srs/ccp4srs_base.h	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_base.h	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_base.h, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_base.h $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,16 +22,16 @@
 //
 //  =================================================================
 //
-//    26.02.13   <--  Date of Last Modification.
+//    03.02.14   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_base  <interface>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSBase - SRS base manager class
+//  **** Classes :  ccp4srs::Base - SRS base manager class
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010-2013
+//  (C) E. Krissinel 2010-2014
 //
 //  =================================================================
 //
@@ -40,211 +40,218 @@
 #define CCP4SRS_BASE_H
 
 #include "ccp4srs_index.h"
-#include "mmdb/mmdb_graph.h"
+#include "mmdb2/mmdb_math_graph.h"
 
+namespace ccp4srs  {
 
-// ==================================================================
+  // ==================================================================
 
-DefineClass(CCP4SRSBase)
+  DefineClass(Base);
 
-class CCP4SRSBase  {
+  class Base  {
+
+    public:
+
+      Base ();  //!< Constructor
+      ~Base();  //!< Destructor
+
+      //   LoadIndex() loads index of the structural database. 'srsPath'
+      // must point on the directory containing the database files.
+      // The index must be loaded once before retrieving any
+      // information from the database.
+      //   LoadIndex() may return either CCP4SRS_Ok, CCP4SRS_CorruptIndex
+      // or CCP4SRS_FileNotFound.
+      int loadIndex ( mmdb::cpstr srsPath );
+
+      //   LoadStructure(..) reads structure from *.srs files and
+      // stores it in RAM for faster access. There is no special
+      // functions to access loaded structures, all requests to
+      // *.sbase files and RAM-storage are dispatched automatically.
+      int  loadStructure   ( mmdb::cpstr entryID );
+
+      PIndex getIndex ( mmdb::cpstr entryID );
+      PIndex getIndex ( int n         );
+
+      //   UnloadStructure(..) deletes strtucture from RAM and releases
+      // its memory. The structure is then accessible in the normal
+      // way from *.srs files, which is slower.
+      int  unloadStructure ( mmdb::cpstr entryID );
+
+      //   GetPath() returns full path to a file with file name FName
+      // in the database directory.  Length of S should suffice for
+      // accomodating the path. The function returns S.
+      //   GetPath() will work only after loading the database index.
+      mmdb::pstr getPath ( mmdb::pstr & S, mmdb::cpstr FName );
+
+      //   GetStructFile() creates and opens the database structure
+      // file and returns its pointer. In the case of errors returns
+      // NULL. Application is responsible for deleting this class.
+      mmdb::io::PFile getStructFile();
+
+      //   GetGraphFile() creates and opens the database graph
+      // file and returns its pointer. In the case of errors returns
+      // NULL. Application is responsible for deleting this class.
+      mmdb::io::PFile getGraphFile();
+
+      //   n_entries() returns number of entries in the database index.
+      inline int  n_entries() { return nEntries; }
+
+      //   getEntryNo() returns position of the structure with
+      // (3-letter) name 'name' as found in the database index.
+      //   Non-negative return means success, otherwise
+      // CCP4SRS_EntryNotFound indicates that the requested structure
+      // was not found in the database index.
+      int  getEntryNo ( mmdb::cpstr entryID );
+
+      //   getMonomer returns pointer to the monomer structure
+      // identified by 3-letter entryID. If such structure is not
+      // found, the function returns NULL.
+      //   The function returns a pointer to a private copy of the
+      // structure. Modifying it will not change data in the structural
+      // database. The application is responsible for deallocating
+      // the structure after use (simply use delete).
+      //   See description of CCP4SRSMonomer for the explanation of
+      // its fields.
+      PMonomer getMonomer ( mmdb::cpstr entryID );
+
+      //   Another form of getMonomer(..) uses an open structure
+      // file, which allows to save on opening/closing file if
+      // multiple access to SRS structures is required.
+      PMonomer getMonomer ( int entryNo,  // 0...nEntries-1
+                            mmdb::io::PFile structFile );
+      PMonomer getMonomer ( mmdb::cpstr entryID,
+                            mmdb::io::PFile structFile );
+
+
+      /// \brief Returns the number of atoms in the references monomer
+      /// \param[inp] entryID 3-letter cif code
+      /// \return Non-negative return delivers the number of atoms,
+      /// otherwise CCP4SRS_EntryNotFound indicates that the requested
+      /// structure was not found in the database
+      int getNofAtoms ( mmdb::cpstr entryID );
+
+      /// \brief Returns the number of atoms in the references monomer
+      /// \param[in] entryNo entry number (0...n_entries()-1)
+      /// \return Non-negative return delivers the number of atoms,
+      /// otherwise CCP4SRS_EntryNotFound indicates that the requested
+      /// structure was not found in the database
+      int getNofAtoms ( int entryNo );
+
+      /// \brief Returns number of non-hydrogen and hydrogen atoms
+      ///        for referenced structure.
+      /// \param[in] entryNo entry number (0...n_entries()-1)
+      /// \param[out] nNonHAtoms number of non-hydrogen atoms
+      /// \param[out] nHAtoms number of hydrogen atoms
+      /// \return CCP4SRS_Ok or CCP4SRS_EntryNotFound.
+      int  getNofAtoms ( int entryNo, int & nNonHAtoms, int & nHAtoms );
+
+      /// \brief Returns atom names, total number of atoms and number of
+      /// hydrogens (nH) for referenced monomer.
+      /// \param[in] entryNo entry number (0...n_entries()-1)
+      /// \param[out] AtName array of atom names, prealocated with
+      /// sufficient length
+      /// \param[out] nAtoms total number of atoms
+      /// \param[out] nH number of hydrogens
+      /// \return CCP4SRS_Ok, CCP4SRS_FileNotFound, CCP4SRS_EntryNotFound
+      /// and CCP4SRS_ReadErrors.
+      int  getAtNames ( int  entryNo, mmdb::PAtomName AtName,
+                        int & nAtoms, int & nH );
+
+      /// \brief Returns atom names, total number of atoms and number of
+      /// hydrogens (nH) for referenced monomer.
+      /// \param[in] structFile pre-open SRS structure file
+      /// \param[in] entryNo entry number (0...n_entries()-1)
+      /// \param[out] AtName array of atom names, prealocated with
+      /// sufficient length
+      /// \param[out] nAtoms total number of atoms
+      /// \param[out] nH number of hydrogens
+      /// \return CCP4SRS_Ok, CCP4SRS_FileNotFound, CCP4SRS_EntryNotFound
+      /// and CCP4SRS_ReadErrors.
+      int  getAtNames  ( mmdb::io::PFile structFile, int entryNo,
+                         mmdb::PAtomName  AtName, int & nAtoms, int & nH  );
+
+      /// \brief Retrieves various atom properties for referenced
+      ///        structure.
+      /// \param[in] entryID monomer's cif id
+      /// \param[out] nNonHAtoms number of non-hydrogen atoms
+      /// \param[out] nNonHAtomName non-hydrogen atom names
+      /// \param[out] nHAtoms number of hydrogen atoms
+      /// \param[out] nNonHAtomName hydrogen atom names
+      /// \param[out] Hconnect connectivity to non-hydrogen atoms:
+      ///             hydrogen HAtName[i] is connected to non-hydrogen
+      ///             NonHAtom[Hconnect[i]], if Hconnect[i]>=0.
+      /// \param[out] Elem element IDs
+      /// \param[out] Chiral chirality IDs
+      /// \return CCP4SRS_Ok, CCP4SRS_FileNotFound, CCP4SRS_EntryNotFound,
+      /// CCP4SRS_ReadErrors and CCP4SRS_BrokenBonds.
+      int  getAtoms ( mmdb::cpstr entryID,
+                      int & nNonHAtoms, mmdb::PAtomName NonHAtName,
+                      int & nHAtoms,    mmdb::PAtomName HAtName,
+                      mmdb::ivector Hconnect, mmdb::ivector Elem,
+                      mmdb::ivector Chiral );
+
+      /// \brief Retrieves bonds for referenced structure.
+      /// \param[in] entryID monomer's cif id
+      /// \param[out] nBonds   number of bonds for ith atom
+      /// \param[out] bondPair bonded atoms: bondPair[i][j] (0<=i<nAtoms,
+      ///             0<=j<=nBonds[i]) gives the number of atom connected
+      ///             to ith atom; only pairs i<j are returned
+      /// \param[in] maxNAtoms length of nBonds[] and bondPairs[]
+      /// \param[in] maxNBonds length of bondPairs[][]
+      /// \return CCP4SRS_Ok, CCP4SRS_FileNotFound, CCP4SRS_EntryNotFound
+      /// and CCP4SRS_ReadErrors.
+      int  getBonds ( mmdb::cpstr   entryID,
+                      mmdb::ivector nBonds, mmdb::imatrix bondPair,
+                      int &   nAtoms, int maxNAtoms,
+                      int     maxNBonds );
+
+      int  getHetInfo ( mmdb::cpstr       entryID,
+                        mmdb::pstr        Formula,
+                        mmdb::pstr        Hname,
+                        mmdb::pstr        Hsynonym,
+                        mmdb::pstr        Hcharge,
+                        mmdb::PAtomName & ClinkAtom,  // will
+                        mmdb::PElement  & ClinkEle,   //   be
+                        mmdb::PAtomName & SlinkAtom,  //     allocated
+                        mmdb::PElement  & SlinkEle,   //       or NULL
+                        int             & nLeavingAtoms );
+
+      //   getGraph(..) retrieves data for chemical structure number
+      // entryNo (as in Index) from graph file graphFile, then
+      // allocates and builds the corresponding graph, which is
+      // returned in G.
+      //   If Hflag is set >= 1, all hydrogens are removed from
+      // the graph. If Hflag is set to 2, element types of atoms,
+      // to which hydrogens are bonded, are modified with flag
+      // HYDROGEN_BOND.
+      //   Returns CCP4SRS_Ok in case of success. Other return code are
+      // CCP4SRS_WrongIndex and CCP4SRS_ReadError.
+      int  getGraph ( mmdb::io::PFile graphFile, mmdb::math::RPGraph G );
+      int  getGraph ( mmdb::io::PFile graphFile, int entryNo,
+                      mmdb::math::RPGraph G, int Hflag );
+      int  getGraph ( mmdb::io::PFile graphFile, mmdb::math::RPGraph G,
+                      int Hflag );
+      int  getGraph ( int    entryNo, mmdb::math::RPGraph G, int Hflag );
+      int  getGraph ( mmdb::cpstr entryID, mmdb::math::RPGraph G,
+                      int Hflag );
+
+
+    protected:
+      MemIO      memIO;
+      PPIndex    index;
+      mmdb::pstr srsDir;
+      int        srsVersion;
+      int        nEntries;
+
+      void init_base ();
+      void freeMemory();
 
-  public:
-
-    CCP4SRSBase ();  //!< Constructor
-    ~CCP4SRSBase();  //!< Destructor
-
-    //   LoadIndex() loads index of the structural database. 'srsPath'
-    // must point on the directory containing the database files.
-    // The index must be loaded once before retrieving any
-    // information from the database.
-    //   LoadIndex() may return either CCP4SRS_Ok, CCP4SRS_CorruptIndex
-    // or CCP4SRS_FileNotFound.
-    int loadIndex ( cpstr srsPath );
-
-    //   LoadStructure(..) reads structure from *.srs files and
-    // stores it in RAM for faster access. There is no special
-    // functions to access loaded structures, all requests to
-    // *.sbase files and RAM-storage are dispatched automatically.
-    int  loadStructure   ( cpstr entryID );
-
-    PCCP4SRSIndex getIndex ( cpstr entryID );
-    PCCP4SRSIndex getIndex ( int n         );
-
-    //   UnloadStructure(..) deletes strtucture from RAM and releases
-    // its memory. The structure is then accessible in the normal
-    // way from *.srs files, which is slower.
-    int  unloadStructure ( cpstr entryID );
-
-    //   GetPath() returns full path to a file with file name FName
-    // in the database directory.  Length of S should suffice for
-    // accomodating the path. The function returns S.
-    //   GetPath() will work only after loading the database index.
-    pstr getPath ( pstr & S, cpstr FName );
-
-    //   GetStructFile() creates and opens the database structure
-    // file and returns its pointer. In the case of errors returns
-    // NULL. Application is responsible for deleting this class.
-    PCFile getStructFile();
-
-    //   GetGraphFile() creates and opens the database graph
-    // file and returns its pointer. In the case of errors returns
-    // NULL. Application is responsible for deleting this class.
-    PCFile getGraphFile();
-
-    //   n_entries() returns number of entries in the database index.
-    inline int  n_entries() { return nEntries; }
-
-    //   getEntryNo() returns position of the structure with
-    // (3-letter) name 'name' as found in the database index.
-    //   Non-negative return means success, otherwise
-    // CCP4SRS_EntryNotFound indicates that the requested structure
-    // was not found in the database index.
-    int  getEntryNo ( cpstr entryID );
-
-    //   getMonomer returns pointer to the monomer structure
-    // identified by 3-letter entryID. If such structure is not
-    // found, the function returns NULL.
-    //   The function returns a pointer to a private copy of the
-    // structure. Modifying it will not change data in the structural
-    // database. The application is responsible for deallocating
-    // the structure after use (simply use delete).
-    //   See description of CCP4SRSMonomer for the explanation of
-    // its fields.
-    PCCP4SRSMonomer getMonomer ( cpstr entryID );
-
-    //   Another form of getMonomer(..) uses an open structure
-    // file, which allows to save on opening/closing file if
-    // multiple access to SRS structures is required.
-    PCCP4SRSMonomer getMonomer ( int entryNo, PCFile structFile );
-                                 // 0...nEntries-1
-    PCCP4SRSMonomer getMonomer ( cpstr entryID, PCFile structFile );
-
-
-    /// \brief Returns the number of atoms in the references monomer
-    /// \param[inp] entryID 3-letter cif code
-    /// \return Non-negative return delivers the number of atoms,
-    /// otherwise CCP4SRS_EntryNotFound indicates that the requested
-    /// structure was not found in the database
-    int getNofAtoms ( cpstr entryID );
-
-    /// \brief Returns the number of atoms in the references monomer
-    /// \param[in] entryNo entry number (0...n_entries()-1)
-    /// \return Non-negative return delivers the number of atoms,
-    /// otherwise CCP4SRS_EntryNotFound indicates that the requested
-    /// structure was not found in the database
-    int getNofAtoms ( int entryNo );
-
-    /// \brief Returns number of non-hydrogen and hydrogen atoms
-    ///        for referenced structure.
-    /// \param[in] entryNo entry number (0...n_entries()-1)
-    /// \param[out] nNonHAtoms number of non-hydrogen atoms
-    /// \param[out] nHAtoms number of hydrogen atoms
-    /// \return CCP4SRS_Ok or CCP4SRS_EntryNotFound.
-    int  getNofAtoms ( int entryNo, int & nNonHAtoms, int & nHAtoms );
-
-    /// \brief Returns atom names, total number of atoms and number of
-    /// hydrogens (nH) for referenced monomer.
-    /// \param[in] entryNo entry number (0...n_entries()-1)
-    /// \param[out] AtName array of atom names, prealocated with
-    /// sufficient length
-    /// \param[out] nAtoms total number of atoms
-    /// \param[out] nH number of hydrogens
-    /// \return CCP4SRS_Ok, CCP4SRS_FileNotFound, CCP4SRS_EntryNotFound
-    /// and CCP4SRS_ReadErrors.
-    int  getAtNames ( int  entryNo, PAtomName AtName,
-                      int & nAtoms, int & nH );
-
-    /// \brief Returns atom names, total number of atoms and number of
-    /// hydrogens (nH) for referenced monomer.
-    /// \param[in] structFile pre-open SRS structure file
-    /// \param[in] entryNo entry number (0...n_entries()-1)
-    /// \param[out] AtName array of atom names, prealocated with
-    /// sufficient length
-    /// \param[out] nAtoms total number of atoms
-    /// \param[out] nH number of hydrogens
-    /// \return CCP4SRS_Ok, CCP4SRS_FileNotFound, CCP4SRS_EntryNotFound
-    /// and CCP4SRS_ReadErrors.
-    int  getAtNames  ( PCFile structFile, int entryNo,
-                       PAtomName  AtName, int & nAtoms, int & nH  );
-
-    /// \brief Retrieves various atom properties for referenced
-    ///        structure.
-    /// \param[in] entryID monomer's cif id
-    /// \param[out] nNonHAtoms number of non-hydrogen atoms
-    /// \param[out] nNonHAtomName non-hydrogen atom names
-    /// \param[out] nHAtoms number of hydrogen atoms
-    /// \param[out] nNonHAtomName hydrogen atom names
-    /// \param[out] Hconnect connectivity to non-hydrogen atoms:
-    ///             hydrogen HAtName[i] is connected to non-hydrogen
-    ///             NonHAtom[Hconnect[i]], if Hconnect[i]>=0.
-    /// \param[out] Elem element IDs
-    /// \param[out] Chiral chirality IDs
-    /// \return CCP4SRS_Ok, CCP4SRS_FileNotFound, CCP4SRS_EntryNotFound,
-    /// CCP4SRS_ReadErrors and CCP4SRS_BrokenBonds.
-    int  getAtoms ( cpstr entryID,
-                    int & nNonHAtoms, PAtomName NonHAtName,
-                    int & nHAtoms,    PAtomName HAtName,
-                    ivector Hconnect, ivector Elem,
-                    ivector Chiral );
-
-    /// \brief Retrieves bonds for referenced structure.
-    /// \param[in] entryID monomer's cif id
-    /// \param[out] nBonds   number of bonds for ith atom
-    /// \param[out] bondPair bonded atoms: bondPair[i][j] (0<=i<nAtoms,
-    ///             0<=j<=nBonds[i]) gives the number of atom connected
-    ///             to ith atom; only pairs i<j are returned
-    /// \param[in] maxNAtoms length of nBonds[] and bondPairs[]
-    /// \param[in] maxNBonds length of bondPairs[][]
-    /// \return CCP4SRS_Ok, CCP4SRS_FileNotFound, CCP4SRS_EntryNotFound
-    /// and CCP4SRS_ReadErrors.
-    int  getBonds ( cpstr   entryID,
-                    ivector nBonds, imatrix bondPair,
-                    int &   nAtoms, int     maxNAtoms,
-                    int     maxNBonds );
-
-    int  getHetInfo ( cpstr       entryID,
-                      pstr        Formula,
-                      pstr        Hname,
-                      pstr        Hsynonym,
-                      pstr        Hcharge,
-                      PAtomName & ClinkAtom,  // will
-                      PElement  & ClinkEle,   //   be
-                      PAtomName & SlinkAtom,  //     allocated
-                      PElement  & SlinkEle,   //       or NULL
-                      int       & nLeavingAtoms );
-
-    //   getGraph(..) retrieves data for chemical structure number
-    // entryNo (as in Index) from graph file graphFile, then
-    // allocates and builds the corresponding graph, which is
-    // returned in G.
-    //   If Hflag is set >= 1, all hydrogens are removed from
-    // the graph. If Hflag is set to 2, element types of atoms,
-    // to which hydrogens are bonded, are modified with flag
-    // HYDROGEN_BOND.
-    //   Returns CCP4SRS_Ok in case of success. Other return code are
-    // CCP4SRS_WrongIndex and CCP4SRS_ReadError.
-    int  getGraph ( PCFile graphFile, RPCGraph G );
-    int  getGraph ( PCFile graphFile, int entryNo, RPCGraph G,
-                    int Hflag );
-    int  getGraph ( PCFile graphFile, RPCGraph G, int Hflag );
-    int  getGraph ( int    entryNo  , RPCGraph G, int Hflag );
-    int  getGraph ( cpstr  entryID  , RPCGraph G, int Hflag );
-
-
-  protected:
-    CMemIO         memIO;
-    PPCCP4SRSIndex index;
-    pstr           srsDir;
-    int            srsVersion;
-    int            nEntries;
+    private:
+      int index_alloc;
 
-    void init_base ();
-    void freeMemory();
+  };
 
-  private:
-    int index_alloc;
+} // namespace ccp4srs
 
-};
 
 #endif // CCP4SRS_BASE_H
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_bond.cpp ccp4srs/ccp4srs/ccp4srs_bond.cpp
--- ccp4srs-old/ccp4srs/ccp4srs_bond.cpp	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_bond.cpp	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_bond.cpp, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_bond.cpp $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010-2011.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,310 +22,317 @@
 //
 //  =================================================================
 //
-//    18.10.11   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_bond  <implementation>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSBond  - atom description class
+//  **** Classes :  ccp4srs::Bond  - atom description class
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010-2011
+//  (C) E. Krissinel 2010-2013
 //
 //  =================================================================
 //
 
-#ifndef  __STRING_H
 #include <string.h>
-#endif
 
 #include "ccp4srs_bond.h"
+#include "ccp4srs_types.h"
 #include "ccp4srs_defs.h"
 
-CCP4SRSBond::CCP4SRSBond()  {
-  atom_1          = -1;
-  atom_2          = -1;
-  bond_order      = CCP4SRSBond::noOrder;
-//  bond_type       = CCP4SRSBond::noType;
-  bond_length     = 0.0;
-  bond_length_esd = 0.0;
-}
-
-CCP4SRSBond::~CCP4SRSBond()  {
-}
-
-
-void  get_bond_type_from_cif_ccp4 ( int & type, PCMMCIFLoop loop,
-                                    cpstr Tag, int row, int & rc )  {
-pstr p;
-   p = loop->GetString ( Tag,row,rc );
-   if (!p)                         type = CCP4SRSBond::noOrder;
-   else if (!strcmp(p,"single"))   type = CCP4SRSBond::Single;
-   else if (!strcmp(p,"aromatic")) type = CCP4SRSBond::Aromatic;
-   else if (!strcmp(p,"aromat"))   type = CCP4SRSBond::Aromatic;
-   else if (!strcmp(p,"double"))   type = CCP4SRSBond::Double;
-   else if (!strcmp(p,"triple"))   type = CCP4SRSBond::Triple;
-   else if (!strcmp(p,"deloc"))    type = CCP4SRSBond::Deloc;
-   else if (!strcmp(p,"coval"))    type = CCP4SRSBond::Covalent;
-   else if (!strcmp(p,"metal"))    type = CCP4SRSBond::Metal;
-   else  {
-     type = CCP4SRSBond::noOrder;
-     rc   = CCP4SRS_WrongBondType;
-   }
-}
-
-void  get_bond_type_from_cif_rcsb ( int & type, PCMMCIFLoop loop,
-                                    cpstr Tag, int row, int & rc )  {
-pstr p;
-   p = loop->GetString ( Tag,row,rc );
-   if (!p)                         type = CCP4SRSBond::noOrder;
-   else if (!strcmp(p,"SING"))   type = CCP4SRSBond::Single;
-   else if (!strcmp(p,"AROM"))   type = CCP4SRSBond::Aromatic;
-   else if (!strcmp(p,"DOUB"))   type = CCP4SRSBond::Double;
-   else if (!strcmp(p,"TRIP"))   type = CCP4SRSBond::Triple;
-   else  {
-     type = CCP4SRSBond::noOrder;
-     rc   = CCP4SRS_WrongBondType;
-   }
-}
-
-void  get_bond_type_from_cif ( int & type, PCMMCIFStruct mmCIFStruct,
-                               cpstr Tag, int & rc )  {
-pstr p;
-   p = mmCIFStruct->GetString ( Tag,rc );
-   if (!p)                       type = CCP4SRSBond::noOrder;
-   else if (!strcmp(p,"SING"))   type = CCP4SRSBond::Single;
-   else if (!strcmp(p,"AROM"))   type = CCP4SRSBond::Aromatic;
-   else if (!strcmp(p,"DOUB"))   type = CCP4SRSBond::Double;
-   else if (!strcmp(p,"TRIP"))   type = CCP4SRSBond::Triple;
-   else  {
-     type = CCP4SRSBond::noOrder;
-     rc   = CCP4SRS_WrongBondType;
-   }
-}
-
-void add_bond_type_to_cif ( PCMMCIFLoop loop, int type )  {
-  switch (type)  {
-    default:
-    case CCP4SRSBond::noOrder:  loop->AddNoData ( CIF_NODATA_DOT   );
-                              break;
-    case CCP4SRSBond::Single:   loop->AddString ( "single"  ,False );
-                              break;
-    case CCP4SRSBond::Aromatic: loop->AddString ( "aromatic",False );
-                              break;
-    case CCP4SRSBond::Double:   loop->AddString ( "double"  ,False );
-                              break;
-    case CCP4SRSBond::Triple:   loop->AddString ( "triple"  ,False );
-                              break;
-    case CCP4SRSBond::Deloc:    loop->AddString ( "deloc"   ,False );
-  }
-}
-
-
-int CCP4SRSBond::readFromCIF_ccp4 ( PCMMCIFLoop mmCIFLoop, int bondNo,
-                             CCP4SRSContainer<CCP4SRSAtom> & atoms )  {
-int rc;
-
-  rc = 0;
-
-  get_atom_from_cif ( atom_1,mmCIFLoop,MMCIF_TAG_ATOM_ID_1,
-                      bondNo,atoms,rc );
-  get_atom_from_cif ( atom_2,mmCIFLoop,MMCIF_TAG_ATOM_ID_2,
-                      bondNo,atoms,rc );
-  get_bond_type_from_cif_ccp4 ( bond_order,mmCIFLoop,MMCIF_TAG_TYPE,
-                      bondNo,rc );
-
-  if (mmCIFLoop->GetTagNo(MMCIF_TAG_VALUE_DIST)>=0)  {
-    mmCIFLoop->CopyReal ( bond_length    ,MMCIF_TAG_VALUE_DIST    ,
-                          bondNo,rc );
-    mmCIFLoop->CopyReal ( bond_length_esd,MMCIF_TAG_VALUE_DIST_ESD,
-                          bondNo,rc );
-  } else  {
+namespace ccp4srs  {
+
+  Bond::Bond()  {
+    atom_1          = -1;
+    atom_2          = -1;
+    bond_order      = Bond::noOrder;
+  //  bond_type       = Bond::noType;
     bond_length     = 0.0;
     bond_length_esd = 0.0;
   }
 
-  return rc;
+  Bond::~Bond()  {
+  }
 
-}
 
+  void  get_bond_type_from_cif_ccp4 ( int & type, mmdb::mmcif::PLoop loop,
+                                      mmdb::cpstr Tag, int row, int & rc )  {
+  mmdb::pstr p;
+     p = loop->GetString ( Tag,row,rc );
+     if (!p)                         type = Bond::noOrder;
+     else if (!strcmp(p,"single"))   type = Bond::Single;
+     else if (!strcmp(p,"aromatic")) type = Bond::Aromatic;
+     else if (!strcmp(p,"aromat"))   type = Bond::Aromatic;
+     else if (!strcmp(p,"double"))   type = Bond::Double;
+     else if (!strcmp(p,"triple"))   type = Bond::Triple;
+     else if (!strcmp(p,"deloc"))    type = Bond::Deloc;
+     else if (!strcmp(p,"coval"))    type = Bond::Covalent;
+     else if (!strcmp(p,"metal"))    type = Bond::Metal;
+     else  {
+       type = Bond::noOrder;
+       rc   = CCP4SRS_WrongBondType;
+     }
+  }
 
-int CCP4SRSBond::readFromCIF_rcsb ( PCMMCIFLoop mmCIFLoop, int bondNo,
-                             CCP4SRSContainer<CCP4SRSAtom> & atoms )  {
-pstr p;
-int  rc;
-
-  rc = 0;
-
-  get_atom_from_cif ( atom_1,mmCIFLoop,MMCIF_TAG_ATOM_ID_1,
-                      bondNo,atoms,rc );
-  get_atom_from_cif ( atom_2,mmCIFLoop,MMCIF_TAG_ATOM_ID_2,
-                      bondNo,atoms,rc );
-  get_bond_type_from_cif_rcsb ( bond_order,mmCIFLoop,
-                      MMCIF_TAG_VALUE_ORDER,bondNo,rc );
-
-  if ((bond_order==CCP4SRSBond::Single) ||
-      (bond_order==CCP4SRSBond::Double))  {
-    p = mmCIFLoop->GetString ( MMCIF_TAG_PDBX_AROMATIC_FLAG,bondNo,rc );
-    if (p)  {
-      if (p[0]=='Y')
-        bond_order = CCP4SRSBond::Aromatic;
-    }
+  void  get_bond_type_from_cif_rcsb ( int & type,
+                                      mmdb::mmcif::PLoop loop,
+                                      mmdb::cpstr Tag,
+                                      int row, int & rc )  {
+  mmdb::pstr p;
+     p = loop->GetString ( Tag,row,rc );
+     if (!p)                       type = Bond::noOrder;
+     else if (!strcmp(p,"SING"))   type = Bond::Single;
+     else if (!strcmp(p,"AROM"))   type = Bond::Aromatic;
+     else if (!strcmp(p,"DOUB"))   type = Bond::Double;
+     else if (!strcmp(p,"TRIP"))   type = Bond::Triple;
+     else  {
+       type = Bond::noOrder;
+       rc   = CCP4SRS_WrongBondType;
+     }
   }
 
-  bond_length     = 0.0;
-  bond_length_esd = 0.0;
+  void  get_bond_type_from_cif ( int & type,
+                                 mmdb::mmcif::PStruct mmCIFStruct,
+                                 mmdb::cpstr Tag, int & rc )  {
+  mmdb::pstr p;
+     p = mmCIFStruct->GetString ( Tag,rc );
+     if (!p)                       type = Bond::noOrder;
+     else if (!strcmp(p,"SING"))   type = Bond::Single;
+     else if (!strcmp(p,"AROM"))   type = Bond::Aromatic;
+     else if (!strcmp(p,"DOUB"))   type = Bond::Double;
+     else if (!strcmp(p,"TRIP"))   type = Bond::Triple;
+     else  {
+       type = Bond::noOrder;
+       rc   = CCP4SRS_WrongBondType;
+     }
+  }
 
-  return rc;
+  void add_bond_type_to_cif ( mmdb::mmcif::PLoop loop, int type )  {
+    switch (type)  {
+      default:
+      case Bond::noOrder:  loop->AddNoData ( mmdb::mmcif::CIF_NODATA_DOT );
+                                break;
+      case Bond::Single:   loop->AddString ( "single"  ,false );
+                                break;
+      case Bond::Aromatic: loop->AddString ( "aromatic",false );
+                                break;
+      case Bond::Double:   loop->AddString ( "double"  ,false );
+                                break;
+      case Bond::Triple:   loop->AddString ( "triple"  ,false );
+                                break;
+      case Bond::Deloc:    loop->AddString ( "deloc"   ,false );
+    }
+  }
 
-}
 
-int CCP4SRSBond::readFromCIF ( PCMMCIFStruct mmCIFStruct,
-                               CCP4SRSContainer<CCP4SRSAtom> & atoms ) {
-pstr p;
-int  rc;
-
-  rc = 0;
-
-  get_atom_from_cif ( atom_1,mmCIFStruct,MMCIF_TAG_ATOM_ID_1,
-                      atoms,rc );
-  get_atom_from_cif ( atom_2,mmCIFStruct,MMCIF_TAG_ATOM_ID_2,
-                      atoms,rc );
-  get_bond_type_from_cif ( bond_order,mmCIFStruct,
-                      MMCIF_TAG_VALUE_ORDER,rc );
-
-  if ((bond_order==CCP4SRSBond::Single) ||
-      (bond_order==CCP4SRSBond::Double))  {
-    p = mmCIFStruct->GetString ( MMCIF_TAG_PDBX_AROMATIC_FLAG,rc );
-    if (p)  {
-      if (p[0]=='Y')
-        bond_order = CCP4SRSBond::Aromatic;
+  int Bond::readFromCIF_ccp4 ( mmdb::mmcif::PLoop mmCIFLoop,
+                               int bondNo,
+                               Container<Atom> & atoms )  {
+  int rc;
+
+    rc = 0;
+
+    get_atom_from_cif ( atom_1,mmCIFLoop,MMCIF_TAG_ATOM_ID_1,
+                        bondNo,atoms,rc );
+    get_atom_from_cif ( atom_2,mmCIFLoop,MMCIF_TAG_ATOM_ID_2,
+                        bondNo,atoms,rc );
+    get_bond_type_from_cif_ccp4 ( bond_order,mmCIFLoop,MMCIF_TAG_TYPE,
+                        bondNo,rc );
+
+    if (mmCIFLoop->GetTagNo(MMCIF_TAG_VALUE_DIST)>=0)  {
+      mmCIFLoop->CopyReal ( bond_length    ,MMCIF_TAG_VALUE_DIST    ,
+                            bondNo,rc );
+      mmCIFLoop->CopyReal ( bond_length_esd,MMCIF_TAG_VALUE_DIST_ESD,
+                            bondNo,rc );
+    } else  {
+      bond_length     = 0.0;
+      bond_length_esd = 0.0;
     }
+
+    return rc;
+
   }
 
-  bond_length     = 0.0;
-  bond_length_esd = 0.0;
 
-  return rc;
+  int Bond::readFromCIF_rcsb ( mmdb::mmcif::PLoop mmCIFLoop,
+                               int bondNo,
+                               Container<Atom> & atoms )  {
+  mmdb::pstr p;
+  int        rc;
+
+    rc = 0;
+
+    get_atom_from_cif ( atom_1,mmCIFLoop,MMCIF_TAG_ATOM_ID_1,
+                        bondNo,atoms,rc );
+    get_atom_from_cif ( atom_2,mmCIFLoop,MMCIF_TAG_ATOM_ID_2,
+                        bondNo,atoms,rc );
+    get_bond_type_from_cif_rcsb ( bond_order,mmCIFLoop,
+                        MMCIF_TAG_VALUE_ORDER,bondNo,rc );
+
+    if ((bond_order==Bond::Single) ||
+        (bond_order==Bond::Double))  {
+      p = mmCIFLoop->GetString ( MMCIF_TAG_PDBX_AROMATIC_FLAG,bondNo,rc );
+      if (p)  {
+        if (p[0]=='Y')
+          bond_order = Bond::Aromatic;
+      }
+    }
 
-}
+    bond_length     = 0.0;
+    bond_length_esd = 0.0;
 
-/*
-loop_
-_chem_comp_bond.comp_id
-_chem_comp_bond.atom_id_1
-_chem_comp_bond.atom_id_2
-_chem_comp_bond.type
-_chem_comp_bond.value_dist
-_chem_comp_bond.value_dist_esd
- ATP      O1G    PG        deloc       1.510    0.020
-*/
+    return rc;
 
+  }
 
-Boolean CCP4SRSBond::compare ( CCP4SRSContainer<CCP4SRSAtom> & atoms,
-                       PCCP4SRSBond bond,
-                       CCP4SRSContainer<CCP4SRSAtom> & bond_atoms )  {
-AtomName a11,a12, a21,a22;
+  int Bond::readFromCIF ( mmdb::mmcif::PStruct mmCIFStruct,
+                                 Container<Atom> & atoms ) {
+  mmdb::pstr p;
+  int        rc;
+
+    rc = 0;
+
+    get_atom_from_cif ( atom_1,mmCIFStruct,MMCIF_TAG_ATOM_ID_1,
+                        atoms,rc );
+    get_atom_from_cif ( atom_2,mmCIFStruct,MMCIF_TAG_ATOM_ID_2,
+                        atoms,rc );
+    get_bond_type_from_cif ( bond_order,mmCIFStruct,
+                        MMCIF_TAG_VALUE_ORDER,rc );
+
+    if ((bond_order==Bond::Single) ||
+        (bond_order==Bond::Double))  {
+      p = mmCIFStruct->GetString ( MMCIF_TAG_PDBX_AROMATIC_FLAG,rc );
+      if (p)  {
+        if (p[0]=='Y')
+          bond_order = Bond::Aromatic;
+      }
+    }
 
-  strcpy ( a11,atoms.at(atom_1)->id() );
-  strcpy ( a12,atoms.at(atom_2)->id() );
+    bond_length     = 0.0;
+    bond_length_esd = 0.0;
 
-  strcpy ( a21,bond_atoms.at(bond->atom1())->id() );
-  strcpy ( a22,bond_atoms.at(bond->atom2())->id() );
+    return rc;
 
-  if (!strcmp(a11,a21))
-    return (strcmp(a12,a22)==0);
-  else if (!strcmp(a11,a22))
-    return (strcmp(a12,a21)==0);
+  }
 
-  return False;
+  /*
+  loop_
+  _chem_comp_bond.comp_id
+  _chem_comp_bond.atom_id_1
+  _chem_comp_bond.atom_id_2
+  _chem_comp_bond.type
+  _chem_comp_bond.value_dist
+  _chem_comp_bond.value_dist_esd
+   ATP      O1G    PG        deloc       1.510    0.020
+  */
+
+
+  bool Bond::compare ( Container<Atom> & atoms, PBond bond,
+                       Container<Atom> & bond_atoms )  {
+  mmdb::AtomName a11,a12, a21,a22;
+
+    strcpy ( a11,atoms.at(atom_1)->id() );
+    strcpy ( a12,atoms.at(atom_2)->id() );
+
+    strcpy ( a21,bond_atoms.at(bond->atom1())->id() );
+    strcpy ( a22,bond_atoms.at(bond->atom2())->id() );
+
+    if (!strcmp(a11,a21))
+      return (strcmp(a12,a22)==0);
+    else if (!strcmp(a11,a22))
+      return (strcmp(a12,a21)==0);
 
-}
+    return false;
 
-Boolean CCP4SRSBond::copy ( CCP4SRSContainer<CCP4SRSAtom> & atoms,
-                       PCCP4SRSBond bond,
-                       CCP4SRSContainer<CCP4SRSAtom> & bond_atoms )  {
-AtomName a1,a2;
-int      i;
+  }
 
-  strcpy ( a1,bond_atoms.at(bond->atom1())->id() );
-  strcpy ( a2,bond_atoms.at(bond->atom2())->id() );
+  bool Bond::copy ( Container<Atom> & atoms,
+                         PBond bond,
+                         Container<Atom> & bond_atoms )  {
+  mmdb::AtomName a1,a2;
+  int      i;
+
+    strcpy ( a1,bond_atoms.at(bond->atom1())->id() );
+    strcpy ( a2,bond_atoms.at(bond->atom2())->id() );
+
+    atom_1 = -1;
+    atom_2 = -1;
+
+    for (i=0;(i<atoms.numberOf());i++)  {
+      if (!strcmp(atoms.at(i)->id(),a1))  atom_1 = i;
+      if (!strcmp(atoms.at(i)->id(),a2))  atom_2 = i;
+    }
 
-  atom_1 = -1;
-  atom_2 = -1;
+    if ((atom_1>=0) && (atom_2>=0))  {
+      bond_order      = bond->order ();
+      bond_length     = bond->length();
+      bond_length_esd = bond->length_esd();
+      return true;
+    }
+
+    return false;
 
-  for (i=0;(i<atoms.numberOf());i++)  {
-    if (!strcmp(atoms.at(i)->id(),a1))  atom_1 = i;
-    if (!strcmp(atoms.at(i)->id(),a2))  atom_2 = i;
   }
 
-  if ((atom_1>=0) && (atom_2>=0))  {
-    bond_order      = bond->order ();
-    bond_length     = bond->length();
+  void Bond::copy ( PBond bond, mmdb::ivector anmatch )  {
+    if (anmatch)  {
+      atom_1 = anmatch[bond->atom1()];
+      atom_2 = anmatch[bond->atom2()];
+    } else  {
+      atom_1 = bond->atom1();
+      atom_2 = bond->atom2();
+    }
+    bond_order      = bond->order     ();
+    bond_length     = bond->length    ();
     bond_length_esd = bond->length_esd();
-    return True;
   }
 
-  return False;
 
-}
+  void Bond::makeCIFTags ( mmdb::mmcif::PLoop mmCIFLoop )  {
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_COMP_ID        );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_1      );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_2      );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_TYPE           );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_VALUE_DIST     );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_VALUE_DIST_ESD );
+  }
+
+  void Bond::writeToCIF ( mmdb::mmcif::PLoop mmCIFLoop,
+                              mmdb::cpstr monID,
+                              Container<Atom> & atoms )  {
+    mmCIFLoop->AddString ( monID,false              );
+    add_atom_to_cif      ( mmCIFLoop,atom_1,atoms   );
+    add_atom_to_cif      ( mmCIFLoop,atom_2,atoms   );
+    add_bond_type_to_cif ( mmCIFLoop,bond_order     );
+    mmCIFLoop->AddReal   ( bond_length    ,"%10.3f" );
+    mmCIFLoop->AddReal   ( bond_length_esd,"%10.3f" );
+  }
+
+  void Bond::write_mem ( PMemIO memIO, int version )  {
+  UNUSED_ARGUMENT(version);
+    memIO->put_integer ( atom_1          );
+    memIO->put_integer ( atom_2          );
+    memIO->put_ibyte   ( bond_order      );
+  //  memIO->put_ibyte   ( bond_type       );
+    memIO->put_float   ( bond_length     );
+    memIO->put_float   ( bond_length_esd );
+  }
+
+  bool Bond::read_mem ( PMemIO memIO, int version, bool * Ok )  {
+  UNUSED_ARGUMENT(version);
+  bool success;
+    if (Ok)  success = *Ok;
+       else  success = true;
+    memIO->get_integer ( atom_1         ,&success );
+    memIO->get_integer ( atom_2         ,&success );
+    memIO->get_ibyte   ( bond_order     ,&success );
+  //  memIO->get_ibyte   ( bond_type      ,&success );
+    memIO->get_float   ( bond_length    ,&success );
+    memIO->get_float   ( bond_length_esd,&success );
+    if (Ok)  *Ok = success;
+    return success;
+  }
 
-void CCP4SRSBond::copy ( PCCP4SRSBond bond, ivector anmatch )  {
-  if (anmatch)  {
-    atom_1 = anmatch[bond->atom1()];
-    atom_2 = anmatch[bond->atom2()];
-  } else  {
-    atom_1 = bond->atom1();
-    atom_2 = bond->atom2();
-  }
-  bond_order      = bond->order     ();
-  bond_length     = bond->length    ();
-  bond_length_esd = bond->length_esd();
-}
-
-
-void CCP4SRSBond::makeCIFTags ( PCMMCIFLoop mmCIFLoop )  {
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_COMP_ID        );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_1      );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_2      );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_TYPE           );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_VALUE_DIST     );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_VALUE_DIST_ESD );
-}
-
-void CCP4SRSBond::writeToCIF ( PCMMCIFLoop mmCIFLoop, cpstr monID,
-                            CCP4SRSContainer<CCP4SRSAtom> & atoms )  {
-  mmCIFLoop->AddString ( monID,False              );
-  add_atom_to_cif      ( mmCIFLoop,atom_1,atoms   );
-  add_atom_to_cif      ( mmCIFLoop,atom_2,atoms   );
-  add_bond_type_to_cif ( mmCIFLoop,bond_order     );
-  mmCIFLoop->AddReal   ( bond_length    ,"%10.3f" );
-  mmCIFLoop->AddReal   ( bond_length_esd,"%10.3f" );
-}
-
-void CCP4SRSBond::write_mem ( PCMemIO memIO, int version )  {
-UNUSED_ARGUMENT(version);
-  memIO->put_integer ( atom_1          );
-  memIO->put_integer ( atom_2          );
-  memIO->put_ibyte   ( bond_order      );
-//  memIO->put_ibyte   ( bond_type       );
-  memIO->put_float   ( bond_length     );
-  memIO->put_float   ( bond_length_esd );
-}
-
-Boolean CCP4SRSBond::read_mem ( PCMemIO memIO, int version,
-                                Boolean * Ok )  {
-UNUSED_ARGUMENT(version);
-Boolean success;
-  if (Ok)  success = *Ok;
-     else  success = True;
-  memIO->get_integer ( atom_1         ,&success );
-  memIO->get_integer ( atom_2         ,&success );
-  memIO->get_ibyte   ( bond_order     ,&success );
-//  memIO->get_ibyte   ( bond_type      ,&success );
-  memIO->get_float   ( bond_length    ,&success );
-  memIO->get_float   ( bond_length_esd,&success );
-  if (Ok)  *Ok = success;
-  return success;
-}
+}  // namespace ccp4srs
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_bond.h ccp4srs/ccp4srs/ccp4srs_bond.h
--- ccp4srs-old/ccp4srs/ccp4srs_bond.h	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_bond.h	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_bond.h, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_bond.h $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,16 +22,16 @@
 //
 //  =================================================================
 //
-//    18.10.11   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_bond  <interface>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSBond  - atom description class
+//  **** Classes :  ccp4srs::Bond  - atom description class
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010-2011
+//  (C) E. Krissinel 2010-2013
 //
 //  =================================================================
 //
@@ -41,56 +41,58 @@
 
 #include "ccp4srs_atom.h"
 
-DefineClass(CCP4SRSBond);
+namespace ccp4srs  {
 
-class CCP4SRSBond  {
+  DefineClass(Bond);
 
-  public:
+  class Bond  {
 
-    //  bond orders
-    enum {noOrder,Single,Aromatic,Double,Triple,Deloc,Covalent,Metal};
+    public:
 
-    CCP4SRSBond();
-    virtual ~CCP4SRSBond();
-
-    inline int      atom1     () { return atom_1;          }
-    inline int      atom2     () { return atom_2;          }
-    inline int      order     () { return bond_order;      }
-    inline realtype length    () { return bond_length;     }
-    inline realtype length_esd() { return bond_length_esd; }
-
-    static void makeCIFTags ( PCMMCIFLoop mmCIFLoop );
-    int  readFromCIF_ccp4 ( PCMMCIFLoop mmCIFLoop, int bondNo,
-                            CCP4SRSContainer<CCP4SRSAtom> & atoms );
-    int  readFromCIF_rcsb ( PCMMCIFLoop mmCIFLoop, int bondNo,
-                            CCP4SRSContainer<CCP4SRSAtom> & atoms );
-    int  readFromCIF ( PCMMCIFStruct mmCIFStruct,
-                       CCP4SRSContainer<CCP4SRSAtom> & atoms );
-    void writeToCIF  ( PCMMCIFLoop mmCIFLoop, cpstr monID,
-                       CCP4SRSContainer<CCP4SRSAtom> & atoms );
-
-    Boolean compare ( CCP4SRSContainer<CCP4SRSAtom> & atoms,
-                      PCCP4SRSBond bond,
-                      CCP4SRSContainer<CCP4SRSAtom> & bond_atoms );
-
-    Boolean copy    ( CCP4SRSContainer<CCP4SRSAtom> & atoms,
-                      PCCP4SRSBond bond,
-                      CCP4SRSContainer<CCP4SRSAtom> & bond_atoms );
-
-    void    write_mem ( PCMemIO memIO, int version );
-    Boolean read_mem  ( PCMemIO memIO, int version,
-                        Boolean * Ok = NULL );
-
-    void copy  ( PCCP4SRSBond bond, ivector anmatch=NULL );
-
-  protected:
-    int      atom_1,atom_2;   //!< ordinal numbers of bonded atoms [0,1,.]
-    int      bond_order;      //!< bond order
-    realtype bond_length;     //!< bond length in A; set to 0.0 if
-                              ///< not provided
-    realtype bond_length_esd; //!< bond length esd in A; set to 0.0 if
-                              /// not provided
+      //  bond orders
+      enum {noOrder,Single,Aromatic,Double,Triple,Deloc,Covalent,Metal};
 
-};
+      Bond();
+      virtual ~Bond();
+
+      inline int      atom1     () { return atom_1;          }
+      inline int      atom2     () { return atom_2;          }
+      inline int      order     () { return bond_order;      }
+      inline mmdb::realtype length    () { return bond_length;     }
+      inline mmdb::realtype length_esd() { return bond_length_esd; }
+
+      static void makeCIFTags ( mmdb::mmcif::PLoop mmCIFLoop );
+      int  readFromCIF_ccp4 ( mmdb::mmcif::PLoop mmCIFLoop, int bondNo,
+                              Container<Atom> & atoms );
+      int  readFromCIF_rcsb ( mmdb::mmcif::PLoop mmCIFLoop, int bondNo,
+                              Container<Atom> & atoms );
+      int  readFromCIF ( mmdb::mmcif::PStruct mmCIFStruct,
+                         Container<Atom> & atoms );
+      void writeToCIF  ( mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID,
+                         Container<Atom> & atoms );
+
+      bool compare ( Container<Atom> & atoms, PBond bond,
+                     Container<Atom> & bond_atoms );
+
+      bool copy    ( Container<Atom> & atoms, PBond bond,
+                     Container<Atom> & bond_atoms );
+
+      void write_mem ( PMemIO memIO, int version );
+      bool read_mem  ( PMemIO memIO, int version,
+                          bool * Ok = NULL );
+
+      void copy  ( PBond bond, mmdb::ivector anmatch=NULL );
+
+    protected:
+      int            atom_1,atom_2;   //!< ordinal numbers of bonded atoms [0,1,.]
+      int            bond_order;      //!< bond order
+      mmdb::realtype bond_length;     //!< bond length in A; set to 0.0 if
+                                      ///< not provided
+      mmdb::realtype bond_length_esd; //!< bond length esd in A; set to 0.0 if
+                                      /// not provided
+
+  };
+
+}  // namespace ccp4srs
 
 #endif // CCP4SRS_BOND_H
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_chem.cpp ccp4srs/ccp4srs/ccp4srs_chem.cpp
--- ccp4srs-old/ccp4srs/ccp4srs_chem.cpp	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_chem.cpp	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_chem.cpp, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_chem.cpp $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,13 +22,13 @@
 //
 //  =================================================================
 //
-//    26.02.13   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_chem  <implementation>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSChem - SRS chemistry manager class
+//  **** Classes :  ccp4srs::Chem - SRS chemistry manager class
 //       ~~~~~~~~~
 //
 //  (C) E. Krissinel 2010-2013
@@ -36,711 +36,729 @@
 //  =================================================================
 //
 
-#ifndef  __STRING_H
 #include <string.h>
-#endif
-
-//#ifndef  __File__
-//#include "file_.h"
-//#endif
 
 #include "ccp4srs_chem.h"
 #include "ccp4srs_defs.h"
 
-CCP4SRSChem::CCP4SRSChem() : CCP4SRSBase()  {
-  init_chem();
-}
-
-CCP4SRSChem::~CCP4SRSChem()  {}
-
-void CCP4SRSChem::init_chem()  {
-
-  minDAdist  = 2.0;
-  maxDAdist  = 3.9;  // max distance for H-bonds
-  maxSBdist  = 4.0;  // max distance for salt bridges
-  maxHAdist2 = 2.5*2.5;
-  maxDHAcos  = 0.0;
-  maxHAAcos  = 0.0;
-  maxDAAcos  = 0.0;
-  maxDDAcos  = 0.0;
-
-}
-
-
-int CCP4SRSChem::getEnergyTypes ( PCResidue R, PCFile structFile ) {
-PCCP4SRSMonomer monomer;
-PCCP4SRSAtom    srs_atom;
-PPCAtom         A;
-AtomName        aname;
-int             i,j,rc,natoms,nat;
-
-  R->GetAtomTable ( A,natoms );
-  if (!A)  return CCP4SRS_EmptyResidue;
-
-  for (i=0;i<natoms;i++)
-    if (A[i])  A[i]->energyType[0] = char(0);
-
-  monomer = getMonomer ( R->GetResName(),structFile );
-  if (monomer)  {
-    nat = monomer->n_atoms();
-    if (nat>0)  {
-      for (i=0;i<natoms;i++)
-        if (A[i])  {
-          for (j=0;j<nat;j++)  {
-            srs_atom = monomer->atom(j);
-            if (srs_atom)  {
-              if (!strcmp(A[i]->name,srs_atom->name_pdb(aname)))  {
-                strcpy ( A[i]->energyType,srs_atom->energy_type() );
-                A[i]->charge = srs_atom->charge();
+namespace ccp4srs  {
+
+  Chem::Chem() : Base()  {
+    init_chem();
+  }
+
+  Chem::~Chem()  {}
+
+  void Chem::init_chem()  {
+
+    minDAdist  = 2.0;
+    maxDAdist  = 3.9;  // max distance for H-bonds
+    maxSBdist  = 4.0;  // max distance for salt bridges
+    maxHAdist2 = 2.5*2.5;
+    maxDHAcos  = 0.0;
+    maxHAAcos  = 0.0;
+    maxDAAcos  = 0.0;
+    maxDDAcos  = 0.0;
+
+  }
+
+
+  CCP4SRS_RC Chem::getEnergyTypes ( mmdb::PResidue R,
+                                    mmdb::io::PFile structFile ) {
+  PMonomer       monomer;
+  PAtom          srs_atom;
+  mmdb::PPAtom   A;
+  mmdb::AtomName aname;
+  int            i,j,natoms,nat;
+  CCP4SRS_RC     rc;
+
+    R->GetAtomTable ( A,natoms );
+    if (!A)  return CCP4SRS_EmptyResidue;
+
+    for (i=0;i<natoms;i++)
+      if (A[i])  A[i]->energyType[0] = char(0);
+
+    monomer = getMonomer ( R->GetResName(),structFile );
+    if (monomer)  {
+      nat = monomer->n_atoms();
+      if (nat>0)  {
+        for (i=0;i<natoms;i++)
+          if (A[i])  {
+            for (j=0;j<nat;j++)  {
+              srs_atom = monomer->atom(j);
+              if (srs_atom)  {
+                if (!strcmp(A[i]->name,srs_atom->name_pdb(aname)))  {
+                  strcpy ( A[i]->energyType,srs_atom->energy_type() );
+                  A[i]->charge = srs_atom->charge();
+                }
               }
             }
           }
-        }
-      rc = CCP4SRS_Ok;
+        rc = CCP4SRS_Ok;
+      } else
+        rc = CCP4SRS_NoAtomsFound;
+      delete monomer;
     } else
-      rc = CCP4SRS_NoAtomsFound;
-    delete monomer;
-  } else
-    rc = CCP4SRS_EntryNotFound;
+      rc = CCP4SRS_EntryNotFound;
 
-  return rc;
+    return rc;
 
-}
+  }
 
 
-int CCP4SRSChem::getEnergyTypes ( PPCResidue R, int nRes,
-                                     PCFile structFile )  {
-PCFile          sFile;
-PCCP4SRSMonomer monomer;
-PCCP4SRSAtom    srs_atom;
-PPCAtom         A;
-AtomName        aname;
-bvector         B;
-int             i,j,k,n,natoms,nat;
-
-  GetVectorMemory ( B,nRes,0 );
-  for (i=0;i<nRes;i++)
-    B[i] = (!R[i]);
-
-  if (structFile)  sFile = structFile;
-             else  sFile = getStructFile();
-  if (!sFile)  return CCP4SRS_FileNotFound;
-
-  i = 0;
-  while (i<nRes)  {
-    while (i<nRes)
-      if (B[i])  i++;
-           else  break;
-    if (i<nRes)  {
-      monomer = getMonomer ( R[i]->GetResName(),sFile );
-      j   = i;
-      while (j<nRes)  {
-        B[j] = True;
-        R[j]->GetAtomTable ( A,natoms );
-        if (A)  {
-          for (k=0;k<natoms;k++)
-            if (A[k])  A[k]->energyType[0] = char(0);
-          if (monomer)  {
-            nat = monomer->n_atoms();
-            if (nat>0)  {
-              for (k=0;k<natoms;k++)
-                if (A[k])  {
-                  for (n=0;n<nat;n++)  {
-                    srs_atom = monomer->atom(n);
-                    if (srs_atom) {
-                      if (!strcmp(A[k]->name,
-                                  srs_atom->name_pdb(aname))) {
-                        strcpy ( A[k]->energyType,
-                                 srs_atom->energy_type() );
-                        A[k]->charge = srs_atom->charge();
+  CCP4SRS_RC Chem::getEnergyTypes ( mmdb::PPResidue R, int nRes,
+                                    mmdb::io::PFile structFile )  {
+  mmdb::io::PFile sFile;
+  PMonomer        monomer;
+  PAtom           srs_atom;
+  mmdb::PPAtom    A;
+  mmdb::AtomName  aname;
+  mmdb::ovector   B;
+  int             i,j,k,n,natoms,nat;
+
+    mmdb::GetVectorMemory ( B,nRes,0 );
+    for (i=0;i<nRes;i++)
+      B[i] = (!R[i]);
+
+    if (structFile)  sFile = structFile;
+               else  sFile = getStructFile();
+    if (!sFile)  return CCP4SRS_FileNotFound;
+
+    i = 0;
+    while (i<nRes)  {
+      while (i<nRes)
+        if (B[i])  i++;
+             else  break;
+      if (i<nRes)  {
+        monomer = getMonomer ( R[i]->GetResName(),sFile );
+        j   = i;
+        while (j<nRes)  {
+          B[j] = true;
+          R[j]->GetAtomTable ( A,natoms );
+          if (A)  {
+            for (k=0;k<natoms;k++)
+              if (A[k])  A[k]->energyType[0] = char(0);
+            if (monomer)  {
+              nat = monomer->n_atoms();
+              if (nat>0)  {
+                for (k=0;k<natoms;k++)
+                  if (A[k])  {
+                    for (n=0;n<nat;n++)  {
+                      srs_atom = monomer->atom(n);
+                      if (srs_atom) {
+                        if (!strcmp(A[k]->name,
+                                    srs_atom->name_pdb(aname))) {
+                          strcpy ( A[k]->energyType,
+                                   srs_atom->energy_type() );
+                          A[k]->charge = srs_atom->charge();
+                        }
                       }
                     }
                   }
-                }
+              }
             }
           }
+          j++;
+          while (j<nRes)
+            if (!B[j])  {
+              if (!strcmp(R[i]->name,R[j]->name))  break;
+                                             else  j++;
+            } else
+              j++;
         }
-        j++;
-        while (j<nRes)
-          if (!B[j])  {
-            if (!strcmp(R[i]->name,R[j]->name))  break;
-                                           else  j++;
-          } else
-            j++;
-      }
-      if (monomer)  {
-        delete monomer;
-        monomer = NULL;
+        if (monomer)  {
+          delete monomer;
+          monomer = NULL;
+        }
+        i++;
       }
-      i++;
     }
+
+    if (!structFile)  delete sFile;
+    mmdb::FreeVectorMemory ( B,0 );
+
+    return CCP4SRS_Ok;
+
   }
 
-  if (!structFile)  delete sFile;
-  FreeVectorMemory ( B,0 );
 
-  return CCP4SRS_Ok;
+  CCP4SRS_RC Chem::getEnergyTypes ( mmdb::PChain chain,
+                                    mmdb::io::PFile structFile )  {
+  mmdb::PPResidue Res;
+  int             nRes;
+    chain->GetResidueTable ( Res,nRes );
+    if (nRes>0)
+          return getEnergyTypes ( Res,nRes,structFile );
+    else  return CCP4SRS_EmptyResSet;
+  }
+
+  CCP4SRS_RC Chem::getEnergyTypes ( mmdb::PModel model,
+                                    mmdb::io::PFile structFile )  {
+  mmdb::PPResidue Res;
+  mmdb::PPChain   chain;
+  mmdb::PManager  MMDB;
+  int             selHnd,i,nRes,nChains;
+  CCP4SRS_RC      rc;
+
+    rc   = CCP4SRS_Ok;
+    MMDB = mmdb::PManager(model->GetCoordHierarchy());
+
+    if (MMDB)  {
+
+      selHnd = MMDB->NewSelection();
+      MMDB->Select ( selHnd,mmdb::STYPE_RESIDUE,model->GetSerNum(),
+                     "*",mmdb::ANY_RES,"*",mmdb::ANY_RES,"*",
+                     "*","*","*","*",mmdb::SKEY_NEW );
+      MMDB->GetSelIndex ( selHnd,Res,nRes );
+      if (nRes>0)  rc = getEnergyTypes ( Res,nRes,structFile );
+             else  rc = CCP4SRS_EmptyResSet;
+      MMDB->DeleteSelection ( selHnd );
+
+    } else  {
 
-}
+      model->GetChainTable ( chain,nChains );
+      for (i=0;i<nChains;i++)
+        if (chain[i])  {
+          chain[i]->GetResidueTable ( Res,nRes );
+          if (nRes>0) getEnergyTypes ( Res,nRes,structFile );
+        }
 
+    }
 
-int CCP4SRSChem::getEnergyTypes ( PCChain chain,
-                                     PCFile structFile )  {
-PPCResidue Res;
-int        nRes;
-  chain->GetResidueTable ( Res,nRes );
-  if (nRes>0)
-        return getEnergyTypes ( Res,nRes,structFile );
-  else  return CCP4SRS_EmptyResSet;
-}
+    return rc;
 
-int CCP4SRSChem::getEnergyTypes ( PCModel model,
-                                     PCFile structFile )  {
-PPCResidue    Res;
-PPCChain      chain;
-PCMMDBManager MMDB;
-int           rc,selHnd,i,nRes,nChains;
+  }
 
-  rc   = CCP4SRS_Ok;
-  MMDB = PCMMDBManager(model->GetCoordHierarchy());
+  CCP4SRS_RC Chem::getEnergyTypes ( mmdb::PManager  MMDB,
+                                    mmdb::io::PFile structFile ) {
+  mmdb::PPResidue Res;
+  int             selHnd,nRes;
+  CCP4SRS_RC      rc;
 
-  if (MMDB)  {
+    rc = CCP4SRS_Ok;
 
     selHnd = MMDB->NewSelection();
-    MMDB->Select ( selHnd,STYPE_RESIDUE,model->GetSerNum(),
-                   "*",ANY_RES,"*",ANY_RES,"*",
-                   "*","*","*","*",SKEY_NEW );
+    MMDB->Select ( selHnd,mmdb::STYPE_RESIDUE,0,
+                   "*",mmdb::ANY_RES,"*",mmdb::ANY_RES,"*",
+                   "*","*","*","*",mmdb::SKEY_NEW );
     MMDB->GetSelIndex ( selHnd,Res,nRes );
     if (nRes>0)  rc = getEnergyTypes ( Res,nRes,structFile );
            else  rc = CCP4SRS_EmptyResSet;
-    MMDB->DeleteSelection ( selHnd );
 
-  } else  {
+    MMDB->DeleteSelection ( selHnd );
 
-    model->GetChainTable ( chain,nChains );
-    for (i=0;i<nChains;i++)
-      if (chain[i])  {
-        chain[i]->GetResidueTable ( Res,nRes );
-        if (nRes>0) getEnergyTypes ( Res,nRes,structFile );
-      }
+    return rc;
 
   }
 
-  return rc;
 
-}
+  CCP4SRS_RC Chem::addHydrogens ( mmdb::PResidue R,
+                                  mmdb::io::PFile structFile )  {
+  //   Return:
+  //     CCP4SRS_Ok             success
+  //     CCP4SRS_EmptyResidue   residue R does not contain atoms
+  //     CCP4SRS_NoAtomsFound   SBStructure does not contain atoms
+  //     CCP4SRS_NoBonds        SBStructure does not contain bonds
+  //     CCP4SRS_NoAtomsData    SBStructure is not complete
+  //     CCP4SRS_NoSimilarity   too few coomon atom names in R and SBase
+  //                          entry with the same structure name
+  //     CCP4SRS_SuperpositionFailed  failed residue superposition
+  // NOTE: the function does not rearranges existing atoms in the
+  // residue, but places the hydrogens on top of them (leaving the
+  // Ter pseudoatom, if found, on top of the list)
+  mmdb::io::PFile sFile;
+  PMonomer        monomer;
+  CCP4SRS_RC      rc;
 
-int CCP4SRSChem::getEnergyTypes ( PCMMDBManager MMDB,
-                                     PCFile structFile ) {
-PPCResidue Res;
-int        rc,selHnd,nRes;
+    if (structFile)  sFile = structFile;
+               else  sFile = getStructFile();
 
-  rc = CCP4SRS_Ok;
+    if (!sFile)  return CCP4SRS_FileNotFound;
 
-  selHnd = MMDB->NewSelection();
-  MMDB->Select ( selHnd,STYPE_RESIDUE,0,
-                 "*",ANY_RES,"*",ANY_RES,"*",
-                 "*","*","*","*",SKEY_NEW );
-  MMDB->GetSelIndex ( selHnd,Res,nRes );
-  if (nRes>0)  rc = getEnergyTypes ( Res,nRes,structFile );
-         else  rc = CCP4SRS_EmptyResSet;
+    monomer = getMonomer ( R->GetResName(),sFile );
+    if (!structFile)  delete sFile;
 
-  MMDB->DeleteSelection ( selHnd );
+    if (!monomer)  return CCP4SRS_EntryNotFound;
 
-  return rc;
-
-}
+    rc = monomer->addHydrogens ( R );
 
+    delete monomer;
 
-int CCP4SRSChem::addHydrogens ( PCResidue R, PCFile structFile )  {
-//   Return:
-//     CCP4SRS_Ok             success
-//     CCP4SRS_EmptyResidue   residue R does not contain atoms
-//     CCP4SRS_NoAtomsFound   SBStructure does not contain atoms
-//     CCP4SRS_NoBonds        SBStructure does not contain bonds
-//     CCP4SRS_NoAtomsData    SBStructure is not complete
-//     CCP4SRS_NoSimilarity   too few coomon atom names in R and SBase
-//                          entry with the same structure name
-//     CCP4SRS_SuperpositionFailed  failed residue superposition
-// NOTE: the function does not rearranges existing atoms in the
-// residue, but places the hydrogens on top of them (leaving the
-// Ter pseudoatom, if found, on top of the list)
-PCFile          sFile;
-PCCP4SRSMonomer monomer;
-int             rc;
+    return rc;
 
-  if (structFile)  sFile = structFile;
-             else  sFile = getStructFile();
+  }
 
-  if (!sFile)  return CCP4SRS_FileNotFound;
+  CCP4SRS_RC Chem::addHydrogens ( mmdb::PChain chain,
+                                  mmdb::io::PFile structFile )  {
+  mmdb::io::PFile sFile;
+  mmdb::PPResidue Res;
+  int             i,k,nRes;
+  bool            B;
+  CCP4SRS_RC      rc;
+
+    if (structFile)  sFile = structFile;
+               else  sFile = getStructFile();
+
+    if (!sFile)  return CCP4SRS_FileNotFound;
+
+    rc = CCP4SRS_Ok;
+    B  = false;
+    chain->GetResidueTable ( Res,nRes );
+    for (i=0;i<nRes;i++)
+      if (Res[i])  {
+        k = addHydrogens ( Res[i],sFile );
+        if (k==CCP4SRS_Ok)  B = true;
+                      else  rc = CCP4SRS_Incomplete;
+      }
+    if (!B)  rc = CCP4SRS_Fail;
 
-  monomer = getMonomer ( R->GetResName(),sFile );
-  if (!structFile)  delete sFile;
+    if (!structFile)  delete sFile;
 
-  if (!monomer)  return CCP4SRS_EntryNotFound;
+    return rc;
 
-  rc = monomer->addHydrogens ( R );
+  }
 
-  delete monomer;
 
-  return rc;
+  CCP4SRS_RC Chem::addHydrogens ( mmdb::PModel    model,
+                                  mmdb::io::PFile structFile )  {
+  mmdb::io::PFile sFile;
+  mmdb::PPChain   chain;
+  mmdb::PPResidue Res;
+  int             i,j,k,nChains,nRes;
+  bool            B;
+  CCP4SRS_RC      rc;
 
-}
+    if (structFile)  sFile = structFile;
+               else  sFile = getStructFile();
 
-int CCP4SRSChem::addHydrogens ( PCChain chain, PCFile structFile )  {
-PCFile     sFile;
-PPCResidue Res;
-int        i,k,nRes,rc;
-Boolean    B;
+    if (!sFile)  return CCP4SRS_FileNotFound;
 
-  if (structFile)  sFile = structFile;
-             else  sFile = getStructFile();
+    rc = CCP4SRS_Ok;
+    B  = false;
+    model->GetChainTable ( chain,nChains );
+    for (i=0;i<nChains;i++)
+      if (chain[i])  {
+        chain[i]->GetResidueTable ( Res,nRes );
+        for (j=0;j<nRes;j++)
+          if (Res[j])  {
+            k = addHydrogens ( Res[j],sFile );
+            if (k==CCP4SRS_Ok)  B = true;
+                          else  rc = CCP4SRS_Incomplete;
+          }
+      }
+    if (!B)  rc = CCP4SRS_Fail;
 
-  if (!sFile)  return CCP4SRS_FileNotFound;
+    if (!structFile)  delete sFile;
 
-  rc = CCP4SRS_Ok;
-  B  = False;
-  chain->GetResidueTable ( Res,nRes );
-  for (i=0;i<nRes;i++)
-    if (Res[i])  {
-      k = addHydrogens ( Res[i],sFile );
-      if (k==CCP4SRS_Ok)  B = True;
-                    else  rc = CCP4SRS_Incomplete;
-    }
-  if (!B)  rc = CCP4SRS_Fail;
+    return rc;
 
-  if (!structFile)  delete sFile;
+  }
 
-  return rc;
+  CCP4SRS_RC Chem::addHydrogens ( mmdb::PManager MMDB,
+                                  mmdb::io::PFile structFile )  {
+  mmdb::io::PFile sFile;
+  mmdb::PPModel   model;
+  mmdb::PPChain   chain;
+  mmdb::PPResidue Res;
+  int             i,j,n,k,nModels,nChains,nRes;
+  bool            B;
+  CCP4SRS_RC      rc;
+
+    if (structFile)  sFile = structFile;
+               else  sFile = getStructFile();
+
+    if (!sFile)  return CCP4SRS_FileNotFound;
+
+    rc = CCP4SRS_Ok;
+    B  = false;
+    MMDB->GetModelTable ( model,nModels );
+    for (i=0;i<nModels;i++)
+      if (model[i])  {
+        model[i]->GetChainTable ( chain,nChains );
+        for (j=0;j<nChains;j++)
+          if (chain[j])  {
+            chain[j]->GetResidueTable ( Res,nRes );
+            for (n=0;n<nRes;n++)
+              if (Res[n])  {
+                k = addHydrogens ( Res[n],sFile );
+                if (k==CCP4SRS_Ok)  B = true;
+                              else  rc = CCP4SRS_Incomplete;
+              }
+          }
+      }
+    if (!B)  rc = CCP4SRS_Fail;
 
-}
+    if (!structFile)  delete sFile;
 
+    return rc;
 
-int CCP4SRSChem::addHydrogens ( PCModel model, PCFile structFile )  {
-PCFile     sFile;
-PPCChain   chain;
-PPCResidue Res;
-int        i,j,k,nChains,nRes,rc;
-Boolean    B;
+  }
 
-  if (structFile)  sFile = structFile;
-             else  sFile = getStructFile();
 
-  if (!sFile)  return CCP4SRS_FileNotFound;
 
-  rc = CCP4SRS_Ok;
-  B  = False;
-  model->GetChainTable ( chain,nChains );
-  for (i=0;i<nChains;i++)
-    if (chain[i])  {
-      chain[i]->GetResidueTable ( Res,nRes );
-      for (j=0;j<nRes;j++)
-        if (Res[j])  {
-          k = addHydrogens ( Res[j],sFile );
-          if (k==CCP4SRS_Ok)  B = True;
-                        else  rc = CCP4SRS_Incomplete;
-        }
+  CCP4SRS_RC Chem::makeBonds ( mmdb::PResidue  R,
+                               mmdb::pstr      altLoc,
+                               mmdb::io::PFile structFile,
+                               PDASelHnds      selHandles,
+                               bool            ignoreNegSigOcc )  {
+  //   MakeBonds(..) makes bonds between atoms in MMDB's residue R
+  // from data found in SBase. Residue R must be associated with
+  // coordinate hierarchy. Data is retrieved from SBase on the basis
+  // of residue name only. In case of multiple conformations, if
+  // altLoc:
+  //    NULL  - the highest occupancy atom will be taken
+  //            if all occupancies are equal then atom with
+  //            first altLoc taken
+  //    other - atoms with given altLoc are taken. If such
+  //            altLoc is not found, the function does as if
+  //            NULL value for altLoc is given.
+  //   If selHandles is not NULL, the function also selects atoms
+  // in the residue according to their hydrogen bond attributes.
+  // This is a special option for hydrogen bond calculations.
+  //   If ignoreNegSigOcc is set true then the function will ignore
+  // atoms with negative occupancy standard deviation. Such atoms
+  // may be hydrogens added by CSBase0::AddHydrogens(..) function,
+  // in general any atoms added by CSBAtom::MakeCAtom(..) function.
+  // Added hydrogens may be ignored if MakeBonds is used in
+  // CSbase::CalcHBonds(..) function.
+  //   Return:
+  //     SBASE_Ok             success
+  //     SBASE_FileNotFound   non-initiated SBase
+  //     SBASE_StructNotFound the residue's name is not found in SBase
+  //     SBASE_EmptyResidue   residue R does not contain atoms
+  //     SBASE_NoAtomsFound   SBase entry does not contain atoms
+  //     SBASE_BrokenBonds    some bonds could not be set up because
+  //                          of missing atoms in R. This could be
+  //                          a result of residue R named wrongly.
+  PMonomer       monomer;
+  PBond          bondi;
+  mmdb::PManager MMDB;
+  mmdb::PPAtom   A;
+  mmdb::ivector  anmatch;
+  int            natoms, mon_natoms, i,i1,i2;
+  mmdb::SELECTION_KEY sk;
+  CCP4SRS_RC     rc;
+
+    R->GetAtomTable ( A,natoms );
+    if (!A)  return CCP4SRS_EmptyResidue;
+
+    for (i=0;i<natoms;i++)
+      if (A[i])  A[i]->FreeBonds();
+
+    monomer = getMonomer ( R->GetResName(),structFile );
+    if (!monomer)  return CCP4SRS_EntryNotFound;
+
+    mon_natoms = monomer->n_atoms();
+    if (mon_natoms<=0)  {
+      delete monomer;
+      return CCP4SRS_NoAtomsFound;
     }
-  if (!B)  rc = CCP4SRS_Fail;
 
-  if (!structFile)  delete sFile;
-
-  return rc;
-
-}
+    mmdb::GetVectorMemory ( anmatch,mon_natoms,0 );
+    monomer->getAtomNameMatch ( A,natoms,altLoc,anmatch );
+    if (ignoreNegSigOcc)
+      for (i=0;i<mon_natoms;i++)  {
+        i1 = anmatch[i];
+        if (i1>=0)  {
+          if (A[i1]->sigOcc<0.0)  anmatch[i] = -1;
+        }
+      }
 
-int CCP4SRSChem::addHydrogens ( PCMMDBManager MMDB,
-                                PCFile structFile )  {
-PCFile     sFile;
-PPCModel   model;
-PPCChain   chain;
-PPCResidue Res;
-int        i,j,n,k,nModels,nChains,nRes,rc;
-Boolean    B;
-
-  if (structFile)  sFile = structFile;
-             else  sFile = getStructFile();
-
-  if (!sFile)  return CCP4SRS_FileNotFound;
-
-  rc = CCP4SRS_Ok;
-  B  = False;
-  MMDB->GetModelTable ( model,nModels );
-  for (i=0;i<nModels;i++)
-    if (model[i])  {
-      model[i]->GetChainTable ( chain,nChains );
-      for (j=0;j<nChains;j++)
-        if (chain[j])  {
-          chain[j]->GetResidueTable ( Res,nRes );
-          for (n=0;n<nRes;n++)
-            if (Res[n])  {
-              k = addHydrogens ( Res[n],sFile );
-              if (k==CCP4SRS_Ok)  B = True;
-                            else  rc = CCP4SRS_Incomplete;
+    if (selHandles)  {
+      MMDB = mmdb::PManager(R->GetCoordHierarchy());
+      if (MMDB)  {
+        sk = selHandles->selKey;
+        for (i=0;i<mon_natoms;i++)  {
+          i1 = anmatch[i];
+          if (i1>=0)
+            switch (monomer->atom(i)->hb_type())  {
+              case 'D' :  MMDB->SelectAtom ( selHandles->selHndDonor,
+                                             A[i1],sk,false );
+                        break;
+              case 'A' :  MMDB->SelectAtom ( selHandles->selHndAcceptor,
+                                             A[i1],sk,false );
+                        break;
+              case 'B' :  MMDB->SelectAtom ( selHandles->selHndDonor,
+                                             A[i1],sk,false );
+                          MMDB->SelectAtom ( selHandles->selHndAcceptor,
+                                             A[i1],sk,false );
+                        break;
+              case 'H' :  MMDB->SelectAtom ( selHandles->selHndHydrogen,
+                                             A[i1],sk,false );
+                        break;
+              default  :
+              case 'N' : ;
             }
         }
+      }
     }
-  if (!B)  rc = CCP4SRS_Fail;
 
-  if (!structFile)  delete sFile;
-
-  return rc;
-
-}
-
-
-
-int CCP4SRSChem::makeBonds ( PCResidue R, pstr altLoc,
-                             PCFile       structFile,
-                             PSDASelHnds  selHandles,
-                             Boolean      ignoreNegSigOcc )  {
-//   MakeBonds(..) makes bonds between atoms in MMDB's residue R
-// from data found in SBase. Residue R must be associated with
-// coordinate hierarchy. Data is retrieved from SBase on the basis
-// of residue name only. In case of multiple conformations, if
-// altLoc:
-//    NULL  - the highest occupancy atom will be taken
-//            if all occupancies are equal then atom with
-//            first altLoc taken
-//    other - atoms with given altLoc are taken. If such
-//            altLoc is not found, the function does as if
-//            NULL value for altLoc is given.
-//   If selHandles is not NULL, the function also selects atoms
-// in the residue according to their hydrogen bond attributes.
-// This is a special option for hydrogen bond calculations.
-//   If ignoreNegSigOcc is set True then the function will ignore
-// atoms with negative occupancy standard deviation. Such atoms
-// may be hydrogens added by CSBase0::AddHydrogens(..) function,
-// in general any atoms added by CSBAtom::MakeCAtom(..) function.
-// Added hydrogens may be ignored if MakeBonds is used in
-// CSbase::CalcHBonds(..) function.
-//   Return:
-//     SBASE_Ok             success
-//     SBASE_FileNotFound   non-initiated SBase
-//     SBASE_StructNotFound the residue's name is not found in SBase
-//     SBASE_EmptyResidue   residue R does not contain atoms
-//     SBASE_NoAtomsFound   SBase entry does not contain atoms
-//     SBASE_BrokenBonds    some bonds could not be set up because
-//                          of missing atoms in R. This could be
-//                          a result of residue R named wrongly.
-PCCP4SRSMonomer monomer;
-PCCP4SRSBond    bondi;
-PCMMDBManager   MMDB;
-PPCAtom         A;
-ivector         anmatch;
-int             natoms, mon_natoms, i,i1,i2,rc;
-
-  R->GetAtomTable ( A,natoms );
-  if (!A)  return CCP4SRS_EmptyResidue;
+    rc = CCP4SRS_Ok;
+    for (i=0;i<monomer->n_bonds();i++)  {
+      bondi = monomer->bond(i);
+      i1 = anmatch[bondi->atom1()];
+      i2 = anmatch[bondi->atom2()];
+      if ((i1>=0) && (i2>=0))  {
+        A[i1]->AddBond ( A[i2],bondi->order(),2 );
+        A[i2]->AddBond ( A[i1],bondi->order(),2 );
+      } else
+        rc = CCP4SRS_BrokenBonds;
+    }
 
-  for (i=0;i<natoms;i++)
-    if (A[i])  A[i]->FreeBonds();
+    mmdb::FreeVectorMemory ( anmatch,0 );
+    delete monomer;
 
-  monomer = getMonomer ( R->GetResName(),structFile );
-  if (!monomer)  return CCP4SRS_EntryNotFound;
+    return rc;
 
-  mon_natoms = monomer->n_atoms();
-  if (mon_natoms<=0)  {
-    delete monomer;
-    return CCP4SRS_NoAtomsFound;
   }
 
-  GetVectorMemory ( anmatch,mon_natoms,0 );
-  monomer->getAtomNameMatch ( A,natoms,altLoc,anmatch );
-  if (ignoreNegSigOcc)
-    for (i=0;i<mon_natoms;i++)  {
-      i1 = anmatch[i];
-      if (i1>=0)  {
-        if (A[i1]->sigOcc<0.0)  anmatch[i] = -1;
-      }
+  void _addAtomPair ( mmdb::PAtom a1, mmdb::PAtom a2,
+                      PAtomPair & Pair, int & nPairs, int & nPAlloc )  {
+  PAtomPair AP;
+  int       i,i1,i2,j1,j2;
+  bool      Found;
+
+    Found = false;
+    i1    = a1->GetIndex();
+    i2    = a2->GetIndex();
+    for (i=0;(i<nPairs) && (!Found);i++)  {
+      j1 = Pair[i].a1->GetIndex();
+      j2 = Pair[i].a2->GetIndex();
+      Found = (((i1==j1) && (i2==j2)) ||
+               ((i1==j2) && (i2==j1)));
     }
 
-  if (selHandles)  {
-    MMDB = PCMMDBManager(R->GetCoordHierarchy());
-    if (MMDB)  {
-      i2 = selHandles->selKey;
-      for (i=0;i<mon_natoms;i++)  {
-        i1 = anmatch[i];
-        if (i1>=0)
-          switch (monomer->atom(i)->hb_type())  {
-            case 'D' :  MMDB->SelectAtom ( selHandles->selHndDonor,
-                                           A[i1],i2,False );
-                      break;
-            case 'A' :  MMDB->SelectAtom ( selHandles->selHndAcceptor,
-                                           A[i1],i2,False );
-                      break;
-            case 'B' :  MMDB->SelectAtom ( selHandles->selHndDonor,
-                                           A[i1],i2,False );
-                        MMDB->SelectAtom ( selHandles->selHndAcceptor,
-                                           A[i1],i2,False );
-                      break;
-            case 'H' :  MMDB->SelectAtom ( selHandles->selHndHydrogen,
-                                           A[i1],i2,False );
-                      break;
-            default  :
-            case 'N' : ;
-          }
+    if (!Found)  {
+      if (nPairs>=nPAlloc)  {
+        nPAlloc = nPairs+20;
+        AP = new AtomPair[nPAlloc];
+        for (i=0;i<nPairs;i++)  {
+          AP[i].a1 = Pair[i].a1;
+          AP[i].a2 = Pair[i].a2;
+        }
+        if (Pair)  delete[] Pair;
+        Pair = AP;
       }
+      Pair[nPairs].a1 = a1;
+      Pair[nPairs].a2 = a2;
+      nPairs++;
     }
-  }
 
-  rc = CCP4SRS_Ok;
-  for (i=0;i<monomer->n_bonds();i++)  {
-    bondi = monomer->bond(i);
-    i1 = anmatch[bondi->atom1()];
-    i2 = anmatch[bondi->atom2()];
-    if ((i1>=0) && (i2>=0))  {
-      A[i1]->AddBond ( A[i2],bondi->order(),2 );
-      A[i2]->AddBond ( A[i1],bondi->order(),2 );
-    } else
-      rc = CCP4SRS_BrokenBonds;
   }
 
-  FreeVectorMemory ( anmatch,0 );
-  delete monomer;
+  CCP4SRS_RC Chem::CalcHBonds ( mmdb::PPResidue Res1, int nres1,
+                                mmdb::PPResidue Res2, int nres2,
+                                RPAtomPair     HBond, int & nHBonds,
+                                RPAtomPair   SBridge, int & nSBridges,
+                                mmdb::io::PFile structFile,
+                                mmdb::pstr altLoc,
+                                bool ignoreNegSigOcc )  {
+  mmdb::io::PFile sFile;
+  mmdb::PManager  MMDB;
+  mmdb::PPAtom    Donor1,Acceptor1, Donor2,Acceptor2;
+  mmdb::PAtom     D,A,H;
+  mmdb::PContact  Contact;
+  mmdb::PAtomBond ABond,DBond;
+  DASelHnds       selHandles1,selHandles2;
+  mmdb::pstr      resName;
+  int             nDonors1,nAcceptors1, nDonors2,nAcceptors2, nContacts;
+  int             i,j,k,nDBonds,nABonds,nHBAlloc,nSBAlloc;
+  bool            isHBond,isSBridge;
+
+    if (HBond)  {
+      delete[] HBond;
+      HBond = NULL;
+    }
+    nHBonds  = 0;
+    nHBAlloc = 0;
+
+    if (SBridge)  {
+      delete[] SBridge;
+      SBridge = NULL;
+    }
+    nSBridges = 0;
+    nSBAlloc  = 0;
 
-  return rc;
+    //  1. Calculate bonds between atoms in given residues and
+    //     select donors and acceptors
 
-}
-
-void _addAtomPair ( PCAtom a1, PCAtom a2,
-                   PSAtomPair & Pair, int & nPairs, int & nPAlloc )  {
-PSAtomPair AP;
-int        i,i1,i2,j1,j2;
-Boolean    Found;
-
-  Found = False;
-  i1    = a1->GetIndex();
-  i2    = a2->GetIndex();
-  for (i=0;(i<nPairs) && (!Found);i++)  {
-    j1 = Pair[i].a1->GetIndex();
-    j2 = Pair[i].a2->GetIndex();
-    Found = (((i1==j1) && (i2==j2)) ||
-             ((i1==j2) && (i2==j1)));
-  }
-
-  if (!Found)  {
-    if (nPairs>=nPAlloc)  {
-      nPAlloc = nPairs+20;
-      AP = new SAtomPair[nPAlloc];
-      for (i=0;i<nPairs;i++)  {
-        AP[i].a1 = Pair[i].a1;
-        AP[i].a2 = Pair[i].a2;
-      }
-      if (Pair)  delete[] Pair;
-      Pair = AP;
+    i = 0;
+    while ((i<nres1) && (!Res1[i]))  i++;
+    if (i>=nres1)  return CCP4SRS_EmptyResSet;
+
+    MMDB = mmdb::PManager(Res1[i]->GetCoordHierarchy());
+    if (!MMDB)  return CCP4SRS_noCoordHierarchy;
+
+    if (structFile)  sFile = structFile;
+               else  sFile = getStructFile();
+
+    if (!sFile)  return CCP4SRS_FileNotFound;
+
+    selHandles1.getNewHandles ( MMDB );
+    for (i=0;i<nres1;i++)
+      if (Res1[i])
+        makeBonds ( Res1[i],altLoc,sFile,&selHandles1,ignoreNegSigOcc );
+    selHandles1.makeSelIndexes ( MMDB );
+
+    selHandles2.getNewHandles ( MMDB );
+    for (i=0;i<nres2;i++)
+      if (Res2[i])
+        makeBonds ( Res2[i],altLoc,sFile,&selHandles2,ignoreNegSigOcc );
+    selHandles2.makeSelIndexes ( MMDB );
+
+    if (!structFile)  delete sFile;
+
+    // 2. Calculate contacts between donors and acceptors as
+    //    potential hydrogen bond contacts
+
+    MMDB->GetSelIndex ( selHandles1.selHndDonor,Donor1,nDonors1 );
+    MMDB->GetSelIndex ( selHandles2.selHndDonor,Donor2,nDonors2 );
+    if ((nDonors1<=0) && (nDonors2<=0))  {
+      selHandles1.deleteSelections ( MMDB );
+      selHandles2.deleteSelections ( MMDB );
+      return CCP4SRS_noDonors;
     }
-    Pair[nPairs].a1 = a1;
-    Pair[nPairs].a2 = a2;
-    nPairs++;
-  }
-
-}
-
-int  CCP4SRSChem::CalcHBonds ( PPCResidue Res1, int nres1,
-                                  PPCResidue Res2, int nres2,
-                                  RPSAtomPair   HBond, int & nHBonds,
-                                  RPSAtomPair SBridge, int & nSBridges,
-                                  PCFile structFile, pstr altLoc,
-                                  Boolean ignoreNegSigOcc )  {
-PCFile        sFile;
-PCMMDBManager MMDB;
-PPCAtom       Donor1,Acceptor1, Donor2,Acceptor2;
-PCAtom        D,A,H;
-PSContact     Contact;
-PSAtomBond    ABond,DBond;
-SDASelHnds    selHandles1,selHandles2;
-pstr          resName;
-int           nDonors1,nAcceptors1, nDonors2,nAcceptors2, nContacts;
-int           i,j,k,nDBonds,nABonds,nHBAlloc,nSBAlloc;
-Boolean       isHBond,isSBridge;
-
-  if (HBond)  {
-    delete[] HBond;
-    HBond = NULL;
-  }
-  nHBonds  = 0;
-  nHBAlloc = 0;
-
-  if (SBridge)  {
-    delete[] SBridge;
-    SBridge = NULL;
-  }
-  nSBridges = 0;
-  nSBAlloc  = 0;
-
-  //  1. Calculate bonds between atoms in given residues and
-  //     select donors and acceptors
-
-  i = 0;
-  while ((i<nres1) && (!Res1[i]))  i++;
-  if (i>=nres1)  return CCP4SRS_EmptyResSet;
-
-  MMDB = PCMMDBManager(Res1[i]->GetCoordHierarchy());
-  if (!MMDB)  return CCP4SRS_noCoordHierarchy;
-
-  if (structFile)  sFile = structFile;
-             else  sFile = getStructFile();
-
-  if (!sFile)  return CCP4SRS_FileNotFound;
-
-  selHandles1.getNewHandles ( MMDB );
-  for (i=0;i<nres1;i++)
-    if (Res1[i])
-      makeBonds ( Res1[i],altLoc,sFile,&selHandles1,ignoreNegSigOcc );
-  selHandles1.makeSelIndexes ( MMDB );
-
-  selHandles2.getNewHandles ( MMDB );
-  for (i=0;i<nres2;i++)
-    if (Res2[i])
-      makeBonds ( Res2[i],altLoc,sFile,&selHandles2,ignoreNegSigOcc );
-  selHandles2.makeSelIndexes ( MMDB );
-
-  if (!structFile)  delete sFile;
-
-  // 2. Calculate contacts between donors and acceptors as
-  //    potential hydrogen bond contacts
-
-  MMDB->GetSelIndex ( selHandles1.selHndDonor,Donor1,nDonors1 );
-  MMDB->GetSelIndex ( selHandles2.selHndDonor,Donor2,nDonors2 );
-  if ((nDonors1<=0) && (nDonors2<=0))  {
-    selHandles1.deleteSelections ( MMDB );
-    selHandles2.deleteSelections ( MMDB );
-    return CCP4SRS_noDonors;
-  }
 
-  MMDB->GetSelIndex(selHandles1.selHndAcceptor,Acceptor1,nAcceptors1);
-  MMDB->GetSelIndex(selHandles2.selHndAcceptor,Acceptor2,nAcceptors2);
-  if ((nAcceptors1<=0) && (nAcceptors2<=0))  {
-    selHandles1.deleteSelections ( MMDB );
-    selHandles2.deleteSelections ( MMDB );
-    return CCP4SRS_noAcceptors;
-  }
+    MMDB->GetSelIndex(selHandles1.selHndAcceptor,Acceptor1,nAcceptors1);
+    MMDB->GetSelIndex(selHandles2.selHndAcceptor,Acceptor2,nAcceptors2);
+    if ((nAcceptors1<=0) && (nAcceptors2<=0))  {
+      selHandles1.deleteSelections ( MMDB );
+      selHandles2.deleteSelections ( MMDB );
+      return CCP4SRS_noAcceptors;
+    }
 
-  if ((nDonors1*nAcceptors2<=0) && (nDonors2*nAcceptors1<=0))  {
-    selHandles1.deleteSelections ( MMDB );
-    selHandles2.deleteSelections ( MMDB );
-    return CCP4SRS_noHBonds;
-  }
+    if ((nDonors1*nAcceptors2<=0) && (nDonors2*nAcceptors1<=0))  {
+      selHandles1.deleteSelections ( MMDB );
+      selHandles2.deleteSelections ( MMDB );
+      return CCP4SRS_noHBonds;
+    }
 
-  //   We now calculate contacts such that 1st contacting atom, either
-  // acceptor or donor, belongs to 1st set of residues, and the second
-  // one - to 2nd set of residues. Therefore we run SeekContacts on
-  // two sets of donors and acceptors, identified by different group
-  // id, merging the array of contacts for convenience.
-  Contact   = NULL;
-  nContacts = 0;
-  MMDB->SeekContacts ( Donor1,nDonors1,Acceptor2,nAcceptors2,
-                       minDAdist,RMax(maxDAdist,maxSBdist),0,Contact,
-                       nContacts,0,NULL,1,0 );
-  MMDB->SeekContacts ( Acceptor1,nAcceptors1,Donor2,nDonors2,
-                       minDAdist,RMax(maxDAdist,maxSBdist),0,Contact,
-                       nContacts,0,NULL,2,0 );
-  if (nContacts<=0)  {
-    selHandles1.deleteSelections ( MMDB );
-    selHandles2.deleteSelections ( MMDB );
-    return CCP4SRS_noHBonds;
-  }
+    //   We now calculate contacts such that 1st contacting atom, either
+    // acceptor or donor, belongs to 1st set of residues, and the second
+    // one - to 2nd set of residues. Therefore we run SeekContacts on
+    // two sets of donors and acceptors, identified by different group
+    // id, merging the array of contacts for convenience.
+    Contact   = NULL;
+    nContacts = 0;
+    MMDB->SeekContacts ( Donor1,nDonors1,Acceptor2,nAcceptors2,
+                         minDAdist,mmdb::RMax(maxDAdist,maxSBdist),0,
+                         Contact,nContacts,0,NULL,1,0 );
+    MMDB->SeekContacts ( Acceptor1,nAcceptors1,Donor2,nDonors2,
+                         minDAdist,mmdb::RMax(maxDAdist,maxSBdist),0,
+                         Contact,nContacts,0,NULL,2,0 );
+    if (nContacts<=0)  {
+      selHandles1.deleteSelections ( MMDB );
+      selHandles2.deleteSelections ( MMDB );
+      return CCP4SRS_noHBonds;
+    }
 
 
-  // 3. Check all contacts for h-bond geometry
+    // 3. Check all contacts for h-bond geometry
 
-  // merge all hydrogens into one selection as it is used
-  // for checking with only
-  MMDB->Select ( selHandles1.selHndHydrogen,STYPE_ATOM,
-                 selHandles2.selHndHydrogen,SKEY_OR );
+    // merge all hydrogens into one selection as it is used
+    // for checking with only
+    MMDB->Select ( selHandles1.selHndHydrogen,mmdb::STYPE_ATOM,
+                   selHandles2.selHndHydrogen,mmdb::SKEY_OR );
+
+    for (i=0;i<nContacts;i++)  {
+
+      if (Contact[i].group<=1)  {
+        D = Donor1   [Contact[i].id1];
+        A = Acceptor2[Contact[i].id2];
+      } else  {
+        A = Acceptor1[Contact[i].id1];
+        D = Donor2   [Contact[i].id2];
+      }
 
-  for (i=0;i<nContacts;i++)  {
-    if (Contact[i].group<=1)  {
-      D = Donor1   [Contact[i].id1];
-      A = Acceptor2[Contact[i].id2];
-    } else  {
-      A = Acceptor1[Contact[i].id1];
-      D = Donor2   [Contact[i].id2];
-    }
-    if (Contact[i].dist<=maxDAdist)  {
-      // Check for H-bond
-      D->GetBonds ( DBond,nDBonds );
-      A->GetBonds ( ABond,nABonds );
-      if (nABonds>0)  {
-        // Check whether there are hydrogens bound to the donor,
-        // and if they are then calculate h-bonds using them
-        H = NULL;
-        for (j=0;j<nDBonds;j++)
-          if ((DBond[j].atom->occupancy>0.0)  &&
-               DBond[j].atom->isInSelection(
-                                selHandles1.selHndHydrogen))  {
-            H = DBond[j].atom;
-            if ((H->GetDist2(A)<maxHAdist2) &&
-                (H->GetCosine(D,A)<=maxDHAcos))  {
-              // Check angles with all acceptor neighbours
-              isHBond = True;
-              for (k=0;(k<nABonds) && isHBond;k++)
-                isHBond = (A->GetCosine(H,ABond[k].atom)<=maxHAAcos);
-              if (isHBond)  {
-                if (Contact[i].group<=1)
-                      _addAtomPair ( H,A,HBond,nHBonds,nHBAlloc );
-                else  _addAtomPair ( A,H,HBond,nHBonds,nHBAlloc );
-              }
-            }
+      isSBridge = false;
+
+      if ((Contact[i].dist<=maxSBdist)       &&
+          (D->GetResidue()!=A->GetResidue()) &&
+          (!strcmp(D->element," N")) && (!strcmp(A->element," O")))  {
+        // Check for salt bridge, which may be formed only by N-O
+        // pairs of aminoacid atoms at distances less then maxSBdist
+        if (!strcmp(D->name," N  "))  {
+          // mainchain nitrogen can form salt bridge only at N-terminus
+          isSBridge = D->isNTerminus();
+        } else  {
+          // other nitrogens can form salt bridge only in LYS, ARG
+          // and HIS
+          resName   = D->GetResName();
+          isSBridge = ((!strcmp(resName,"LYS")) ||
+                       (!strcmp(resName,"ARG")) ||
+                       (!strcmp(resName,"HIS")));
+        }
+        if (isSBridge)  {
+          if ((!strcmp(A->name," O  ")) || (!strcmp(A->name," OXT")))  {
+            // mainchain oxygens can form salt bridge only at C-terminus
+            isSBridge = A->isCTerminus();
+          } else  {
+            // other oxygens can form salt bridge only in GLU and ASP
+            resName   = A->GetResName();
+            isSBridge = ((!strcmp(resName,"GLU")) ||
+                         (!strcmp(resName,"ASP")));
           }
-        if ((!H) && (nDBonds>0))  {
-          // There were no hydrogens bonded to donor, assume that
-          // the structure is incomplete and check donor-acceptor
-          // geometry for possible h-bonding.
-          isHBond = True;
-          for (j=0;(j<nDBonds) && isHBond;j++)
-            isHBond = (D->GetCosine(DBond[j].atom,A)<=maxDDAcos);
-          for (j=0;(j<nABonds) && isHBond;j++)
-            isHBond = (A->GetCosine(D,ABond[j].atom)<=maxDAAcos);
-          if (isHBond)  {
+          if (isSBridge)  {
             if (Contact[i].group<=1)
-                  _addAtomPair ( D,A,HBond,nHBonds,nHBAlloc );
-            else  _addAtomPair ( A,D,HBond,nHBonds,nHBAlloc );
+                  _addAtomPair ( D,A,SBridge,nSBridges,nSBAlloc );
+            else  _addAtomPair ( A,D,SBridge,nSBridges,nSBAlloc );
           }
         }
       }
-    }
-    if ((Contact[i].dist<=maxSBdist)       &&
-        (D->GetResidue()!=A->GetResidue()) &&
-        (!strcmp(D->element," N")) && (!strcmp(A->element," O")))  {
-      // Check for salt bridge, which may be formed only by N-O
-      // pairs of aminoacid atoms at distances less then maxSBdist
-      if (!strcmp(D->name," N  "))  {
-        // mainchain nitrogen can form salt bridge only at N-terminus
-        isSBridge = D->isNTerminus();
-      } else  {
-        // other nitrogens can form salt bridge only in LYS, ARG
-        // and HIS
-        resName   = D->GetResName();
-        isSBridge = ((!strcmp(resName,"LYS")) ||
-                     (!strcmp(resName,"ARG")) ||
-                     (!strcmp(resName,"HIS")));
-      }
-      if (isSBridge)  {
-        if ((!strcmp(A->name," O  ")) || (!strcmp(A->name," OXT")))  {
-          // mainchain oxygens can form salt bridge only at C-terminus
-          isSBridge = A->isCTerminus();
-        } else  {
-          // other oxygens can form salt bridge only in GLU and ASP
-          resName   = A->GetResName();
-          isSBridge = ((!strcmp(resName,"GLU")) ||
-                       (!strcmp(resName,"ASP")));
-        }
-        if (isSBridge)  {
-          if (Contact[i].group<=1)
-                _addAtomPair ( D,A,SBridge,nSBridges,nSBAlloc );
-          else  _addAtomPair ( A,D,SBridge,nSBridges,nSBAlloc );
+
+      if ((Contact[i].dist<=maxDAdist) && (!isSBridge))  {
+        // Check for H-bond if salt bridge was not identified
+        D->GetBonds ( DBond,nDBonds );
+        A->GetBonds ( ABond,nABonds );
+        if (nABonds>0)  {
+          // Check whether there are hydrogens bound to the donor,
+          // and if they are then calculate h-bonds using them
+          H = NULL;
+          for (j=0;j<nDBonds;j++)
+            if ((DBond[j].atom->occupancy>0.0)  &&
+                 DBond[j].atom->isInSelection(
+                                  selHandles1.selHndHydrogen))  {
+              H = DBond[j].atom;
+              if ((H->GetDist2(A)<maxHAdist2) &&
+                  (H->GetCosine(D,A)<=maxDHAcos))  {
+                // Check angles with all acceptor neighbours
+                isHBond = true;
+                for (k=0;(k<nABonds) && isHBond;k++)
+                  isHBond = (A->GetCosine(H,ABond[k].atom)<=maxHAAcos);
+                if (isHBond)  {
+                  if (Contact[i].group<=1)
+                        _addAtomPair ( H,A,HBond,nHBonds,nHBAlloc );
+                  else  _addAtomPair ( A,H,HBond,nHBonds,nHBAlloc );
+                }
+              }
+            }
+          if ((!H) && (nDBonds>0))  {
+            // There were no hydrogens bonded to donor, assume that
+            // the structure is incomplete and check donor-acceptor
+            // geometry for possible h-bonding.
+            isHBond = true;
+            for (j=0;(j<nDBonds) && isHBond;j++)
+              isHBond = (D->GetCosine(DBond[j].atom,A)<=maxDDAcos);
+            for (j=0;(j<nABonds) && isHBond;j++)
+              isHBond = (A->GetCosine(D,ABond[j].atom)<=maxDAAcos);
+            if (isHBond)  {
+              if (Contact[i].group<=1)
+                    _addAtomPair ( D,A,HBond,nHBonds,nHBAlloc );
+              else  _addAtomPair ( A,D,HBond,nHBonds,nHBAlloc );
+            }
+          }
         }
       }
+
     }
-  }
 
-  if (Contact)  delete[] Contact;
+    if (Contact)  delete[] Contact;
 
-  selHandles1.deleteSelections ( MMDB );
-  selHandles2.deleteSelections ( MMDB );
+    selHandles1.deleteSelections ( MMDB );
+    selHandles2.deleteSelections ( MMDB );
+
+    return CCP4SRS_Ok;
 
-  return CCP4SRS_Ok;
+  }
 
-}
+}  // namespace ccp4srs
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_chem.h ccp4srs/ccp4srs/ccp4srs_chem.h
--- ccp4srs-old/ccp4srs/ccp4srs_chem.h	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_chem.h	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_chem.h, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_chem.h $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,13 +22,13 @@
 //
 //  =================================================================
 //
-//    26.02.13   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_chem  <interface>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSChem - SRS chemistry manager class
+//  **** Classes :  ccp4srs::Chem - SRS chemistry manager class
 //       ~~~~~~~~~
 //
 //  (C) E. Krissinel 2010-2013
@@ -42,133 +42,146 @@
 #include "ccp4srs_base.h"
 #include "ccp4srs_types.h"
 
+namespace ccp4srs  {
 
-// ==================================================================
+  // ==================================================================
 
-DefineClass(CCP4SRSChem)
+  DefineClass(Chem);
 
-class CCP4SRSChem : public CCP4SRSBase  {
+  class Chem : public Base  {
 
-  public:
-    CCP4SRSChem ();
-    ~CCP4SRSChem();
-
-    int  getEnergyTypes ( PCResidue  R,           PCFile structFile );
-    int  getEnergyTypes ( PPCResidue R, int nRes, PCFile structFile );
-    int  getEnergyTypes ( PCChain      chain,     PCFile structFile );
-    int  getEnergyTypes ( PCModel      model,     PCFile structFile );
-    int  getEnergyTypes ( PCMMDBManager MMDB,     PCFile structFile );
-
-    int  addHydrogens   ( PCResidue        R, PCFile structFile );
-    int  addHydrogens   ( PCChain      chain, PCFile structFile );
-    int  addHydrogens   ( PCModel      model, PCFile structFile );
-    int  addHydrogens   ( PCMMDBManager MMDB, PCFile structFile );
-
-
-    //   MakeBonds(..) makes bonds between atoms in MMDB's residue R
-    // from data found in SBase. Residue R must be associated with
-    // coordinate hierarchy. Data is retrieved from SBase on the basis
-    // of residue name only. In case of multiple conformations, if
-    // altLoc:
-    //    NULL  - the highest occupancy atom will be taken
-    //            if all occupancies are equal then atom with
-    //            first altLoc taken
-    //    other - atoms with given altLoc are taken. If such
-    //            altLoc is not found, the function does as if
-    //            NULL value for altLoc is given.
-    //   If selHandles is not NULL, the function also selects atoms
-    // in the residue according to their hydrogen bond attributes.
-    // This is a special option for hydrogen bond calculations
-    //   If ignoreNegSigOcc is set True then the function will ignore
-    // atoms with negative occupancy standard deviation. Such atoms
-    // may be hydrogens added by CSBase0::AddHydrogen(..) function,
-    // in general any atoms added by CSBAtom::MakeCAtom(..) function.
-    // Added hydrogens may be ignored if MakeBonds is used in
-    // CSbase::CalcHBonds(..) function.
-    //   Return:
-    //     SBASE_Ok             success
-    //     SBASE_FileNotFound   non-initiated SBase
-    //     SBASE_StructNotFound the residue's name is not found
-    //                          in SBase
-    //     SBASE_EmptyResidue   residue R does not contain atoms
-    //     SBASE_NoAtomsFound   SBase entry does not contain atoms
-    //     SBASE_BrokenBonds    some bonds could not be set up because
-    //                          of missing atoms in R. This could be
-    //                          a result of residue R named wrongly.
-    int  makeBonds ( PCResidue   R,
-                     pstr        altLoc,
-                     PCFile      structFile,
-                     PSDASelHnds selHandles,
-                     Boolean     ignoreNegSigOcc );
-
-    //   CalcHBonds(..) calculates hydrogen bonds and salt bridges
-    // between atoms of residues given in Res1[0..nres1-1] and
-    // Res2[0..nres2-1]. H-bonds are returned in HBond[0..nHBonds-1]
-    // and salt bridges are returned in SBridge[0..nSBridges-1].
-    //
-    //   On input:
-    //     Res1, Res2         must belong to the same MMDB
-    //     HBond, SBridge     should be set NULL, otherwise the
-    //                        function attempts to deallocate them
-    //     nHBonds, nSBridges ignored
-    //     structFile         may be a pointer to open SBase stucture
-    //                        file in order to save on file open
-    //                        operation. If structFile is set NULL,
-    //                        the function will open the SBase
-    //                        structure file by itself
-    //     altLoc             specifies the alternative location for
-    //                        donors and acceptors.
-    //                          altLoc==NULL  the highest occupancy
-    //                                        atoms are taken. If all
-    //                                        occupancies are equal
-    //                                        equal then atom with
-    //                                        first altLoc taken
-    //                          altLoc!=NULL  atoms with given altLoc
-    //                                        are taken. If such
-    //                                        altLoc is not found,
-    //                                        the function acts as
-    //                                        if NULL value for altLoc
-    //                                        were given.
-    //     ignoreNegSigOcc    if it is set True, then the function
-    //                        ignores atoms with negative occupancy
-    //                        standard deviation. Such atoms may be
-    //                        hydrogens added by addHydrogen(..)
-    //                        function, or, in general, any atoms added
-    //                        by CCP4SRSAtom::MakeCAtom(..) function.
-    //                        Such added hydrogens are not guaranteed to
-    //                        be in correct place, therefore the
-    //                        function may mistake on some hydrogen
-    //                        bonds if they are not neglected.
-    //
-    //   On output:
-    //     Allocated arrays HBond[0..nHBonds-1] and
-    //     SBridge[0..nSBridges-1]. If no bonds/bridges were found,
-    //     the corresponding array is not allocated and set NULL.
-    //     Application is responsible for deallocation of the arrays,
-    //     when not needed, using statements
-    //       if (HBond)    delete[] HBond;
-    //       if (SBridge)  delete[] SBridge;
-    //     HBond[i].a1, SBridge[i].a1 always refer atom from Res1[],
-    //     and HBond[i].a2, SBridge[i].a2 always refer atom from
-    //     Res2[].
-    //
-    int  CalcHBonds ( PPCResidue Res1, int nres1,
-                      PPCResidue Res2, int nres2,
-                      RPSAtomPair   HBond, int & nHBonds,
-                      RPSAtomPair SBridge, int & nSBridges,
-                      PCFile structFile=NULL, pstr altLoc=NULL,
-                      Boolean ignoreNegSigOcc=False );
-
-  protected:
-    // Geometry parameters for H-bond calculations
-    realtype minDAdist,maxSBdist,maxDAdist,maxHAdist2;
-    realtype maxDHAcos,maxHAAcos,maxDAAcos,maxDDAcos;
+    public:
+      Chem ();
+      ~Chem();
+
+      CCP4SRS_RC getEnergyTypes ( mmdb::PResidue  R,
+                                  mmdb::io::PFile structFile );
+      CCP4SRS_RC getEnergyTypes ( mmdb::PPResidue R, int nRes,
+                                  mmdb::io::PFile structFile );
+      CCP4SRS_RC getEnergyTypes ( mmdb::PChain  chain,
+                                  mmdb::io::PFile structFile );
+      CCP4SRS_RC getEnergyTypes ( mmdb::PModel  model,
+                                  mmdb::io::PFile structFile );
+      CCP4SRS_RC getEnergyTypes ( mmdb::PManager MMDB,
+                                  mmdb::io::PFile structFile );
+
+      CCP4SRS_RC addHydrogens   ( mmdb::PResidue    R,
+                                  mmdb::io::PFile structFile );
+      CCP4SRS_RC addHydrogens   ( mmdb::PChain  chain,
+                                  mmdb::io::PFile structFile );
+      CCP4SRS_RC addHydrogens   ( mmdb::PModel  model,
+                                  mmdb::io::PFile structFile );
+      CCP4SRS_RC addHydrogens   ( mmdb::PManager MMDB,
+                                  mmdb::io::PFile structFile );
+
+
+      //   MakeBonds(..) makes bonds between atoms in MMDB's residue R
+      // from data found in SBase. Residue R must be associated with
+      // coordinate hierarchy. Data is retrieved from SBase on the basis
+      // of residue name only. In case of multiple conformations, if
+      // altLoc:
+      //    NULL  - the highest occupancy atom will be taken
+      //            if all occupancies are equal then atom with
+      //            first altLoc taken
+      //    other - atoms with given altLoc are taken. If such
+      //            altLoc is not found, the function does as if
+      //            NULL value for altLoc is given.
+      //   If selHandles is not NULL, the function also selects atoms
+      // in the residue according to their hydrogen bond attributes.
+      // This is a special option for hydrogen bond calculations
+      //   If ignoreNegSigOcc is set True then the function will ignore
+      // atoms with negative occupancy standard deviation. Such atoms
+      // may be hydrogens added by CSBase0::AddHydrogen(..) function,
+      // in general any atoms added by CSBAtom::MakeCAtom(..) function.
+      // Added hydrogens may be ignored if MakeBonds is used in
+      // CSbase::CalcHBonds(..) function.
+      //   Return:
+      //     SBASE_Ok             success
+      //     SBASE_FileNotFound   non-initiated SBase
+      //     SBASE_StructNotFound the residue's name is not found
+      //                          in SBase
+      //     SBASE_EmptyResidue   residue R does not contain atoms
+      //     SBASE_NoAtomsFound   SBase entry does not contain atoms
+      //     SBASE_BrokenBonds    some bonds could not be set up because
+      //                          of missing atoms in R. This could be
+      //                          a result of residue R named wrongly.
+      CCP4SRS_RC makeBonds ( mmdb::PResidue  R,
+                             mmdb::pstr      altLoc,
+                             mmdb::io::PFile structFile,
+                             PDASelHnds      selHandles,
+                             bool            ignoreNegSigOcc );
+
+      //   CalcHBonds(..) calculates hydrogen bonds and salt bridges
+      // between atoms of residues given in Res1[0..nres1-1] and
+      // Res2[0..nres2-1]. H-bonds are returned in HBond[0..nHBonds-1]
+      // and salt bridges are returned in SBridge[0..nSBridges-1].
+      //
+      //   On input:
+      //     Res1, Res2         must belong to the same MMDB
+      //     HBond, SBridge     should be set NULL, otherwise the
+      //                        function attempts to deallocate them
+      //     nHBonds, nSBridges ignored
+      //     structFile         may be a pointer to open SBase stucture
+      //                        file in order to save on file open
+      //                        operation. If structFile is set NULL,
+      //                        the function will open the SBase
+      //                        structure file by itself
+      //     altLoc             specifies the alternative location for
+      //                        donors and acceptors.
+      //                          altLoc==NULL  the highest occupancy
+      //                                        atoms are taken. If all
+      //                                        occupancies are equal
+      //                                        equal then atom with
+      //                                        first altLoc taken
+      //                          altLoc!=NULL  atoms with given altLoc
+      //                                        are taken. If such
+      //                                        altLoc is not found,
+      //                                        the function acts as
+      //                                        if NULL value for altLoc
+      //                                        were given.
+      //     ignoreNegSigOcc    if it is set True, then the function
+      //                        ignores atoms with negative occupancy
+      //                        standard deviation. Such atoms may be
+      //                        hydrogens added by addHydrogen(..)
+      //                        function, or, in general, any atoms added
+      //                        by CCP4SRSAtom::MakeCAtom(..) function.
+      //                        Such added hydrogens are not guaranteed to
+      //                        be in correct place, therefore the
+      //                        function may mistake on some hydrogen
+      //                        bonds if they are not neglected.
+      //
+      //   On output:
+      //     Allocated arrays HBond[0..nHBonds-1] and
+      //     SBridge[0..nSBridges-1]. If no bonds/bridges were found,
+      //     the corresponding array is not allocated and set NULL.
+      //     Application is responsible for deallocation of the arrays,
+      //     when not needed, using statements
+      //       if (HBond)    delete[] HBond;
+      //       if (SBridge)  delete[] SBridge;
+      //     HBond[i].a1, SBridge[i].a1 always refer atom from Res1[],
+      //     and HBond[i].a2, SBridge[i].a2 always refer atom from
+      //     Res2[].
+      //
+      CCP4SRS_RC CalcHBonds ( mmdb::PPResidue Res1, int nres1,
+                              mmdb::PPResidue Res2, int nres2,
+                              RPAtomPair     HBond, int & nHBonds,
+                              RPAtomPair   SBridge, int & nSBridges,
+                              mmdb::io::PFile structFile=NULL,
+                              mmdb::pstr      altLoc=NULL,
+                              bool ignoreNegSigOcc=false );
+
+    protected:
+      // Geometry parameters for H-bond calculations
+      mmdb::realtype minDAdist,maxSBdist,maxDAdist,maxHAdist2;
+      mmdb::realtype maxDHAcos,maxHAAcos,maxDAAcos,maxDDAcos;
 
-    void init_chem();
+      void init_chem();
 
-  private:
-    int index_alloc;
+    private:
+      int index_alloc;
 
-};
+  };
+
+}  // namespace ccp4srs
 
 #endif // CCP4SRS_CHEM_H
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_chicenter.cpp ccp4srs/ccp4srs/ccp4srs_chicenter.cpp
--- ccp4srs-old/ccp4srs/ccp4srs_chicenter.cpp	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_chicenter.cpp	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_chicenter.cpp, v1.00 2010/03/11 15:28:14 Eugene Exp$
+//  $Id: ccp4srs_chicenter.cpp $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,183 +22,183 @@
 //
 //  =================================================================
 //
-//    11.03.10   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_chicenter  <implementation>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSChiCenter - chiral center class
+//  **** Classes :  ccp4srs::ChiCenter - chiral center class
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010
+//  (C) E. Krissinel 2010-2013
 //
 //  =================================================================
 //
 
-#ifndef  __STRING_H
 #include <string.h>
-#endif
-
 
 #include "ccp4srs_chicenter.h"
 #include "ccp4srs_defs.h"
 
-CCP4SRSChiCenter::CCP4SRSChiCenter()  {
-  chicenter_id[0] = char(0);  // chiral center id
-  atom_center     = -1;       // chiral center atom
-  atom_1          = -1;       // ordinal numbers of atoms
-  atom_2          = -1;       //   that form
-  atom_3          = -1;       //     the center
-  volume_sign     = CCP4SRSChiCenter::noSign;
-}
-
-CCP4SRSChiCenter::~CCP4SRSChiCenter()  {
-}
-
-
-#define  VOLUME_SIGN_POSITIVE  "positiv"
-#define  VOLUME_SIGN_NEGATIVE  "negativ"
-#define  VOLUME_SIGN_BOTH      "both"
-
-char CCP4SRSChiCenter::get_chirality()  {
-  switch (volume_sign)  {
-    default:
-    case noSign   : break;
-    case Positive : return 'R';
-    case Negative : return 'S';
-    case Both     : return 'B';
-  }
-  return 'N';
-}
-
-
-int CCP4SRSChiCenter::readFromCIF ( PCMMCIFLoop mmCIFLoop, int chiNo,
-                             CCP4SRSContainer<CCP4SRSAtom> & atoms )  {
-char S[100];
-int  rc;
-
-  rc = 0;
-
-  mmCIFLoop->CopyString ( chicenter_id,sizeof(ChiCenterID)-1,
-                          MMCIF_TAG_ID,chiNo,rc );
-
-  get_atom_from_cif ( atom_center,mmCIFLoop,MMCIF_TAG_ATOM_ID_CENTRE,
-                      chiNo,atoms,rc );
-  get_atom_from_cif ( atom_1,mmCIFLoop,MMCIF_TAG_ATOM_ID_1,
-                      chiNo,atoms,rc );
-  get_atom_from_cif ( atom_2,mmCIFLoop,MMCIF_TAG_ATOM_ID_2,
-                      chiNo,atoms,rc );
-  get_atom_from_cif ( atom_3,mmCIFLoop,MMCIF_TAG_ATOM_ID_3,
-                      chiNo,atoms,rc );
-
-  S[0] = char(0);
-  mmCIFLoop->CopyString ( S,sizeof(S)-1,MMCIF_TAG_VOLUME_SIGN,
-                          chiNo,rc );
-  LowerCase ( S );
-  if (!strcmp(S,VOLUME_SIGN_POSITIVE))
-    volume_sign = CCP4SRSChiCenter::Positive;
-  else if (!strcmp(S,VOLUME_SIGN_NEGATIVE))
-    volume_sign = CCP4SRSChiCenter::Negative;
-  else if (!strcmp(S,VOLUME_SIGN_BOTH))
-    volume_sign = CCP4SRSChiCenter::Both;
-  else
-    volume_sign = CCP4SRSChiCenter::noSign;
-
-  return rc;
-
-}
-
-
-
-/*
-loop_
-_chem_comp_chir.comp_id
-_chem_comp_chir.id
-_chem_comp_chir.atom_id_centre
-_chem_comp_chir.atom_id_1
-_chem_comp_chir.atom_id_2
-_chem_comp_chir.atom_id_3
-_chem_comp_chir.volume_sign
- ATP      chir_01  C4*    C5*    O4*    C3*       negativ
- ATP      chir_02  C3*    C4*    O3*    C2*       negativ
- ATP      chir_03  C2*    C3*    O2*    C1*       negativ
- ATP      chir_04  C1*    O4*    C2*    N9        positiv
-*/
-
-void CCP4SRSChiCenter::makeCIFTags ( PCMMCIFLoop mmCIFLoop )  {
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_COMP_ID        );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_ID             );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_CENTRE );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_1      );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_2      );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_3      );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_VOLUME_SIGN    );
-}
-
-void CCP4SRSChiCenter::writeToCIF ( PCMMCIFLoop mmCIFLoop, cpstr monID,
-                             CCP4SRSContainer<CCP4SRSAtom> & atoms )  {
-
-  mmCIFLoop->AddString ( monID,False                 );
-  mmCIFLoop->AddString ( chicenter_id,False          );
-
-  add_atom_to_cif      ( mmCIFLoop,atom_center,atoms );
-  add_atom_to_cif      ( mmCIFLoop,atom_1,atoms      );
-  add_atom_to_cif      ( mmCIFLoop,atom_2,atoms      );
-  add_atom_to_cif      ( mmCIFLoop,atom_3,atoms      );
-
-  switch (volume_sign)  {
-    case CCP4SRSChiCenter::Positive :
-      mmCIFLoop->AddString ( VOLUME_SIGN_POSITIVE,False ); break;
-    case CCP4SRSChiCenter::Negative :
-      mmCIFLoop->AddString ( VOLUME_SIGN_NEGATIVE,False ); break;
-    case CCP4SRSChiCenter::Both :
-      mmCIFLoop->AddString ( VOLUME_SIGN_BOTH,False );     break;
-    default :
-      mmCIFLoop->AddNoData ( CIF_NODATA_DOT );
-  }
-
-}
-
-void  CCP4SRSChiCenter::copy ( PCCP4SRSChiCenter chicenter,
-                               ivector anmatch )  {
-  strcpy ( chicenter_id,chicenter->id() );
-  if (anmatch)  {
-    atom_center = anmatch[chicenter->center()];
-    atom_1 = anmatch[chicenter->atom1()];
-    atom_2 = anmatch[chicenter->atom2()];
-    atom_3 = anmatch[chicenter->atom3()];
-  } else  {
-    atom_1 = chicenter->atom1();
-    atom_2 = chicenter->atom2();
-    atom_3 = chicenter->atom3();
-  }
-  volume_sign = chicenter->sign();
-}
-
-void  CCP4SRSChiCenter::write_mem ( PCMemIO memIO, int version )  {
-UNUSED_ARGUMENT(version);
-  memIO->put_line    ( chicenter_id );
-  memIO->put_integer ( atom_center  );
-  memIO->put_integer ( atom_1       );
-  memIO->put_integer ( atom_2       );
-  memIO->put_integer ( atom_3       );
-  memIO->put_ibyte   ( volume_sign  );
-}
-
-Boolean CCP4SRSChiCenter::read_mem ( PCMemIO memIO, int version,
-                                     Boolean * Ok )  {
-UNUSED_ARGUMENT(version);
-Boolean success;
-  if (Ok)  success = *Ok;
-     else  success = True;
-  memIO->get_line    ( chicenter_id,&success );
-  memIO->get_integer ( atom_center ,&success );
-  memIO->get_integer ( atom_1      ,&success );
-  memIO->get_integer ( atom_2      ,&success );
-  memIO->get_integer ( atom_3      ,&success );
-  memIO->get_ibyte   ( volume_sign ,&success );
-  if (Ok)  *Ok = success;
-  return success;
-}
+namespace ccp4srs  {
+
+  ChiCenter::ChiCenter()  {
+    chicenter_id[0] = char(0);  // chiral center id
+    atom_center     = -1;       // chiral center atom
+    atom_1          = -1;       // ordinal numbers of atoms
+    atom_2          = -1;       //   that form
+    atom_3          = -1;       //     the center
+    volume_sign     = ChiCenter::noSign;
+  }
+
+  ChiCenter::~ChiCenter()  {
+  }
+
+
+  #define  VOLUME_SIGN_POSITIVE  "positiv"
+  #define  VOLUME_SIGN_NEGATIVE  "negativ"
+  #define  VOLUME_SIGN_BOTH      "both"
+
+  char ChiCenter::get_chirality()  {
+    switch (volume_sign)  {
+      default:
+      case noSign   : break;
+      case Positive : return 'R';
+      case Negative : return 'S';
+      case Both     : return 'B';
+    }
+    return 'N';
+  }
+
+
+  int ChiCenter::readFromCIF ( mmdb::mmcif::PLoop mmCIFLoop,
+                               int chiNo, Container<Atom> & atoms )  {
+  char S[100];
+  int  rc;
+
+    rc = 0;
+
+    mmCIFLoop->CopyString ( chicenter_id,sizeof(ChiCenterID)-1,
+                            MMCIF_TAG_ID,chiNo,rc );
+
+    get_atom_from_cif ( atom_center,mmCIFLoop,MMCIF_TAG_ATOM_ID_CENTRE,
+                        chiNo,atoms,rc );
+    get_atom_from_cif ( atom_1,mmCIFLoop,MMCIF_TAG_ATOM_ID_1,
+                        chiNo,atoms,rc );
+    get_atom_from_cif ( atom_2,mmCIFLoop,MMCIF_TAG_ATOM_ID_2,
+                        chiNo,atoms,rc );
+    get_atom_from_cif ( atom_3,mmCIFLoop,MMCIF_TAG_ATOM_ID_3,
+                        chiNo,atoms,rc );
+
+    S[0] = char(0);
+    mmCIFLoop->CopyString ( S,sizeof(S)-1,MMCIF_TAG_VOLUME_SIGN,
+                            chiNo,rc );
+    mmdb::LowerCase ( S );
+    if (!strcmp(S,VOLUME_SIGN_POSITIVE))
+      volume_sign = ChiCenter::Positive;
+    else if (!strcmp(S,VOLUME_SIGN_NEGATIVE))
+      volume_sign = ChiCenter::Negative;
+    else if (!strcmp(S,VOLUME_SIGN_BOTH))
+      volume_sign = ChiCenter::Both;
+    else
+      volume_sign = ChiCenter::noSign;
+
+    return rc;
+
+  }
+
+
+
+  /*
+  loop_
+  _chem_comp_chir.comp_id
+  _chem_comp_chir.id
+  _chem_comp_chir.atom_id_centre
+  _chem_comp_chir.atom_id_1
+  _chem_comp_chir.atom_id_2
+  _chem_comp_chir.atom_id_3
+  _chem_comp_chir.volume_sign
+   ATP      chir_01  C4*    C5*    O4*    C3*       negativ
+   ATP      chir_02  C3*    C4*    O3*    C2*       negativ
+   ATP      chir_03  C2*    C3*    O2*    C1*       negativ
+   ATP      chir_04  C1*    O4*    C2*    N9        positiv
+  */
+
+  void ChiCenter::makeCIFTags ( mmdb::mmcif::PLoop mmCIFLoop )  {
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_COMP_ID        );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_ID             );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_CENTRE );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_1      );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_2      );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_3      );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_VOLUME_SIGN    );
+  }
+
+  void ChiCenter::writeToCIF ( mmdb::mmcif::PLoop mmCIFLoop,
+                               mmdb::cpstr monID,
+                               Container<Atom> & atoms )  {
+
+    mmCIFLoop->AddString ( monID,false                 );
+    mmCIFLoop->AddString ( chicenter_id,false          );
+
+    add_atom_to_cif      ( mmCIFLoop,atom_center,atoms );
+    add_atom_to_cif      ( mmCIFLoop,atom_1,atoms      );
+    add_atom_to_cif      ( mmCIFLoop,atom_2,atoms      );
+    add_atom_to_cif      ( mmCIFLoop,atom_3,atoms      );
+
+    switch (volume_sign)  {
+      case ChiCenter::Positive :
+        mmCIFLoop->AddString ( VOLUME_SIGN_POSITIVE,false ); break;
+      case ChiCenter::Negative :
+        mmCIFLoop->AddString ( VOLUME_SIGN_NEGATIVE,false ); break;
+      case ChiCenter::Both :
+        mmCIFLoop->AddString ( VOLUME_SIGN_BOTH,false );     break;
+      default :
+        mmCIFLoop->AddNoData ( mmdb::mmcif::CIF_NODATA_DOT );
+    }
+
+  }
+
+  void  ChiCenter::copy ( PChiCenter chicenter,
+                          mmdb::ivector anmatch )  {
+    strcpy ( chicenter_id,chicenter->id() );
+    if (anmatch)  {
+      atom_center = anmatch[chicenter->center()];
+      atom_1 = anmatch[chicenter->atom1()];
+      atom_2 = anmatch[chicenter->atom2()];
+      atom_3 = anmatch[chicenter->atom3()];
+    } else  {
+      atom_1 = chicenter->atom1();
+      atom_2 = chicenter->atom2();
+      atom_3 = chicenter->atom3();
+    }
+    volume_sign = chicenter->sign();
+  }
+
+  void  ChiCenter::write_mem ( PMemIO memIO, int version )  {
+  UNUSED_ARGUMENT(version);
+    memIO->put_line    ( chicenter_id );
+    memIO->put_integer ( atom_center  );
+    memIO->put_integer ( atom_1       );
+    memIO->put_integer ( atom_2       );
+    memIO->put_integer ( atom_3       );
+    memIO->put_ibyte   ( volume_sign  );
+  }
+
+  bool ChiCenter::read_mem ( PMemIO memIO, int version, bool * Ok )  {
+  UNUSED_ARGUMENT(version);
+  bool success;
+    if (Ok)  success = *Ok;
+       else  success = true;
+    memIO->get_line    ( chicenter_id,&success );
+    memIO->get_integer ( atom_center ,&success );
+    memIO->get_integer ( atom_1      ,&success );
+    memIO->get_integer ( atom_2      ,&success );
+    memIO->get_integer ( atom_3      ,&success );
+    memIO->get_ibyte   ( volume_sign ,&success );
+    if (Ok)  *Ok = success;
+    return success;
+  }
 
+}  // namespace ccp4srs
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_chicenter.h ccp4srs/ccp4srs/ccp4srs_chicenter.h
--- ccp4srs-old/ccp4srs/ccp4srs_chicenter.h	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_chicenter.h	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_chicenter.h, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_chicenter.h $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,16 +22,16 @@
 //
 //  =================================================================
 //
-//    11.03.10   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_chicenter  <interface>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSChiCenter - chiral center class
+//  **** Classes :  ccp4srs::ChiCenter - chiral center class
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010
+//  (C) E. Krissinel 2010-2013
 //
 //  =================================================================
 //
@@ -41,47 +41,50 @@
 
 #include "ccp4srs_atom.h"
 
-DefineClass(CCP4SRSChiCenter)
+namespace ccp4srs  {
 
-typedef char ChiCenterID[20];
+  DefineClass(ChiCenter);
 
-class CCP4SRSChiCenter  {
+  typedef char ChiCenterID[20];
 
-  // Chiral center signs
-  enum  {noSign,Positive,Negative,Both};
+  class ChiCenter  {
 
-  public:
-    CCP4SRSChiCenter();
-    virtual ~CCP4SRSChiCenter();
+    // Chiral center signs
+    enum  {noSign,Positive,Negative,Both};
 
-    inline cpstr    id    () { return chicenter_id; }
-    inline int      center() { return atom_center;  }
-    inline int      atom1 () { return atom_1;       }
-    inline int      atom2 () { return atom_2;       }
-    inline int      atom3 () { return atom_3;       }
-    inline int      sign  () { return volume_sign;  }
+    public:
+      ChiCenter();
+      virtual ~ChiCenter();
 
-    char get_chirality();
+      inline mmdb::cpstr id    () { return chicenter_id; }
+      inline int         center() { return atom_center;  }
+      inline int         atom1 () { return atom_1;       }
+      inline int         atom2 () { return atom_2;       }
+      inline int         atom3 () { return atom_3;       }
+      inline int         sign  () { return volume_sign;  }
 
-    static void makeCIFTags ( PCMMCIFLoop mmCIFLoop );
-    int  readFromCIF ( PCMMCIFLoop mmCIFLoop, int chiNo,
-                       CCP4SRSContainer<CCP4SRSAtom> & atoms );
-    void writeToCIF  ( PCMMCIFLoop mmCIFLoop, cpstr monID,
-                       CCP4SRSContainer<CCP4SRSAtom> & atoms );
+      char get_chirality();
 
-    void    write_mem ( PCMemIO memIO, int version );
-    Boolean read_mem  ( PCMemIO memIO, int version,
-                        Boolean * Ok = NULL );
+      static void makeCIFTags ( mmdb::mmcif::PLoop mmCIFLoop );
+      int  readFromCIF ( mmdb::mmcif::PLoop mmCIFLoop, int chiNo,
+                         Container<Atom> & atoms );
+      void writeToCIF  ( mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID,
+                         Container<Atom> & atoms );
 
-    void copy ( PCCP4SRSChiCenter chicenter, ivector anmatch=NULL );
+      void write_mem ( PMemIO memIO, int version );
+      bool read_mem  ( PMemIO memIO, int version, bool * Ok = NULL );
 
-  protected:
-    ChiCenterID chicenter_id;    //!< chiral center id
-    int         atom_center;     //!< chiral center atom [0,1,...]
-    int         atom_1,atom_2;   //!< ordinal numbers of atoms that
-    int         atom_3;          //!< form the center [0,1,...]
-    int         volume_sign;     //!< chirality
+      void copy ( PChiCenter chicenter, mmdb::ivector anmatch=NULL );
 
-};
+    protected:
+      ChiCenterID chicenter_id;    //!< chiral center id
+      int         atom_center;     //!< chiral center atom [0,1,...]
+      int         atom_1,atom_2;   //!< ordinal numbers of atoms that
+      int         atom_3;          //!< form the center [0,1,...]
+      int         volume_sign;     //!< chirality
+
+  };
+
+}  // namespace ccp4srs
 
 #endif // CCP4SRS_CHICENTER_H
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_container.h ccp4srs/ccp4srs/ccp4srs_container.h
--- ccp4srs-old/ccp4srs/ccp4srs_container.h	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_container.h	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_container.h, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_container.h $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,16 +22,16 @@
 //
 //  =================================================================
 //
-//    29.04.10   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_container  <interface>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSContainer  - template container class
+//  **** Classes :  ccp4srs::Container  - template container class
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010
+//  (C) E. Krissinel 2010-2013
 //
 //  =================================================================
 //
@@ -41,96 +41,100 @@
 
 #include "memio_.h"
 
-template <class T>
+namespace ccp4srs  {
 
-class CCP4SRSContainer  {
+  template <class T>
 
-  protected:
-    int  n_objects;
-    T  **object;
-
-  private:
-    int  n_alloc;
-
-  public:
-
-    CCP4SRSContainer()  {
-      object    = NULL;
-      n_objects = 0;
-      n_alloc   = 0;
-    }
-
-    virtual ~CCP4SRSContainer()  {
-      empty();
-    }
-
-    void empty()  {
-    int i;
-      if (object)  {
-        for (i=0;i<n_alloc;i++)
-          if (object[i])  delete object[i];
-        delete[] object;
-        object = NULL;
-      }
-      n_objects = 0;
-      n_alloc   = 0;
-    }
-
-    inline int numberOf()      { return n_objects;   }
-    inline T*  at ( int pos )  { return object[pos]; }
-
-    int  index ( cpstr id )  {
-    int  i,k;
-      k = -1;
-      if (id)  {
-        for (i=0;(i<n_objects) && (k<0);i++)
-          if (!strcmp(id,object[i]->id()))  k = i;
-      }
-      return k;
-    }
-
-    void add ( T* obj )  {
-    T**  tobject;
-    int  i;
-      if (n_objects>=n_alloc)  {
-        n_alloc = n_objects+10;
-        tobject = new T*[n_alloc];
+  class Container  {
+
+    protected:
+      int  n_objects;
+      T  **object;
+
+    private:
+      int  n_alloc;
+
+    public:
+
+      Container()  {
+        object    = NULL;
+        n_objects = 0;
+        n_alloc   = 0;
+      }
+
+      virtual ~Container()  {
+        empty();
+      }
+
+      void empty()  {
+      int i;
+        if (object)  {
+          for (i=0;i<n_alloc;i++)
+            if (object[i])  delete object[i];
+          delete[] object;
+          object = NULL;
+        }
+        n_objects = 0;
+        n_alloc   = 0;
+      }
+
+      inline int numberOf()      { return n_objects;   }
+      inline T*  at ( int pos )  { return object[pos]; }
+
+      int  index ( mmdb::cpstr id )  {
+      int  i,k;
+        k = -1;
+        if (id)  {
+          for (i=0;(i<n_objects) && (k<0);i++)
+            if (!strcmp(id,object[i]->id()))  k = i;
+        }
+        return k;
+      }
+
+      void add ( T* obj )  {
+      T**  tobject;
+      int  i;
+        if (n_objects>=n_alloc)  {
+          n_alloc = n_objects+10;
+          tobject = new T*[n_alloc];
+          for (i=0;i<n_objects;i++)
+            tobject[i] = object[i];
+          for (i=n_objects;i<n_alloc;i++)
+            tobject[i] = NULL;
+          delete[] object;
+          object = tobject;
+        }
+        object[n_objects++] = obj;
+      }
+
+      void  write_mem ( PMemIO memIO, int version )  {
+      int i;
+        memIO->put_integer ( n_objects );
         for (i=0;i<n_objects;i++)
-          tobject[i] = object[i];
-        for (i=n_objects;i<n_alloc;i++)
-          tobject[i] = NULL;
-        delete[] object;
-        object = tobject;
-      }
-      object[n_objects++] = obj;
-    }
-
-    void  write_mem ( PCMemIO memIO, int version )  {
-    int i;
-      memIO->put_integer ( n_objects );
-      for (i=0;i<n_objects;i++)
-        object[i]->write_mem ( memIO,version );
-    }
-
-    Boolean read_mem ( PCMemIO memIO, int version, Boolean * Ok )  {
-    int     i;
-    Boolean success;
-      empty();
-      if (Ok)  success = *Ok;
-         else  success = True;
-      memIO->get_integer ( n_objects,&success );
-      n_alloc = n_objects;
-      if (n_objects>0)  {
-        object = new T*[n_alloc];
-        for (i=0;i<n_objects;i++)  {
-          object[i] = new T();
-          object[i]->read_mem ( memIO,version,&success );
+          object[i]->write_mem ( memIO,version );
+      }
+
+      bool read_mem ( PMemIO memIO, int version, bool * Ok )  {
+      int  i;
+      bool success;
+        empty();
+        if (Ok)  success = *Ok;
+           else  success = true;
+        memIO->get_integer ( n_objects,&success );
+        n_alloc = n_objects;
+        if (n_objects>0)  {
+          object = new T*[n_alloc];
+          for (i=0;i<n_objects;i++)  {
+            object[i] = new T();
+            object[i]->read_mem ( memIO,version,&success );
+          }
         }
+        if (Ok)  *Ok = success;
+        return success;
       }
-      if (Ok)  *Ok = success;
-      return success;
-    }
 
-};
+  };
+
+}  // namespace ccp4srs
 
 #endif // CCP4SRS_CONTAINER_H
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_defs.h ccp4srs/ccp4srs/ccp4srs_defs.h
--- ccp4srs-old/ccp4srs/ccp4srs_defs.h	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_defs.h	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_defs.h, v 1.00 2010/03/11 15:28:14 eugene Exp $
+//  $Id: ccp4srs_defs.h $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrievak and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010-2011.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,7 +22,7 @@
 //
 //  =================================================================
 //
-//    26.02.13   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
@@ -39,35 +39,8 @@
 #ifndef CCP4SRS_DEFS_H
 #define CCP4SRS_DEFS_H
 
-#define  CCP4SRS_file_version            2
-
-#define  CCP4SRS_noDonors               (4)
-#define  CCP4SRS_noAcceptors            (3)
-#define  CCP4SRS_noHBonds               (2)
-#define  CCP4SRS_Incomplete             (1)
-#define  CCP4SRS_Ok                     (0)
-#define  CCP4SRS_WrongBondType          (-1)
-#define  CCP4SRS_IndexCorrupt           (-2)
-#define  CCP4SRS_FileNotFound           (-3)
-#define  CCP4SRS_EntryNotFound          (-4)
-#define  CCP4SRS_ReadErrors             (-5)
-#define  CCP4SRS_EmptyResidue           (-6)
-#define  CCP4SRS_NoAtomsFound           (-7)
-#define  CCP4SRS_NoBonds                (-8)
-#define  CCP4SRS_EmptyResSet            (-9)
-#define  CCP4SRS_Fail                   (-10)
-#define  CCP4SRS_SVD_Fail               (-11)
-#define  CCP4SRS_noCoordHierarchy       (-12)
-#define  CCP4SRS_BrokenBonds            (-13)
-
-
-#define  srsIndexFile   "index.srs"
-#define  srsGraphFile   "graph.srs"
-#define  srsStructFile  "struct.srs"
-
-
-//  special atom ids
-#define CCP4SRSAtomID_NA             (-10000)
+// THIS FILE SHOULD BE NEVER UNCLUDED IN HEADERS. USE CCP4SRS_TYPES.H
+// INSTEAD
 
 //  mmCIF tags
 #define MMCIF_COMP                   "comp_"
@@ -129,6 +102,11 @@
 #define MMCIF_TAG_PLANE_ID               "plane_id"
 #define MMCIF_TAG_DIST_ESD               "dist_esd"
 
+#define MMCIF_LOOP_CHEM_COMP_DESCRIPTOR  "_pdbx_chem_comp_descriptor"
+#define MMCIF_TAG_PROGRAM                "program"
+#define MMCIF_TAG_PROGRAM_VERSION        "program_version"
+#define MMCIF_TAG_DESCRIPTOR             "descriptor"
+
 
 //   Entry types
 /*
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_entry.cpp ccp4srs/ccp4srs/ccp4srs_entry.cpp
--- ccp4srs-old/ccp4srs/ccp4srs_entry.cpp	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_entry.cpp	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_entry.cpp, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_entry.cpp $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,16 +22,16 @@
 //
 //  =================================================================
 //
-//    11.03.10   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_entry  <implementation>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSEntry  - base class for all SRS entries
+//  **** Classes :  ccp4srs::Entry  - base class for all SRS entries
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010
+//  (C) E. Krissinel 2010-2013
 //
 //  =================================================================
 //
@@ -39,56 +39,60 @@
 #include "ccp4srs_entry.h"
 #include "ccp4srs_defs.h"
 
-CCP4SRSEntry::CCP4SRSEntry()  {}
+namespace ccp4srs  {
 
-CCP4SRSEntry::~CCP4SRSEntry() {}
+  Entry::Entry()  {}
 
-int CCP4SRSEntry::write ( RCFile f, int version, PCMemIO memIO ) {
-PCMemIO mem_io;
-int     rc;
+  Entry::~Entry() {}
 
-  if (memIO)  mem_io = memIO;
-        else  mem_io = new CMemIO();
+  int Entry::write ( mmdb::io::RFile f, int version, PMemIO memIO ) {
+  PMemIO mem_io;
+  int    rc;
 
-  write_mem ( mem_io,version );
-  rc = mem_io->write ( f );
+    if (memIO)  mem_io = memIO;
+          else  mem_io = new MemIO();
 
-  if (!memIO)
-    delete mem_io;
+    write_mem ( mem_io,version );
+    rc = mem_io->write ( f );
 
-  return rc;
+    if (!memIO)
+      delete mem_io;
 
-}
+    return rc;
 
-int CCP4SRSEntry::read ( RCFile f, int version, PCMemIO memIO )  {
-PCMemIO mem_io;
-int     rc;
+  }
+
+  int Entry::read ( mmdb::io::RFile f, int version, PMemIO memIO )  {
+  PMemIO mem_io;
+  int    rc;
+
+    if (memIO)  mem_io = memIO;
+          else  mem_io = new MemIO();
+
+    rc = mem_io->read ( f );
+    if (rc==MemIO::Ok)  {
+      if (!read_mem(mem_io,version))
+        rc = MemIO::MemReadError;
+    }
+
+    if (!memIO)
+      delete mem_io;
 
-  if (memIO)  mem_io = memIO;
-        else  mem_io = new CMemIO();
+    return rc;
 
-  rc = mem_io->read ( f );
-  if (rc==CMemIO::Ok)  {
-    if (!read_mem(mem_io,version))
-      rc = CMemIO::MemReadError;
   }
 
-  if (!memIO)
-    delete mem_io;
+  void Entry::write_mem ( PMemIO memIO, int version )  {
+  UNUSED_ARGUMENT(memIO);
+  UNUSED_ARGUMENT(version);
+  }
 
-  return rc;
+  bool Entry::read_mem ( PMemIO memIO, int version, bool * Ok )  {
+  UNUSED_ARGUMENT(memIO);
+  UNUSED_ARGUMENT(version);
+  UNUSED_ARGUMENT(Ok);
+    return true;
+  }
 
-}
+}  // namespace ccp4srs
 
-void CCP4SRSEntry::write_mem ( PCMemIO memIO, int version )  {
-UNUSED_ARGUMENT(memIO);
-UNUSED_ARGUMENT(version);
-}
-
-Boolean CCP4SRSEntry::read_mem ( PCMemIO memIO, int version,
-                                 Boolean * Ok )  {
-UNUSED_ARGUMENT(memIO);
-UNUSED_ARGUMENT(version);
-UNUSED_ARGUMENT(Ok);
-  return True;
-}
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_entry.h ccp4srs/ccp4srs/ccp4srs_entry.h
--- ccp4srs-old/ccp4srs/ccp4srs_entry.h	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_entry.h	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_entry.h, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_entry.h $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,16 +22,16 @@
 //
 //  =================================================================
 //
-//    11.03.10   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_entry  <interface>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSEntry  - base class for all SRS entries
+//  **** Classes :  ccp4srs::Entry  - base class for all SRS entries
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010
+//  (C) E. Krissinel 2010-2013
 //
 //  =================================================================
 //
@@ -41,29 +41,34 @@
 
 #include "memio_.h"
 
-DefineClass(CCP4SRSEntry)
+namespace ccp4srs  {
 
-class CCP4SRSEntry  {
+  DefineClass(Entry);
 
-  public:
+  class Entry  {
 
-    // entry types
-    enum {None,Monomer,Link};
+    public:
 
-    CCP4SRSEntry();
-    virtual ~CCP4SRSEntry();
+      // entry types
+      enum {None,Monomer,Link};
 
-    virtual int type()  { return CCP4SRSEntry::None; }
+      Entry();
+      virtual ~Entry();
 
-    int write ( RCFile f, int version, PCMemIO memIO=NULL );
-    int read  ( RCFile f, int version, PCMemIO memIO=NULL );
+      virtual int type()  { return Entry::None; }
 
-  protected:
+      int write ( mmdb::io::RFile f, int version, PMemIO memIO=NULL );
+      int read  ( mmdb::io::RFile f, int version, PMemIO memIO=NULL );
 
-    virtual void    write_mem ( PCMemIO memIO, int version );
-    virtual Boolean read_mem  ( PCMemIO memIO, int version,
-                                Boolean * Ok = NULL );
+    protected:
+
+      virtual void write_mem ( PMemIO memIO, int version );
+      virtual bool read_mem  ( PMemIO memIO, int version,
+                               bool * Ok = NULL );
+
+  };
+
+}  // namespace ccp4srs
 
-};
 
 #endif // CCP4SRS_ENTRY_H
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_index.cpp ccp4srs/ccp4srs/ccp4srs_index.cpp
--- ccp4srs-old/ccp4srs/ccp4srs_index.cpp	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_index.cpp	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_index.cpp, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_index.cpp $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,184 +22,185 @@
 //
 //  =================================================================
 //
-//    26.02.13   <--  Date of Last Modification.
+//    03.02.14   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_index  <implementation>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSIndex - SRS data index class
+//  **** Classes :  ccp4srs::Index - SRS data index class
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010-2013
+//  (C) E. Krissinel 2010-2014
 //
 //  =================================================================
 //
 
 #include <string.h>
 
-#include "mmdb/mmdb_tables.h"
-
+#include "mmdb2/mmdb_tables.h"
 #include "ccp4srs_index.h"
 
-CCP4SRSIndex::CCP4SRSIndex()  {
-  CCP4SRSIndexInit();
-}
-
-CCP4SRSIndex::~CCP4SRSIndex() {
-  if (Comp1)  delete[] Comp1;
-  if (Comp2)  delete[] Comp2;
-}
-
-void CCP4SRSIndex::CCP4SRSIndexInit ()  {
-  entryID[0] = char(0);
-  nAtoms     = 0;
-  nNonHAtoms = 0;
-  nBonds     = 0;
-  fGraphPos  = -1;
-  fStructPos = -1;
-  Comp1      = NULL;
-  Comp2      = NULL;
-}
-
-int CCP4SRSIndex::MakeCompositions ( PCCP4SRSMonomer mon )  {
-//    MakeCompositions(..) makes the compositions strings for the
-//  given structure.
-//    A composition string consists of records E(N), where E stands
-//  for chemical element name, and N - for the number of atoms of this
-//  element in the structure. The records E(N) follow in alphabetical
-//  order of E without spaces and contain no spaces, records with N=0
-//  are excluded.
-//    Comp2 differs of Comp1 only if there are leaving atoms and
-//  represents the composition with leaving atoms taken into account.
-//  If there is no leaving atoms, Comp2==Comp1.
-//    The function returns the number of leaving atoms in the.
-//  structure.
-char    Cmp1[1000];
-char    Cmp2[1000];
-char    N[50];
-ivector elem;
-int     i,k,x,l,nl;
-short   n0,n;
-
-  nAtoms = mon->n_atoms();
-  nBonds = mon->n_bonds();
-
-  strcpy ( Cmp1,"" );
-  strcpy ( Cmp2,"" );
-
-  GetVectorMemory ( elem,nAtoms,0 );
-  nNonHAtoms = 0;
-  for (i=0;i<nAtoms;i++)  {
-    elem[i] = getElementNo ( mon->atom(i)->element() );
-    if (elem[i]>1)  nNonHAtoms++;
-  }
-
-  n0 = -1;
-  n  = 0;
-  nl = 0;
-  for (i=0;(i<nAtoms) && (n<nElementNames);i++)  {
-    n = 10000;
-    for (k=0;k<nAtoms;k++)
-      if ((elem[k]>n0) && (elem[k]<n))  n = elem[k];
-    if (n<nElementNames)   {
-      x = 0;
-      l = 0;
-      for (k=0;k<nAtoms;k++)
-        if (elem[k]==n)  {
-          x++;
-          if (mon->atom(k)->leaving()=='Y')  l++;
-        }
-      nl += l;
-      sprintf ( N,"%s(%i)",ElementName[n-1],x );
-      strcat  ( Cmp1,N );
-      sprintf ( N,"%s(%i)",ElementName[n-1],x-l );
-      strcat  ( Cmp2,N );
-      n0 = n;
-    }
+namespace ccp4srs  {
+
+  Index::Index()  {
+    IndexInit();
   }
 
-  FreeVectorMemory ( elem,0 );
+  Index::~Index() {
+    if (Comp1)  delete[] Comp1;
+    if (Comp2)  delete[] Comp2;
+  }
+
+  void Index::IndexInit ()  {
+    entryID[0] = char(0);
+    nAtoms     = 0;
+    nNonHAtoms = 0;
+    nBonds     = 0;
+    fGraphPos  = -1;
+    fStructPos = -1;
+    Comp1      = NULL;
+    Comp2      = NULL;
+  }
 
-  CreateCopy ( Comp1,Cmp1 );
-  CreateCopy ( Comp2,Cmp2 );
+  int Index::MakeCompositions ( PMonomer mon )  {
+  //    MakeCompositions(..) makes the compositions strings for the
+  //  given structure.
+  //    A composition string consists of records E(N), where E stands
+  //  for chemical element name, and N - for the number of atoms of this
+  //  element in the structure. The records E(N) follow in alphabetical
+  //  order of E without spaces and contain no spaces, records with N=0
+  //  are excluded.
+  //    Comp2 differs of Comp1 only if there are leaving atoms and
+  //  represents the composition with leaving atoms taken into account.
+  //  If there is no leaving atoms, Comp2==Comp1.
+  //    The function returns the number of leaving atoms in the.
+  //  structure.
+  char          Cmp1[1000];
+  char          Cmp2[1000];
+  char          N[50];
+  mmdb::ivector elem;
+  int           i,k,x,l,nl;
+  short         n0,n;
+
+    nAtoms = mon->n_atoms();
+    nBonds = mon->n_bonds();
+
+    strcpy ( Cmp1,"" );
+    strcpy ( Cmp2,"" );
+
+    mmdb::GetVectorMemory ( elem,nAtoms,0 );
+    nNonHAtoms = 0;
+    for (i=0;i<nAtoms;i++)  {
+      elem[i] = mmdb::getElementNo ( mon->atom(i)->element() );
+      if (elem[i]>1)  nNonHAtoms++;
+    }
 
-  return nl;
+    n0 = -1;
+    n  = 0;
+    nl = 0;
+    for (i=0;(i<nAtoms) && (n<mmdb::nElementNames);i++)  {
+      n = 10000;
+      for (k=0;k<nAtoms;k++)
+        if ((elem[k]>n0) && (elem[k]<n))  n = elem[k];
+      if (n<mmdb::nElementNames)   {
+        x = 0;
+        l = 0;
+        for (k=0;k<nAtoms;k++)
+          if (elem[k]==n)  {
+            x++;
+            if (mon->atom(k)->leaving()=='Y')  l++;
+          }
+        nl += l;
+        sprintf ( N,"%s(%i)",mmdb::ElementName[n-1],x );
+        strcat  ( Cmp1,N );
+        sprintf ( N,"%s(%i)",mmdb::ElementName[n-1],x-l );
+        strcat  ( Cmp2,N );
+        n0 = n;
+      }
+    }
 
-}
+    mmdb::FreeVectorMemory ( elem,0 );
 
+    mmdb::CreateCopy ( Comp1,Cmp1 );
+    mmdb::CreateCopy ( Comp2,Cmp2 );
 
+    return nl;
 
-int CCP4SRSIndex::write ( RCFile f, int version, PCMemIO memIO ) {
-PCMemIO mem_io;
-int     rc;
+  }
 
-  if (memIO)  mem_io = memIO;
-        else  mem_io = new CMemIO();
 
-  write_mem ( mem_io,version );
-  rc = mem_io->write ( f );
 
-  if (!memIO)
-    delete mem_io;
+  int Index::write ( mmdb::io::RFile f, int version, PMemIO memIO ) {
+  PMemIO mem_io;
+  int    rc;
 
-  return rc;
+    if (memIO)  mem_io = memIO;
+          else  mem_io = new MemIO();
 
-}
+    write_mem ( mem_io,version );
+    rc = mem_io->write ( f );
 
-int CCP4SRSIndex::read ( RCFile f, int version, PCMemIO memIO )  {
-PCMemIO mem_io;
-int     rc;
+    if (!memIO)
+      delete mem_io;
 
-  if (memIO)  mem_io = memIO;
-        else  mem_io = new CMemIO();
+    return rc;
 
-  rc = mem_io->read ( f );
-  if (rc==CMemIO::Ok)  {
-    if (!read_mem(mem_io,version))
-      rc = CMemIO::MemReadError;
   }
 
-  if (!memIO)
-    delete mem_io;
-
-  return rc;
+  int Index::read ( mmdb::io::RFile f, int version, PMemIO memIO )  {
+  PMemIO mem_io;
+  int    rc;
+
+    if (memIO)  mem_io = memIO;
+          else  mem_io = new MemIO();
+
+    rc = mem_io->read ( f );
+    if (rc==MemIO::Ok)  {
+      if (!read_mem(mem_io,version))
+        rc = MemIO::MemReadError;
+    }
 
-}
+    if (!memIO)
+      delete mem_io;
 
-void CCP4SRSIndex::write_mem ( PCMemIO memIO, int version )  {
-UNUSED_ARGUMENT(version);
+    return rc;
 
-  memIO->put_line    ( entryID    );
-  memIO->put_integer ( nAtoms     );
-  memIO->put_integer ( nNonHAtoms );
-  memIO->put_integer ( nBonds     );
-  memIO->put_long    ( fGraphPos  );
-  memIO->put_long    ( fStructPos );
-  memIO->put_string  ( Comp1      );
-  memIO->put_string  ( Comp2      );
+  }
 
-}
+  void Index::write_mem ( PMemIO memIO, int version )  {
+  UNUSED_ARGUMENT(version);
 
-Boolean CCP4SRSIndex::read_mem ( PCMemIO memIO, int version,
-                                 Boolean * Ok )  {
-UNUSED_ARGUMENT(version);
-Boolean success;
+    memIO->put_line    ( entryID    );
+    memIO->put_integer ( nAtoms     );
+    memIO->put_integer ( nNonHAtoms );
+    memIO->put_integer ( nBonds     );
+    memIO->put_long    ( fGraphPos  );
+    memIO->put_long    ( fStructPos );
+    memIO->put_string  ( Comp1      );
+    memIO->put_string  ( Comp2      );
 
-  if (Ok)  success = *Ok;
-     else  success = True;
+  }
 
-  memIO->get_line    ( entryID   ,&success );
-  memIO->get_integer ( nAtoms    ,&success );
-  memIO->get_integer ( nNonHAtoms,&success );
-  memIO->get_integer ( nBonds    ,&success );
-  memIO->get_long    ( fGraphPos ,&success );
-  memIO->get_long    ( fStructPos,&success );
-  memIO->get_string  ( Comp1     ,&success );
-  memIO->get_string  ( Comp2     ,&success );
+  bool Index::read_mem ( PMemIO memIO, int version, bool * Ok )  {
+  UNUSED_ARGUMENT(version);
+  bool success;
+
+    if (Ok)  success = *Ok;
+       else  success = true;
+
+    memIO->get_line    ( entryID   ,&success );
+    memIO->get_integer ( nAtoms    ,&success );
+    memIO->get_integer ( nNonHAtoms,&success );
+    memIO->get_integer ( nBonds    ,&success );
+    memIO->get_long    ( fGraphPos ,&success );
+    memIO->get_long    ( fStructPos,&success );
+    memIO->get_string  ( Comp1     ,&success );
+    memIO->get_string  ( Comp2     ,&success );
 
-  if (Ok) *Ok = success;
-  return success;
+    if (Ok) *Ok = success;
+    return success;
 
-}
+  }
 
+}  // namespace ccp4srs
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_index.h ccp4srs/ccp4srs/ccp4srs_index.h
--- ccp4srs-old/ccp4srs/ccp4srs_index.h	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_index.h	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_index.h, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_index.h $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,13 +22,13 @@
 //
 //  =================================================================
 //
-//    26.02.13   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_index  <interface>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSIndex - SRS data index class
+//  **** Classes :  ccp4srs::Index - SRS data index class
 //       ~~~~~~~~~
 //
 //  (C) E. Krissinel 2010-2013
@@ -41,39 +41,41 @@
 
 #include "ccp4srs_monomer.h"
 
-#include "mmdb/mmdb_defs.h"
+namespace ccp4srs  {
 
-DefineClass(CCP4SRSIndex)
+  DefineClass(Index);
 
-class CCP4SRSIndex  {
+  class Index  {
 
-  public :
-    ResName  entryID;    //!< monomer or link ID
-    int      nAtoms;     //!< number of atoms in the entry
-    int      nNonHAtoms; //!< number of non-hydrogen atoms in the entry
-    int      nBonds;     //!< number of bonds in the entry
-    long     fGraphPos;  //!< file offset for CGraph
-    long     fStructPos; //!< file offset for CCP4SRSMonomer
-    pstr     Comp1;      //!< composition string
-    pstr     Comp2;      //!< composition string with leaving atom
+    public :
+      mmdb::ResName entryID;    //!< monomer or link ID
+      int           nAtoms;     //!< number of atoms in the entry
+      int           nNonHAtoms; //!< number of non-hydrogen atoms in the entry
+      int           nBonds;     //!< number of bonds in the entry
+      long          fGraphPos;  //!< file offset for CGraph
+      long          fStructPos; //!< file offset for CCP4SRSMonomer
+      mmdb::pstr    Comp1;      //!< composition string
+      mmdb::pstr    Comp2;      //!< composition string with leaving atom
 
-    CCP4SRSIndex ();
-    virtual ~CCP4SRSIndex();
+      Index ();
+      virtual ~Index();
 
-    int   MakeCompositions ( PCCP4SRSMonomer monomer );
+      int   MakeCompositions ( PMonomer monomer );
 
-    int write ( RCFile f, int version, PCMemIO memIO=NULL );
-    int read  ( RCFile f, int version, PCMemIO memIO=NULL );
+      int write ( mmdb::io::RFile f, int version, PMemIO memIO=NULL );
+      int read  ( mmdb::io::RFile f, int version, PMemIO memIO=NULL );
 
-  protected:
+    protected:
 
-    void  CCP4SRSIndexInit();
+      void  IndexInit();
 
-    virtual void    write_mem ( PCMemIO memIO, int version );
-    virtual Boolean read_mem  ( PCMemIO memIO, int version,
-                                Boolean * Ok = NULL );
+      virtual void write_mem ( PMemIO memIO, int version );
+      virtual bool read_mem  ( PMemIO memIO, int version,
+                               bool * Ok = NULL );
 
-};
+  };
+
+}  // namespace ccp4srs
 
 
 #endif // CCP4SRS_INDEX_H
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_manager.cpp ccp4srs/ccp4srs/ccp4srs_manager.cpp
--- ccp4srs-old/ccp4srs/ccp4srs_manager.cpp	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_manager.cpp	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_manager.cpp, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_manager.cpp $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,13 +22,13 @@
 //
 //  =================================================================
 //
-//    26.02.13   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_manager  <implementation>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSManager - SRS general manager class
+//  **** Classes :  ccp4srs::Manager - SRS general manager class
 //       ~~~~~~~~~
 //
 //  (C) E. Krissinel 2010-2013
@@ -36,12 +36,15 @@
 //  =================================================================
 //
 
-#ifndef  __STRING_H
 #include <string.h>
-#endif
 
 #include "ccp4srs_manager.h"
 
-CCP4SRSManager::CCP4SRSManager() : CCP4SRSChem()  {}
+namespace ccp4srs  {
+
+  Manager::Manager() : Chem()  {}
+
+  Manager::~Manager()  {}
+
+}  // namespace ccp4srs
 
-CCP4SRSManager::~CCP4SRSManager()  {}
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_manager.h ccp4srs/ccp4srs/ccp4srs_manager.h
--- ccp4srs-old/ccp4srs/ccp4srs_manager.h	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_manager.h	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_manager.h, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_manager.h $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,13 +22,13 @@
 //
 //  =================================================================
 //
-//    26.02.13   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_manager  <interface>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSManager - SRS general manager class
+//  **** Classes :  ccp4srs::Manager - SRS general manager class
 //       ~~~~~~~~~
 //
 //  (C) E. Krissinel 2010-2013
@@ -41,17 +41,20 @@
 
 #include "ccp4srs_chem.h"
 
+namespace ccp4srs  {
 
-// ==================================================================
+  // ==================================================================
 
-DefineClass(CCP4SRSManager);
+  DefineClass(Manager);
 
-class CCP4SRSManager : public CCP4SRSChem {
+  class Manager : public Chem {
 
-  public:
-    CCP4SRSManager ();
-    ~CCP4SRSManager();
+    public:
+      Manager ();
+      ~Manager();
 
-};
+  };
+
+}  // namespace ccp4srs
 
 #endif // CCP4SRS_MANAGER_H
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_monomer.cpp ccp4srs/ccp4srs/ccp4srs_monomer.cpp
--- ccp4srs-old/ccp4srs/ccp4srs_monomer.cpp	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_monomer.cpp	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_monomer.h, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_monomer.cpp $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010-2011.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,674 +22,587 @@
 //
 //  =================================================================
 //
-//    17.04.12   <--  Date of Last Modification.
+//    03.02.14   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
-//  **** Module  :  ccp4srs_monomer  <interface>
+//  **** Module  :  ccp4srs_monomer  <implementation>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSMonomer  - monomer structure
+//  **** Classes :  ccp4srs::Monomer  - monomer structure
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010-2012
+//  (C) E. Krissinel 2010-2014
 //
 //  =================================================================
 //
 
-#ifndef  __STRING_H
 #include <string.h>
-#endif
 
 #include "ccp4srs_monomer.h"
 #include "ccp4srs_defs.h"
 
-#include "mmdb/linalg_.h"
-#include "mmdb/mmdb_tables.h"
+#include "mmdb2/mmdb_math_linalg.h"
+#include "mmdb2/mmdb_tables.h"
 
+namespace ccp4srs  {
 
-CCP4SRSMonomer::CCP4SRSMonomer() : CCP4SRSEntry()  {
-  Init();
-}
-
-CCP4SRSMonomer::~CCP4SRSMonomer()  {
-  reset();
-}
-
-void CCP4SRSMonomer::Init()  {
-  monID   [0] = char(0);
-  oldMonID[0] = char(0);
-  monName     = NULL;
-  monType     = NULL;
-  monFormula  = NULL;
-}
-
-void CCP4SRSMonomer::reset()  {
-
-  atoms      .empty();
-  bonds      .empty();
-  angles     .empty();
-  torsions   .empty();
-  chicenters .empty();
-  planes     .empty();
-  struct_tree.empty();
-
-  if (monName)     delete[] monName;
-  if (monType)     delete[] monType;
-  if (monFormula)  delete[] monFormula;
-
-  Init();
-
-}
-
-void CCP4SRSMonomer::setOldID ( cpstr oldID )  {
-  strcpy ( oldMonID,oldID );
-}
-
-cpstr  CCP4SRSMonomer::chem_name()  {
-  if (monName)  return monName;
-  return "";
-}
-
-cpstr  CCP4SRSMonomer::chem_type()  {
-  if (monType)  return monType;
-  return "";
-}
-
-cpstr  CCP4SRSMonomer::chem_formula()  {
-  if (monFormula)  return monFormula;
-  return "";
-}
-
-void CCP4SRSMonomer::getLeavingAtoms ( int & nLeavingAtoms,
-                                       ivector & leavingAtom,
-                                       ivector & bondedAtom )  {
-//  should be called after all atoms and bonds are set up
-int i,j;
-
-  FreeVectorMemory ( leavingAtom,0 );
-  FreeVectorMemory ( bondedAtom ,0 );
-
-  nLeavingAtoms = 0;
-  for (i=0;i<atoms.numberOf();i++)
-    if (atom(i)->isLeaving())
-      nLeavingAtoms++;
-
-  if (nLeavingAtoms>0)  {
-    GetVectorMemory ( leavingAtom,nLeavingAtoms,0 );
-    GetVectorMemory ( bondedAtom ,nLeavingAtoms,0 );
-    j = 0;
-    for (i=0;i<atoms.numberOf();i++)
-      if (atom(i)->isLeaving())  {
-        leavingAtom[j] =  i;
-        bondedAtom [j] = -1;
-        j++;
-      }
-    for (i=0;i<nLeavingAtoms;i++)
-      for (j=0;j<bonds.numberOf();j++)  {
-        if ((leavingAtom[i]==bond(j)->atom1()) &&
-            (strcmp(atom(bond(j)->atom2())->element(),"H")))
-          bondedAtom[i] = bond(j)->atom2();
-        else if ((leavingAtom[i]==bond(j)->atom2()) &&
-            (strcmp(atom(bond(j)->atom1())->element(),"H")))
-          bondedAtom[i] = bond(j)->atom1();
-      }
+  Monomer::Monomer() : Entry()  {
+    Init();
   }
 
-}
-
-
-int  superpose_atoms ( mat44 & T, PPCCP4SRSAtom A1, PPCAtom A2,
-                       int nAtoms,
-                       rmatrix & A, rmatrix & U, rmatrix & V,
-                       rvector & W, rvector & RV1 )  {
-//   Given two sets of atoms, A1 and A2, superpose_atoms(...)
-// calculates the rotational-translational matrix T such that
-// |T*A1 - A2| is minimal in least-square terms. The transfomation
-// superposes exactly the atoms A1[0] and A2[0].
-realtype det,B;
-vect3    vc1,vc2;
-int      i,j,k;
+  Monomer::~Monomer()  {
+    reset();
+  }
 
-  //  1.  Calculate the correlation matrix. The rotation will be
-  //      done around
+  void Monomer::Init()  {
+    monID   [0] = char(0);
+    oldMonID[0] = char(0);
+    monName     = NULL;
+    monType     = NULL;
+    monFormula  = NULL;
+  }
 
-  for (i=1;i<=3;i++)
-    for (j=1;j<=3;j++)
-      A[i][j] = 0.0;
+  void Monomer::reset()  {
 
-  for (k=1;k<nAtoms;k++)  {
-    vc1[0] = A1[k]->x() - A1[0]->x();
-    vc1[1] = A1[k]->y() - A1[0]->y();
-    vc1[2] = A1[k]->z() - A1[0]->z();
-    vc2[0] = A2[k]->x - A2[0]->x;
-    vc2[1] = A2[k]->y - A2[0]->y;
-    vc2[2] = A2[k]->z - A2[0]->z;
-    for (i=1;i<=3;i++)
-      for (j=1;j<=3;j++)
-        A[i][j] += vc1[j-1]*vc2[i-1];
-  }
+    atoms      .empty();
+    bonds      .empty();
+    angles     .empty();
+    torsions   .empty();
+    chicenters .empty();
+    planes     .empty();
+    struct_tree.empty();
 
-  //  2. Calculate transformation matrix (to be applied to A1)
+    if (monName)     delete[] monName;
+    if (monType)     delete[] monType;
+    if (monFormula)  delete[] monFormula;
 
-  det = A[1][1]*A[2][2]*A[3][3] +
-        A[1][2]*A[2][3]*A[3][1] +
-        A[2][1]*A[3][2]*A[1][3] -
-        A[1][3]*A[2][2]*A[3][1] -
-        A[1][1]*A[2][3]*A[3][2] -
-        A[3][3]*A[1][2]*A[2][1];
+    Init();
 
-  //  2.1 SV-decompose the correlation matrix
+  }
 
-  SVD ( 3,3,3,A,U,V,W,RV1,True,True,i );
+  void Monomer::setOldID ( mmdb::cpstr oldID )  {
+    strcpy ( oldMonID,oldID );
+  }
 
-  if (i!=0)  return CCP4SRS_SVD_Fail;
+  mmdb::cpstr  Monomer::chem_name()  {
+    if (monName)  return monName;
+    return "";
+  }
 
-  //  2.2 Check for parasite inversion and fix it if found
+  mmdb::cpstr  Monomer::chem_type()  {
+    if (monType)  return monType;
+    return "";
+  }
 
-  if (det<=0.0)  {
-    k = 0;
-    B = MaxReal;
-    for (j=1;j<=3;j++)
-      if (W[j]<B)  {
-        B = W[j];
-        k = j;
-      }
-    for (j=1;j<=3;j++)
-      V[j][k] = -V[j][k];
+  mmdb::cpstr  Monomer::chem_formula()  {
+    if (monFormula)  return monFormula;
+    return "";
   }
 
-  //  2.3 Calculate rotational part of T
+  void Monomer::getLeavingAtoms ( int & nLeavingAtoms,
+                                         mmdb::ivector & leavingAtom,
+                                         mmdb::ivector & bondedAtom )  {
+  //  should be called after all atoms and bonds are set up
+  int i,j;
 
-  for (j=1;j<=3;j++)
-    for (k=1;k<=3;k++)  {
-      B = 0.0;
-      for (i=1;i<=3;i++)
-        B += U[j][i]*V[k][i];
-      T[j-1][k-1] = B;
-    }
+    mmdb::FreeVectorMemory ( leavingAtom,0 );
+    mmdb::FreeVectorMemory ( bondedAtom ,0 );
 
-  //  2.4 Add translational part to T
+    nLeavingAtoms = 0;
+    for (i=0;i<atoms.numberOf();i++)
+      if (atom(i)->isLeaving())
+        nLeavingAtoms++;
 
-  T[0][3] = A2[0]->x - T[0][0]*A1[0]->x() - T[0][1]*A1[0]->y() -
-                       T[0][2]*A1[0]->z();
-  T[1][3] = A2[0]->y - T[1][0]*A1[0]->x() - T[1][1]*A1[0]->y() -
-                       T[1][2]*A1[0]->z();
-  T[2][3] = A2[0]->z - T[2][0]*A1[0]->x() - T[2][1]*A1[0]->y() -
-                       T[2][2]*A1[0]->z();
-
-  return CCP4SRS_Ok;
-
-}
-
-int CCP4SRSMonomer::atom_no ( cpstr aname )  {
-// returns number of atom with given name [0...], or -1 if atom
-// is not found
-int i,n;
-
-  n = -1;
-  for (i=0;(i<atoms.numberOf()) && (n<0);i++)
-    if (!strcmp(atoms.at(i)->name(),aname))
-      n = i;
-
-  return n;
-
-}
-
-int CCP4SRSMonomer::get_bound ( int atomNo, cpstr elem, int serNo ) {
-// returns number of atom with chemical element 'elem', bound to
-// atom number 'atomNo' [0,1,..]. serNo==0 returns 1st atom found,
-// serNo==1 returns second atom and so on. If atom not found, -1 is
-// returned.
-int i,j,n, atm1,atm2;
-
-  n = -1;
-  j = 0;
-  for (i=0;(i<bonds.numberOf()) && (n<0);i++)  {
-    atm2 = bonds.at(i)->atom2();
-    if (atm2==atomNo)  {
-      atm1 = atm2;
-      atm2 = bonds.at(i)->atom1();
-    } else
-      atm1 = bonds.at(i)->atom1();
-    if (atm1==atomNo)  {
-      if (!strcmp(atoms.at(atm2)->element(),elem))  {
-        if (j==serNo)  n = atm2;
-                 else  j++;
-      }
+    if (nLeavingAtoms>0)  {
+      mmdb::GetVectorMemory ( leavingAtom,nLeavingAtoms,0 );
+      mmdb::GetVectorMemory ( bondedAtom ,nLeavingAtoms,0 );
+      j = 0;
+      for (i=0;i<atoms.numberOf();i++)
+        if (atom(i)->isLeaving())  {
+          leavingAtom[j] =  i;
+          bondedAtom [j] = -1;
+          j++;
+        }
+      for (i=0;i<nLeavingAtoms;i++)
+        for (j=0;j<bonds.numberOf();j++)  {
+          if ((leavingAtom[i]==bond(j)->atom1()) &&
+              (strcmp(atom(bond(j)->atom2())->element(),"H")))
+            bondedAtom[i] = bond(j)->atom2();
+          else if ((leavingAtom[i]==bond(j)->atom2()) &&
+              (strcmp(atom(bond(j)->atom1())->element(),"H")))
+            bondedAtom[i] = bond(j)->atom1();
+        }
     }
+
   }
 
-  return n;
 
-}
+  int  superpose_atoms ( mmdb::mat44 & T, PPAtom A1,
+                  mmdb::PPAtom A2, int nAtoms,
+                  mmdb::rmatrix & A, mmdb::rmatrix & U, mmdb::rmatrix & V,
+                  mmdb::rvector & W, mmdb::rvector & RV1 )  {
+  //   Given two sets of atoms, A1 and A2, superpose_atoms(...)
+  // calculates the rotational-translational matrix T such that
+  // |T*A1 - A2| is minimal in least-square terms. The transfomation
+  // superposes exactly the atoms A1[0] and A2[0].
+  mmdb::realtype det,B;
+  mmdb::vect3    vc1,vc2;
+  int            i,j,k;
 
-int CCP4SRSMonomer::get_bound ( int atomNo, int n ) {
-// returns nth [0,1,..] atom bound to atom with name 'aname'
-int  i,j,k,atm1,atm2;
+    //  1.  Calculate the correlation matrix. The rotation will be
+    //      done around
 
-  k = -1;
-  j = 0;
-  for (i=0;(i<bonds.numberOf()) && (k<0);i++)  {
-    atm1 = bonds.at(i)->atom1();
-    atm2 = bonds.at(i)->atom2();
-    if (atm1==atomNo)  {
-      if (j==n) k = atm2;
-           else j++;
-    } else if (atm2==atomNo)  {
-      if (j==n) k = atm1;
-           else j++;
-    }
-  }
+    for (i=1;i<=3;i++)
+      for (j=1;j<=3;j++)
+        A[i][j] = 0.0;
 
-  return k;
+    for (k=1;k<nAtoms;k++)  {
+      vc1[0] = A1[k]->x() - A1[0]->x();
+      vc1[1] = A1[k]->y() - A1[0]->y();
+      vc1[2] = A1[k]->z() - A1[0]->z();
+      vc2[0] = A2[k]->x - A2[0]->x;
+      vc2[1] = A2[k]->y - A2[0]->y;
+      vc2[2] = A2[k]->z - A2[0]->z;
+      for (i=1;i<=3;i++)
+        for (j=1;j<=3;j++)
+          A[i][j] += vc1[j-1]*vc2[i-1];
+    }
 
-}
+    //  2. Calculate transformation matrix (to be applied to A1)
 
-int CCP4SRSMonomer::get_bound ( cpstr aname, int n ) {
-// returns nth [0,1,..] atom bound to atom with name 'aname'
-int  i,j,k,atm1,atm2;
+    det = A[1][1]*A[2][2]*A[3][3] +
+          A[1][2]*A[2][3]*A[3][1] +
+          A[2][1]*A[3][2]*A[1][3] -
+          A[1][3]*A[2][2]*A[3][1] -
+          A[1][1]*A[2][3]*A[3][2] -
+          A[3][3]*A[1][2]*A[2][1];
 
-  k = -1;
-  j = 0;
-  for (i=0;(i<bonds.numberOf()) && (k<0);i++)  {
-    atm1 = bonds.at(i)->atom1();
-    atm2 = bonds.at(i)->atom2();
-    if (!strcmp(atoms.at(atm1)->name(),aname))  {
-      if (j==n) k = atm2;
-           else j++;
-    } else if (!strcmp(atoms.at(atm2)->name(),aname))  {
-      if (j==n) k = atm1;
-           else j++;
-    }
-  }
+    //  2.1 SV-decompose the correlation matrix
 
-  return k;
+    mmdb::math::SVD ( 3,3,3,A,U,V,W,RV1,true,true,i );
 
-}
+    if (i!=0)  return CCP4SRS_SVD_Fail;
 
+    //  2.2 Check for parasite inversion and fix it if found
 
-int CCP4SRSMonomer::addHydrogens ( PCResidue R )  {
-//
-//   Return:
-//     CCP4SRS_Ok             success
-//     CCP4SRS_EmptyResidue   residue R does not contain atoms
-//     CCP4SRS_NoAtomsFound   monomer does not contain atoms
-//     CCP4SRS_NoBonds        monomer does not contain bonds
-//     CCP4SRS_NoAtomsData    monomer is not complete
-//     CCP4SRS_NoSimilarity   too few coomon atom names in R and SRS
-//                            entry with the same structure name
-//     CCP4SRS_SuperpositionFailed  failed residue superposition
-//
-// NOTE1: the function does not rearranges existing atoms in the
-// residue, but places the hydrogens on top of them (leaving the
-// Ter pseudoatom, if found, on top of the list).
-//
-// NOTE2: in case of alternative locations, the first one in the
-// residue is chosen.
-//
-PPCAtom      H;
-PCCP4SRSAtom sa1[10];
-PCCP4SRSAtom atomi;
-PCAtom       sa2[10];
-AtomName     aname;
-rmatrix      D,U,V;
-rvector      W,RV1;
-imatrix      c;
-ivector      A,nb;
-mat44        T;
-int          natoms,nbonds, i,j,k,m,n,mm,nTer,nH;
-
-
-  //  1.  Make simple checks first
-
-  natoms = atoms.numberOf();
-  nbonds = bonds.numberOf();
-
-  if (natoms<=2)          return CCP4SRS_NoAtomsFound;
-  if (nbonds<=0)          return CCP4SRS_NoBonds;
-  if (R->nAtoms<=2)       return CCP4SRS_EmptyResidue;
-  if (natoms==R->nAtoms)  return CCP4SRS_Ok;
-
-
-  //  2.  Map existing atoms from the residue onto a local array
-
-  GetVectorMemory ( A,natoms,0 );
-  nTer = 20000;
-  for (i=0;i<natoms;i++)  {
-    A[i] = -1;  // signal "no atom"
-    for (j=0;(j<R->nAtoms) && (A[i]<0);j++)
-      if (R->atom[j])  {
-        if (R->atom[j]->Ter)
-          nTer = j;
-        else if (!strcmp(atoms.at(i)->name_pdb(aname),R->atom[j]->name))
-          A[i] = j;  // here is the place to check for altlocs
-      }
-  }
-
-
-  //  3.  Make bond matrix
-
-  GetMatrixMemory ( c ,natoms,10,0,0 );
-  GetVectorMemory ( nb,natoms,0 );
-
-  for (i=0;i<natoms;i++)
-    nb[i] = 0;  // number of bonds at ith atom
-
-  for (i=0;i<nbonds;i++)  {
-    j = bonds.at(i)->atom1();
-    k = bonds.at(i)->atom2();
-    c[j][nb[j]] = k;
-    c[k][nb[k]] = j;
-    nb[j]++;
-    nb[k]++;
-  }
-
-
-  //  4.  Loop over all hydrogens. Locate core atoms bonded to
-  //      hydrogen in SBStructure and superpose them with the
-  //      corresponding atoms in the residue. Using the superposition
-  //      matrix, add hydrogens to the residue.
-
-  GetMatrixMemory ( D  ,3,3,1,1 );
-  GetMatrixMemory ( U  ,3,3,1,1 );
-  GetMatrixMemory ( V  ,3,3,1,1 );
-  GetVectorMemory ( W  ,3,1 );
-  GetVectorMemory ( RV1,3,1 );
-
-  H  = new PCAtom[natoms];
-  nH = 0;
-
-  for (i=0;i<natoms;i++)  {
-    atomi = atoms.at(i);
-    if ((!strcmp(atomi->element(),"H")) && (A[i]<0) && (nb[i]>0) &&
-        (atomi->x()>-MaxShortReal)) {
-      // ith atom is a hydrogen which is not found in the residue.
-      // Find 3+ core atoms that are most closely bonded to this one.
-      n = c[i][0];  // core atom bonded to the hydrogen
-      if (A[n]>=0)  {
-        sa1[0] = atoms.at(n);
-        sa2[0] = R->atom[A[n]];
-        mm = 1;
-        m  = 1;
-        while ((m<3) && (mm<2))  {
-          k = n;
-          for (j=0;(j<nb[k]) && (m<10);j++)  {
-            n = c[k][j];
-            if (A[n]>=0)  {
-              sa1[m] = atoms.at(n);
-              sa2[m] = R->atom[A[n]];
-              m++;
-            }
-          }
-          mm++;
-        }
-        if (m>=3)  {
-          // superpose atoms and add the hydrogen to the residue
-          k = superpose_atoms ( T,sa1,sa2,m,D,U,V,W,RV1 );
-          if (k==CCP4SRS_Ok)  {
-            H[nH] = atomi->makeCAtom();
-            H[nH]->Transform ( T );
-            nH++;
-          }
+    if (det<=0.0)  {
+      k = 0;
+      B = mmdb::MaxReal;
+      for (j=1;j<=3;j++)
+        if (W[j]<B)  {
+          B = W[j];
+          k = j;
         }
-      }
+      for (j=1;j<=3;j++)
+        V[j][k] = -V[j][k];
     }
-  }
 
-  //  5.  Put hydrogens into the residue
+    //  2.3 Calculate rotational part of T
 
-  for (i=0;i<nH;i++)  {
-    R->InsertAtom ( H[i],nTer );
-    nTer++;
-  }
+    for (j=1;j<=3;j++)
+      for (k=1;k<=3;k++)  {
+        B = 0.0;
+        for (i=1;i<=3;i++)
+          B += U[j][i]*V[k][i];
+        T[j-1][k-1] = B;
+      }
 
+    //  2.4 Add translational part to T
 
-  //  6.  Release memory and return
+    T[0][3] = A2[0]->x - T[0][0]*A1[0]->x() - T[0][1]*A1[0]->y() -
+                         T[0][2]*A1[0]->z();
+    T[1][3] = A2[0]->y - T[1][0]*A1[0]->x() - T[1][1]*A1[0]->y() -
+                         T[1][2]*A1[0]->z();
+    T[2][3] = A2[0]->z - T[2][0]*A1[0]->x() - T[2][1]*A1[0]->y() -
+                         T[2][2]*A1[0]->z();
 
-  if (H)  delete[] H;
-  FreeVectorMemory ( A,0 );
+    return CCP4SRS_Ok;
 
-  FreeVectorMemory ( RV1,1 );
-  FreeVectorMemory ( W  ,1 );
-  FreeMatrixMemory ( V  ,3,1,1 );
-  FreeMatrixMemory ( U  ,3,1,1 );
-  FreeMatrixMemory ( D  ,3,1,1 );
+  }
 
-  FreeVectorMemory ( nb,0 );
-  FreeMatrixMemory ( c ,natoms,0,0 );
+  int Monomer::atom_no ( mmdb::cpstr aname )  {
+  // returns number of atom with given name [0...], or -1 if atom
+  // is not found
+  int i,n;
 
-  return CCP4SRS_Ok;
+    n = -1;
+    for (i=0;(i<atoms.numberOf()) && (n<0);i++)
+      if (!strcmp(atoms.at(i)->name(),aname))
+        n = i;
 
-}
+    return n;
 
+  }
 
-void CCP4SRSMonomer::getAtomNameMatch ( PPCAtom A, int nat,
-                                        pstr altLoc,
-                                        ivector anmatch )  {
-AtomName anamei;
-int      i,j,k, natoms;
-Boolean  done;
+  int Monomer::get_bound ( int atomNo, mmdb::cpstr elem, int serNo ) {
+  // returns number of atom with chemical element 'elem', bound to
+  // atom number 'atomNo' [0,1,..]. serNo==0 returns 1st atom found,
+  // serNo==1 returns second atom and so on. If atom not found, -1 is
+  // returned.
+  int i,j,n, atm1,atm2;
 
-  natoms = atoms.numberOf();
-  for (i=0;i<natoms;i++)  {
-    k    = -1;
-    j    = 0;
-    done = False;
-    while ((j<nat) && (!done))  {
-      if (A[j])  {
-        atoms.at(i)->name_pdb ( anamei );
-        if ((!A[j]->Ter) && (!strcmp(A[j]->name,anamei)))  {
-          k = j;  // atom found
-          // check now for altLocs
-          j++;
-          while ((j<nat) && (!done))  {
-            if (A[j])  {
-              done = (A[j]->Ter || (strcmp(A[j]->name,anamei)));
-              if (!done)  {
-                if (A[j]->occupancy>A[k]->occupancy)  k = j;
-                if (altLoc)  {
-                  if (!strcmp(A[j]->altLoc,altLoc))  {
-                    k    = j;
-                    done = True;
-                  }
-                }
-              }
-            }
-            j++;
-          }
+    n = -1;
+    j = 0;
+    for (i=0;(i<bonds.numberOf()) && (n<0);i++)  {
+      atm2 = bonds.at(i)->atom2();
+      if (atm2==atomNo)  {
+        atm1 = atm2;
+        atm2 = bonds.at(i)->atom1();
+      } else
+        atm1 = bonds.at(i)->atom1();
+      if (atm1==atomNo)  {
+        if (!strcmp(atoms.at(atm2)->element(),elem))  {
+          if (j==serNo)  n = atm2;
+                   else  j++;
         }
       }
-      j++;
     }
-    anmatch[i] = k;
+
+    return n;
+
   }
 
-}
+  int Monomer::get_bound ( int atomNo, int n ) {
+  // returns nth [0,1,..] atom bound to atom with name 'aname'
+  int  i,j,k,atm1,atm2;
+
+    k = -1;
+    j = 0;
+    for (i=0;(i<bonds.numberOf()) && (k<0);i++)  {
+      atm1 = bonds.at(i)->atom1();
+      atm2 = bonds.at(i)->atom2();
+      if (atm1==atomNo)  {
+        if (j==n) k = atm2;
+             else j++;
+      } else if (atm2==atomNo)  {
+        if (j==n) k = atm1;
+             else j++;
+      }
+    }
 
-void CCP4SRSMonomer::getAtomNameMatch ( CCP4SRSContainer<CCP4SRSAtom> *A,
-                                        ivector anmatch )  {
-int i,j,n,nat;
+    return k;
 
-  n   = A->numberOf();
-  nat = atoms.numberOf();
-  for (i=0;i<n;i++)  {
-    anmatch[i] = -1;
-    for (j=0;(j<nat) && (anmatch[i]<0);j++)
-      if (!strcmp(A->at(i)->id(),atoms.at(j)->id()))
-        anmatch[i] = j;
   }
 
-}
+  int Monomer::get_bound ( mmdb::cpstr aname, int n ) {
+  // returns nth [0,1,..] atom bound to atom with name 'aname'
+  int  i,j,k,atm1,atm2;
 
+    k = -1;
+    j = 0;
+    for (i=0;(i<bonds.numberOf()) && (k<0);i++)  {
+      atm1 = bonds.at(i)->atom1();
+      atm2 = bonds.at(i)->atom2();
+      if (!strcmp(atoms.at(atm1)->name(),aname))  {
+        if (j==n) k = atm2;
+             else j++;
+      } else if (!strcmp(atoms.at(atm2)->name(),aname))  {
+        if (j==n) k = atm1;
+             else j++;
+      }
+    }
 
-void CCP4SRSMonomer::readMonIDFromCIF ( PCMMCIFLoop loop )  {
-pstr p;
-int  rc;
-  if (loop && (!monID[0]))  {
-    p  = loop->GetString ( MMCIF_TAG_COMP_ID,0,rc );
-    if (p) strcpy ( monID,p );
-  }
-}
+    return k;
 
-void CCP4SRSMonomer::readMonIDFromCIF ( PCMMCIFStruct mmCIFStruct )  {
-pstr p;
-int  rc;
-  if (mmCIFStruct && (!monID[0]))  {
-    p  = mmCIFStruct->GetString ( MMCIF_TAG_COMP_ID,rc );
-    if (p) strcpy ( monID,p );
   }
-}
 
-// Return code:
-//     CCP4SRS_Ok    success
-int CCP4SRSMonomer::readFromCIF ( PCMMCIFData mmCIFData,
-                                  pstr error_desc )  {
-  reset();
-  if (mmCIFData->GetStructure(MMCIF_STRUCT_CHEM_COMP))
-        return readFromCIF_rcsb ( mmCIFData,error_desc );
-  else  return readFromCIF_ccp4 ( mmCIFData,error_desc );
-}
 
-int CCP4SRSMonomer::readFromCIF_rcsb ( PCMMCIFData mmCIFData,
-                                       pstr error_desc )  {
-PCMMCIFStruct mmCIFStruct;
-PCMMCIFLoop   mmCIFLoop;
-PCCP4SRSAtom  atom;
-PCCP4SRSBond  bond;
-int           rc,loop_len,i;
+  CCP4SRS_RC Monomer::addHydrogens ( mmdb::PResidue R )  {
+  //
+  //   Return:
+  //     _Ok             success
+  //     _EmptyResidue   residue R does not contain atoms
+  //     _NoAtomsFound   monomer does not contain atoms
+  //     _NoBonds        monomer does not contain bonds
+  //     _NoAtomsData    monomer is not complete
+  //     _NoSimilarity   too few coomon atom names in R and SRS
+  //                            entry with the same structure name
+  //     _SuperpositionFailed  failed residue superposition
+  //
+  // NOTE1: the function does not rearranges existing atoms in the
+  // residue, but places the hydrogens on top of them (leaving the
+  // Ter pseudoatom, if found, on top of the list).
+  //
+  // NOTE2: in case of alternative locations, the first one in the
+  // residue is chosen.
+  //
+  mmdb::PPAtom   H;
+  PAtom          sa1[10];
+  PAtom          atomi;
+  mmdb::PAtom    sa2[10];
+  mmdb::AtomName aname;
+  mmdb::rmatrix  D,U,V;
+  mmdb::rvector  W,RV1;
+  mmdb::imatrix  c;
+  mmdb::ivector  A,nb;
+  mmdb::mat44    T;
+  int            natoms,nbonds, i,j,k,m,n,mm,nTer,nH;
+
+    //  1.  Make simple checks first
+
+    natoms = atoms.numberOf();
+    nbonds = bonds.numberOf();
+
+    if (natoms<=2)          return CCP4SRS_NoAtomsFound;
+    if (nbonds<=0)          return CCP4SRS_NoBonds;
+    if (R->nAtoms<=2)       return CCP4SRS_EmptyResidue;
+    if (natoms==R->nAtoms)  return CCP4SRS_Ok;
+
+
+    //  2.  Map existing atoms from the residue onto a local array
+
+    mmdb::GetVectorMemory ( A,natoms,0 );
+    nTer = 20000;
+    for (i=0;i<natoms;i++)  {
+      A[i] = -1;  // signal "no atom"
+      for (j=0;(j<R->nAtoms) && (A[i]<0);j++)
+        if (R->atom[j])  {
+          if (R->atom[j]->Ter)
+            nTer = j;
+          else if (!strcmp(atoms.at(i)->name_pdb(aname),R->atom[j]->name))
+            A[i] = j;  // here is the place to check for altlocs
+        }
+    }
 
-  rc = 0;
 
-  mmCIFStruct = mmCIFData->GetStructure ( MMCIF_STRUCT_CHEM_COMP );
-  if (mmCIFStruct)  {
-    CreateCopy ( monName,mmCIFStruct->GetString(MMCIF_TAG_Name,rc) );
-    CreateCopy ( monType,mmCIFStruct->GetString(MMCIF_TAG_Type,rc) );
-    CreateCopy ( monFormula,mmCIFStruct->GetString(MMCIF_TAG_Formula,
-                                                   rc) );
-  }
+    //  3.  Make bond matrix
 
-  // take atoms
-  mmCIFLoop = mmCIFData->GetLoop ( MMCIF_LOOP_CHEM_COMP_ATOM );
-  if (!mmCIFLoop)
-    mmCIFStruct = mmCIFData->GetStructure ( MMCIF_LOOP_CHEM_COMP_ATOM );
+    mmdb::GetMatrixMemory ( c ,natoms,10,0,0 );
+    mmdb::GetVectorMemory ( nb,natoms,0 );
 
-  if (mmCIFLoop)  {
+    for (i=0;i<natoms;i++)
+      nb[i] = 0;  // number of bonds at ith atom
 
-    readMonIDFromCIF ( mmCIFLoop );
+    for (i=0;i<nbonds;i++)  {
+      j = bonds.at(i)->atom1();
+      k = bonds.at(i)->atom2();
+      c[j][nb[j]] = k;
+      c[k][nb[k]] = j;
+      nb[j]++;
+      nb[k]++;
+    }
 
-    loop_len = mmCIFLoop->GetLoopLength();
-    rc       = 0;
-    for (i=0;(i<loop_len) && (!rc);i++)  {
-      atom = new CCP4SRSAtom();
-      rc   = atom->readFromCIF_rcsb ( mmCIFLoop,i );
-      if (!rc)  atoms.add ( atom );
-      else  {
-        if (error_desc)
-          sprintf ( error_desc,"Error %i in row %i of %s loop",
-                    rc,i+1,MMCIF_LOOP_CHEM_COMP_ATOM );
-        delete atom;
+
+    //  4.  Loop over all hydrogens. Locate core atoms bonded to
+    //      hydrogen in SBStructure and superpose them with the
+    //      corresponding atoms in the residue. Using the superposition
+    //      matrix, add hydrogens to the residue.
+
+    mmdb::GetMatrixMemory ( D  ,3,3,1,1 );
+    mmdb::GetMatrixMemory ( U  ,3,3,1,1 );
+    mmdb::GetMatrixMemory ( V  ,3,3,1,1 );
+    mmdb::GetVectorMemory ( W  ,3,1 );
+    mmdb::GetVectorMemory ( RV1,3,1 );
+
+    H  = new mmdb::PAtom[natoms];
+    nH = 0;
+
+    for (i=0;i<natoms;i++)  {
+      atomi = atoms.at(i);
+      if ((!strcmp(atomi->element(),"H")) && (A[i]<0) && (nb[i]>0) &&
+          (atomi->x()>-mmdb::MaxShortReal)) {
+        // ith atom is a hydrogen which is not found in the residue.
+        // Find 3+ core atoms that are most closely bonded to this one.
+        n = c[i][0];  // core atom bonded to the hydrogen
+        if (A[n]>=0)  {
+          sa1[0] = atoms.at(n);
+          sa2[0] = R->atom[A[n]];
+          mm = 1;
+          m  = 1;
+          while ((m<3) && (mm<2))  {
+            k = n;
+            for (j=0;(j<nb[k]) && (m<10);j++)  {
+              n = c[k][j];
+              if (A[n]>=0)  {
+                sa1[m] = atoms.at(n);
+                sa2[m] = R->atom[A[n]];
+                m++;
+              }
+            }
+            mm++;
+          }
+          if (m>=3)  {
+            // superpose atoms and add the hydrogen to the residue
+            k = superpose_atoms ( T,sa1,sa2,m,D,U,V,W,RV1 );
+            if (k==CCP4SRS_Ok)  {
+              H[nH] = atomi->makeAtom();
+              H[nH]->Transform ( T );
+              nH++;
+            }
+          }
+        }
       }
     }
 
-  } else if (mmCIFStruct)  {
-
-    readMonIDFromCIF ( mmCIFStruct );
+    //  5.  Put hydrogens into the residue
 
-    atom = new CCP4SRSAtom();
-    rc = atom->readFromCIF ( mmCIFStruct );
-    if (!rc)  atoms.add ( atom );
-    else  {
-      if (error_desc)
-        sprintf ( error_desc,"Error %i in %s structure",
-                  rc,MMCIF_LOOP_CHEM_COMP_ATOM );
-      delete atom;
+    for (i=0;i<nH;i++)  {
+      R->InsertAtom ( H[i],nTer );
+      nTer++;
     }
 
-  }
 
-  if (rc)  {
-    reset();
-    return rc;
-  }
+    //  6.  Release memory and return
 
+    if (H)  delete[] H;
+    mmdb::FreeVectorMemory ( A,0 );
 
-  // take bonds
-  mmCIFLoop =  mmCIFData->GetLoop ( MMCIF_LOOP_CHEM_COMP_BOND );
-  if (!mmCIFLoop)
-    mmCIFStruct = mmCIFData->GetStructure ( MMCIF_LOOP_CHEM_COMP_BOND );
+    mmdb::FreeVectorMemory ( RV1,1 );
+    mmdb::FreeVectorMemory ( W  ,1 );
+    mmdb::FreeMatrixMemory ( V  ,3,1,1 );
+    mmdb::FreeMatrixMemory ( U  ,3,1,1 );
+    mmdb::FreeMatrixMemory ( D  ,3,1,1 );
 
-  if (mmCIFLoop)  {
+    mmdb::FreeVectorMemory ( nb,0 );
+    mmdb::FreeMatrixMemory ( c ,natoms,0,0 );
 
-    readMonIDFromCIF ( mmCIFLoop );
+    return CCP4SRS_Ok;
 
-    loop_len = mmCIFLoop->GetLoopLength();
-    rc       = 0;
-    for (i=0;(i<loop_len) && (!rc);i++)  {
-      bond = new CCP4SRSBond();
-      rc = bond->readFromCIF_rcsb ( mmCIFLoop,i,atoms );
-      if (!rc)  bonds.add ( bond );
-      else  {
-        if (error_desc)
-          sprintf ( error_desc,"Error %i in row %i of %s loop",
-                    rc,i+1,MMCIF_LOOP_CHEM_COMP_BOND );
-        delete bond;
+  }
+
+
+  void Monomer::getAtomNameMatch ( mmdb::PPAtom A, int nat,
+                                          mmdb::pstr    altLoc,
+                                          mmdb::ivector anmatch )  {
+  mmdb::AtomName anamei;
+  int            i,j,k, natoms;
+  bool           done;
+
+    natoms = atoms.numberOf();
+    for (i=0;i<natoms;i++)  {
+      k    = -1;
+      j    = 0;
+      done = false;
+      while ((j<nat) && (!done))  {
+        if (A[j])  {
+          atoms.at(i)->name_pdb ( anamei );
+          if ((!A[j]->Ter) && (!strcmp(A[j]->name,anamei)))  {
+            k = j;  // atom found
+            // check now for altLocs
+            j++;
+            while ((j<nat) && (!done))  {
+              if (A[j])  {
+                done = (A[j]->Ter || (strcmp(A[j]->name,anamei)));
+                if (!done)  {
+                  if (A[j]->occupancy>A[k]->occupancy)  k = j;
+                  if (altLoc)  {
+                    if (!strcmp(A[j]->altLoc,altLoc))  {
+                      k    = j;
+                      done = true;
+                    }
+                  }
+                }
+              }
+              j++;
+            }
+          }
+        }
+        j++;
       }
+      anmatch[i] = k;
     }
 
-  } else if (mmCIFStruct)  {
+  }
 
-    readMonIDFromCIF ( mmCIFStruct );
+  void Monomer::getAtomNameMatch ( Container<Atom> *A,
+                                   mmdb::ivector anmatch )  {
+  int i,j,n,nat;
 
-    bond = new CCP4SRSBond();
-    rc = bond->readFromCIF ( mmCIFStruct,atoms );
-    if (!rc)  bonds.add ( bond );
-    else  {
-      if (error_desc)
-        sprintf ( error_desc,"Error %i in %s structure",
-                  rc,MMCIF_LOOP_CHEM_COMP_BOND );
-      delete bond;
+    n   = A->numberOf();
+    nat = atoms.numberOf();
+    for (i=0;i<n;i++)  {
+      anmatch[i] = -1;
+      for (j=0;(j<nat) && (anmatch[i]<0);j++)
+        if (!strcmp(A->at(i)->id(),atoms.at(j)->id()))
+          anmatch[i] = j;
     }
 
   }
 
-  if (rc)  {
-    reset();
-    return rc;
+
+  void Monomer::readMonIDFromCIF ( mmdb::mmcif::PLoop loop )  {
+  mmdb::pstr p;
+  int        rc;
+    if (loop && (!monID[0]))  {
+      p  = loop->GetString ( MMCIF_TAG_COMP_ID,0,rc );
+      if (p) strcpy ( monID,p );
+    }
+  }
+
+  void Monomer::readMonIDFromCIF ( mmdb::mmcif::PStruct mmCIFStruct )  {
+  mmdb::pstr p;
+  int        rc;
+    if (mmCIFStruct && (!monID[0]))  {
+      p  = mmCIFStruct->GetString ( MMCIF_TAG_COMP_ID,rc );
+      if (p) strcpy ( monID,p );
+    }
   }
 
-  return CCP4SRS_Ok;
+  // Return code:
+  //     _Ok    success
+  int Monomer::readFromCIF ( mmdb::mmcif::PData mmCIFData,
+                                    mmdb::pstr error_desc )  {
+    reset();
+    if (mmCIFData->GetStructure(MMCIF_STRUCT_CHEM_COMP))
+          return readFromCIF_rcsb ( mmCIFData,error_desc );
+    else  return readFromCIF_ccp4 ( mmCIFData,error_desc );
+  }
+
+  int Monomer::readFromCIF_rcsb ( mmdb::mmcif::PData mmCIFData,
+                                         mmdb::pstr error_desc )  {
+  mmdb::mmcif::PStruct mmCIFStruct;
+  mmdb::mmcif::PLoop   mmCIFLoop;
+  PAtom                atom;
+  PBond                bond;
+  int                  rc,loop_len,i;
+
+    rc = 0;
+
+    mmCIFStruct = mmCIFData->GetStructure ( MMCIF_STRUCT_CHEM_COMP );
+    if (mmCIFStruct)  {
+      mmdb::CreateCopy ( monName,mmCIFStruct->GetString(MMCIF_TAG_Name,rc) );
+      mmdb::CreateCopy ( monType,mmCIFStruct->GetString(MMCIF_TAG_Type,rc) );
+      mmdb::CreateCopy ( monFormula,mmCIFStruct->GetString(MMCIF_TAG_Formula,
+                                                     rc) );
+    }
+
+    // take atoms
+    mmCIFLoop = mmCIFData->GetLoop ( MMCIF_LOOP_CHEM_COMP_ATOM );
+    if (!mmCIFLoop)
+      mmCIFStruct = mmCIFData->GetStructure ( MMCIF_LOOP_CHEM_COMP_ATOM );
+
+    if (mmCIFLoop)  {
+
+      readMonIDFromCIF ( mmCIFLoop );
+
+      loop_len = mmCIFLoop->GetLoopLength();
+      rc       = 0;
+      for (i=0;(i<loop_len) && (!rc);i++)  {
+        atom = new Atom();
+        rc   = atom->readFromCIF_rcsb ( mmCIFLoop,i );
+        if (!rc)  atoms.add ( atom );
+        else  {
+          if (error_desc)
+            sprintf ( error_desc,"Error %i in row %i of %s loop",
+                      rc,i+1,MMCIF_LOOP_CHEM_COMP_ATOM );
+          delete atom;
+        }
+      }
 
-}
+    } else if (mmCIFStruct)  {
 
-int CCP4SRSMonomer::readFromCIF_ccp4 ( PCMMCIFData mmCIFData,
-                                       pstr error_desc )  {
-PCMMCIFLoop       loop;
-PCCP4SRSAtom      atom;
-PCCP4SRSBond      bond;
-PCCP4SRSAngle     angle;
-PCCP4SRSChiCenter chicenter;
-PCCP4SRSTorsion   torsion;
-PCCP4SRSPlane     plane;
-int               loop_len, i,n, rc;
-
-  // take atoms
-  loop =  mmCIFData->GetLoop ( MMCIF_LOOP_CHEM_COMP_ATOM );
-  readMonIDFromCIF ( loop );
-
-  if (loop)  {
-
-    loop_len = loop->GetLoopLength();
-    rc       = 0;
-    for (i=0;(i<loop_len) && (!rc);i++)  {
-      atom = new CCP4SRSAtom();
-      rc = atom->readFromCIF_ccp4 ( loop,i );
+      readMonIDFromCIF ( mmCIFStruct );
+
+      atom = new Atom();
+      rc = atom->readFromCIF ( mmCIFStruct );
       if (!rc)  atoms.add ( atom );
       else  {
         if (error_desc)
-          sprintf ( error_desc,"Error %i in row %i of %s loop",
-                    rc,i+1,MMCIF_LOOP_CHEM_COMP_ATOM );
+          sprintf ( error_desc,"Error %i in %s structure",
+                    rc,MMCIF_LOOP_CHEM_COMP_ATOM );
         delete atom;
       }
+
     }
 
     if (rc)  {
@@ -697,427 +610,557 @@
       return rc;
     }
 
-  }
 
-  // take tree records
-  loop =  mmCIFData->GetLoop ( MMCIF_LOOP_CHEM_COMP_TREE );
-  readMonIDFromCIF ( loop );
-  rc = struct_tree.readFromCIF ( loop,atoms );
-
-  if (rc)  {
-    reset();
-    return rc;
-  }
+    // take bonds
+    mmCIFLoop =  mmCIFData->GetLoop ( MMCIF_LOOP_CHEM_COMP_BOND );
+    if (!mmCIFLoop)
+      mmCIFStruct = mmCIFData->GetStructure ( MMCIF_LOOP_CHEM_COMP_BOND );
+
+    if (mmCIFLoop)  {
+
+      readMonIDFromCIF ( mmCIFLoop );
+
+      loop_len = mmCIFLoop->GetLoopLength();
+      rc       = 0;
+      for (i=0;(i<loop_len) && (!rc);i++)  {
+        bond = new Bond();
+        rc = bond->readFromCIF_rcsb ( mmCIFLoop,i,atoms );
+        if (!rc)  bonds.add ( bond );
+        else  {
+          if (error_desc)
+            sprintf ( error_desc,"Error %i in row %i of %s loop",
+                      rc,i+1,MMCIF_LOOP_CHEM_COMP_BOND );
+          delete bond;
+        }
+      }
 
-  // take bonds
-  loop =  mmCIFData->GetLoop ( MMCIF_LOOP_CHEM_COMP_BOND );
-  readMonIDFromCIF ( loop );
+    } else if (mmCIFStruct)  {
 
-  if (loop)  {
+      readMonIDFromCIF ( mmCIFStruct );
 
-    loop_len = loop->GetLoopLength();
-    rc       = 0;
-    for (i=0;(i<loop_len) && (!rc);i++)  {
-      bond = new CCP4SRSBond();
-      rc = bond->readFromCIF_ccp4 ( loop,i,atoms );
+      bond = new Bond();
+      rc = bond->readFromCIF ( mmCIFStruct,atoms );
       if (!rc)  bonds.add ( bond );
       else  {
         if (error_desc)
-          sprintf ( error_desc,"Error %i in row %i of %s loop",
-                    rc,i+1,MMCIF_LOOP_CHEM_COMP_BOND );
-        delete bond;
-      }
-      /*
-      if ((!rc) || (rc==CCP4SRS_WrongBondType))  {
-        bonds.add ( bond );
-        rc = 0;
-      } else  {
-        if (error_desc)
-          sprintf ( error_desc,"Error %i in row %i of %s loop",
-                    rc,i+1,MMCIF_LOOP_CHEM_COMP_BOND );
+          sprintf ( error_desc,"Error %i in %s structure",
+                    rc,MMCIF_LOOP_CHEM_COMP_BOND );
         delete bond;
       }
-      */
+
     }
 
+    // take bonds
+    mmCIFLoop =  mmCIFData->GetLoop ( MMCIF_LOOP_CHEM_COMP_DESCRIPTOR );
+    if (mmCIFLoop)  {
+      ACDLabs.readFromCIF_rcsb ( mmCIFLoop,"ACDLabs" );
+      CACTVS .readFromCIF_rcsb ( mmCIFLoop,"CACTVS"  );
+      OpenEye.readFromCIF_rcsb ( mmCIFLoop,"OpenEye OEToolkits" );
+      InChI  .readFromCIF_rcsb ( mmCIFLoop,"InChI"   );
+    } else  {
+      ACDLabs.freeSmiles();
+      CACTVS .freeSmiles();
+      OpenEye.freeSmiles();
+      InChI  .freeSmiles();
+    }
+
+/*
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+000 SMILES           ACDLabs              12.01 "O=C(O)OC"
+000 SMILES_CANONICAL CACTVS               3.370 "COC(O)=O"
+000 SMILES           CACTVS               3.370 "COC(O)=O"
+000 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "COC(=O)O"
+000 SMILES           "OpenEye OEToolkits" 1.7.0 "COC(=O)O"
+000 InChI            InChI                1.03  "InChI=1S/C2H4O3/c1-5-2(3)4/h1H3,(H,3,4)"
+000 InChIKey         InChI                1.03  CXHHBNMLPJOKQD-UHFFFAOYSA-N
+*/
+
     if (rc)  {
       reset();
       return rc;
     }
 
+    return CCP4SRS_Ok;
+
   }
 
-  // take angles
-  loop =  mmCIFData->GetLoop ( MMCIF_LOOP_CHEM_COMP_ANGLE );
-  readMonIDFromCIF ( loop );
-
-  if (loop)  {
-
-    loop_len = loop->GetLoopLength();
-    rc       = 0;
-    for (i=0;(i<loop_len) && (!rc);i++)  {
-      angle = new CCP4SRSAngle();
-      rc = angle->readFromCIF ( loop,i,atoms );
-      if (!rc)  angles.add ( angle );
-      else  {
-        if (error_desc)
-          sprintf ( error_desc,"Error %i in row %i of %s loop",
-                    rc,i+1,MMCIF_LOOP_CHEM_COMP_ANGLE );
-        delete angle;
+  int Monomer::readFromCIF_ccp4 ( mmdb::mmcif::PData mmCIFData,
+                                  mmdb::pstr error_desc )  {
+  mmdb::mmcif::PLoop loop;
+  PAtom       atom;
+  PBond       bond;
+  PAngle      angle;
+  PChiCenter  chicenter;
+  PTorsion    torsion;
+  PPlane      plane;
+  int                loop_len, i,n, rc;
+
+    // take atoms
+    loop =  mmCIFData->GetLoop ( MMCIF_LOOP_CHEM_COMP_ATOM );
+    readMonIDFromCIF ( loop );
+
+    if (loop)  {
+
+      loop_len = loop->GetLoopLength();
+      rc       = 0;
+      for (i=0;(i<loop_len) && (!rc);i++)  {
+        atom = new Atom();
+        rc = atom->readFromCIF_ccp4 ( loop,i );
+        if (!rc)  atoms.add ( atom );
+        else  {
+          if (error_desc)
+            sprintf ( error_desc,"Error %i in row %i of %s loop",
+                      rc,i+1,MMCIF_LOOP_CHEM_COMP_ATOM );
+          delete atom;
+        }
+      }
+
+      if (rc)  {
+        reset();
+        return rc;
       }
+
     }
 
+    // take tree records
+    loop =  mmCIFData->GetLoop ( MMCIF_LOOP_CHEM_COMP_TREE );
+    readMonIDFromCIF ( loop );
+    rc = struct_tree.readFromCIF ( loop,atoms );
+
     if (rc)  {
       reset();
       return rc;
     }
 
-  }
+    // take bonds
+    loop =  mmCIFData->GetLoop ( MMCIF_LOOP_CHEM_COMP_BOND );
+    readMonIDFromCIF ( loop );
+
+    if (loop)  {
+
+      loop_len = loop->GetLoopLength();
+      rc       = 0;
+      for (i=0;(i<loop_len) && (!rc);i++)  {
+        bond = new Bond();
+        rc = bond->readFromCIF_ccp4 ( loop,i,atoms );
+        if (!rc)  bonds.add ( bond );
+        else  {
+          if (error_desc)
+            sprintf ( error_desc,"Error %i in row %i of %s loop",
+                      rc,i+1,MMCIF_LOOP_CHEM_COMP_BOND );
+          delete bond;
+        }
+        /*
+        if ((!rc) || (rc==_WrongBondType))  {
+          bonds.add ( bond );
+          rc = 0;
+        } else  {
+          if (error_desc)
+            sprintf ( error_desc,"Error %i in row %i of %s loop",
+                      rc,i+1,MMCIF_LOOP_CHEM_COMP_BOND );
+          delete bond;
+        }
+        */
+      }
 
-  // take chiral centers
-  loop =  mmCIFData->GetLoop ( MMCIF_LOOP_CHEM_COMP_CHIR );
-  readMonIDFromCIF ( loop );
+      if (rc)  {
+        reset();
+        return rc;
+      }
 
-  if (loop)  {
+    }
 
-    // reset atom chirality signs
-    for (i=0;i<atoms.numberOf();i++)
-      atoms.at(i)->set_chirality ( 'N' );
+    // take angles
+    loop =  mmCIFData->GetLoop ( MMCIF_LOOP_CHEM_COMP_ANGLE );
+    readMonIDFromCIF ( loop );
+
+    if (loop)  {
+
+      loop_len = loop->GetLoopLength();
+      rc       = 0;
+      for (i=0;(i<loop_len) && (!rc);i++)  {
+        angle = new Angle();
+        rc = angle->readFromCIF ( loop,i,atoms );
+        if (!rc)  angles.add ( angle );
+        else  {
+          if (error_desc)
+            sprintf ( error_desc,"Error %i in row %i of %s loop",
+                      rc,i+1,MMCIF_LOOP_CHEM_COMP_ANGLE );
+          delete angle;
+        }
+      }
 
-    loop_len = loop->GetLoopLength();
-    rc       = 0;
-    for (i=0;(i<loop_len) && (!rc);i++)  {
-      chicenter = new CCP4SRSChiCenter();
-      rc = chicenter->readFromCIF ( loop,i,atoms );
-      if (!rc)  {
-        chicenters.add ( chicenter );
-        atoms.at(chicenter->center())->set_chirality (
-                                          chicenter->get_chirality() );
-      } else  {
-        if (error_desc)
-          sprintf ( error_desc,"Error %i in row %i of %s loop",
-                    rc,i+1,MMCIF_LOOP_CHEM_COMP_CHIR );
-        delete chicenter;
+      if (rc)  {
+        reset();
+        return rc;
       }
+
     }
 
-    if (rc)  {
-      reset();
-      return rc;
+    // take chiral centers
+    loop =  mmCIFData->GetLoop ( MMCIF_LOOP_CHEM_COMP_CHIR );
+    readMonIDFromCIF ( loop );
+
+    if (loop)  {
+
+      // reset atom chirality signs
+      for (i=0;i<atoms.numberOf();i++)
+        atoms.at(i)->set_chirality ( 'N' );
+
+      loop_len = loop->GetLoopLength();
+      rc       = 0;
+      for (i=0;(i<loop_len) && (!rc);i++)  {
+        chicenter = new ChiCenter();
+        rc = chicenter->readFromCIF ( loop,i,atoms );
+        if (!rc)  {
+          chicenters.add ( chicenter );
+          atoms.at(chicenter->center())->set_chirality (
+                                            chicenter->get_chirality() );
+        } else  {
+          if (error_desc)
+            sprintf ( error_desc,"Error %i in row %i of %s loop",
+                      rc,i+1,MMCIF_LOOP_CHEM_COMP_CHIR );
+          delete chicenter;
+        }
+      }
+
+      if (rc)  {
+        reset();
+        return rc;
+      }
+
     }
 
-  }
 
+    // take torsions
+    loop =  mmCIFData->GetLoop ( MMCIF_LOOP_CHEM_COMP_TOR );
+    readMonIDFromCIF ( loop );
+
+    if (loop)  {
+
+      loop_len = loop->GetLoopLength();
+      rc       = 0;
+      for (i=0;(i<loop_len) && (!rc);i++)  {
+        torsion = new Torsion();
+        rc = torsion->readFromCIF ( loop,i,atoms );
+        if (!rc)  torsions.add ( torsion );
+        else  {
+          if (error_desc)
+            sprintf ( error_desc,"Error %i in row %i of %s loop",
+                      rc,i+1,MMCIF_LOOP_CHEM_COMP_TOR );
+          delete torsion;
+        }
+      }
 
-  // take torsions
-  loop =  mmCIFData->GetLoop ( MMCIF_LOOP_CHEM_COMP_TOR );
-  readMonIDFromCIF ( loop );
-
-  if (loop)  {
-
-    loop_len = loop->GetLoopLength();
-    rc       = 0;
-    for (i=0;(i<loop_len) && (!rc);i++)  {
-      torsion = new CCP4SRSTorsion();
-      rc = torsion->readFromCIF ( loop,i,atoms );
-      if (!rc)  torsions.add ( torsion );
-      else  {
-        if (error_desc)
-          sprintf ( error_desc,"Error %i in row %i of %s loop",
-                    rc,i+1,MMCIF_LOOP_CHEM_COMP_TOR );
-        delete torsion;
+      if (rc)  {
+        reset();
+        return rc;
       }
-    }
 
-    if (rc)  {
-      reset();
-      return rc;
     }
 
-  }
 
+    // take planes
+    loop =  mmCIFData->GetLoop ( MMCIF_LOOP_CHEM_COMP_PLANE_ATOM );
+    readMonIDFromCIF ( loop );
+
+    if (loop)  {
+
+      n  = 0;
+      rc = Plane::Ok;
+      while (rc==Plane::Ok)  {
+        plane = new Plane();
+        rc = plane->readFromCIF ( loop,n,atoms );
+        if (rc==Plane::Ok)  {
+          planes.add ( plane );
+          n++;
+        } else  {
+          if (error_desc && (rc!=Plane::NoMorePlanes))
+            sprintf ( error_desc,"Error %i in plane %s of %s loop",
+                      rc,plane->id(),MMCIF_LOOP_CHEM_COMP_PLANE_ATOM );
+          delete plane;
+        }
+      }
 
-  // take planes
-  loop =  mmCIFData->GetLoop ( MMCIF_LOOP_CHEM_COMP_PLANE_ATOM );
-  readMonIDFromCIF ( loop );
-
-  if (loop)  {
-
-    n  = 0;
-    rc = CCP4SRSPlane::Ok;
-    while (rc==CCP4SRSPlane::Ok)  {
-      plane = new CCP4SRSPlane();
-      rc = plane->readFromCIF ( loop,n,atoms );
-      if (rc==CCP4SRSPlane::Ok)  {
-        planes.add ( plane );
-        n++;
-      } else  {
-        if (error_desc && (rc!=CCP4SRSPlane::NoMorePlanes))
-          sprintf ( error_desc,"Error %i in plane %s of %s loop",
-                    rc,plane->id(),MMCIF_LOOP_CHEM_COMP_PLANE_ATOM );
-        delete plane;
+      if (rc!=Plane::NoMorePlanes)  {
+        reset();
+        return rc;
       }
-    }
 
-    if (rc!=CCP4SRSPlane::NoMorePlanes)  {
-      reset();
-      return rc;
     }
 
+    return CCP4SRS_Ok;
+
   }
 
-  return CCP4SRS_Ok;
 
-}
+  mmdb::mmcif::PData Monomer::makeCIF()  {
+  mmdb::mmcif::PData data;
+  mmdb::mmcif::PLoop loop;
+  char        S[100];
+  int         i;
 
+    strcpy ( S,MMCIF_COMP );
+    strcat ( S,monID );
+    data = new mmdb::mmcif::Data ( S );
 
-PCMMCIFData CCP4SRSMonomer::makeCIF()  {
-PCMMCIFData data;
-PCMMCIFLoop loop;
-char        S[100];
-int         i;
-
-  strcpy ( S,MMCIF_COMP );
-  strcat ( S,monID );
-  data = new CMMCIFData ( S );
-
-  data->AddLoop ( MMCIF_LOOP_CHEM_COMP_ATOM,loop );
-  CCP4SRSAtom::makeCIFTags ( loop );
-  for (i=0;i<atoms.numberOf();i++)
-    atoms.at(i)->writeToCIF ( loop,monID );
-
-  struct_tree.writeToCIF ( data,monID,atoms );
-
-  data->AddLoop ( MMCIF_LOOP_CHEM_COMP_BOND,loop );
-  CCP4SRSBond::makeCIFTags ( loop );
-  for (i=0;i<bonds.numberOf();i++)
-    bonds.at(i)->writeToCIF ( loop,monID,atoms );
-
-  data->AddLoop ( MMCIF_LOOP_CHEM_COMP_ANGLE,loop );
-  CCP4SRSAngle::makeCIFTags ( loop );
-  for (i=0;i<angles.numberOf();i++)
-    angles.at(i)->writeToCIF ( loop,monID,atoms );
-
-  data->AddLoop ( MMCIF_LOOP_CHEM_COMP_CHIR,loop );
-  CCP4SRSChiCenter::makeCIFTags ( loop );
-  for (i=0;i<chicenters.numberOf();i++)
-    chicenters.at(i)->writeToCIF ( loop,monID,atoms );
-
-  data->AddLoop ( MMCIF_LOOP_CHEM_COMP_TOR,loop );
-  CCP4SRSTorsion::makeCIFTags ( loop );
-  for (i=0;i<torsions.numberOf();i++)
-    torsions.at(i)->writeToCIF ( loop,monID,atoms );
-
-  data->AddLoop ( MMCIF_LOOP_CHEM_COMP_PLANE_ATOM,loop );
-  CCP4SRSPlane::makeCIFTags ( loop );
-  for (i=0;i<planes.numberOf();i++)
-    planes.at(i)->writeToCIF ( loop,monID,atoms );
-
-  return data;
-
-}
-
-void CCP4SRSMonomer::write_mem ( PCMemIO memIO, int version )  {
-  memIO->put_line   ( monID      );
-  memIO->put_line   ( oldMonID   );
-  memIO->put_string ( monName    );
-  memIO->put_string ( monType    );
-  memIO->put_string ( monFormula );
-  atoms      .write_mem ( memIO,version );
-  bonds      .write_mem ( memIO,version );
-  angles     .write_mem ( memIO,version );
-  torsions   .write_mem ( memIO,version );
-  chicenters .write_mem ( memIO,version );
-  planes     .write_mem ( memIO,version );
-  struct_tree.write_mem ( memIO,version );
-}
-
-Boolean CCP4SRSMonomer::read_mem ( PCMemIO memIO, int version,
-                                   Boolean * Ok )  {
-Boolean success;
-  if (Ok)  success = *Ok;
-     else  success = True;
-  memIO->get_line   ( monID     ,&success );
-  memIO->get_line   ( oldMonID  ,&success );
-  memIO->get_string ( monName   ,&success );
-  memIO->get_string ( monType   ,&success );
-  memIO->get_string ( monFormula,&success );
-  atoms      .read_mem ( memIO,version,&success );
-  bonds      .read_mem ( memIO,version,&success );
-  angles     .read_mem ( memIO,version,&success );
-  torsions   .read_mem ( memIO,version,&success );
-  chicenters .read_mem ( memIO,version,&success );
-  planes     .read_mem ( memIO,version,&success );
-  struct_tree.read_mem ( memIO,version,&success );
-  if (Ok)  *Ok = success;
-  return success;
-}
-
-
-int makeElementType ( int ElType, char chirality )  {
-  if (chirality=='S')  return ElType | CHIRAL_LEFT;
-  if (chirality=='R')  return ElType | CHIRAL_RIGHT;
-  return ElType;
-}
-
-
-PCGraph CCP4SRSMonomer::getGraph ( int *retCode )  {
-// Generate chemical graph
-PCGraph      graph;
-PCVertex     vertex;
-PCEdge       edge;
-PCCP4SRSAtom a;
-PCCP4SRSBond b;
-int          i,n,rc,vtype,vx1,vx2;
-
-  graph = new CGraph();
-  graph->SetName ( ID() );
-  rc = 0;
-
-  n = n_atoms();
-  for (i=0;(i<n) && (!rc);i++)  {
-
-    a = atom(i);
-
-    vtype = getElementNo ( a->element() );
-    if (vtype!=ELEMENT_UNKNOWN)  {
-
-      if (a->leaving()=='Y')
-        vtype |= ATOM_LEAVING;
-
-      vertex = new CVertex ( makeElementType(vtype,a->chirality()) );
-      vertex->SetName   ( a->name() );
-      vertex->SetUserID ( i );
-      graph->AddVertex  ( vertex );
-
-    } else
-      rc = 10000 + i;
-
-  }
-
-  n = n_bonds();
-  for (i=0;(i<n) && (!rc);i++)  {
-
-    b   = bond(i);
-    vx1 = b->atom1();
-    vx2 = b->atom2();
-
-    if (vx1<0)  rc = 20000 + i;
-    if (vx2<0)  rc = 30000 + i;
-
-    vx1++;
-    vx2++;
-
-    if (!rc)  {
-      edge = new CEdge ( vx1,vx2,b->order() );
-      graph->AddEdge ( edge );
-    }
-
-  }
-
-  if (rc)  {
-    delete graph;
-    graph = NULL;
-  }
-
-  if (retCode)  *retCode = rc;
-
-  return graph;
-
-}
-
-// service function, assume merging rcsb monomer with monlib one
-void CCP4SRSMonomer::merge ( PCCP4SRSMonomer monomer )  {
-PCCP4SRSAtom                   tatom;
-PCCP4SRSBond                   mbond,tbond;
-PCCP4SRSAngle                  angle;
-PCCP4SRSPlane                  plane;
-PCCP4SRSTorsion                torsion;
-PCCP4SRSChiCenter              chicenter;
-CCP4SRSContainer<CCP4SRSAtom> *matoms;
-AtomName                       aname;
-ivector                        anmatch;
-int                            i,j,k;
-
-  if (!monID[0])  strcpy ( monID,monomer->ID() );
-  else if (strcmp(monID,monomer->ID()))
-    return;  // can't merge dufferent monomers
-
-  if (!oldMonID[0])  strcpy ( oldMonID,monomer->oldID() );
-
-  if (!chem_name()[0])  CreateCopy ( monName,monomer->chem_name() );
-  if (!chem_type()[0])  CreateCopy ( monType,monomer->chem_type() );
-  if (!chem_formula()[0])
-                  CreateCopy ( monFormula,monomer->chem_formula() );
+    data->AddLoop ( MMCIF_LOOP_CHEM_COMP_ATOM,loop );
+    Atom::makeCIFTags ( loop );
+    for (i=0;i<atoms.numberOf();i++)
+      atoms.at(i)->writeToCIF ( loop,monID );
 
-  for (i=0;i<monomer->n_atoms();i++)  {
-    k = -1;
-    strcpy ( aname,monomer->atom(i)->id() );
-    for (j=0;(j<atoms.numberOf()) && (k<0);j++)
-      if (!strcmp(atoms.at(j)->id(),aname))
-        k = j;
-    if (k<0)  {
-      tatom = new CCP4SRSAtom();
-      tatom->copy ( monomer->atom(i) );
-      add ( tatom );
-    } else
-      atoms.at(k)->merge ( monomer->atom(i) );
-  }
+    struct_tree.writeToCIF ( data,monID,atoms );
 
-  GetVectorMemory ( anmatch,monomer->n_atoms(),0 );
-  getAtomNameMatch ( monomer->get_atoms(),anmatch );
+    data->AddLoop ( MMCIF_LOOP_CHEM_COMP_BOND,loop );
+    Bond::makeCIFTags ( loop );
+    for (i=0;i<bonds.numberOf();i++)
+      bonds.at(i)->writeToCIF ( loop,monID,atoms );
+
+    data->AddLoop ( MMCIF_LOOP_CHEM_COMP_ANGLE,loop );
+    Angle::makeCIFTags ( loop );
+    for (i=0;i<angles.numberOf();i++)
+      angles.at(i)->writeToCIF ( loop,monID,atoms );
+
+    data->AddLoop ( MMCIF_LOOP_CHEM_COMP_CHIR,loop );
+    ChiCenter::makeCIFTags ( loop );
+    for (i=0;i<chicenters.numberOf();i++)
+      chicenters.at(i)->writeToCIF ( loop,monID,atoms );
+
+    data->AddLoop ( MMCIF_LOOP_CHEM_COMP_TOR,loop );
+    Torsion::makeCIFTags ( loop );
+    for (i=0;i<torsions.numberOf();i++)
+      torsions.at(i)->writeToCIF ( loop,monID,atoms );
+
+    data->AddLoop ( MMCIF_LOOP_CHEM_COMP_PLANE_ATOM,loop );
+    Plane::makeCIFTags ( loop );
+    for (i=0;i<planes.numberOf();i++)
+      planes.at(i)->writeToCIF ( loop,monID,atoms );
+
+    return data;
+
+  }
+
+  void Monomer::write_mem ( PMemIO memIO, int version )  {
+    memIO->put_line   ( monID      );
+    memIO->put_line   ( oldMonID   );
+    memIO->put_string ( monName    );
+    memIO->put_string ( monType    );
+    memIO->put_string ( monFormula );
+    atoms      .write_mem ( memIO,version );
+    bonds      .write_mem ( memIO,version );
+    angles     .write_mem ( memIO,version );
+    torsions   .write_mem ( memIO,version );
+    chicenters .write_mem ( memIO,version );
+    planes     .write_mem ( memIO,version );
+    struct_tree.write_mem ( memIO,version );
+    ACDLabs    .write_mem ( memIO,version );
+    CACTVS     .write_mem ( memIO,version );
+    OpenEye    .write_mem ( memIO,version );
+    InChI      .write_mem ( memIO,version );
+  }
+
+  bool Monomer::read_mem ( PMemIO memIO, int version, bool * Ok )  {
+  bool success;
+    if (Ok)  success = *Ok;
+       else  success = true;
+    memIO->get_line   ( monID     ,&success );
+    memIO->get_line   ( oldMonID  ,&success );
+    memIO->get_string ( monName   ,&success );
+    memIO->get_string ( monType   ,&success );
+    memIO->get_string ( monFormula,&success );
+    atoms      .read_mem ( memIO,version,&success );
+    bonds      .read_mem ( memIO,version,&success );
+    angles     .read_mem ( memIO,version,&success );
+    torsions   .read_mem ( memIO,version,&success );
+    chicenters .read_mem ( memIO,version,&success );
+    planes     .read_mem ( memIO,version,&success );
+    struct_tree.read_mem ( memIO,version,&success );
+    ACDLabs    .read_mem ( memIO,version,&success );
+    CACTVS     .read_mem ( memIO,version,&success );
+    OpenEye    .read_mem ( memIO,version,&success );
+    InChI      .read_mem ( memIO,version,&success );
+
+    if (Ok)  *Ok = success;
+    return success;
+  }
+
+
+  int makeElementType ( int ElType, char chirality )  {
+    if (chirality=='S')  return ElType | mmdb::math::CHIRAL_LEFT;
+    if (chirality=='R')  return ElType | mmdb::math::CHIRAL_RIGHT;
+    return ElType;
+  }
+
+
+  mmdb::math::PGraph Monomer::getGraph ( int *retCode )  {
+  // Generate chemical graph
+  mmdb::math::PGraph  graph;
+  mmdb::math::PVertex vertex;
+  mmdb::math::PEdge   edge;
+  PAtom        a;
+  PBond        b;
+  int                 i,n,rc,vtype,vx1,vx2;
+
+    graph = new mmdb::math::Graph();
+    graph->SetName ( ID() );
+    rc = 0;
+
+    n = n_atoms();
+    for (i=0;(i<n) && (!rc);i++)  {
+
+      a = atom(i);
+
+      vtype = mmdb::getElementNo ( a->element() );
+      if (vtype!=mmdb::ELEMENT_UNKNOWN)  {
+
+        if (a->leaving()=='Y')
+          vtype |= mmdb::math::ATOM_LEAVING;
+
+        vertex = new mmdb::math::Vertex (
+                     makeElementType(vtype,a->chirality()) );
+        vertex->SetName   ( a->name() );
+        vertex->SetUserID ( i );
+        graph->AddVertex  ( vertex );
+
+      } else
+        rc = 10000 + i;
+
+    }
+
+    n = n_bonds();
+    for (i=0;(i<n) && (!rc);i++)  {
+
+      b   = bond(i);
+      vx1 = b->atom1();
+      vx2 = b->atom2();
 
-  matoms = monomer->get_atoms();
-  for (i=0;i<monomer->n_bonds();i++)  {
-    k     = -1;
-    mbond = monomer->bond(i);
-    for (j=0;(j<bonds.numberOf()) && (k<0);j++)
-      if (mbond->compare(*matoms,bonds.at(j),atoms))
-        k = j;
-    if (k<0)  {
-      tbond = new CCP4SRSBond();
-      if (tbond->copy(atoms,mbond,*matoms))
-            bonds.add ( tbond );
-      else  delete tbond;
-    } else if (bonds.at(k)->length()<=1.0e-10)
-      bonds.at(k)->copy ( mbond,anmatch );
-  }
+      if (vx1<0)  rc = 20000 + i;
+      if (vx2<0)  rc = 30000 + i;
+
+      vx1++;
+      vx2++;
+
+      if (!rc)  {
+        edge = new mmdb::math::Edge ( vx1,vx2,b->order() );
+        graph->AddEdge ( edge );
+      }
 
-  if (angles.numberOf()<=0)  {
-    for (i=0;i<monomer->n_angles();i++)  {
-      angle = new CCP4SRSAngle();
-      angle->copy ( monomer->angle(i),anmatch );
-      angles.add ( angle );
     }
-  }
 
-  if (torsions.numberOf()<=0)  {
-    for (i=0;i<monomer->n_torsions();i++)  {
-      torsion = new CCP4SRSTorsion();
-      torsion->copy ( monomer->torsion(i),anmatch );
-      torsions.add ( torsion );
+    if (rc)  {
+      delete graph;
+      graph = NULL;
     }
+
+    if (retCode)  *retCode = rc;
+
+    return graph;
+
   }
 
-  if (chicenters.numberOf()<=0)  {
-    for (i=0;i<monomer->n_chicenters();i++)  {
-      chicenter = new CCP4SRSChiCenter();
-      chicenter->copy ( monomer->chicenter(i),anmatch );
-      chicenters.add ( chicenter );
+  // service function, assume merging rcsb monomer with monlib one
+  void Monomer::merge ( PMonomer monomer )  {
+  PAtom            tatom;
+  PBond            mbond,tbond;
+  PAngle           angle;
+  PPlane           plane;
+  PTorsion         torsion;
+  PChiCenter       chicenter;
+  Container<Atom> *matoms;
+  mmdb::AtomName   aname;
+  mmdb::ivector    anmatch;
+  int              i,j,k;
+
+    if (!monID[0])  strcpy ( monID,monomer->ID() );
+    else if (strcmp(monID,monomer->ID()))
+      return;  // can't merge dufferent monomers
+
+    if (!oldMonID[0])  strcpy ( oldMonID,monomer->oldID() );
+
+    if (!chem_name()[0])  mmdb::CreateCopy ( monName,monomer->chem_name() );
+    if (!chem_type()[0])  mmdb::CreateCopy ( monType,monomer->chem_type() );
+    if (!chem_formula()[0])
+                    mmdb::CreateCopy ( monFormula,monomer->chem_formula() );
+    if (ACDLabs.isEmpty())  ACDLabs.copy ( monomer->getACDLabs() );
+    if (CACTVS .isEmpty())  CACTVS .copy ( monomer->getCACTVS () );
+    if (OpenEye.isEmpty())  OpenEye.copy ( monomer->getOpenEye() );
+    if (InChI  .isEmpty())  InChI  .copy ( monomer->getInChI  () );
+
+    for (i=0;i<monomer->n_atoms();i++)  {
+      k = -1;
+      strcpy ( aname,monomer->atom(i)->id() );
+      for (j=0;(j<atoms.numberOf()) && (k<0);j++)
+        if (!strcmp(atoms.at(j)->id(),aname))
+          k = j;
+      if (k<0)  {
+        tatom = new Atom();
+        tatom->copy ( monomer->atom(i) );
+        add ( tatom );
+      } else
+        atoms.at(k)->merge ( monomer->atom(i) );
+    }
+
+    mmdb::GetVectorMemory ( anmatch,monomer->n_atoms(),0 );
+    getAtomNameMatch ( monomer->get_atoms(),anmatch );
+
+    matoms = monomer->get_atoms();
+    for (i=0;i<monomer->n_bonds();i++)  {
+      k     = -1;
+      mbond = monomer->bond(i);
+      for (j=0;(j<bonds.numberOf()) && (k<0);j++)
+        if (mbond->compare(*matoms,bonds.at(j),atoms))
+          k = j;
+      if (k<0)  {
+        tbond = new Bond();
+        if (tbond->copy(atoms,mbond,*matoms))
+              bonds.add ( tbond );
+        else  delete tbond;
+      } else if (bonds.at(k)->length()<=1.0e-10)
+        bonds.at(k)->copy ( mbond,anmatch );
+    }
+
+    if (angles.numberOf()<=0)  {
+      for (i=0;i<monomer->n_angles();i++)  {
+        angle = new Angle();
+        angle->copy ( monomer->angle(i),anmatch );
+        angles.add ( angle );
+      }
     }
-  }
 
-  if (planes.numberOf()<=0)  {
-    for (i=0;i<monomer->n_planes();i++)  {
-      plane = new CCP4SRSPlane();
-      plane->copy ( monomer->plane(i),anmatch );
-      planes.add ( plane );
+    if (torsions.numberOf()<=0)  {
+      for (i=0;i<monomer->n_torsions();i++)  {
+        torsion = new Torsion();
+        torsion->copy ( monomer->torsion(i),anmatch );
+        torsions.add ( torsion );
+      }
+    }
+
+    if (chicenters.numberOf()<=0)  {
+      for (i=0;i<monomer->n_chicenters();i++)  {
+        chicenter = new ChiCenter();
+        chicenter->copy ( monomer->chicenter(i),anmatch );
+        chicenters.add ( chicenter );
+      }
     }
-  }
 
-  if (struct_tree.size()<=0)
-    struct_tree.copy ( monomer->tree(),anmatch );
+    if (planes.numberOf()<=0)  {
+      for (i=0;i<monomer->n_planes();i++)  {
+        plane = new Plane();
+        plane->copy ( monomer->plane(i),anmatch );
+        planes.add ( plane );
+      }
+    }
 
-  FreeVectorMemory ( anmatch,0 );
+    if (struct_tree.size()<=0)
+      struct_tree.copy ( monomer->tree(),anmatch );
+
+    mmdb::FreeVectorMemory ( anmatch,0 );
+
+  }
 
-}
+}  // namespace
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_monomer.h ccp4srs/ccp4srs/ccp4srs_monomer.h
--- ccp4srs-old/ccp4srs/ccp4srs_monomer.h	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_monomer.h	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_monomer.h, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_monomer.h $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010-2011.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,16 +22,16 @@
 //
 //  =================================================================
 //
-//    18.10.11   <--  Date of Last Modification.
+//    03.02.14   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_monomer  <interface>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSMonomer  - monomer structure
+//  **** Classes :  ccp4srs::Monomer  - monomer structure
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010-2011
+//  (C) E. Krissinel 2010-2014
 //
 //  =================================================================
 //
@@ -39,9 +39,8 @@
 #ifndef CCP4SRS_MONOMER_H
 #define CCP4SRS_MONOMER_H
 
-#include "mmdb/mmdb_mmcif.h"
-#include "mmdb/mmdb_graph.h"
-#include "mmdb/mmdb_defs.h"
+#include "mmdb2/mmdb_mmcif_.h"
+#include "mmdb2/mmdb_math_graph.h"
 
 #include "ccp4srs_entry.h"
 #include "ccp4srs_bond.h"
@@ -50,148 +49,158 @@
 #include "ccp4srs_chicenter.h"
 #include "ccp4srs_plane.h"
 #include "ccp4srs_tree.h"
+#include "ccp4srs_smiles.h"
+#include "ccp4srs_types.h"
 
-DefineClass(CCP4SRSMonomer)
+namespace ccp4srs  {
 
-class CCP4SRSMonomer : public CCP4SRSEntry  {
+  DefineClass(Monomer);
 
-  public:
-    CCP4SRSMonomer();
-    ~CCP4SRSMonomer();
-
-    virtual int type()  { return CCP4SRSEntry::Monomer; }
-
-    void   reset();  // deletes all data
-
-    inline cpstr ID   ()  { return monID;    }
-    inline cpstr oldID()  { return oldMonID; }
-    void   setOldID   ( cpstr oldID );
-
-    cpstr  chem_name   ();
-    cpstr  chem_type   ();
-    cpstr  chem_formula();
-
-    inline int n_atoms     () { return atoms     .numberOf(); }
-    inline int n_bonds     () { return bonds     .numberOf(); }
-    inline int n_angles    () { return angles    .numberOf(); }
-    inline int n_torsions  () { return torsions  .numberOf(); }
-    inline int n_chicenters() { return chicenters.numberOf(); }
-    inline int n_planes    () { return planes    .numberOf(); }
-
-    inline PCCP4SRSAtom  atom  ( int n ) { return atoms   .at(n); }
-    inline PCCP4SRSBond  bond  ( int n ) { return bonds   .at(n); }
-    inline PCCP4SRSAngle angle ( int n ) { return angles  .at(n); }
-    inline PCCP4SRSPlane plane ( int n ) { return planes  .at(n); }
-    inline PCCP4SRSTree  tree  ()        { return &struct_tree;   }
-    inline PCCP4SRSTorsion torsion ( int n )
-                                         { return torsions.at(n); }
-    inline PCCP4SRSChiCenter chicenter ( int n )
-                                       { return chicenters.at(n); }
-
-    inline void add ( PCCP4SRSAtom  atom    ) { atoms .add(atom ); }
-    inline void add ( PCCP4SRSBond  bond    ) { bonds .add(bond ); }
-    inline void add ( PCCP4SRSAngle angle   ) { angles.add(angle); }
-    inline void add ( PCCP4SRSPlane plane   ) { planes.add(plane); }
-    inline void add ( PCCP4SRSTree  stree   )
-                                        { struct_tree.copy(stree); }
-    inline void add ( PCCP4SRSTorsion torsion )
-                                          { torsions.add(torsion); }
-    inline void add ( PCCP4SRSChiCenter chicenter )
-                                      { chicenters.add(chicenter); }
-
-    inline CCP4SRSContainer<CCP4SRSAtom> *get_atoms()
-                                                { return &atoms;      }
-    inline CCP4SRSContainer<CCP4SRSBond> *get_bonds()
-                                                { return &bonds;      }
-    inline CCP4SRSContainer<CCP4SRSAngle> *get_angles()
-                                                { return &angles;     }
-    inline CCP4SRSContainer<CCP4SRSTorsion> *get_torsions()
-                                                { return &torsions;   }
-    inline CCP4SRSContainer<CCP4SRSChiCenter> *get_chicenters()
-                                                { return &chicenters; }
-    inline CCP4SRSContainer<CCP4SRSPlane> *get_planes()
-                                                { return &planes;     }
-    inline CCP4SRSTree *get_tree() { return &struct_tree; }
-
-    int atom_no   ( cpstr aname );
-    int get_bound ( int  atomNo, cpstr elem, int serNo );
-    int get_bound ( int  atomNo, int n );
-    int get_bound ( cpstr aname, int n );
-
-    int addHydrogens ( PCResidue R );
-
-    //  getAtomNameMatch(..) returns anmatch[i], i=0..nAtoms-1, equal
-    // to j such that name(Atom[i])==name(A[j]). Note that atom names
-    // are similarly aligned and space-padded in MMDB, but not in SRS.
-    // However, the proper alignment is done on fly. If ith atom in
-    // the structue is not found in A, anmatch[i] is set -1.
-    //   If array A contains atoms in different alternative
-    // conformations, the the value of altLoc is interpreted as
-    // follows:
-    //    NULL  - the highest occupancy atom will be taken
-    //            if all occupancies are equal then atom with
-    //            first altLoc taken
-    //    other - atoms with given altLoc are taken. If such
-    //            altLoc is not found, the function does as if
-    //            NULL value for altLoc is given.
-    //   A clean PDB file is anticipated, so that atoms with
-    // alternative conformations are grouped together.
-    //   It is Ok to have NULL pointers in A.
-    void getAtomNameMatch ( PPCAtom A, int nat, pstr altLoc,
-                            ivector anmatch );
-
-    /// \brief Matches atoms in given container with atoms in the
-    ///   monomer by atom names.
-    ///  \param[in] A pointer to atom container
-    ///  \param[out] anmatch allocated integer vector
-    ///         [0..A->numberOf()-1], where the match will be returned:
-    /// \arg \b anmatch[i]>=0 : atom A->at(i) matches anmathch[i]-th
-    ///         atom in the monomer
-    /// \arg \b anmatch[i]<0  : atom A->at(i) does not have a name match
-    ///         in the monomer
-    void getAtomNameMatch ( CCP4SRSContainer<CCP4SRSAtom> *A,
-                            ivector anmatch );
-
-    PCGraph getGraph ( int *retCode );
-
-    void getLeavingAtoms ( int & nLeavingAtoms,
-                           ivector & leavingAtom,
-                           ivector & bondedAtom );
-
-    // Return code:
-    //     CCP4SRS_Ok    success
-    int readFromCIF ( PCMMCIFData mmCIFData, pstr error_desc = NULL );
-
-    PCMMCIFData makeCIF();  // return to be deleted by application
-
-    // service function
-    void merge ( PCCP4SRSMonomer monomer );
-
-  protected:
-    ResName                            monID;
-    ResName                            oldMonID;
-    pstr                               monName;
-    pstr                               monType;
-    pstr                               monFormula;
-    CCP4SRSContainer<CCP4SRSAtom>      atoms;
-    CCP4SRSContainer<CCP4SRSBond>      bonds;
-    CCP4SRSContainer<CCP4SRSAngle>     angles;
-    CCP4SRSContainer<CCP4SRSTorsion>   torsions;
-    CCP4SRSContainer<CCP4SRSChiCenter> chicenters;
-    CCP4SRSContainer<CCP4SRSPlane>     planes;
-    CCP4SRSTree                        struct_tree;
-
-    void  Init();
-
-    void  readMonIDFromCIF ( PCMMCIFLoop   loop );
-    void  readMonIDFromCIF ( PCMMCIFStruct mmCIFStruct );
-    int   readFromCIF_ccp4 ( PCMMCIFData   mmCIFData, pstr error_desc );
-    int   readFromCIF_rcsb ( PCMMCIFData   mmCIFData, pstr error_desc );
-
-    virtual void    write_mem ( PCMemIO memIO, int version );
-    virtual Boolean read_mem  ( PCMemIO memIO, int version,
-                                Boolean * Ok = NULL );
+  class Monomer : public Entry  {
 
-};
+    public:
+      Monomer();
+      ~Monomer();
+
+      virtual int type()  { return Entry::Monomer; }
+
+      void   reset();  // deletes all data
+
+      inline mmdb::cpstr ID   ()  { return monID;    }
+      inline mmdb::cpstr oldID()  { return oldMonID; }
+      void   setOldID   ( mmdb::cpstr oldID );
+
+      mmdb::cpstr  chem_name   ();
+      mmdb::cpstr  chem_type   ();
+      mmdb::cpstr  chem_formula();
+
+      inline int n_atoms     () { return atoms     .numberOf(); }
+      inline int n_bonds     () { return bonds     .numberOf(); }
+      inline int n_angles    () { return angles    .numberOf(); }
+      inline int n_torsions  () { return torsions  .numberOf(); }
+      inline int n_chicenters() { return chicenters.numberOf(); }
+      inline int n_planes    () { return planes    .numberOf(); }
+
+      inline PAtom  atom  ( int n ) { return atoms   .at(n); }
+      inline PBond  bond  ( int n ) { return bonds   .at(n); }
+      inline PAngle angle ( int n ) { return angles  .at(n); }
+      inline PPlane plane ( int n ) { return planes  .at(n); }
+      inline PTree  tree  ()        { return &struct_tree;   }
+      inline PTorsion torsion ( int n )
+                                           { return torsions.at(n); }
+      inline PChiCenter chicenter ( int n )
+                                         { return chicenters.at(n); }
+
+      inline void add ( PAtom  atom    ) { atoms .add(atom ); }
+      inline void add ( PBond  bond    ) { bonds .add(bond ); }
+      inline void add ( PAngle angle   ) { angles.add(angle); }
+      inline void add ( PPlane plane   ) { planes.add(plane); }
+      inline void add ( PTree  stree   ) { struct_tree.copy(stree); }
+      inline void add ( PTorsion torsion )
+                                            { torsions.add(torsion); }
+      inline void add ( PChiCenter chicenter )
+                                        { chicenters.add(chicenter); }
+
+      inline Container<Atom>    *get_atoms   () { return &atoms;      }
+      inline Container<Bond>    *get_bonds   () { return &bonds;      }
+      inline Container<Angle>   *get_angles  () { return &angles;     }
+      inline Container<Torsion> *get_torsions() { return &torsions;   }
+      inline Container<ChiCenter> *get_chicenters() { return &chicenters; }
+      inline Container<Plane>   *get_planes  () { return &planes;     }
+      inline Tree *get_tree() { return &struct_tree; }
+
+      inline Smiles *getACDLabs()  { return &ACDLabs; }
+      inline Smiles *getCACTVS ()  { return &CACTVS;  }
+      inline Smiles *getOpenEye()  { return &OpenEye; }
+      inline Smiles *getInChI  ()  { return &InChI;   }
+
+      int atom_no   ( mmdb::cpstr aname );
+      int get_bound ( int  atomNo, mmdb::cpstr elem, int serNo );
+      int get_bound ( int  atomNo, int n );
+      int get_bound ( mmdb::cpstr aname, int n );
+
+      CCP4SRS_RC addHydrogens ( mmdb::PResidue R );
+
+      //  getAtomNameMatch(..) returns anmatch[i], i=0..nAtoms-1, equal
+      // to j such that name(Atom[i])==name(A[j]). Note that atom names
+      // are similarly aligned and space-padded in MMDB, but not in SRS.
+      // However, the proper alignment is done on fly. If ith atom in
+      // the structue is not found in A, anmatch[i] is set -1.
+      //   If array A contains atoms in different alternative
+      // conformations, the the value of altLoc is interpreted as
+      // follows:
+      //    NULL  - the highest occupancy atom will be taken
+      //            if all occupancies are equal then atom with
+      //            first altLoc taken
+      //    other - atoms with given altLoc are taken. If such
+      //            altLoc is not found, the function does as if
+      //            NULL value for altLoc is given.
+      //   A clean PDB file is anticipated, so that atoms with
+      // alternative conformations are grouped together.
+      //   It is Ok to have NULL pointers in A.
+      void getAtomNameMatch ( mmdb::PPAtom A, int nat, mmdb::pstr altLoc,
+                              mmdb::ivector anmatch );
+
+      /// \brief Matches atoms in given container with atoms in the
+      ///   monomer by atom names.
+      ///  \param[in] A pointer to atom container
+      ///  \param[out] anmatch allocated integer vector
+      ///         [0..A->numberOf()-1], where the match will be returned:
+      /// \arg \b anmatch[i]>=0 : atom A->at(i) matches anmathch[i]-th
+      ///         atom in the monomer
+      /// \arg \b anmatch[i]<0  : atom A->at(i) does not have a name match
+      ///         in the monomer
+      void getAtomNameMatch ( Container<Atom> *A, mmdb::ivector anmatch );
+
+      mmdb::math::PGraph getGraph ( int *retCode );
+
+      void getLeavingAtoms ( int & nLeavingAtoms,
+                             mmdb::ivector & leavingAtom,
+                             mmdb::ivector & bondedAtom );
+
+      // Return code:
+      //     CCP4SRS_Ok    success
+      int readFromCIF ( mmdb::mmcif::PData mmCIFData,
+                        mmdb::pstr error_desc = NULL );
+
+      mmdb::mmcif::PData makeCIF();  // return to be deleted by application
+
+      // service function
+      void merge ( PMonomer monomer );
+
+    protected:
+      mmdb::ResName        monID;
+      mmdb::ResName        oldMonID;
+      mmdb::pstr           monName;
+      mmdb::pstr           monType;
+      mmdb::pstr           monFormula;
+      Container<Atom>      atoms;
+      Container<Bond>      bonds;
+      Container<Angle>     angles;
+      Container<Torsion>   torsions;
+      Container<ChiCenter> chicenters;
+      Container<Plane>     planes;
+      Tree                 struct_tree;
+      Smiles               ACDLabs;
+      Smiles               CACTVS;
+      Smiles               OpenEye;
+      Smiles               InChI;
+
+      void  Init();
+
+      void  readMonIDFromCIF ( mmdb::mmcif::PLoop   loop );
+      void  readMonIDFromCIF ( mmdb::mmcif::PStruct mmCIFStruct );
+      int   readFromCIF_ccp4 ( mmdb::mmcif::PData   mmCIFData,
+                               mmdb::pstr error_desc );
+      int   readFromCIF_rcsb ( mmdb::mmcif::PData   mmCIFData,
+                               mmdb::pstr error_desc );
+
+      virtual void write_mem ( PMemIO memIO, int version );
+      virtual bool read_mem  ( PMemIO memIO, int version,
+                               bool * Ok = NULL );
+
+  };
+
+}  // namespace ccp4srs
 
 #endif // CCP4SRS_MONOMER_H
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_plane.cpp ccp4srs/ccp4srs/ccp4srs_plane.cpp
--- ccp4srs-old/ccp4srs/ccp4srs_plane.cpp	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_plane.cpp	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_plane.cpp, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_plane.cpp $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010-2011.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,181 +22,181 @@
 //
 //  =================================================================
 //
-//    18.10.11   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_plane  <implementation>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSPlane  - plain group of atoms
+//  **** Classes :  ccp4srs::Plane  - plain group of atoms
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010-2011
+//  (C) E. Krissinel 2010-2013
 //
 //  =================================================================
 //
 
-
-#ifndef __STRING_H
 #include <string.h>
-#endif
 
 #include "ccp4srs_plane.h"
 #include "ccp4srs_defs.h"
 
-CCP4SRSPlane::CCP4SRSPlane()  {
-  plane_id[0] = char(0);
-  n_atoms     = 0;
-  plane_atoms = NULL;
-  dist_esd    = NULL;
-}
-
-CCP4SRSPlane::~CCP4SRSPlane()  {
-  empty();
-}
-
-void CCP4SRSPlane::empty()  {
-  FreeVectorMemory ( plane_atoms,0 );
-  FreeVectorMemory ( dist_esd   ,0 );
-  n_atoms = 0;
-}
-
-
-void CCP4SRSPlane::makeCIFTags ( PCMMCIFLoop mmCIFLoop )  {
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_COMP_ID  );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_PLANE_ID );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID  );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_DIST_ESD );
-}
-
-int CCP4SRSPlane::readFromCIF ( PCMMCIFLoop mmCIFLoop, int planeNo,
-                             CCP4SRSContainer<CCP4SRSAtom> & atoms )  {
-PlaneID planeId;
-int     i,j,k,n,i1,loop_len;
-int     rc;
-
-  empty();
-
-  rc = 0;
-  loop_len = mmCIFLoop->GetLoopLength();
-  if (loop_len<=0)
-    return CCP4SRSPlane::EmptyLoop;
-
-  i1 = -1;
-  n  = 0;
-  for (i=0;(i<loop_len) && (n<=planeNo);i++)  {
-    mmCIFLoop->CopyString ( plane_id,sizeof(PlaneID)-1,
-                            MMCIF_TAG_PLANE_ID,i,rc );
-    k = -1;
-    for (j=i-1;(j>=0) && (k<0);j--)  {
-      mmCIFLoop->CopyString ( planeId,sizeof(PlaneID)-1,
-                              MMCIF_TAG_PLANE_ID,j,rc );
-      if (!strcmp(plane_id,planeId))
-        k = j;
-    }
-    if (k<0)  {
-      n++;
-      i1 = i;
-    }
+namespace ccp4srs  {
+
+  Plane::Plane()  {
+    plane_id[0] = char(0);
+    n_atoms     = 0;
+    plane_atoms = NULL;
+    dist_esd    = NULL;
   }
 
-  if (n<=planeNo)
-    return CCP4SRSPlane::NoMorePlanes;
+  Plane::~Plane()  {
+    empty();
+  }
+
+  void Plane::empty()  {
+    mmdb::FreeVectorMemory ( plane_atoms,0 );
+    mmdb::FreeVectorMemory ( dist_esd   ,0 );
+    n_atoms = 0;
+  }
 
-  GetVectorMemory ( plane_atoms,loop_len-i1,0 );
-  GetVectorMemory ( dist_esd   ,loop_len-i1,0 );
 
-  for (i=i1;i<loop_len;i++)  {
-    mmCIFLoop->CopyString ( planeId,sizeof(PlaneID)-1,
-                            MMCIF_TAG_PLANE_ID,i,rc );
-    if (!strcmp(planeId,plane_id))  {
-      get_atom_from_cif ( plane_atoms[n_atoms],mmCIFLoop,
-                          MMCIF_TAG_ATOM_ID,i,atoms,rc );
-      mmCIFLoop->CopyReal ( dist_esd[n_atoms],MMCIF_TAG_DIST_ESD,i,rc );
-      n_atoms++;
-    }
+  void Plane::makeCIFTags ( mmdb::mmcif::PLoop mmCIFLoop )  {
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_COMP_ID  );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_PLANE_ID );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID  );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_DIST_ESD );
   }
 
-  return rc;
+  int Plane::readFromCIF ( mmdb::mmcif::PLoop mmCIFLoop,
+                          int planeNo, Container<Atom> & atoms )  {
+  PlaneID planeId;
+  int     i,j,k,n,i1,loop_len;
+  int     rc;
+
+    empty();
+
+    rc = 0;
+    loop_len = mmCIFLoop->GetLoopLength();
+    if (loop_len<=0)
+      return Plane::EmptyLoop;
+
+    i1 = -1;
+    n  = 0;
+    for (i=0;(i<loop_len) && (n<=planeNo);i++)  {
+      mmCIFLoop->CopyString ( plane_id,sizeof(PlaneID)-1,
+                              MMCIF_TAG_PLANE_ID,i,rc );
+      k = -1;
+      for (j=i-1;(j>=0) && (k<0);j--)  {
+        mmCIFLoop->CopyString ( planeId,sizeof(PlaneID)-1,
+                                MMCIF_TAG_PLANE_ID,j,rc );
+        if (!strcmp(plane_id,planeId))
+          k = j;
+      }
+      if (k<0)  {
+        n++;
+        i1 = i;
+      }
+    }
+
+    if (n<=planeNo)
+      return Plane::NoMorePlanes;
+
+    mmdb::GetVectorMemory ( plane_atoms,loop_len-i1,0 );
+    mmdb::GetVectorMemory ( dist_esd   ,loop_len-i1,0 );
 
-}
+    for (i=i1;i<loop_len;i++)  {
+      mmCIFLoop->CopyString ( planeId,sizeof(PlaneID)-1,
+                              MMCIF_TAG_PLANE_ID,i,rc );
+      if (!strcmp(planeId,plane_id))  {
+        get_atom_from_cif ( plane_atoms[n_atoms],mmCIFLoop,
+                            MMCIF_TAG_ATOM_ID,i,atoms,rc );
+        mmCIFLoop->CopyReal ( dist_esd[n_atoms],MMCIF_TAG_DIST_ESD,i,rc );
+        n_atoms++;
+      }
+    }
 
-/*
-loop_
-_chem_comp_plane_atom.comp_id
-_chem_comp_plane_atom.plane_id
-_chem_comp_plane_atom.atom_id
-_chem_comp_plane_atom.dist_esd
- ATP      plan-1    N9        0.020
-*/
+    return rc;
 
-void CCP4SRSPlane::writeToCIF ( PCMMCIFLoop mmCIFLoop, cpstr monID,
-                             CCP4SRSContainer<CCP4SRSAtom> & atoms )  {
-int i;
-  for (i=0;i<n_atoms;i++)  {
-    mmCIFLoop->AddString ( monID,False     );
-    mmCIFLoop->AddString ( plane_id,False  );
-    add_atom_to_cif      ( mmCIFLoop,plane_atoms[i],atoms );
-    mmCIFLoop->AddReal   ( dist_esd[i],"%10.3f" );
   }
-}
 
+  /*
+  loop_
+  _chem_comp_plane_atom.comp_id
+  _chem_comp_plane_atom.plane_id
+  _chem_comp_plane_atom.atom_id
+  _chem_comp_plane_atom.dist_esd
+   ATP      plan-1    N9        0.020
+  */
+
+  void Plane::writeToCIF ( mmdb::mmcif::PLoop mmCIFLoop,
+                           mmdb::cpstr monID,
+                           Container<Atom> & atoms )  {
+  int i;
+    for (i=0;i<n_atoms;i++)  {
+      mmCIFLoop->AddString ( monID,false     );
+      mmCIFLoop->AddString ( plane_id,false  );
+      add_atom_to_cif      ( mmCIFLoop,plane_atoms[i],atoms );
+      mmCIFLoop->AddReal   ( dist_esd[i],"%10.3f" );
+    }
+  }
 
-void CCP4SRSPlane::copy ( PCCP4SRSPlane plane, ivector anmatch )  {
-int i;
 
-  empty();
+  void Plane::copy ( PPlane plane, mmdb::ivector anmatch )  {
+  int i;
 
-  strcpy ( plane_id,plane->id() );
-  n_atoms = plane->size();
-  if (n_atoms>0)  {
-    GetVectorMemory ( plane_atoms,n_atoms,0 );
-    GetVectorMemory ( dist_esd   ,n_atoms,0 );
-    if (anmatch)  {
-      for (i=0;i<n_atoms;i++)  {
-        plane_atoms[i] = anmatch[plane->atom(i)];
-        dist_esd   [i] = plane->esd  ( i );
-      }
-    } else  {
-      for (i=0;i<n_atoms;i++)  {
-        plane_atoms[i] = plane->atom ( i );
-        dist_esd   [i] = plane->esd  ( i );
+    empty();
+
+    strcpy ( plane_id,plane->id() );
+    n_atoms = plane->size();
+    if (n_atoms>0)  {
+      mmdb::GetVectorMemory ( plane_atoms,n_atoms,0 );
+      mmdb::GetVectorMemory ( dist_esd   ,n_atoms,0 );
+      if (anmatch)  {
+        for (i=0;i<n_atoms;i++)  {
+          plane_atoms[i] = anmatch[plane->atom(i)];
+          dist_esd   [i] = plane->esd  ( i );
+        }
+      } else  {
+        for (i=0;i<n_atoms;i++)  {
+          plane_atoms[i] = plane->atom ( i );
+          dist_esd   [i] = plane->esd  ( i );
+        }
       }
     }
-  }
 
-}
+  }
 
-void  CCP4SRSPlane::write_mem ( PCMemIO memIO, int version )  {
-UNUSED_ARGUMENT(version);
-int  i;
-  memIO->put_line   ( plane_id );
-  memIO->put_ishort ( n_atoms  );
-  for (i=0;i<n_atoms;i++)  {
-    memIO->put_integer ( plane_atoms[i] );
-    memIO->put_float   ( dist_esd   [i] );
-  }
-}
-
-Boolean CCP4SRSPlane::read_mem ( PCMemIO memIO, int version,
-                                 Boolean * Ok )  {
-UNUSED_ARGUMENT(version);
-int     i;
-Boolean success;
-  empty();
-  if (Ok)  success = *Ok;
-     else  success = True;
-  memIO->get_line   ( plane_id,&success );
-  memIO->get_ishort ( n_atoms ,&success );
-  if (n_atoms>0)  {
-    GetVectorMemory ( plane_atoms,n_atoms,0 );
-    GetVectorMemory ( dist_esd   ,n_atoms,0 );
+  void  Plane::write_mem ( PMemIO memIO, int version )  {
+  UNUSED_ARGUMENT(version);
+  int  i;
+    memIO->put_line   ( plane_id );
+    memIO->put_ishort ( n_atoms  );
     for (i=0;i<n_atoms;i++)  {
-      memIO->get_integer ( plane_atoms[i],&success );
-      memIO->get_float   ( dist_esd   [i],&success );
+      memIO->put_integer ( plane_atoms[i] );
+      memIO->put_float   ( dist_esd   [i] );
+    }
+  }
+
+  bool Plane::read_mem ( PMemIO memIO, int version, bool * Ok )  {
+  UNUSED_ARGUMENT(version);
+  int     i;
+  bool success;
+    empty();
+    if (Ok)  success = *Ok;
+       else  success = true;
+    memIO->get_line   ( plane_id,&success );
+    memIO->get_ishort ( n_atoms ,&success );
+    if (n_atoms>0)  {
+      mmdb::GetVectorMemory ( plane_atoms,n_atoms,0 );
+      mmdb::GetVectorMemory ( dist_esd   ,n_atoms,0 );
+      for (i=0;i<n_atoms;i++)  {
+        memIO->get_integer ( plane_atoms[i],&success );
+        memIO->get_float   ( dist_esd   [i],&success );
+      }
     }
+    if (Ok)  *Ok = success;
+    return success;
   }
-  if (Ok)  *Ok = success;
-  return success;
-}
 
+}  // namespace ccp4srs
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_plane.h ccp4srs/ccp4srs/ccp4srs_plane.h
--- ccp4srs-old/ccp4srs/ccp4srs_plane.h	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_plane.h	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_plane.h, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_plane.h $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010-2011.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,16 +22,16 @@
 //
 //  =================================================================
 //
-//    18.10.11   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_plane  <interface>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSPlane  - plain group of atoms
+//  **** Classes :  ccp4srs::Plane  - plain group of atoms
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010-2011
+//  (C) E. Krissinel 2010-2013
 //
 //  =================================================================
 //
@@ -41,46 +41,49 @@
 
 #include "ccp4srs_atom.h"
 
-DefineClass(CCP4SRSPlane)
+namespace ccp4srs  {
 
-typedef char PlaneID[20];
+  DefineClass(Plane);
 
-class CCP4SRSPlane  {
+  typedef char PlaneID[20];
 
-  public:
+  class Plane  {
 
-    enum { Ok=0,EmptyLoop=-11111,NoMorePlanes=-11112 };
+    public:
 
-    CCP4SRSPlane();
-    virtual ~CCP4SRSPlane();
+      enum { Ok=0,EmptyLoop=-11111,NoMorePlanes=-11112 };
 
-    inline cpstr    id   () { return plane_id;    }
-    inline int      size () { return n_atoms;     }
-    inline ivector  atoms() { return plane_atoms; }
-    inline rvector  esds () { return dist_esd;    }
-    inline int      atom ( int atomNo ) { return plane_atoms[atomNo]; }
-    inline realtype esd  ( int atomNo ) { return dist_esd   [atomNo]; }
+      Plane();
+      virtual ~Plane();
 
-    static void makeCIFTags ( PCMMCIFLoop mmCIFLoop );
-    int  readFromCIF ( PCMMCIFLoop mmCIFLoop, int planeNo,
-                       CCP4SRSContainer<CCP4SRSAtom> & atoms );
-    void writeToCIF  ( PCMMCIFLoop mmCIFLoop, cpstr monID,
-                       CCP4SRSContainer<CCP4SRSAtom> & atoms );
+      inline mmdb::cpstr    id   () { return plane_id;    }
+      inline int            size () { return n_atoms;     }
+      inline mmdb::ivector  atoms() { return plane_atoms; }
+      inline mmdb::rvector  esds () { return dist_esd;    }
+      inline int            atom ( int atomNo ) { return plane_atoms[atomNo]; }
+      inline mmdb::realtype esd  ( int atomNo ) { return dist_esd   [atomNo]; }
 
-    void    write_mem ( PCMemIO memIO, int version );
-    Boolean read_mem  ( PCMemIO memIO, int version,
-                        Boolean * Ok = NULL );
+      static void makeCIFTags ( mmdb::mmcif::PLoop mmCIFLoop );
+      int  readFromCIF ( mmdb::mmcif::PLoop mmCIFLoop, int planeNo,
+                         Container<Atom> & atoms );
+      void writeToCIF  ( mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID,
+                         Container<Atom> & atoms );
 
-    void copy ( PCCP4SRSPlane plane, ivector anmatch=NULL );
+      void write_mem ( PMemIO memIO, int version );
+      bool read_mem  ( PMemIO memIO, int version, bool * Ok = NULL );
 
-  protected:
-    PlaneID  plane_id;     //!< plane id
-    int      n_atoms;      //!< plane size
-    ivector  plane_atoms;  //!< vector of plain's atom names
-    rvector  dist_esd;     //!< vector of distance esds from the plane
+      void copy ( PPlane plane, mmdb::ivector anmatch=NULL );
 
-    void  empty();
+    protected:
+      PlaneID       plane_id;     //!< plane id
+      int           n_atoms;      //!< plane size
+      mmdb::ivector plane_atoms;  //!< vector of plain's atom names
+      mmdb::rvector dist_esd;     //!< vector of distance esds from the plane
 
-};
+      void  empty();
+
+  };
+
+}  // namespace ccp4srs
 
 #endif // CCP4SRS_PLANE_H
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_smiles.cpp ccp4srs/ccp4srs/ccp4srs_smiles.cpp
--- ccp4srs-old/ccp4srs/ccp4srs_smiles.cpp	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/ccp4srs/ccp4srs_smiles.cpp	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,370 @@
+//  $Id: ccp4srs_smiles.cpp $
+//  =================================================================
+//
+//   CCP4 SRS Library: Storage, Retrieval and Search support for
+//   CCP4 ligand data.
+//
+//   Copyright (C) Eugene Krissinel 2010-2013.
+//
+//   This library is free software: you can redistribute it and/or
+//   modify it under the terms of the GNU Lesser General Public
+//   License version 3, modified in accordance with the provisions
+//   of the license to address the requirements of UK law.
+//
+//   You should have received a copy of the modified GNU Lesser
+//   General Public License along with this library. If not, copies
+//   may be downloaded from http://www.ccp4.ac.uk/ccp4license.php
+//
+//   This program is distributed in the hope that it will be useful,
+//   but WITHOUT ANY WARRANTY; without even the implied warranty of
+//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+//   GNU Lesser General Public License for more details.
+//
+//  =================================================================
+//
+//    12.04.14   <--  Date of Last Modification.
+//                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//  -----------------------------------------------------------------
+//
+//  **** Module  :  ccp4srs_smiles  <implementation>
+//       ~~~~~~~~~
+//  **** Classes :  ccp4srs::Smiles  - atom description class
+//       ~~~~~~~~~
+//
+//  (C) E. Krissinel 2010-2014
+//
+//  =================================================================
+//
+
+#include <string.h>
+
+#include "ccp4srs_smiles.h"
+#include "ccp4srs_defs.h"
+
+namespace ccp4srs  {
+
+  Smiles::Smiles()  {
+    ver       = NULL; //!< software version
+    plain     = NULL; //!< plain smiles
+    canonical = NULL; //!< canonical smiles
+  }
+
+  Smiles::~Smiles()  {
+    freeSmiles();
+  }
+
+  void Smiles::freeSmiles()  {
+    if (ver)       delete[] ver;
+    if (plain)     delete[] plain;
+    if (canonical) delete[] canonical;
+    ver       = NULL; //!< software version
+    plain     = NULL; //!< plain smiles
+    canonical = NULL; //!< canonical smiles
+  }
+
+  void Smiles::write_mem ( PMemIO memIO, int version )  {
+  UNUSED_ARGUMENT(version);
+    memIO->put_string ( ver       );
+    memIO->put_string ( plain     );
+    memIO->put_string ( canonical );
+  }
+
+  bool Smiles::read_mem ( PMemIO memIO, int version, bool * Ok )  {
+  UNUSED_ARGUMENT(version);
+  bool success;
+    if (Ok)  success = *Ok;
+       else  success = true;
+    if (version>=3)  {
+      memIO->get_string ( ver      ,&success );
+      memIO->get_string ( plain    ,&success );
+      memIO->get_string ( canonical,&success );
+    } else
+      freeSmiles();
+    if (Ok)  *Ok = success;
+    return success;
+  }
+
+  int Smiles::readFromCIF_rcsb ( mmdb::mmcif::PLoop mmCIFLoop,
+                                 mmdb::cpstr  program )  {
+  mmdb::pstr p;
+  int        i,loop_len,rc;
+
+    rc = 0;
+    loop_len = mmCIFLoop->GetLoopLength();
+    for (i=0;(i<loop_len) && (!rc);i++)  {
+      p = mmCIFLoop->GetString ( MMCIF_TAG_PROGRAM,i,rc );
+      if (p)  {
+        if (!strcmp(p,program))  {
+          mmdb::CreateCopy( ver,
+                mmCIFLoop->GetString(MMCIF_TAG_PROGRAM_VERSION,i,rc) );
+          p = mmCIFLoop->GetString ( MMCIF_TAG_TYPE,i,rc );
+          if (p)  {
+            if ((!strcmp(p,"SMILES")) || (!strcmp(p,"InChI")))
+                  mmdb::CreateCopy( plain,
+                     mmCIFLoop->GetString(MMCIF_TAG_DESCRIPTOR,i,rc) );
+            else  mmdb::CreateCopy( canonical,
+                     mmCIFLoop->GetString(MMCIF_TAG_DESCRIPTOR,i,rc) );
+          }
+        }
+      }
+    }
+
+    return rc;
+
+  }
+
+  void Smiles::copy ( PSmiles smiles )  {
+    mmdb::CreateCopy ( ver      ,smiles->getVersion  () );
+    mmdb::CreateCopy ( plain    ,smiles->getSmiles   () );
+    mmdb::CreateCopy ( canonical,smiles->getCanonical() );
+  }
+
+  bool Smiles::isEmpty()  {
+    return ((!ver) && (!plain) && (!canonical));
+  }
+
+/*
+  void  get_bond_type_from_cif_ccp4 ( int & type, mmdb::mmcif::PLoop loop,
+                                      mmdb::cpstr Tag, int row, int & rc )  {
+  mmdb::pstr p;
+     p = loop->GetString ( Tag,row,rc );
+     if (!p)                         type = Smiles::noOrder;
+     else if (!strcmp(p,"single"))   type = Smiles::Single;
+     else if (!strcmp(p,"aromatic")) type = Smiles::Aromatic;
+     else if (!strcmp(p,"aromat"))   type = Smiles::Aromatic;
+     else if (!strcmp(p,"double"))   type = Smiles::Double;
+     else if (!strcmp(p,"triple"))   type = Smiles::Triple;
+     else if (!strcmp(p,"deloc"))    type = Smiles::Deloc;
+     else if (!strcmp(p,"coval"))    type = Smiles::Covalent;
+     else if (!strcmp(p,"metal"))    type = Smiles::Metal;
+     else  {
+       type = Smiles::noOrder;
+       rc   = CCP4SRS_WrongBondType;
+     }
+  }
+
+  void  get_bond_type_from_cif_rcsb ( int & type,
+                                      mmdb::mmcif::PLoop loop,
+                                      mmdb::cpstr Tag,
+                                      int row, int & rc )  {
+  mmdb::pstr p;
+     p = loop->GetString ( Tag,row,rc );
+     if (!p)                       type = Smiles::noOrder;
+     else if (!strcmp(p,"SING"))   type = Smiles::Single;
+     else if (!strcmp(p,"AROM"))   type = Smiles::Aromatic;
+     else if (!strcmp(p,"DOUB"))   type = Smiles::Double;
+     else if (!strcmp(p,"TRIP"))   type = Smiles::Triple;
+     else  {
+       type = Smiles::noOrder;
+       rc   = CCP4SRS_WrongBondType;
+     }
+  }
+
+  void  get_bond_type_from_cif ( int & type,
+                                 mmdb::mmcif::PStruct mmCIFStruct,
+                                 mmdb::cpstr Tag, int & rc )  {
+  mmdb::pstr p;
+     p = mmCIFStruct->GetString ( Tag,rc );
+     if (!p)                       type = Smiles::noOrder;
+     else if (!strcmp(p,"SING"))   type = Smiles::Single;
+     else if (!strcmp(p,"AROM"))   type = Smiles::Aromatic;
+     else if (!strcmp(p,"DOUB"))   type = Smiles::Double;
+     else if (!strcmp(p,"TRIP"))   type = Smiles::Triple;
+     else  {
+       type = Smiles::noOrder;
+       rc   = CCP4SRS_WrongBondType;
+     }
+  }
+
+  void add_bond_type_to_cif ( mmdb::mmcif::PLoop loop, int type )  {
+    switch (type)  {
+      default:
+      case Smiles::noOrder:  loop->AddNoData ( mmdb::mmcif::CIF_NODATA_DOT );
+                                break;
+      case Smiles::Single:   loop->AddString ( "single"  ,false );
+                                break;
+      case Smiles::Aromatic: loop->AddString ( "aromatic",false );
+                                break;
+      case Smiles::Double:   loop->AddString ( "double"  ,false );
+                                break;
+      case Smiles::Triple:   loop->AddString ( "triple"  ,false );
+                                break;
+      case Smiles::Deloc:    loop->AddString ( "deloc"   ,false );
+    }
+  }
+
+
+  int Smiles::readFromCIF_ccp4 ( mmdb::mmcif::PLoop mmCIFLoop,
+                               int bondNo,
+                               Container<Atom> & atoms )  {
+  int rc;
+
+    rc = 0;
+
+    get_atom_from_cif ( atom_1,mmCIFLoop,MMCIF_TAG_ATOM_ID_1,
+                        bondNo,atoms,rc );
+    get_atom_from_cif ( atom_2,mmCIFLoop,MMCIF_TAG_ATOM_ID_2,
+                        bondNo,atoms,rc );
+    get_bond_type_from_cif_ccp4 ( bond_order,mmCIFLoop,MMCIF_TAG_TYPE,
+                        bondNo,rc );
+
+    if (mmCIFLoop->GetTagNo(MMCIF_TAG_VALUE_DIST)>=0)  {
+      mmCIFLoop->CopyReal ( bond_length    ,MMCIF_TAG_VALUE_DIST    ,
+                            bondNo,rc );
+      mmCIFLoop->CopyReal ( bond_length_esd,MMCIF_TAG_VALUE_DIST_ESD,
+                            bondNo,rc );
+    } else  {
+      bond_length     = 0.0;
+      bond_length_esd = 0.0;
+    }
+
+    return rc;
+
+  }
+
+
+  int Smiles::readFromCIF_rcsb ( mmdb::mmcif::PLoop mmCIFLoop,
+                               int bondNo,
+                               Container<Atom> & atoms )  {
+  mmdb::pstr p;
+  int        rc;
+
+    rc = 0;
+
+    get_atom_from_cif ( atom_1,mmCIFLoop,MMCIF_TAG_ATOM_ID_1,
+                        bondNo,atoms,rc );
+    get_atom_from_cif ( atom_2,mmCIFLoop,MMCIF_TAG_ATOM_ID_2,
+                        bondNo,atoms,rc );
+    get_bond_type_from_cif_rcsb ( bond_order,mmCIFLoop,
+                        MMCIF_TAG_VALUE_ORDER,bondNo,rc );
+
+    if ((bond_order==Smiles::Single) ||
+        (bond_order==Smiles::Double))  {
+      p = mmCIFLoop->GetString ( MMCIF_TAG_PDBX_AROMATIC_FLAG,bondNo,rc );
+      if (p)  {
+        if (p[0]=='Y')
+          bond_order = Smiles::Aromatic;
+      }
+    }
+
+    bond_length     = 0.0;
+    bond_length_esd = 0.0;
+
+    return rc;
+
+  }
+
+  int Smiles::readFromCIF ( mmdb::mmcif::PStruct mmCIFStruct,
+                                 Container<Atom> & atoms ) {
+  mmdb::pstr p;
+  int        rc;
+
+    rc = 0;
+
+    get_atom_from_cif ( atom_1,mmCIFStruct,MMCIF_TAG_ATOM_ID_1,
+                        atoms,rc );
+    get_atom_from_cif ( atom_2,mmCIFStruct,MMCIF_TAG_ATOM_ID_2,
+                        atoms,rc );
+    get_bond_type_from_cif ( bond_order,mmCIFStruct,
+                        MMCIF_TAG_VALUE_ORDER,rc );
+
+    if ((bond_order==Smiles::Single) ||
+        (bond_order==Smiles::Double))  {
+      p = mmCIFStruct->GetString ( MMCIF_TAG_PDBX_AROMATIC_FLAG,rc );
+      if (p)  {
+        if (p[0]=='Y')
+          bond_order = Smiles::Aromatic;
+      }
+    }
+
+    bond_length     = 0.0;
+    bond_length_esd = 0.0;
+
+    return rc;
+
+  }
+
+  bool Smiles::compare ( Container<Atom> & atoms, PBond bond,
+                       Container<Atom> & bond_atoms )  {
+  mmdb::AtomName a11,a12, a21,a22;
+
+    strcpy ( a11,atoms.at(atom_1)->id() );
+    strcpy ( a12,atoms.at(atom_2)->id() );
+
+    strcpy ( a21,bond_atoms.at(bond->atom1())->id() );
+    strcpy ( a22,bond_atoms.at(bond->atom2())->id() );
+
+    if (!strcmp(a11,a21))
+      return (strcmp(a12,a22)==0);
+    else if (!strcmp(a11,a22))
+      return (strcmp(a12,a21)==0);
+
+    return false;
+
+  }
+
+  bool Smiles::copy ( Container<Atom> & atoms,
+                         PBond bond,
+                         Container<Atom> & bond_atoms )  {
+  mmdb::AtomName a1,a2;
+  int      i;
+
+    strcpy ( a1,bond_atoms.at(bond->atom1())->id() );
+    strcpy ( a2,bond_atoms.at(bond->atom2())->id() );
+
+    atom_1 = -1;
+    atom_2 = -1;
+
+    for (i=0;(i<atoms.numberOf());i++)  {
+      if (!strcmp(atoms.at(i)->id(),a1))  atom_1 = i;
+      if (!strcmp(atoms.at(i)->id(),a2))  atom_2 = i;
+    }
+
+    if ((atom_1>=0) && (atom_2>=0))  {
+      bond_order      = bond->order ();
+      bond_length     = bond->length();
+      bond_length_esd = bond->length_esd();
+      return true;
+    }
+
+    return false;
+
+  }
+
+  void Smiles::copy ( PBond bond, mmdb::ivector anmatch )  {
+    if (anmatch)  {
+      atom_1 = anmatch[bond->atom1()];
+      atom_2 = anmatch[bond->atom2()];
+    } else  {
+      atom_1 = bond->atom1();
+      atom_2 = bond->atom2();
+    }
+    bond_order      = bond->order     ();
+    bond_length     = bond->length    ();
+    bond_length_esd = bond->length_esd();
+  }
+
+
+  void Smiles::makeCIFTags ( mmdb::mmcif::PLoop mmCIFLoop )  {
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_COMP_ID        );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_1      );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_2      );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_TYPE           );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_VALUE_DIST     );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_VALUE_DIST_ESD );
+  }
+
+  void Smiles::writeToCIF ( mmdb::mmcif::PLoop mmCIFLoop,
+                              mmdb::cpstr monID,
+                              Container<Atom> & atoms )  {
+    mmCIFLoop->AddString ( monID,false              );
+    add_atom_to_cif      ( mmCIFLoop,atom_1,atoms   );
+    add_atom_to_cif      ( mmCIFLoop,atom_2,atoms   );
+    add_bond_type_to_cif ( mmCIFLoop,bond_order     );
+    mmCIFLoop->AddReal   ( bond_length    ,"%10.3f" );
+    mmCIFLoop->AddReal   ( bond_length_esd,"%10.3f" );
+  }
+
+*/
+
+}  // namespace ccp4srs
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_smiles.h ccp4srs/ccp4srs/ccp4srs_smiles.h
--- ccp4srs-old/ccp4srs/ccp4srs_smiles.h	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/ccp4srs/ccp4srs_smiles.h	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,104 @@
+//  $Id: ccp4srs_smiles.h $
+//  =================================================================
+//
+//   CCP4 SRS Library: Storage, Retrieval and Search support for
+//   CCP4 ligand data.
+//
+//   Copyright (C) Eugene Krissinel 2010-2013.
+//
+//   This library is free software: you can redistribute it and/or
+//   modify it under the terms of the GNU Lesser General Public
+//   License version 3, modified in accordance with the provisions
+//   of the license to address the requirements of UK law.
+//
+//   You should have received a copy of the modified GNU Lesser
+//   General Public License along with this library. If not, copies
+//   may be downloaded from http://www.ccp4.ac.uk/ccp4license.php
+//
+//   This program is distributed in the hope that it will be useful,
+//   but WITHOUT ANY WARRANTY; without even the implied warranty of
+//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+//   GNU Lesser General Public License for more details.
+//
+//  =================================================================
+//
+//    12.04.14   <--  Date of Last Modification.
+//                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//  -----------------------------------------------------------------
+//
+//  **** Module  :  ccp4srs_smiles  <interface>
+//       ~~~~~~~~~
+//  **** Classes :  ccp4srs::Smiles  - atom description class
+//       ~~~~~~~~~
+//
+//  (C) E. Krissinel 2010-2014
+//
+//  =================================================================
+//
+
+#ifndef CCP4SRS_SMILES_H
+#define CCP4SRS_SMILES_H
+
+#include "memio_.h"
+
+#include "mmdb2/mmdb_mattype.h"
+#include "mmdb2/mmdb_mmcif_.h"
+
+namespace ccp4srs  {
+
+  DefineClass(Smiles);
+
+  class Smiles  {
+
+    public:
+
+      Smiles();
+      virtual ~Smiles();
+
+      void freeSmiles();
+
+      int  readFromCIF_rcsb ( mmdb::mmcif::PLoop mmCIFLoop,
+                              mmdb::cpstr program );
+
+      bool   isEmpty();
+
+      inline mmdb::cpstr getVersion  ()  { return ver;       }
+      inline mmdb::cpstr getSmiles   ()  { return plain;     }
+      inline mmdb::cpstr getCanonical()  { return canonical; }
+      inline mmdb::cpstr getInChI    ()  { return plain;     }
+      inline mmdb::cpstr getInChIKey ()  { return canonical; }
+
+      void copy ( PSmiles smiles );
+
+/*
+      static void makeCIFTags ( mmdb::mmcif::PLoop mmCIFLoop );
+      int  readFromCIF_ccp4 ( mmdb::mmcif::PLoop mmCIFLoop, int bondNo,
+                              Container<Atom> & atoms );
+      int  readFromCIF_rcsb ( mmdb::mmcif::PLoop mmCIFLoop, int bondNo,
+                              Container<Atom> & atoms );
+      int  readFromCIF ( mmdb::mmcif::PStruct mmCIFStruct,
+                         Container<Atom> & atoms );
+      void writeToCIF  ( mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID,
+                         Container<Atom> & atoms );
+
+      bool compare ( Container<Atom> & atoms, PBond bond,
+                     Container<Atom> & bond_atoms );
+
+      bool copy    ( Container<Atom> & atoms, PBond bond,
+                     Container<Atom> & bond_atoms );
+*/
+
+      void write_mem ( PMemIO memIO, int version );
+      bool read_mem  ( PMemIO memIO, int version,
+                          bool * Ok = NULL );
+
+    protected:
+      mmdb::pstr  ver;       //!< software version
+      mmdb::pstr  plain;     //!< plain smiles
+      mmdb::pstr  canonical; //!< canonical smiles
+
+  };
+
+}  // namespace ccp4srs
+
+#endif // CCP4SRS_SMILES_H
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_torsion.cpp ccp4srs/ccp4srs/ccp4srs_torsion.cpp
--- ccp4srs-old/ccp4srs/ccp4srs_torsion.cpp	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_torsion.cpp	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_torsion.cpp, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_torsion.cpp $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010-2011.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,158 +22,160 @@
 //
 //  =================================================================
 //
-//    18.10.11   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_torsion  <implementation>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSTorsion  - torsion angle restraint class
+//  **** Classes :  ccp4srs::Torsion  - torsion angle restraint class
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010-2011
+//  (C) E. Krissinel 2010-2013
 //
 //  =================================================================
 //
 
-#ifndef __STRING_H
 #include <string.h>
-#endif
 
 #include "ccp4srs_torsion.h"
 #include "ccp4srs_defs.h"
 
-CCP4SRSTorsion::CCP4SRSTorsion()  {
-  torsion_id[0]  = char(0);
-  atom_1         = -1;
-  atom_2         = -1;
-  atom_3         = -1;
-  atom_4         = -1;
-  torsion_period = 0;
-  torsion        = 0.0;
-  torsion_esd    = 0.0;
-}
-
-CCP4SRSTorsion::~CCP4SRSTorsion()  {
-}
-
-
-void CCP4SRSTorsion::makeCIFTags ( PCMMCIFLoop mmCIFLoop )  {
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_COMP_ID         );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_ID              );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_1       );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_2       );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_3       );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_4       );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_VALUE_ANGLE     );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_VALUE_ANGLE_ESD );
-  mmCIFLoop->AddLoopTag ( MMCIF_TAG_PERIOD          );
-}
-
-int CCP4SRSTorsion::readFromCIF ( PCMMCIFLoop mmCIFLoop, int torsionNo,
-                            CCP4SRSContainer<CCP4SRSAtom> & atoms )  {
-int rc;
-
-  rc = 0;
-
-  mmCIFLoop->CopyString ( torsion_id,sizeof(TorsionID)-1,
-                          MMCIF_TAG_ID,torsionNo,rc );
-
-  get_atom_from_cif ( atom_1,mmCIFLoop,MMCIF_TAG_ATOM_ID_1,
-                      torsionNo,atoms,rc );
-  get_atom_from_cif ( atom_2,mmCIFLoop,MMCIF_TAG_ATOM_ID_2,
-                      torsionNo,atoms,rc );
-  get_atom_from_cif ( atom_3,mmCIFLoop,MMCIF_TAG_ATOM_ID_3,
-                      torsionNo,atoms,rc );
-  get_atom_from_cif ( atom_4,mmCIFLoop,MMCIF_TAG_ATOM_ID_4,
-                      torsionNo,atoms,rc );
-
-  mmCIFLoop->CopyReal ( torsion,MMCIF_TAG_VALUE_ANGLE,torsionNo,rc );
-  mmCIFLoop->CopyReal ( torsion_esd,MMCIF_TAG_VALUE_ANGLE_ESD,
-                                                      torsionNo,rc );
-
-  mmCIFLoop->CopyInteger(torsion_period,MMCIF_TAG_PERIOD,torsionNo,rc);
-
-  return rc;
-
-}
-
-/*
-loop_
-_chem_comp_tor.comp_id
-_chem_comp_tor.id
-_chem_comp_tor.atom_id_1
-_chem_comp_tor.atom_id_2
-_chem_comp_tor.atom_id_3
-_chem_comp_tor.atom_id_4
-_chem_comp_tor.value_angle
-_chem_comp_tor.value_angle_esd
-_chem_comp_tor.period
- ATP      var_1    O2A    PA     O3A    PB       -59.994   20.000   1
-*/
-
-
-void CCP4SRSTorsion::writeToCIF ( PCMMCIFLoop mmCIFLoop, cpstr monID,
-                             CCP4SRSContainer<CCP4SRSAtom> & atoms )  {
-
-  mmCIFLoop->AddString ( monID,False       );
-  mmCIFLoop->AddString ( torsion_id,False  );
-
-  add_atom_to_cif ( mmCIFLoop,atom_1,atoms );
-  add_atom_to_cif ( mmCIFLoop,atom_2,atoms );
-  add_atom_to_cif ( mmCIFLoop,atom_3,atoms );
-  add_atom_to_cif ( mmCIFLoop,atom_4,atoms );
-  mmCIFLoop->AddReal    ( torsion    ,"%10.3f" );
-  mmCIFLoop->AddReal    ( torsion_esd,"%10.3f" );
-  mmCIFLoop->AddInteger ( torsion_period );
-
-}
-
-void  CCP4SRSTorsion::copy ( PCCP4SRSTorsion trs, ivector anmatch )  {
-  strcpy ( torsion_id,trs->id() );
-  if (anmatch)  {
-    atom_1 = anmatch[trs->atom1()];
-    atom_2 = anmatch[trs->atom2()];
-    atom_3 = anmatch[trs->atom3()];
-    atom_4 = anmatch[trs->atom4()];
-  } else  {
-    atom_1 = trs->atom1();
-    atom_2 = trs->atom2();
-    atom_3 = trs->atom3();
-    atom_4 = trs->atom4();
-  }
-  torsion_period = trs->period();
-  torsion        = trs->value ();
-  torsion_esd    = trs->esd   ();
-}
-
-void  CCP4SRSTorsion::write_mem ( PCMemIO memIO, int version )  {
-UNUSED_ARGUMENT(version);
-  memIO->put_line    ( torsion_id     );
-  memIO->put_integer ( atom_1         );
-  memIO->put_integer ( atom_2         );
-  memIO->put_integer ( atom_3         );
-  memIO->put_integer ( atom_4         );
-  memIO->put_ibyte   ( torsion_period );
-  memIO->put_float   ( torsion        );
-  memIO->put_float   ( torsion_esd    );
-}
-
-Boolean CCP4SRSTorsion::read_mem ( PCMemIO memIO, int version,
-                                   Boolean * Ok )  {
-UNUSED_ARGUMENT(version);
-Boolean success;
-  if (Ok)  success = *Ok;
-     else  success = True;
-  memIO->get_line    ( torsion_id    ,&success );
-  memIO->get_integer ( atom_1        ,&success );
-  memIO->get_integer ( atom_2        ,&success );
-  memIO->get_integer ( atom_3        ,&success );
-  memIO->get_integer ( atom_4        ,&success );
-  memIO->get_ibyte   ( torsion_period,&success );
-  memIO->get_float   ( torsion       ,&success );
-  memIO->get_float   ( torsion_esd   ,&success );
-  if (Ok)  *Ok = success;
-  return success;
-}
+namespace ccp4srs  {
 
+  Torsion::Torsion()  {
+    torsion_id[0]  = char(0);
+    atom_1         = -1;
+    atom_2         = -1;
+    atom_3         = -1;
+    atom_4         = -1;
+    torsion_period = 0;
+    torsion        = 0.0;
+    torsion_esd    = 0.0;
+  }
+
+  Torsion::~Torsion()  {
+  }
+
+
+  void Torsion::makeCIFTags ( mmdb::mmcif::PLoop mmCIFLoop )  {
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_COMP_ID         );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_ID              );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_1       );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_2       );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_3       );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_ATOM_ID_4       );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_VALUE_ANGLE     );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_VALUE_ANGLE_ESD );
+    mmCIFLoop->AddLoopTag ( MMCIF_TAG_PERIOD          );
+  }
+
+  int Torsion::readFromCIF ( mmdb::mmcif::PLoop mmCIFLoop,
+                             int torsionNo, Container<Atom> & atoms ) {
+  int rc;
+
+    rc = 0;
+
+    mmCIFLoop->CopyString ( torsion_id,sizeof(TorsionID)-1,
+                            MMCIF_TAG_ID,torsionNo,rc );
+
+    get_atom_from_cif ( atom_1,mmCIFLoop,MMCIF_TAG_ATOM_ID_1,
+                        torsionNo,atoms,rc );
+    get_atom_from_cif ( atom_2,mmCIFLoop,MMCIF_TAG_ATOM_ID_2,
+                        torsionNo,atoms,rc );
+    get_atom_from_cif ( atom_3,mmCIFLoop,MMCIF_TAG_ATOM_ID_3,
+                        torsionNo,atoms,rc );
+    get_atom_from_cif ( atom_4,mmCIFLoop,MMCIF_TAG_ATOM_ID_4,
+                        torsionNo,atoms,rc );
+
+    mmCIFLoop->CopyReal ( torsion,MMCIF_TAG_VALUE_ANGLE,torsionNo,rc );
+    mmCIFLoop->CopyReal ( torsion_esd,MMCIF_TAG_VALUE_ANGLE_ESD,
+                                                        torsionNo,rc );
+
+    mmCIFLoop->CopyInteger(torsion_period,MMCIF_TAG_PERIOD,torsionNo,rc);
+
+    return rc;
+
+  }
+
+  /*
+  loop_
+  _chem_comp_tor.comp_id
+  _chem_comp_tor.id
+  _chem_comp_tor.atom_id_1
+  _chem_comp_tor.atom_id_2
+  _chem_comp_tor.atom_id_3
+  _chem_comp_tor.atom_id_4
+  _chem_comp_tor.value_angle
+  _chem_comp_tor.value_angle_esd
+  _chem_comp_tor.period
+   ATP      var_1    O2A    PA     O3A    PB       -59.994   20.000   1
+  */
+
+
+  void Torsion::writeToCIF ( mmdb::mmcif::PLoop mmCIFLoop,
+                             mmdb::cpstr monID,
+                             Container<Atom> & atoms )  {
+
+    mmCIFLoop->AddString ( monID,false       );
+    mmCIFLoop->AddString ( torsion_id,false  );
+
+    add_atom_to_cif ( mmCIFLoop,atom_1,atoms );
+    add_atom_to_cif ( mmCIFLoop,atom_2,atoms );
+    add_atom_to_cif ( mmCIFLoop,atom_3,atoms );
+    add_atom_to_cif ( mmCIFLoop,atom_4,atoms );
+    mmCIFLoop->AddReal    ( torsion    ,"%10.3f" );
+    mmCIFLoop->AddReal    ( torsion_esd,"%10.3f" );
+    mmCIFLoop->AddInteger ( torsion_period );
+
+  }
+
+  void  Torsion::copy ( PTorsion trs,
+                               mmdb::ivector anmatch )  {
+    strcpy ( torsion_id,trs->id() );
+    if (anmatch)  {
+      atom_1 = anmatch[trs->atom1()];
+      atom_2 = anmatch[trs->atom2()];
+      atom_3 = anmatch[trs->atom3()];
+      atom_4 = anmatch[trs->atom4()];
+    } else  {
+      atom_1 = trs->atom1();
+      atom_2 = trs->atom2();
+      atom_3 = trs->atom3();
+      atom_4 = trs->atom4();
+    }
+    torsion_period = trs->period();
+    torsion        = trs->value ();
+    torsion_esd    = trs->esd   ();
+  }
+
+  void  Torsion::write_mem ( PMemIO memIO, int version )  {
+  UNUSED_ARGUMENT(version);
+    memIO->put_line    ( torsion_id     );
+    memIO->put_integer ( atom_1         );
+    memIO->put_integer ( atom_2         );
+    memIO->put_integer ( atom_3         );
+    memIO->put_integer ( atom_4         );
+    memIO->put_ibyte   ( torsion_period );
+    memIO->put_float   ( torsion        );
+    memIO->put_float   ( torsion_esd    );
+  }
+
+  bool Torsion::read_mem ( PMemIO memIO, int version, bool * Ok )  {
+  UNUSED_ARGUMENT(version);
+  bool success;
+    if (Ok)  success = *Ok;
+       else  success = true;
+    memIO->get_line    ( torsion_id    ,&success );
+    memIO->get_integer ( atom_1        ,&success );
+    memIO->get_integer ( atom_2        ,&success );
+    memIO->get_integer ( atom_3        ,&success );
+    memIO->get_integer ( atom_4        ,&success );
+    memIO->get_ibyte   ( torsion_period,&success );
+    memIO->get_float   ( torsion       ,&success );
+    memIO->get_float   ( torsion_esd   ,&success );
+    if (Ok)  *Ok = success;
+    return success;
+  }
+
+}  // namespace ccp4srs
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_torsion.h ccp4srs/ccp4srs/ccp4srs_torsion.h
--- ccp4srs-old/ccp4srs/ccp4srs_torsion.h	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_torsion.h	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_torsion.h, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_torsion.h $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010-2011.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,16 +22,16 @@
 //
 //  =================================================================
 //
-//    18.10.11   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_torsion  <interface>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSTorsion  - torsion angle restraint class
+//  **** Classes :  ccp4srs::Torsion  - torsion angle restraint class
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010-2011
+//  (C) E. Krissinel 2010-2013
 //
 //  =================================================================
 //
@@ -41,46 +41,49 @@
 
 #include "ccp4srs_atom.h"
 
-DefineClass(CCP4SRSTorsion);
+namespace ccp4srs  {
 
-typedef char TorsionID[20];
+  DefineClass(Torsion);
 
-class CCP4SRSTorsion {
+  typedef char TorsionID[20];
 
-  public:
-    CCP4SRSTorsion();
-    virtual ~CCP4SRSTorsion();
-
-    inline cpstr    id    () { return torsion_id;     }
-    inline int      atom1 () { return atom_1;         }
-    inline int      atom2 () { return atom_2;         }
-    inline int      atom3 () { return atom_3;         }
-    inline int      atom4 () { return atom_4;         }
-    inline int      period() { return torsion_period; }
-    inline realtype value () { return torsion;        }
-    inline realtype esd   () { return torsion_esd;    }
-
-    static void makeCIFTags ( PCMMCIFLoop mmCIFLoop );
-    int  readFromCIF ( PCMMCIFLoop mmCIFLoop, int angleNo,
-                       CCP4SRSContainer<CCP4SRSAtom> & atoms );
-    void writeToCIF  ( PCMMCIFLoop mmCIFLoop, cpstr monID,
-                       CCP4SRSContainer<CCP4SRSAtom> & atoms );
-
-    void    write_mem ( PCMemIO memIO, int version );
-    Boolean read_mem  ( PCMemIO memIO, int version,
-                        Boolean * Ok = NULL );
-
-    void copy ( PCCP4SRSTorsion trs, ivector anmatch=NULL );
-
-  protected:
-    TorsionID  torsion_id;     //!< torsion angle id
-    int        atom_1,atom_2;  //!< ordinal numbers of atoms
-    int        atom_3,atom_4;  ///  that form the angle [0,1,...]
-    int        torsion_period; //!< torsion period
-    realtype   torsion;        //!< torsion angle in degrees
-    realtype   torsion_esd;    //!< torsion angle esd in degrees;
-                               /// set to 0.0 if not provided
+  class Torsion {
 
-};
+    public:
+      Torsion();
+      virtual ~Torsion();
+
+      inline mmdb::cpstr    id    () { return torsion_id;     }
+      inline int            atom1 () { return atom_1;         }
+      inline int            atom2 () { return atom_2;         }
+      inline int            atom3 () { return atom_3;         }
+      inline int            atom4 () { return atom_4;         }
+      inline int            period() { return torsion_period; }
+      inline mmdb::realtype value () { return torsion;        }
+      inline mmdb::realtype esd   () { return torsion_esd;    }
+
+      static void makeCIFTags ( mmdb::mmcif::PLoop mmCIFLoop );
+      int  readFromCIF ( mmdb::mmcif::PLoop mmCIFLoop, int angleNo,
+                         Container<Atom> & atoms );
+      void writeToCIF  ( mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID,
+                         Container<Atom> & atoms );
+
+      void write_mem ( PMemIO memIO, int version );
+      bool read_mem  ( PMemIO memIO, int version, bool * Ok = NULL );
+
+      void copy ( PTorsion trs, mmdb::ivector anmatch=NULL );
+
+    protected:
+      TorsionID   torsion_id;     //!< torsion angle id
+      int         atom_1,atom_2;  //!< ordinal numbers of atoms
+      int         atom_3,atom_4;  ///  that form the angle [0,1,...]
+      int         torsion_period; //!< torsion period
+      mmdb::realtype torsion;     //!< torsion angle in degrees
+      mmdb::realtype torsion_esd; //!< torsion angle esd in degrees;
+                                  /// set to 0.0 if not provided
+
+  };
+
+}  // namespace ccp4srs
 
 #endif // CCP4SRS_TORSION_H
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_tree.cpp ccp4srs/ccp4srs/ccp4srs_tree.cpp
--- ccp4srs-old/ccp4srs/ccp4srs_tree.cpp	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_tree.cpp	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_tree.cpp, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_tree.cpp $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,206 +22,206 @@
 //
 //  =================================================================
 //
-//    11.03.10   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_tree  <implementation>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSTree  - structure tree
+//  **** Classes :  ccp4srs::Tree  - structure tree
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010
+//  (C) E. Krissinel 2010-2013
 //
 //  =================================================================
 //
 
-
-#ifndef  __STRING_H
 #include <string.h>
-#endif
 
 #include "ccp4srs_tree.h"
 #include "ccp4srs_defs.h"
 
-CCP4SRSTree::CCP4SRSTree()  {
-  n_sections    = 0;
-  atom_tree     = NULL;  // tree atom
-  atom_backward = NULL;  // previous atom
-  atom_forward  = NULL;  // next atom
-  connect_type  = NULL;  // type of connection
-}
-
-CCP4SRSTree::~CCP4SRSTree()  {
-  empty();
-}
-
-void CCP4SRSTree::empty()  {
-  FreeVectorMemory ( atom_tree    ,0 );
-  FreeVectorMemory ( atom_backward,0 );
-  FreeVectorMemory ( atom_forward ,0 );
-  n_sections = 0;
-}
-
-
-int CCP4SRSTree::readFromCIF ( PCMMCIFLoop mmCIFLoop,
-                            CCP4SRSContainer<CCP4SRSAtom> & atoms )  {
-pstr p;
-int  rc,i;
+namespace ccp4srs  {
 
-  rc = 0;
+  Tree::Tree()  {
+    n_sections    = 0;
+    atom_tree     = NULL;  // tree atom
+    atom_backward = NULL;  // previous atom
+    atom_forward  = NULL;  // next atom
+    connect_type  = NULL;  // type of connection
+  }
 
-  empty();
+  Tree::~Tree()  {
+    empty();
+  }
 
-  if (mmCIFLoop)  {
+  void Tree::empty()  {
+    mmdb::FreeVectorMemory ( atom_tree    ,0 );
+    mmdb::FreeVectorMemory ( atom_backward,0 );
+    mmdb::FreeVectorMemory ( atom_forward ,0 );
+    n_sections = 0;
+  }
 
-    n_sections = mmCIFLoop->GetLoopLength();
 
-    if (n_sections>0)  {
+  int Tree::readFromCIF ( mmdb::mmcif::PLoop mmCIFLoop,
+                          Container<Atom> & atoms ) {
+  mmdb::pstr p;
+  int        rc,i;
+
+    rc = 0;
+
+    empty();
+
+    if (mmCIFLoop)  {
+
+      n_sections = mmCIFLoop->GetLoopLength();
+
+      if (n_sections>0)  {
+
+        mmdb::GetVectorMemory ( atom_tree,    n_sections,0 );
+        mmdb::GetVectorMemory ( atom_backward,n_sections,0 );
+        mmdb::GetVectorMemory ( atom_forward, n_sections,0 );
+        mmdb::GetVectorMemory ( connect_type, n_sections,0 );
+        for (i=0;(i<n_sections) && (!rc);i++)  {
+          get_atom_from_cif ( atom_tree[i],mmCIFLoop,
+                              MMCIF_TAG_ATOM_ID,i,atoms,rc );
+          get_atom_from_cif ( atom_backward[i],mmCIFLoop,
+                              MMCIF_TAG_ATOM_BACK,i,atoms,rc );
+          get_atom_from_cif ( atom_forward[i],mmCIFLoop,
+                              MMCIF_TAG_ATOM_FORWARD,i,atoms,rc );
+          p = mmCIFLoop->GetString ( MMCIF_TAG_CONNECT_TYPE,i,rc );
+          if (!p)   connect_type[i] = Tree::None;
+          else if (!strcmp(p,"START"))
+                    connect_type[i] = Tree::Start;
+          else if (!strcmp(p,"END"))
+                    connect_type[i] = Tree::End;
+          else if (!strcmp(p,"ADD"))
+                    connect_type[i] = Tree::Add;
+          else      connect_type[i] = Tree::None;
+        }
 
-      GetVectorMemory ( atom_tree,    n_sections,0 );
-      GetVectorMemory ( atom_backward,n_sections,0 );
-      GetVectorMemory ( atom_forward, n_sections,0 );
-      GetVectorMemory ( connect_type, n_sections,0 );
-      for (i=0;(i<n_sections) && (!rc);i++)  {
-        get_atom_from_cif ( atom_tree[i],mmCIFLoop,
-                            MMCIF_TAG_ATOM_ID,i,atoms,rc );
-        get_atom_from_cif ( atom_backward[i],mmCIFLoop,
-                            MMCIF_TAG_ATOM_BACK,i,atoms,rc );
-        get_atom_from_cif ( atom_forward[i],mmCIFLoop,
-                            MMCIF_TAG_ATOM_FORWARD,i,atoms,rc );
-        p = mmCIFLoop->GetString ( MMCIF_TAG_CONNECT_TYPE,i,rc );
-        if (!p)   connect_type[i] = CCP4SRSTree::None;
-        else if (!strcmp(p,"START"))
-                  connect_type[i] = CCP4SRSTree::Start;
-        else if (!strcmp(p,"END"))
-                  connect_type[i] = CCP4SRSTree::End;
-        else if (!strcmp(p,"ADD"))
-                  connect_type[i] = CCP4SRSTree::Add;
-        else      connect_type[i] = CCP4SRSTree::None;
       }
 
     }
 
-  }
-
-  return rc;
+    return rc;
 
-}
+  }
 
-void  CCP4SRSTree::writeToCIF ( PCMMCIFData mmCIFData, cpstr monID,
-                            CCP4SRSContainer<CCP4SRSAtom> & atoms )  {
-PCMMCIFLoop loop;
-int         i;
+  void  Tree::writeToCIF ( mmdb::mmcif::PData mmCIFData,
+                           mmdb::cpstr monID,
+                           Container<Atom> & atoms )  {
+  mmdb::mmcif::PLoop loop;
+  int                i;
 
-  if (n_sections>0)  {
+    if (n_sections>0)  {
 
-    mmCIFData->AddLoop ( MMCIF_LOOP_CHEM_COMP_TREE,loop );
+      mmCIFData->AddLoop ( MMCIF_LOOP_CHEM_COMP_TREE,loop );
 
-    loop->AddLoopTag ( MMCIF_TAG_COMP_ID      );
-    loop->AddLoopTag ( MMCIF_TAG_ATOM_ID      );
-    loop->AddLoopTag ( MMCIF_TAG_ATOM_BACK    );
-    loop->AddLoopTag ( MMCIF_TAG_ATOM_FORWARD );
-    loop->AddLoopTag ( MMCIF_TAG_CONNECT_TYPE );
+      loop->AddLoopTag ( MMCIF_TAG_COMP_ID      );
+      loop->AddLoopTag ( MMCIF_TAG_ATOM_ID      );
+      loop->AddLoopTag ( MMCIF_TAG_ATOM_BACK    );
+      loop->AddLoopTag ( MMCIF_TAG_ATOM_FORWARD );
+      loop->AddLoopTag ( MMCIF_TAG_CONNECT_TYPE );
 
-    for (i=0;i<n_sections;i++)  {
-      loop->AddString ( monID,False );
-      add_atom_to_cif ( loop, atom_tree    [i], atoms );
-      add_atom_to_cif ( loop, atom_backward[i], atoms );
-      add_atom_to_cif ( loop, atom_forward [i], atoms );
-      switch (connect_type[i])  {
-        default :
-        case CCP4SRSTree::None  : loop->AddNoData ( CIF_NODATA_DOT );
-                                  break;
-        case CCP4SRSTree::Start : loop->AddString ( "START",False );
-                                  break;
-        case CCP4SRSTree::End   : loop->AddString ( "END",False );
-                                  break;
-        case CCP4SRSTree::Add   : loop->AddString ( "ADD",False );
+      for (i=0;i<n_sections;i++)  {
+        loop->AddString ( monID,false );
+        add_atom_to_cif ( loop, atom_tree    [i], atoms );
+        add_atom_to_cif ( loop, atom_backward[i], atoms );
+        add_atom_to_cif ( loop, atom_forward [i], atoms );
+        switch (connect_type[i])  {
+          default :
+          case Tree::None  : loop->AddNoData ( mmdb::mmcif::CIF_NODATA_DOT );
+                                    break;
+          case Tree::Start : loop->AddString ( "START",false );
+                                    break;
+          case Tree::End   : loop->AddString ( "END",false );
+                                    break;
+          case Tree::Add   : loop->AddString ( "ADD",false );
+        }
       }
+
     }
 
   }
 
-}
+  /*
+  loop_
+  _chem_comp_tree.comp_id
+  _chem_comp_tree.atom_id
+  _chem_comp_tree.atom_back
+  _chem_comp_tree.atom_forward
+  _chem_comp_tree.connect_type
+   ATP      O2A    n/a    PA     START
+
+  */
+
+
+  void  Tree::write_mem ( PMemIO memIO, int version )  {
+  UNUSED_ARGUMENT(version);
+  int i;
+    memIO->put_integer ( n_sections );
+    for (i=0;i<n_sections;i++)  {
+      memIO->put_integer ( atom_tree    [i] );
+      memIO->put_integer ( atom_backward[i] );
+      memIO->put_integer ( atom_forward [i] );
+      memIO->put_integer ( connect_type [i] );
+    }
+  }
 
-/*
-loop_
-_chem_comp_tree.comp_id
-_chem_comp_tree.atom_id
-_chem_comp_tree.atom_back
-_chem_comp_tree.atom_forward
-_chem_comp_tree.connect_type
- ATP      O2A    n/a    PA     START
-
-*/
-
-
-void  CCP4SRSTree::write_mem ( PCMemIO memIO, int version )  {
-UNUSED_ARGUMENT(version);
-int i;
-  memIO->put_integer ( n_sections );
-  for (i=0;i<n_sections;i++)  {
-    memIO->put_integer ( atom_tree    [i] );
-    memIO->put_integer ( atom_backward[i] );
-    memIO->put_integer ( atom_forward [i] );
-    memIO->put_integer ( connect_type [i] );
-  }
-}
-
-void  CCP4SRSTree::copy ( PCCP4SRSTree tree, ivector anmatch )  {
-int i;
-  empty();
-  n_sections = tree->size();
-  if (n_sections>0)  {
-    GetVectorMemory ( atom_tree,    n_sections,0 );
-    GetVectorMemory ( atom_backward,n_sections,0 );
-    GetVectorMemory ( atom_forward, n_sections,0 );
-    GetVectorMemory ( connect_type, n_sections,0 );
-    if (anmatch)  {
-      for (i=0;i<n_sections;i++)  {
-        if (tree->atom(i)>=0)
-          atom_tree    [i] = anmatch [ tree->atom    (i) ];
-        if (tree->backward(i)>=0)
-          atom_backward[i] = anmatch [ tree->backward(i) ];
-        if (tree->forward(i)>=0)
-          atom_forward [i] = anmatch [ tree->forward (i) ];
-        connect_type [i] = tree->connect (i);
-      }
-    } else  {
-      for (i=0;i<n_sections;i++)  {
-        atom_tree    [i] = tree->atom    (i);
-        atom_backward[i] = tree->backward(i);
-        atom_forward [i] = tree->forward (i);
-        connect_type [i] = tree->connect (i);
+  void  Tree::copy ( PTree tree, mmdb::ivector anmatch )  {
+  int i;
+    empty();
+    n_sections = tree->size();
+    if (n_sections>0)  {
+      mmdb::GetVectorMemory ( atom_tree,    n_sections,0 );
+      mmdb::GetVectorMemory ( atom_backward,n_sections,0 );
+      mmdb::GetVectorMemory ( atom_forward, n_sections,0 );
+      mmdb::GetVectorMemory ( connect_type, n_sections,0 );
+      if (anmatch)  {
+        for (i=0;i<n_sections;i++)  {
+          if (tree->atom(i)>=0)
+            atom_tree    [i] = anmatch [ tree->atom    (i) ];
+          if (tree->backward(i)>=0)
+            atom_backward[i] = anmatch [ tree->backward(i) ];
+          if (tree->forward(i)>=0)
+            atom_forward [i] = anmatch [ tree->forward (i) ];
+          connect_type [i] = tree->connect (i);
+        }
+      } else  {
+        for (i=0;i<n_sections;i++)  {
+          atom_tree    [i] = tree->atom    (i);
+          atom_backward[i] = tree->backward(i);
+          atom_forward [i] = tree->forward (i);
+          connect_type [i] = tree->connect (i);
+        }
       }
     }
   }
-}
 
 
-Boolean  CCP4SRSTree::read_mem ( PCMemIO memIO, int version,
-                                 Boolean * Ok )  {
-UNUSED_ARGUMENT(version);
-int     i;
-Boolean success;
-  empty();
-  if (Ok)  success = *Ok;
-     else  success = True;
-  memIO->get_integer ( n_sections,&success );
-  if (n_sections>0)  {
-    GetVectorMemory ( atom_tree,    n_sections,0 );
-    GetVectorMemory ( atom_backward,n_sections,0 );
-    GetVectorMemory ( atom_forward, n_sections,0 );
-    GetVectorMemory ( connect_type, n_sections,0 );
-    for (i=0;i<n_sections;i++)  {
-      memIO->get_integer ( atom_tree    [i],&success );
-      memIO->get_integer ( atom_backward[i],&success );
-      memIO->get_integer ( atom_forward [i],&success );
-      memIO->get_integer ( connect_type [i],&success );
+  bool  Tree::read_mem ( PMemIO memIO, int version, bool * Ok )  {
+  UNUSED_ARGUMENT(version);
+  int  i;
+  bool success;
+    empty();
+    if (Ok)  success = *Ok;
+       else  success = true;
+    memIO->get_integer ( n_sections,&success );
+    if (n_sections>0)  {
+      mmdb::GetVectorMemory ( atom_tree,    n_sections,0 );
+      mmdb::GetVectorMemory ( atom_backward,n_sections,0 );
+      mmdb::GetVectorMemory ( atom_forward, n_sections,0 );
+      mmdb::GetVectorMemory ( connect_type, n_sections,0 );
+      for (i=0;i<n_sections;i++)  {
+        memIO->get_integer ( atom_tree    [i],&success );
+        memIO->get_integer ( atom_backward[i],&success );
+        memIO->get_integer ( atom_forward [i],&success );
+        memIO->get_integer ( connect_type [i],&success );
+      }
     }
+    if (Ok)  *Ok = success;
+    return success;
   }
-  if (Ok)  *Ok = success;
-  return success;
-}
 
+}  // namespace ccp4srs
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_tree.h ccp4srs/ccp4srs/ccp4srs_tree.h
--- ccp4srs-old/ccp4srs/ccp4srs_tree.h	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_tree.h	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_tree.h, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_tree.h $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,16 +22,16 @@
 //
 //  =================================================================
 //
-//    11.03.10   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_tree  <interface>
 //       ~~~~~~~~~
-//  **** Classes :  CCP4SRSTree  - structure tree
+//  **** Classes :  ccp4srs::Tree  - structure tree
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010
+//  (C) E. Krissinel 2010-2013
 //
 //  =================================================================
 //
@@ -41,43 +41,48 @@
 
 #include "ccp4srs_atom.h"
 
-DefineClass(CCP4SRSTree);
+namespace ccp4srs  {
 
-class CCP4SRSTree  {
+  DefineClass(Tree);
 
-  // atom connectivity types
-  enum  {None,Start,End,Add};
+  class Tree  {
 
-  public:
-    CCP4SRSTree();
-    virtual ~CCP4SRSTree();
+    // atom connectivity types
+    enum  {None,Start,End,Add};
 
-    void  empty();
+    public:
+      Tree();
+      virtual ~Tree();
 
-    inline int size() { return n_sections;    }
-    inline int atom     ( int secNo ) { return atom_tree    [secNo]; }
-    inline int backward ( int secNo ) { return atom_backward[secNo]; }
-    inline int forward  ( int secNo ) { return atom_forward [secNo]; }
-    inline int connect  ( int secNo ) { return connect_type [secNo]; }
+      void  empty();
 
-    int   readFromCIF   ( PCMMCIFLoop mmCIFLoop,
-                          CCP4SRSContainer<CCP4SRSAtom> & atoms );
-    void  writeToCIF    ( PCMMCIFData mmCIFData, cpstr monID,
-                          CCP4SRSContainer<CCP4SRSAtom> & atoms );
+      inline int size() { return n_sections;    }
+      inline int atom     ( int secNo ) { return atom_tree    [secNo]; }
+      inline int backward ( int secNo ) { return atom_backward[secNo]; }
+      inline int forward  ( int secNo ) { return atom_forward [secNo]; }
+      inline int connect  ( int secNo ) { return connect_type [secNo]; }
 
-    void    write_mem   ( PCMemIO memIO, int version );
-    Boolean read_mem    ( PCMemIO memIO, int version,
-                          Boolean * Ok = NULL );
+      int   readFromCIF   ( mmdb::mmcif::PLoop mmCIFLoop,
+                            Container<Atom> & atoms );
+      void  writeToCIF    ( mmdb::mmcif::PData mmCIFData,
+                            mmdb::cpstr monID,
+                            Container<Atom> & atoms );
 
-    void  copy ( PCCP4SRSTree tree, ivector anmatch=NULL );
+      void  write_mem   ( PMemIO memIO, int version );
+      bool  read_mem    ( PMemIO memIO, int version,
+                          bool * Ok = NULL );
 
-  protected:
-    int      n_sections;     //!< number of sections
-    ivector  atom_tree;      //!< tree atom name
-    ivector  atom_backward;  //!< previous atom name
-    ivector  atom_forward;   //!< next atom name
-    ivector  connect_type;   //!< type of connection
+      void  copy ( PTree tree, mmdb::ivector anmatch=NULL );
 
-};
+    protected:
+      int            n_sections;     //!< number of sections
+      mmdb::ivector  atom_tree;      //!< tree atom name
+      mmdb::ivector  atom_backward;  //!< previous atom name
+      mmdb::ivector  atom_forward;   //!< next atom name
+      mmdb::ivector  connect_type;   //!< type of connection
+
+  };
+
+}  // namespace ccp4srs
 
 #endif // CCP4SRS_TREE_H
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_types.cpp ccp4srs/ccp4srs/ccp4srs_types.cpp
--- ccp4srs-old/ccp4srs/ccp4srs_types.cpp	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_types.cpp	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_types.cpp, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_types.cpp $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,14 +22,15 @@
 //
 //  =================================================================
 //
-//    26.02.13   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_types  <implementation>
 //       ~~~~~~~~~
-//  **** Classes :  SAtomPair  - atom pair
-//       ~~~~~~~~~  SDASelHnds - donor-acceptor selection handlers
+//  **** Classes :  ccp4srs::AtomPair  - atom pair
+//       ~~~~~~~~~  ccp4srs::DASelHnds - donor-acceptor selection
+//                                       handlers
 //
 //  (C) E. Krissinel 2010-2013
 //
@@ -38,22 +39,33 @@
 
 #include "ccp4srs_types.h"
 
-void SDASelHnds::getNewHandles ( PCMMDBManager MMDB )  {
-  selHndDonor    = MMDB->NewSelection();
-  selHndAcceptor = MMDB->NewSelection();
-  selHndHydrogen = MMDB->NewSelection();
-  selKey = SKEY_OR;
-}
-
-void SDASelHnds::makeSelIndexes ( PCMMDBManager MMDB )  {
-  MMDB->MakeSelIndex ( selHndDonor    );
-  MMDB->MakeSelIndex ( selHndAcceptor );
-  MMDB->MakeSelIndex ( selHndHydrogen );
-}
-
-void SDASelHnds::deleteSelections ( PCMMDBManager MMDB )  {
-  MMDB->DeleteSelection ( selHndDonor    );
-  MMDB->DeleteSelection ( selHndAcceptor );
-  MMDB->DeleteSelection ( selHndHydrogen );
-}
+namespace ccp4srs  {
 
+  const int CCP4SRS_file_version = 3;
+
+  mmdb::cpstr srsIndexFile  = "index.srs";
+  mmdb::cpstr srsGraphFile  = "graph.srs";
+  mmdb::cpstr srsStructFile = "struct.srs";
+
+  const int AtomID_NA = -10000;
+
+  void DASelHnds::getNewHandles ( mmdb::PManager MMDB )  {
+    selHndDonor    = MMDB->NewSelection();
+    selHndAcceptor = MMDB->NewSelection();
+    selHndHydrogen = MMDB->NewSelection();
+    selKey = mmdb::SKEY_OR;
+  }
+
+  void DASelHnds::makeSelIndexes ( mmdb::PManager MMDB )  {
+    MMDB->MakeSelIndex ( selHndDonor    );
+    MMDB->MakeSelIndex ( selHndAcceptor );
+    MMDB->MakeSelIndex ( selHndHydrogen );
+  }
+
+  void DASelHnds::deleteSelections ( mmdb::PManager MMDB )  {
+    MMDB->DeleteSelection ( selHndDonor    );
+    MMDB->DeleteSelection ( selHndAcceptor );
+    MMDB->DeleteSelection ( selHndHydrogen );
+  }
+
+}  // namespace ccp4srs
diff -ruN ccp4srs-old/ccp4srs/ccp4srs_types.h ccp4srs/ccp4srs/ccp4srs_types.h
--- ccp4srs-old/ccp4srs/ccp4srs_types.h	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/ccp4srs_types.h	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: ccp4srs_types.h, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: ccp4srs_types.h $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,16 +22,17 @@
 //
 //  =================================================================
 //
-//    26.02.13   <--  Date of Last Modification.
+//    03.02.14   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  ccp4srs_types  <interface>
 //       ~~~~~~~~~
-//  **** Classes :  SAtomPair  - atom pair
-//       ~~~~~~~~~  SDASelHnds - donor-acceptor selection handlers
+//  **** Classes :  ccp4srs::AtomPair  - atom pair
+//       ~~~~~~~~~  ccp4srs::DASelHnds - donor-acceptor selection
+//                                       handlers
 //
-//  (C) E. Krissinel 2010-2013
+//  (C) E. Krissinel 2010-2014
 //
 //  =================================================================
 //
@@ -39,31 +40,71 @@
 #ifndef CCP4SRS_TYPES_H
 #define CCP4SRS_TYPES_H
 
+#include "mmdb2/mmdb_manager.h"
 
-#include "mmdb/mmdb_manager.h"
+namespace ccp4srs  {
 
-// ==================================================================
+  enum CCP4SRS_VERSION  {
+    MAJOR_VERSION = 1,  //!< major version
+    MINOR_VERSION = 0,  //!< minor version
+    MICRO_VERSION = 0   //!< micro version
+  };
+
+  extern const int CCP4SRS_file_version;
+
+  enum CCP4SRS_RC  {
+    CCP4SRS_noDonors         =   4,
+    CCP4SRS_noAcceptors      =   3,
+    CCP4SRS_noHBonds         =   2,
+    CCP4SRS_Incomplete       =   1,
+    CCP4SRS_Ok               =   0,
+    CCP4SRS_WrongBondType    =  -1,
+    CCP4SRS_IndexCorrupt     =  -2,
+    CCP4SRS_FileNotFound     =  -3,
+    CCP4SRS_EntryNotFound    =  -4,
+    CCP4SRS_ReadErrors       =  -5,
+    CCP4SRS_EmptyResidue     =  -6,
+    CCP4SRS_NoAtomsFound     =  -7,
+    CCP4SRS_NoBonds          =  -8,
+    CCP4SRS_EmptyResSet      =  -9,
+    CCP4SRS_Fail             = -10,
+    CCP4SRS_SVD_Fail         = -11,
+    CCP4SRS_noCoordHierarchy = -12,
+    CCP4SRS_BrokenBonds      = -13
+  };
+
+  extern mmdb::cpstr srsIndexFile;
+  extern mmdb::cpstr srsGraphFile;
+  extern mmdb::cpstr srsStructFile;
+
+
+  //  special atom ids
+  extern const int AtomID_NA;
+
+  // ==================================================================
+
+  DefineStructure(AtomPair);
+
+  struct AtomPair  {
+    mmdb::PAtom a1,a2;
+  };
+
+  // ==================================================================
+
+  //   SDASelHandles is optionally used in MakeBonds(..), when
+  // the latter works for hydrogen bond calculations.
+  DefineStructure(DASelHnds);
+
+  struct DASelHnds  {
+    int  selHndDonor;
+    int  selHndAcceptor;
+    int  selHndHydrogen;
+    mmdb::SELECTION_KEY selKey;
+    void getNewHandles    ( mmdb::PManager MMDB );
+    void makeSelIndexes   ( mmdb::PManager MMDB );
+    void deleteSelections ( mmdb::PManager MMDB );
+  };
 
-DefineStructure(SAtomPair);
-
-struct SAtomPair  {
-  PCAtom a1,a2;
-};
-
-// ==================================================================
-
-//   SDASelHandles is optionally used in MakeBonds(..), when
-// the latter works for hydrogen bond calculations.
-DefineStructure(SDASelHnds);
-
-struct SDASelHnds  {
-  int selHndDonor;
-  int selHndAcceptor;
-  int selHndHydrogen;
-  int selKey;
-  void getNewHandles    ( PCMMDBManager MMDB );
-  void makeSelIndexes   ( PCMMDBManager MMDB );
-  void deleteSelections ( PCMMDBManager MMDB );
-};
+}  // namespace ccp4srs
 
 #endif // CCP4SRS_TYPES_H
diff -ruN ccp4srs-old/ccp4srs/memio_.cpp ccp4srs/ccp4srs/memio_.cpp
--- ccp4srs-old/ccp4srs/memio_.cpp	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/memio_.cpp	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: memio_.h, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: memio_.cpp $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrievak and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,478 +22,479 @@
 //
 //  =================================================================
 //
-//    11.03.10   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
-//  **** Module  :  memio_  <interface>
+//  **** Module  :  memio_  <implementation>
 //       ~~~~~~~~~
-//  **** Classes :  CMemIO  - buffered I/O
+//  **** Classes :  ccp4srs::MemIO  - buffered I/O
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010
+//  (C) E. Krissinel 2010-2013
 //
 //  =================================================================
 //
 
 #include <string.h>
-
 #include <zlib.h>
 
 #include "memio_.h"
 
+namespace ccp4srs  {
 
-CMemIO::CMemIO()  {
+  MemIO::MemIO()  {
 
-  compression_level  = Z_NO_COMPRESSION;
-  compression_buffer = NULL;
-  compression_alloc  = 0;
+    compression_level  = Z_NO_COMPRESSION;
+    compression_buffer = NULL;
+    compression_alloc  = 0;
 
-  buffer        = NULL;
-  buffer_length = 0;
-  buffer_pos    = 0;
-  alloc_length  = 0;
-  chunk_size    = 10000;
+    buffer        = NULL;
+    buffer_length = 0;
+    buffer_pos    = 0;
+    alloc_length  = 0;
+    chunk_size    = 10000;
 
-}
+  }
 
-CMemIO::~CMemIO()  {
-  free();
-}
+  MemIO::~MemIO()  {
+    free();
+  }
 
-void CMemIO::setCompressionLevel ( int compressionLevel )  {
-  switch (compressionLevel)  {
-    case 0:  compression_level = Z_NO_COMPRESSION;      break;
-    case 1:  compression_level = Z_BEST_SPEED;          break;
-    case 2:  compression_level = Z_DEFAULT_COMPRESSION; break;
-    default: compression_level = Z_BEST_COMPRESSION;
+  void MemIO::setCompressionLevel ( int compressionLevel )  {
+    switch (compressionLevel)  {
+      case 0:  compression_level = Z_NO_COMPRESSION;      break;
+      case 1:  compression_level = Z_BEST_SPEED;          break;
+      case 2:  compression_level = Z_DEFAULT_COMPRESSION; break;
+      default: compression_level = Z_BEST_COMPRESSION;
+    }
   }
-}
 
 
-int CMemIO::read ( cpstr fileName, byte gzMode )  {
-CFile f;
-int   rc;
+  int MemIO::read ( mmdb::cpstr fileName, mmdb::io::GZ_MODE gzMode )  {
+  mmdb::io::File f;
+  int            rc;
 
-  buffer_pos = 0;
-  rc = CMemIO::Ok;
+    buffer_pos = 0;
+    rc = MemIO::Ok;
 
-  f.assign ( fileName,False,True,gzMode );
+    f.assign ( fileName,false,true,gzMode );
 
-  if (f.reset(True))  rc = read ( f );
-                else  rc = CMemIO::CantOpenFile;
+    if (f.reset(true))  rc = read ( f );
+                  else  rc = MemIO::CantOpenFile;
 
-  if (rc!=CMemIO::Ok)
-    free();
+    if (rc!=MemIO::Ok)
+      free();
 
-  f.shut();
+    f.shut();
 
-  return rc;
+    return rc;
 
-}
+  }
 
-int CMemIO::read ( RCFile f )  {
-int    rc,len;
-uLongf dsize;
+  int MemIO::read ( mmdb::io::RFile f )  {
+  int    rc,len;
+  uLongf dsize;
 
-  buffer_pos = 0;
+    buffer_pos = 0;
 
-  if (f.ReadInt(&buffer_length))  {
+    if (f.ReadInt(&buffer_length))  {
 
-    if (buffer_length==0)
-      rc = CMemIO::EmptyFile;
+      if (buffer_length==0)
+        rc = MemIO::EmptyFile;
 
-    else if (buffer_length>0)  { // no compression
+      else if (buffer_length>0)  { // no compression
+
+        if (buffer_length>alloc_length)  {
+          mmdb::FreeVectorMemory ( buffer,0 );
+          alloc_length = buffer_length;
+          mmdb::GetVectorMemory ( buffer,alloc_length,0 );
+        }
+        if (f.ReadFile(buffer,buffer_length))
+              rc = MemIO::Ok;
+        else  rc = MemIO::ReadError;
+
+      } else  { // decompress
+
+        buffer_length = -buffer_length - 1;
+        if (buffer_length>alloc_length)  {
+          mmdb::FreeVectorMemory ( buffer,0 );
+          alloc_length = buffer_length;
+          mmdb::GetVectorMemory ( buffer,alloc_length,0 );
+        }
+
+        if (f.ReadInt(&len))  {
+
+          if (compression_alloc<=len)  {
+            mmdb::FreeVectorMemory ( compression_buffer,0 );
+            compression_alloc = len + 100;
+            mmdb::GetVectorMemory  ( compression_buffer,compression_alloc,0 );
+          }
+
+          if (f.ReadFile(compression_buffer,len))  {
+            dsize = alloc_length;
+            rc = uncompress ( buffer,&dsize,compression_buffer,len );
+            if (rc==Z_OK)  {
+              if (int(dsize)!=buffer_length)  rc = MemIO::SizeError;
+                                        else  rc = MemIO::Ok;
+            } else
+              rc = MemIO::UncompressionError;
+          } else
+            rc = MemIO::ReadError;
+
+        } else
+          rc = MemIO::ReadError;
 
-      if (buffer_length>alloc_length)  {
-        FreeVectorMemory ( buffer,0 );
-        alloc_length = buffer_length;
-        GetVectorMemory ( buffer,alloc_length,0 );
       }
-      if (f.ReadFile(buffer,buffer_length))
-            rc = CMemIO::Ok;
-      else  rc = CMemIO::ReadError;
-
-    } else  { // decompress
-
-      buffer_length = -buffer_length - 1;
-      if (buffer_length>alloc_length)  {
-        FreeVectorMemory ( buffer,0 );
-        alloc_length = buffer_length;
-        GetVectorMemory ( buffer,alloc_length,0 );
+
+    } else
+      rc = MemIO::ReadError;
+
+    return rc;
+
+  }
+
+  int MemIO::write ( mmdb::cpstr fileName, mmdb::io::GZ_MODE gzMode )  {
+  mmdb::io::File f;
+  int            rc;
+
+    rc = MemIO::Ok;
+
+    f.assign ( fileName,false,true,gzMode );
+
+    if (f.rewrite()) rc = write(f);
+                else rc = MemIO::CantOpenFile;
+
+    f.shut();
+
+    return rc;
+
+  }
+
+  int MemIO::write ( mmdb::io::RFile f )  {
+  int    rc,len;
+  uLongf csize;
+
+    rc = MemIO::Ok;
+
+    if ((compression_level==Z_NO_COMPRESSION) || (buffer_length<=0))  {
+
+      if (f.WriteInt(&buffer_length))  {
+        if (!f.WriteFile(buffer,buffer_length))
+          rc = MemIO::WriteError;
       }
 
-      if (f.ReadInt(&len))  {
+    } else  {
+
+      len = -buffer_length - 1;
+      if (f.WriteInt(&len))  {
 
-        if (compression_alloc<=len)  {
-          FreeVectorMemory ( compression_buffer,0 );
-          compression_alloc = len + 100;
-          GetVectorMemory  ( compression_buffer,compression_alloc,0 );
+        csize = (uLongf)(1.1*buffer_length);
+        if (compression_alloc<=int(csize))  {
+          mmdb::FreeVectorMemory ( compression_buffer,0 );
+          mmdb::GetVectorMemory  ( compression_buffer,csize,0 );
         }
 
-        if (f.ReadFile(compression_buffer,len))  {
-          dsize = alloc_length;
-          rc = uncompress ( buffer,&dsize,compression_buffer,len );
-          if (rc==Z_OK)  {
-            if (int(dsize)!=buffer_length)  rc = CMemIO::SizeError;
-                                      else  rc = CMemIO::Ok;
+        rc = compress2 ( compression_buffer,&csize,
+                         buffer,buffer_length,compression_level );
+
+        if (rc==Z_OK)  {
+          len = csize;
+          if (f.WriteInt(&len))  {
+            if (!f.WriteFile(compression_buffer,csize))
+                  rc = MemIO::WriteError;
+            else  rc = MemIO::Ok;
           } else
-            rc = CMemIO::UncompressionError;
+            rc = MemIO::WriteError;
         } else
-          rc = CMemIO::ReadError;
+          rc = MemIO::CompressionError;
 
       } else
-        rc = CMemIO::ReadError;
+        rc = MemIO::WriteError;
+
+    }
+
+    return rc;
+
+  }
+
+  void MemIO::reset()  {
+    buffer_length = 0;
+  }
+
+  void MemIO::free()  {
+    mmdb::FreeVectorMemory ( compression_buffer,0 );
+    mmdb::FreeVectorMemory ( buffer            ,0 );
+    compression_alloc = 0;
+    buffer_length     = 0;
+    buffer_pos        = 0;
+    alloc_length      = 0;
+  }
+
+  void *MemIO::get_buffer ( const int length )  {
+    if (alloc_length<length)  {
+      mmdb::FreeVectorMemory ( buffer,0 );
+      alloc_length = length;
+      mmdb::GetVectorMemory ( buffer,alloc_length,0 );
+    }
+    return buffer;
+  }
+
+  void MemIO::get_buffer ( mmdb::pstr * buf, int * length )  {
+    *buf    = mmdb::pstr(buffer);
+    *length = buffer_length;
+  }
+
 
+  void MemIO::write_buffer ( const void * src, const int length  )  {
+  mmdb::bvector b1;
+    if (buffer_length+length>=alloc_length)  {
+      alloc_length += length+chunk_size;
+      mmdb::GetVectorMemory ( b1,alloc_length,0 );
+      memcpy ( b1,buffer,buffer_length );
+      mmdb::FreeVectorMemory ( buffer,0 );
+      buffer = b1;
     }
+    memcpy ( &(buffer[buffer_length]),src,length );
+    buffer_length += length;
+  }
 
-  } else
-    rc = CMemIO::ReadError;
 
-  return rc;
+  void MemIO::put_integer ( int I )  {
+  mmdb::intUniBin iUB;
+    mmdb::int2UniBin ( I,iUB );
+    write_buffer ( iUB,sizeof(mmdb::intUniBin) );
+  }
 
-}
+  void MemIO::put_ishort ( int I )  {
+  mmdb::shortUniBin sUB;
+    mmdb::short2UniBin ( short(I),sUB );
+    write_buffer ( sUB,sizeof(mmdb::shortUniBin) );
+  }
 
-int CMemIO::write ( cpstr fileName, byte gzMode )  {
-CFile f;
-int   rc;
+  void MemIO::put_ibyte ( int I )  {
+  // here we do not rely only on little-endian architectures
+  mmdb::byte B;
+    B = mmdb::byte(I);
+    write_buffer ( &B,sizeof(mmdb::byte) );
+  }
 
-  rc = CMemIO::Ok;
+  void MemIO::put_byte ( mmdb::byte B )  {
+    write_buffer ( &B,sizeof(mmdb::byte) );
+  }
 
-  f.assign ( fileName,False,True,gzMode );
+  void MemIO::put_short ( short I )  {
+  mmdb::shortUniBin sUB;
+    mmdb::short2UniBin ( I,sUB );
+    write_buffer ( sUB,sizeof(mmdb::shortUniBin) );
+  }
 
-  if (f.rewrite()) rc = write(f);
-              else rc = CMemIO::CantOpenFile;
+  void MemIO::put_long ( long I )  {
+  mmdb::longUniBin lUB;
+    mmdb::long2UniBin ( I,lUB );
+    write_buffer ( lUB,sizeof(mmdb::longUniBin) );
+  }
 
-  f.shut();
+  void MemIO::put_word ( mmdb::word W )  {
+  mmdb::wordUniBin wUB;
+    mmdb::word2UniBin ( W,wUB );
+    write_buffer ( wUB,sizeof(mmdb::wordUniBin) );
+  }
 
-  return rc;
+  void MemIO::put_real ( mmdb::realtype R )  {
+  mmdb::realUniBin rUB;
+    mmdb::real2UniBin ( R,rUB );
+    write_buffer ( rUB,sizeof(mmdb::realUniBin) );
+  }
 
-}
+  void MemIO::put_float ( mmdb::realtype R )  {
+  mmdb::floatUniBin fUB;
+    mmdb::float2UniBin ( R,fUB );
+    write_buffer ( fUB,sizeof(mmdb::floatUniBin) );
+  }
 
-int CMemIO::write ( RCFile f )  {
-int    rc,len;
-uLongf csize;
+  void MemIO::put_shortreal ( mmdb::shortreal R )  {
+  mmdb::shortrealUniBin srUB;
+    mmdb::shortreal2UniBin ( R,srUB );
+    write_buffer ( srUB,sizeof(mmdb::shortrealUniBin) );
+  }
 
-  rc = CMemIO::Ok;
+  void MemIO::put_line ( mmdb::cpstr L )  {
+    write_buffer ( L,strlen(L)+1 );  // null-terminated
+  }
 
-  if ((compression_level==Z_NO_COMPRESSION) || (buffer_length<=0))  {
+  void MemIO::put_string ( mmdb::cpstr S )  {
+  int len;
+    if (S)  len = strlen ( S );
+      else  len = 0;
+    put_integer ( len );
+    if (len>0)
+      write_buffer ( S,len );  // not null-terminated
+  }
 
-    if (f.WriteInt(&buffer_length))  {
-      if (!f.WriteFile(buffer,buffer_length))
-        rc = CMemIO::WriteError;
+  void MemIO::put_bool ( bool B )  {
+  char c;
+    if (B)  c = 'Y';
+      else  c = 'N';
+    write_buffer ( &c,1 );
+  }
+
+
+  bool MemIO::read_buffer ( void * dest, const int length,
+                                      bool * Ok )  {
+    if (buffer_pos+length<=buffer_length)  {
+      memcpy ( dest,&(buffer[buffer_pos]),length );
+      buffer_pos += length;
+      return true;
     }
+    if (Ok) *Ok = false;
+    return false;
+  }
 
-  } else  {
+  bool MemIO::get_integer ( int & I, bool * Ok )  {
+  mmdb::intUniBin iUB;
+    if (read_buffer(iUB,sizeof(mmdb::intUniBin),Ok))  {
+      mmdb::UniBin2int ( iUB,I );
+      return true;
+    } else  {
+      I = 0;
+      return false;
+    }
+  }
 
-    len = -buffer_length - 1;
-    if (f.WriteInt(&len))  {
+  bool MemIO::get_ishort ( int & I, bool * Ok )  {
+  mmdb::shortUniBin sUB;
+  short             Ishort;
+    if (read_buffer(sUB,sizeof(mmdb::shortUniBin),Ok))  {
+      mmdb::UniBin2short ( sUB,Ishort );
+      I = Ishort;
+      return true;
+    } else  {
+      I = 0;
+      return false;
+    }
+  }
 
-      csize = (uLongf)(1.1*buffer_length);
-      if (compression_alloc<=int(csize))  {
-        FreeVectorMemory ( compression_buffer,0 );
-        GetVectorMemory  ( compression_buffer,csize,0 );
-      }
+  bool MemIO::get_ibyte ( int & I, bool * Ok )  {
+  mmdb::byte B;
+    if (read_buffer(&B,sizeof(mmdb::byte),Ok))  {
+      I = B;
+      return true;
+    } else  {
+      I = 0;
+      return false;
+    }
+  }
 
-      rc = compress2 ( compression_buffer,&csize,
-                       buffer,buffer_length,compression_level );
+  bool MemIO::get_byte ( mmdb::byte & B, bool * Ok )  {
+    return read_buffer ( &B,sizeof(mmdb::byte),Ok );
+  }
 
-      if (rc==Z_OK)  {
-        len = csize;
-        if (f.WriteInt(&len))  {
-          if (!f.WriteFile(compression_buffer,csize))
-                rc = CMemIO::WriteError;
-          else  rc = CMemIO::Ok;
-        } else
-          rc = CMemIO::WriteError;
-      } else
-        rc = CMemIO::CompressionError;
+  bool MemIO::get_short ( short & I, bool * Ok )  {
+  mmdb::shortUniBin sUB;
+    if (read_buffer(sUB,sizeof(mmdb::shortUniBin),Ok))  {
+      mmdb::UniBin2short ( sUB,I );
+      return true;
+    } else  {
+      I = 0;
+      return false;
+    }
+  }
 
-    } else
-      rc = CMemIO::WriteError;
+  bool MemIO::get_long ( long & I, bool * Ok )  {
+  mmdb::longUniBin lUB;
+    if (read_buffer(lUB,sizeof(mmdb::longUniBin),Ok))  {
+      mmdb::UniBin2long ( lUB,I );
+      return true;
+    } else  {
+      I = 0;
+      return false;
+    }
+  }
+
+  bool MemIO::get_word ( mmdb::word & W, bool * Ok )  {
+  mmdb::wordUniBin wUB;
+    if (read_buffer(wUB,sizeof(mmdb::wordUniBin),Ok))  {
+      mmdb::UniBin2word ( wUB,W );
+      return true;
+    } else  {
+      W = 0;
+      return false;
+    }
+  }
+
+  bool MemIO::get_real ( mmdb::realtype & R, bool * Ok )  {
+  mmdb::realUniBin rUB;
+    if (read_buffer(rUB,sizeof(mmdb::realUniBin),Ok))  {
+      mmdb::UniBin2real ( rUB,R );
+      return true;
+    } else  {
+      R = 0.0;
+      return false;
+    }
+  }
+
+  bool MemIO::get_float ( mmdb::realtype & R, bool * Ok )  {
+  mmdb::floatUniBin fUB;
+    if (read_buffer(fUB,sizeof(mmdb::floatUniBin),Ok))  {
+      mmdb::UniBin2float ( fUB,R );
+      return true;
+    } else  {
+      R = 0.0;
+      return false;
+    }
+  }
 
+  bool MemIO::get_shortreal ( mmdb::shortreal & R, bool * Ok )  {
+  mmdb::shortrealUniBin srUB;
+    if (read_buffer(srUB,sizeof(mmdb::shortrealUniBin),Ok))  {
+      mmdb::UniBin2shortreal ( srUB,R );
+      return true;
+    } else  {
+      R = 0.0;
+      return false;
+    }
   }
 
-  return rc;
+  bool MemIO::get_line ( mmdb::pstr L, bool * Ok )  {
+  int  i;
+  char c;
+    i = 0;
+    c = ' ';
+    while (c && (buffer_pos<buffer_length))  {
+      c      = buffer[buffer_pos++];
+      L[i++] = c;
+    }
+    if (!c)
+      return true;
+    else  {
+      if (Ok)  Ok = false;
+      return false;
+    }
+  }
 
-}
+  bool MemIO::get_string ( mmdb::pstr & L, bool * Ok )  {
+  int len;
+    if (L)  delete[] L;
+    L = NULL;
+    if (get_integer(len,Ok))  {
+      if (len>0)  {
+        L = new char[len+1];
+        L[len] = char(0);
+        return read_buffer ( L,len,Ok );
+      }
+      return true;
+    }
+    return false;
+  }
 
-void CMemIO::reset()  {
-  buffer_length = 0;
-}
-
-void CMemIO::free()  {
-  FreeVectorMemory ( compression_buffer,0 );
-  FreeVectorMemory ( buffer            ,0 );
-  compression_alloc = 0;
-  buffer_length     = 0;
-  buffer_pos        = 0;
-  alloc_length      = 0;
-}
-
-void *CMemIO::get_buffer ( const int length )  {
-  if (alloc_length<length)  {
-    FreeVectorMemory ( buffer,0 );
-    alloc_length = length;
-    GetVectorMemory ( buffer,alloc_length,0 );
-  }
-  return buffer;
-}
-
-void CMemIO::get_buffer ( pstr * buf, int * length )  {
-  *buf    = pstr(buffer);
-  *length = buffer_length;
-}
-
-
-void CMemIO::write_buffer ( const void * src, const int length  )  {
-bvector b1;
-  if (buffer_length+length>=alloc_length)  {
-    alloc_length += length+chunk_size;
-    GetVectorMemory ( b1,alloc_length,0 );
-    memcpy ( b1,buffer,buffer_length );
-    FreeVectorMemory ( buffer,0 );
-    buffer = b1;
-  }
-  memcpy ( &(buffer[buffer_length]),src,length );
-  buffer_length += length;
-}
-
-
-void CMemIO::put_integer ( int I )  {
-intUniBin iUB;
-  int2UniBin ( I,iUB );
-  write_buffer ( iUB,sizeof(intUniBin) );
-}
-
-void CMemIO::put_ishort ( int I )  {
-shortUniBin sUB;
-  short2UniBin ( short(I),sUB );
-  write_buffer ( sUB,sizeof(shortUniBin) );
-}
-
-void CMemIO::put_ibyte ( int I )  {
-// here we do not rely only on little-endian architectures
-byte B;
-  B = byte(I);
-  write_buffer ( &B,sizeof(byte) );
-}
-
-void CMemIO::put_byte ( byte B )  {
-  write_buffer ( &B,sizeof(byte) );
-}
-
-void CMemIO::put_short ( short I )  {
-shortUniBin sUB;
-  short2UniBin ( I,sUB );
-  write_buffer ( sUB,sizeof(shortUniBin) );
-}
-
-void CMemIO::put_long ( long I )  {
-longUniBin lUB;
-  long2UniBin ( I,lUB );
-  write_buffer ( lUB,sizeof(longUniBin) );
-}
-
-void CMemIO::put_word ( word W )  {
-wordUniBin wUB;
-  word2UniBin ( W,wUB );
-  write_buffer ( wUB,sizeof(wordUniBin) );
-}
-
-void CMemIO::put_real ( realtype R )  {
-realUniBin rUB;
-  real2UniBin ( R,rUB );
-  write_buffer ( rUB,sizeof(realUniBin) );
-}
-
-void CMemIO::put_float ( realtype R )  {
-floatUniBin fUB;
-  float2UniBin ( R,fUB );
-  write_buffer ( fUB,sizeof(floatUniBin) );
-}
-
-void CMemIO::put_shortreal ( shortreal R )  {
-shortrealUniBin srUB;
-  shortreal2UniBin ( R,srUB );
-  write_buffer ( srUB,sizeof(shortrealUniBin) );
-}
-
-void CMemIO::put_line ( cpstr L )  {
-  write_buffer ( L,strlen(L)+1 );  // null-terminated
-}
-
-void CMemIO::put_string ( cpstr S )  {
-int len;
-  if (S)  len = strlen ( S );
-    else  len = 0;
-  put_integer ( len );
-  if (len>0)
-    write_buffer ( S,len );  // not null-terminated
-}
-
-void CMemIO::put_boolean ( Boolean  B )  {
-char c;
-  if (B)  c = 'Y';
-    else  c = 'N';
-  write_buffer ( &c,1 );
-}
-
-
-Boolean CMemIO::read_buffer ( void * dest, const int length,
-                                    Boolean * Ok )  {
-  if (buffer_pos+length<=buffer_length)  {
-    memcpy ( dest,&(buffer[buffer_pos]),length );
-    buffer_pos += length;
-    return True;
-  }
-  if (Ok) *Ok = False;
-  return False;
-}
-
-Boolean CMemIO::get_integer ( int & I, Boolean * Ok )  {
-intUniBin iUB;
-  if (read_buffer(iUB,sizeof(intUniBin),Ok))  {
-    UniBin2int ( iUB,I );
-    return True;
-  } else  {
-    I = 0;
-    return False;
-  }
-}
-
-Boolean CMemIO::get_ishort ( int & I, Boolean * Ok )  {
-shortUniBin sUB;
-short       Ishort;
-  if (read_buffer(sUB,sizeof(shortUniBin),Ok))  {
-    UniBin2short ( sUB,Ishort );
-    I = Ishort;
-    return True;
-  } else  {
-    I = 0;
-    return False;
-  }
-}
-
-Boolean CMemIO::get_ibyte ( int & I, Boolean * Ok )  {
-byte B;
-  if (read_buffer(&B,sizeof(byte),Ok))  {
-    I = B;
-    return True;
-  } else  {
-    I = 0;
-    return False;
-  }
-}
-
-Boolean CMemIO::get_byte ( byte & B, Boolean * Ok )  {
-  return read_buffer ( &B,sizeof(byte),Ok );
-}
-
-Boolean CMemIO::get_short ( short & I, Boolean * Ok )  {
-shortUniBin sUB;
-  if (read_buffer(sUB,sizeof(shortUniBin),Ok))  {
-    UniBin2short ( sUB,I );
-    return True;
-  } else  {
-    I = 0;
-    return False;
-  }
-}
-
-Boolean CMemIO::get_long ( long & I, Boolean * Ok )  {
-longUniBin lUB;
-  if (read_buffer(lUB,sizeof(longUniBin),Ok))  {
-    UniBin2long ( lUB,I );
-    return True;
-  } else  {
-    I = 0;
-    return False;
-  }
-}
-
-Boolean CMemIO::get_word ( word & W, Boolean * Ok )  {
-wordUniBin wUB;
-  if (read_buffer(wUB,sizeof(wordUniBin),Ok))  {
-    UniBin2word ( wUB,W );
-    return True;
-  } else  {
-    W = 0;
-    return False;
-  }
-}
-
-Boolean CMemIO::get_real ( realtype & R, Boolean * Ok )  {
-realUniBin rUB;
-  if (read_buffer(rUB,sizeof(realUniBin),Ok))  {
-    UniBin2real ( rUB,R );
-    return True;
-  } else  {
-    R = 0.0;
-    return False;
-  }
-}
-
-Boolean CMemIO::get_float ( realtype & R, Boolean * Ok )  {
-floatUniBin fUB;
-  if (read_buffer(fUB,sizeof(floatUniBin),Ok))  {
-    UniBin2float ( fUB,R );
-    return True;
-  } else  {
-    R = 0.0;
-    return False;
-  }
-}
-
-Boolean CMemIO::get_shortreal ( shortreal & R, Boolean * Ok )  {
-shortrealUniBin srUB;
-  if (read_buffer(srUB,sizeof(shortrealUniBin),Ok))  {
-    UniBin2shortreal ( srUB,R );
-    return True;
-  } else  {
-    R = 0.0;
-    return False;
-  }
-}
-
-Boolean CMemIO::get_line ( pstr L, Boolean * Ok )  {
-int  i;
-char c;
-  i = 0;
-  c = ' ';
-  while (c && (buffer_pos<buffer_length))  {
-    c      = buffer[buffer_pos++];
-    L[i++] = c;
-  }
-  if (!c)
-    return True;
-  else  {
-    if (Ok)  Ok = False;
-    return False;
-  }
-}
-
-Boolean CMemIO::get_string ( pstr & L, Boolean * Ok )  {
-int len;
-  if (L)  delete[] L;
-  L = NULL;
-  if (get_integer(len,Ok))  {
-    if (len>0)  {
-      L = new char[len+1];
-      L[len] = char(0);
-      return read_buffer ( L,len,Ok );
-    }
-    return True;
-  }
-  return False;
-}
-
-Boolean CMemIO::get_boolean ( Boolean  & B, Boolean * Ok )  {
-char c;
-  if (read_buffer(&c,1,Ok))  {
-    B = (c=='Y');
-    return True;
+  bool MemIO::get_bool ( bool & B, bool * Ok )  {
+  char c;
+    if (read_buffer(&c,1,Ok))  {
+      B = (c=='Y');
+      return true;
+    }
+    return false;
   }
-  return False;
-}
 
+}  // namespace ccp4srs
diff -ruN ccp4srs-old/ccp4srs/memio_.h ccp4srs/ccp4srs/memio_.h
--- ccp4srs-old/ccp4srs/memio_.h	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/memio_.h	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: memio_.h, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: memio_.h $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrievak and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,16 +22,16 @@
 //
 //  =================================================================
 //
-//    11.03.10   <--  Date of Last Modification.
+//    03.02.14   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  memio_  <interface>
 //       ~~~~~~~~~
-//  **** Classes :  CMemIO  - buffered I/O
+//  **** Classes :  ccp4srs::MemIO  - buffered I/O
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010
+//  (C) E. Krissinel 2010-2014
 //
 //  =================================================================
 //
@@ -39,75 +39,81 @@
 #ifndef MEMIO_H
 #define MEMIO_H
 
-#include "mmdb/file_.h"
+#include "mmdb2/mmdb_io_file.h"
 
-DefineClass(CMemIO)
+namespace ccp4srs  {
 
-class CMemIO  {
+  DefineClass(MemIO);
 
-  public:
+  class MemIO  {
 
-    enum { Ok,CantOpenFile,EmptyFile,ReadError,WriteError,MemReadError,
-           CompressionError,UncompressionError,SizeError };
-
-    CMemIO();
-    virtual ~CMemIO();
-
-    void  setCompressionLevel ( int compressionLevel ); // 0,1,2,3
-
-    int   read  ( cpstr  fileName, byte gzMode=GZM_NONE );
-    int   read  ( RCFile f );
-
-    int   write ( cpstr  fileName, byte gzMode=GZM_NONE );
-    int   write ( RCFile f );
-
-    int   length() { return buffer_length; }
-
-    void  reset();
-    void  free ();
-
-    void * get_buffer ( const int length );
-    void   set_buffer_length ( const int len )  { buffer_length = len; }
-    void   get_buffer ( pstr * buf, int * length );
-
-    void    write_buffer ( const void * src,  const int length  );
-    Boolean read_buffer  ( void       * dest, const int length,
-                           Boolean * Ok = NULL);
-
-    void  put_integer   ( int       I );
-    void  put_ishort    ( int       I );  // saves as short
-    void  put_ibyte     ( int       I );  // saves as byte
-    void  put_byte      ( byte      B );
-    void  put_short     ( short     I );
-    void  put_long      ( long      I );
-    void  put_word      ( word      W );
-    void  put_real      ( realtype  R );
-    void  put_float     ( realtype  R );  // stores single precision
-    void  put_shortreal ( shortreal R );
-    void  put_line      ( cpstr     L );  // for static strings
-    void  put_string    ( cpstr     L );  // for dynamic strings
-    void  put_boolean   ( Boolean   B );
-
-    Boolean  get_integer   ( int       & I, Boolean * Ok = NULL );
-    Boolean  get_ishort    ( int       & I, Boolean * Ok = NULL );
-    Boolean  get_ibyte     ( int       & I, Boolean * Ok = NULL );
-    Boolean  get_byte      ( byte      & B, Boolean * Ok = NULL );
-    Boolean  get_short     ( short     & I, Boolean * Ok = NULL );
-    Boolean  get_long      ( long      & I, Boolean * Ok = NULL );
-    Boolean  get_word      ( word      & W, Boolean * Ok = NULL );
-    Boolean  get_real      ( realtype  & R, Boolean * Ok = NULL );
-    Boolean  get_float     ( realtype  & R, Boolean * Ok = NULL );
-    Boolean  get_shortreal ( shortreal & R, Boolean * Ok = NULL );
-    Boolean  get_line      ( pstr        L, Boolean * Ok = NULL );
-    Boolean  get_string    ( pstr      & L, Boolean * Ok = NULL );
-    Boolean  get_boolean   ( Boolean   & B, Boolean * Ok = NULL );
-
-  private:
-    int     compression_level;
-    bvector buffer,compression_buffer;
-    int     buffer_length,buffer_pos,alloc_length,chunk_size;
-    int     compression_alloc;
+    public:
+
+      enum { Ok,CantOpenFile,EmptyFile,ReadError,WriteError,MemReadError,
+             CompressionError,UncompressionError,SizeError };
+
+      MemIO();
+      virtual ~MemIO();
+
+      void  setCompressionLevel ( int compressionLevel ); // 0,1,2,3
+
+      int   read  ( mmdb::cpstr  fileName,
+                    mmdb::io::GZ_MODE gzMode=mmdb::io::GZM_NONE );
+      int   read  ( mmdb::io::RFile f );
+
+      int   write ( mmdb::cpstr  fileName,
+                    mmdb::io::GZ_MODE gzMode=mmdb::io::GZM_NONE );
+      int   write ( mmdb::io::RFile f );
+
+      int   length() { return buffer_length; }
+
+      void  reset();
+      void  free ();
+
+      void * get_buffer        ( const int length );
+      void   set_buffer_length ( const int len )  { buffer_length = len; }
+      void   get_buffer        ( mmdb::pstr * buf, int * length );
+
+      void  write_buffer ( const void * src,  const int length  );
+      bool  read_buffer  ( void       * dest, const int length,
+                           bool * Ok = NULL);
+
+      void  put_integer   ( int        I );
+      void  put_ishort    ( int        I );  // saves as short
+      void  put_ibyte     ( int        I );  // saves as byte
+      void  put_byte      ( mmdb::byte B );
+      void  put_short     ( short      I );
+      void  put_long      ( long       I );
+      void  put_word      ( mmdb::word W );
+      void  put_real      ( mmdb::realtype  R );
+      void  put_float     ( mmdb::realtype  R );  // stores single precision
+      void  put_shortreal ( mmdb::shortreal R );
+      void  put_line      ( mmdb::cpstr     L );  // for static strings
+      void  put_string    ( mmdb::cpstr     L );  // for dynamic strings
+      void  put_bool      ( bool   B );
+
+      bool  get_integer   ( int        & I, bool * Ok = NULL );
+      bool  get_ishort    ( int        & I, bool * Ok = NULL );
+      bool  get_ibyte     ( int        & I, bool * Ok = NULL );
+      bool  get_byte      ( mmdb::byte & B, bool * Ok = NULL );
+      bool  get_short     ( short      & I, bool * Ok = NULL );
+      bool  get_long      ( long       & I, bool * Ok = NULL );
+      bool  get_word      ( mmdb::word      & W, bool * Ok = NULL );
+      bool  get_real      ( mmdb::realtype  & R, bool * Ok = NULL );
+      bool  get_float     ( mmdb::realtype  & R, bool * Ok = NULL );
+      bool  get_shortreal ( mmdb::shortreal & R, bool * Ok = NULL );
+      bool  get_line      ( mmdb::pstr        L, bool * Ok = NULL );
+      bool  get_string    ( mmdb::pstr      & L, bool * Ok = NULL );
+      bool  get_bool      ( bool   & B, bool * Ok = NULL );
+
+    private:
+      int           compression_level;
+      mmdb::bvector buffer,compression_buffer;
+      int           buffer_length,buffer_pos,alloc_length,chunk_size;
+      int           compression_alloc;
 
-};
+  };
+
+}  // namespace ccp4srs
 
 #endif // MEMIO_H
diff -ruN ccp4srs-old/ccp4srs/mpfile_.cpp ccp4srs/ccp4srs/mpfile_.cpp
--- ccp4srs-old/ccp4srs/mpfile_.cpp	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/mpfile_.cpp	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: mpfile_.cpp, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: mpfile_.cpp $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,270 +22,271 @@
 //
 //  =================================================================
 //
-//    11.03.10   <--  Date of Last Modification.
+//    18.09.13   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  mpfile_  <implementation>
 //       ~~~~~~~~~
-//  **** Classes :  CMPFile  - multi-part file support
+//  **** Classes :  ccp4srs::MPFile  - multi-part file support
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010
+//  (C) E. Krissinel 2010-2013
 //
 //  =================================================================
 //
 
-#ifndef  MPFILE_H
 #include "mpfile_.h"
-#endif
 
+namespace ccp4srs  {
 
-//  ==========================  CMPFile  ============================
+  //  ==========================  MPFile  ============================
 
-void SMPFilePos::Copy ( RSMPFilePos dbf_pos )  {
-  chunkNo = dbf_pos.chunkNo;
-  offset  = dbf_pos.offset;
-}
-
-void SMPFilePos::write ( RCFile f )  {
-  f.WriteByte ( &chunkNo );
-  f.WriteLong ( &offset  );
-}
-
-void SMPFilePos::read ( RCFile f )  {
-  f.ReadByte ( &chunkNo );
-  f.ReadLong ( &offset  );
-}
-
-
-CMPFile::CMPFile()  {
-  f         = NULL;
-  fpath     = NULL;
-  chunkPath = NULL;
-  uniBinary = True;
-  readOnly  = False;
-  chunkSize = 1000000000;
-  chunkNo   = 0;
-  nchunks   = 0;
-}
-
-CMPFile::~CMPFile()  {
-  shut();
-  if (fpath)  {
-    delete[] fpath;
-    fpath = NULL;
-  }
-}
-
-void CMPFile::shut()  {
-int i;
-  if (f)  {
-    for (i=0;i<nchunks;i++)
-      if (f[i])  f[i]->shut();
-    delete[] f;
-    f = NULL;
+  void MPFilePos::Copy ( RMPFilePos dbf_pos )  {
+    chunkNo = dbf_pos.chunkNo;
+    offset  = dbf_pos.offset;
+  }
+
+  void MPFilePos::write ( mmdb::io::RFile f )  {
+    f.WriteByte ( &chunkNo );
+    f.WriteLong ( &offset  );
   }
-  if (chunkPath)  {
-    delete[] chunkPath;
+
+  void MPFilePos::read ( mmdb::io::RFile f )  {
+    f.ReadByte ( &chunkNo );
+    f.ReadLong ( &offset  );
+  }
+
+
+  MPFile::MPFile()  {
+    f         = NULL;
+    fpath     = NULL;
     chunkPath = NULL;
+    uniBinary = true;
+    readOnly  = false;
+    chunkSize = 1000000000;
+    chunkNo   = 0;
+    nchunks   = 0;
   }
-  uniBinary = True;
-  readOnly    = False;
-  chunkSize = 1000000000;
-  chunkNo   = 0;
-  nchunks   = 0;
-}
-
-void CMPFile::assign ( cpstr FName, Boolean UniB )  {
-  shut();
-  CreateCopy ( fpath,FName );
-  uniBinary = UniB;
-}
-
-pstr CMPFile::getChunkPath()  {
-char N[50];
-  sprintf ( N,".fp%i",chunkNo+1 );
-  CreateCopCat ( chunkPath,fpath,N );
-  return chunkPath;
-}
-
-Boolean CMPFile::reset ( Boolean readOnly )  {
-  shut();
-  readOnly = readOnly;
-  chunkNo  = 0;
-  nchunks  = 1;
-  f    = new PCFile[nchunks];
-  f[0] = new CFile();
-  f[0]->assign ( getChunkPath(),False,uniBinary,GZM_NONE );
-  if (f[0]->reset(readOnly))
-       return f[0]->ReadLong ( &chunkSize );
-  else return False;
-}
-
-Boolean CMPFile::rewrite ( long chunk_size )  {
-
-  shut();
-
-  readOnly  = False;
-  chunkSize = chunk_size;
-  chunkNo   = 1;
-  nchunks   = 1;
-  f    = new PCFile[nchunks];
-  f[0] = new CFile();
-  while (chunkNo>0)  {
-    f[0]->assign ( getChunkPath(),False,uniBinary,GZM_NONE );
-    if (f[0]->exists())  {
-      f[0]->erase();
-      chunkNo++;
-    } else
-      chunkNo = 0;
+
+  MPFile::~MPFile()  {
+    shut();
+    if (fpath)  {
+      delete[] fpath;
+      fpath = NULL;
+    }
   }
-  f[0]->assign ( getChunkPath(),False,uniBinary,GZM_NONE );
-  if (f[0]->rewrite())  return f[0]->WriteLong ( &chunkSize );
-                  else  return False;
 
-}
+  void MPFile::shut()  {
+  int i;
+    if (f)  {
+      for (i=0;i<nchunks;i++)
+        if (f[i])  f[i]->shut();
+      delete[] f;
+      f = NULL;
+    }
+    if (chunkPath)  {
+      delete[] chunkPath;
+      chunkPath = NULL;
+    }
+    uniBinary = true;
+    readOnly    = false;
+    chunkSize = 1000000000;
+    chunkNo   = 0;
+    nchunks   = 0;
+  }
 
-Boolean CMPFile::append ( long chunk_size )  {
-PCFile fa;
-int    i;
+  void MPFile::assign ( mmdb::cpstr FName, bool UniB )  {
+    shut();
+    mmdb::CreateCopy ( fpath,FName );
+    uniBinary = UniB;
+  }
 
-  shut();
+  mmdb::pstr MPFile::getChunkPath()  {
+  char N[50];
+    sprintf ( N,".fp%i",chunkNo+1 );
+    mmdb::CreateCopCat ( chunkPath,fpath,N );
+    return chunkPath;
+  }
 
-  readOnly = False;
-  chunkNo  = 0;
-  nchunks  = 1;
+  bool MPFile::reset ( bool readOnly )  {
+    shut();
+    readOnly = readOnly;
+    chunkNo  = 0;
+    nchunks  = 1;
+    f    = new mmdb::io::PFile[nchunks];
+    f[0] = new mmdb::io::File();
+    f[0]->assign ( getChunkPath(),false,uniBinary,mmdb::io::GZM_NONE );
+    if (f[0]->reset(readOnly))
+         return f[0]->ReadLong ( &chunkSize );
+    else return false;
+  }
 
-  fa = new CFile();
-  fa->assign ( getChunkPath(),False,uniBinary,GZM_NONE );
+  bool MPFile::rewrite ( long chunk_size )  {
 
-  if (!fa->exists())  {
+    shut();
 
-    f = new PCFile[nchunks];
+    readOnly  = false;
     chunkSize = chunk_size;
-    f[0] = fa;
-    if (f[0]->rewrite())
-         return f[0]->WriteLong ( &chunkSize );
-    else return False;
+    chunkNo   = 1;
+    nchunks   = 1;
+    f    = new mmdb::io::PFile[nchunks];
+    f[0] = new mmdb::io::File();
+    while (chunkNo>0)  {
+      f[0]->assign ( getChunkPath(),false,uniBinary,mmdb::io::GZM_NONE );
+      if (f[0]->exists())  {
+        f[0]->erase();
+        chunkNo++;
+      } else
+        chunkNo = 0;
+    }
+    f[0]->assign ( getChunkPath(),false,uniBinary,mmdb::io::GZM_NONE );
+    if (f[0]->rewrite())  return f[0]->WriteLong ( &chunkSize );
+                    else  return false;
+
+  }
+
+  bool MPFile::append ( long chunk_size )  {
+  mmdb::io::PFile fa;
+  int    i;
+
+    shut();
+
+    readOnly = false;
+    chunkNo  = 0;
+    nchunks  = 1;
+
+    fa = new mmdb::io::File();
+    fa->assign ( getChunkPath(),false,uniBinary,mmdb::io::GZM_NONE );
+
+    if (!fa->exists())  {
 
-  } else if (fa->reset(readOnly))  {
+      f = new mmdb::io::PFile[nchunks];
+      chunkSize = chunk_size;
+      f[0] = fa;
+      if (f[0]->rewrite())
+           return f[0]->WriteLong ( &chunkSize );
+      else return false;
 
-    if (!fa->ReadLong(&chunkSize))  {
-      delete fa;
-      return False;
+    } else if (fa->reset(readOnly))  {
+
+      if (!fa->ReadLong(&chunkSize))  {
+        delete fa;
+        return false;
+      }
+
+    } else
+      return false;
+
+    while (fa->exists())  {
+      chunkNo++;
+      fa->assign ( getChunkPath(),false,uniBinary,mmdb::io::GZM_NONE );
     }
 
-  } else
-    return False;
+    nchunks = chunkNo;
+    chunkNo--;
+
+    f = new mmdb::io::PFile[nchunks];
+    for (i=0;i<nchunks;i++)
+      f[i] = NULL;
+
+    f[chunkNo] = fa;
+    f[chunkNo]->assign ( getChunkPath(),false,uniBinary,mmdb::io::GZM_NONE );
+    return f[chunkNo]->append();
 
-  while (fa->exists())  {
-    chunkNo++;
-    fa->assign ( getChunkPath(),False,uniBinary,GZM_NONE );
   }
 
-  nchunks = chunkNo;
-  chunkNo--;
+  void MPFile::getPosition ( RMPFilePos DBFPos )  {
+    if (f)  {
+      if (f[chunkNo])  {
+        DBFPos.chunkNo = chunkNo;
+        DBFPos.offset  = f[chunkNo]->Position();
+        return;
+      }
+    }
+    DBFPos.chunkNo = 0;
+    DBFPos.offset  = 0;
+  }
 
-  f = new PCFile[nchunks];
-  for (i=0;i<nchunks;i++)
-    f[i] = NULL;
+  bool MPFile::getChunk ( int toChunkNo, bool onRead )  {
+  mmdb::io::PPFile f1;
+  int              i;
+  bool             B;
+    if (toChunkNo>=nchunks)  {
+      f1 = new mmdb::io::PFile[toChunkNo+1];
+      for (i=0;i<nchunks;i++)
+        f1[i] = f[i];
+      for (i=nchunks;i<=toChunkNo;i++)
+        f1[i] = NULL;
+      if (f)  delete[] f;
+      f = f1;
+      nchunks = toChunkNo+1;
+    }
+    chunkNo = toChunkNo;
+    if (!f[chunkNo])  {
+      f[chunkNo] = new mmdb::io::File();
+      f[chunkNo]->assign ( getChunkPath(),false,uniBinary,
+                           mmdb::io::GZM_NONE );
+    }
+    if (!f[chunkNo]->isOpen())  {
+      if (onRead)  {
+        B = f[chunkNo]->reset ( readOnly );
+        if (B && (chunkNo==0))
+          f[chunkNo]->ReadLong ( &chunkSize );
+      } else  {
+        B = f[chunkNo]->rewrite();
+        if (B && (chunkNo==0))
+          f[chunkNo]->WriteLong ( &chunkSize );
+      }
+      if (!B)  {
+        delete f[chunkNo];
+        f[chunkNo] = NULL;
+      }
+      return B;
+    }
+    return true;
+  }
 
-  f[chunkNo] = fa;
-  f[chunkNo]->assign ( getChunkPath(),False,uniBinary,GZM_NONE );
-  return f[chunkNo]->append();
+  bool MPFile::seek ( RMPFilePos DBFPos )  {
+    if (getChunk(DBFPos.chunkNo,true))
+         return f[chunkNo]->seek ( DBFPos.offset );
+    else return false;
+  }
 
-}
+  bool MPFile::MPFileEnd()  {
+    if (f)  {
+      if (f[chunkNo])
+        return f[chunkNo]->FileEnd();
+    }
+    return true;
+  }
 
-void CMPFile::getPosition ( RSMPFilePos DBFPos )  {
-  if (f)  {
-    if (f[chunkNo])  {
-      DBFPos.chunkNo = chunkNo;
-      DBFPos.offset  = f[chunkNo]->Position();
-      return;
+  bool MPFile::Success()  {
+    if (f)  {
+      if (f[chunkNo])
+        return f[chunkNo]->Success();
     }
+    return false;
   }
-  DBFPos.chunkNo = 0;
-  DBFPos.offset  = 0;
-}
 
-Boolean CMPFile::getChunk ( int toChunkNo, Boolean onRead )  {
-PPCFile f1;
-int     i;
-Boolean B;
-  if (toChunkNo>=nchunks)  {
-    f1 = new PCFile[toChunkNo+1];
-    for (i=0;i<nchunks;i++)
-      f1[i] = f[i];
-    for (i=nchunks;i<=toChunkNo;i++)
-      f1[i] = NULL;
-    if (f)  delete[] f;
-    f = f1;
-    nchunks = toChunkNo+1;
-  }
-  chunkNo = toChunkNo;
-  if (!f[chunkNo])  {
-    f[chunkNo] = new CFile();
-    f[chunkNo]->assign ( getChunkPath(),False,uniBinary,GZM_NONE );
-  }
-  if (!f[chunkNo]->isOpen())  {
-    if (onRead)  {
-      B = f[chunkNo]->reset ( readOnly );
-      if (B && (chunkNo==0))
-        f[chunkNo]->ReadLong ( &chunkSize );
-    } else  {
-      B = f[chunkNo]->rewrite();
-      if (B && (chunkNo==0))
-        f[chunkNo]->WriteLong ( &chunkSize );
-    }
-    if (!B)  {
-      delete f[chunkNo];
-      f[chunkNo] = NULL;
-    }
-    return B;
-  }
-  return True;
-}
-
-Boolean CMPFile::seek ( RSMPFilePos DBFPos )  {
-  if (getChunk(DBFPos.chunkNo,True))
-       return f[chunkNo]->seek ( DBFPos.offset );
-  else return False;
-}
-
-Boolean CMPFile::MPFileEnd()  {
-  if (f)  {
-    if (f[chunkNo])
-      return f[chunkNo]->FileEnd();
-  }
-  return True;
-}
-
-Boolean CMPFile::Success()  {
-  if (f)  {
-    if (f[chunkNo])
-      return f[chunkNo]->Success();
-  }
-  return False;
-}
-
-Boolean CMPFile::checkChunkEnd ( Boolean onRead )  {
-  if (getChunk(chunkNo,onRead))  {
-    if (f[chunkNo]->Position()>=chunkSize)
-      return getChunk ( chunkNo+1,onRead );
-    return True;
-  }
-  return False;
-}
-
-
-PCFile CMPFile::getChunkRead()  {
-  if (checkChunkEnd(True))  return f[chunkNo];
-                      else  return NULL;
-}
-
-PCFile CMPFile::getChunkWrite()  {
-  if (checkChunkEnd(False))  return f[chunkNo];
-                       else  return NULL;
-}
+  bool MPFile::checkChunkEnd ( bool onRead )  {
+    if (getChunk(chunkNo,onRead))  {
+      if (f[chunkNo]->Position()>=chunkSize)
+        return getChunk ( chunkNo+1,onRead );
+      return true;
+    }
+    return false;
+  }
+
+
+  mmdb::io::PFile MPFile::getChunkRead()  {
+    if (checkChunkEnd(true))  return f[chunkNo];
+                        else  return NULL;
+  }
+
+  mmdb::io::PFile MPFile::getChunkWrite()  {
+    if (checkChunkEnd(false))  return f[chunkNo];
+                         else  return NULL;
+  }
 
+}  // namespace ccp4srs
diff -ruN ccp4srs-old/ccp4srs/mpfile_.h ccp4srs/ccp4srs/mpfile_.h
--- ccp4srs-old/ccp4srs/mpfile_.h	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/ccp4srs/mpfile_.h	2014-09-09 21:34:12.000000000 -0700
@@ -1,10 +1,10 @@
-//  $Id: mpfile_.h, v 1.00 2010/03/11 15:28:14 Eugene Exp $
+//  $Id: mpfile_.h $
 //  =================================================================
 //
 //   CCP4 SRS Library: Storage, Retrieval and Search support for
 //   CCP4 ligand data.
 //
-//   Copyright (C) Eugene Krissinel 2010.
+//   Copyright (C) Eugene Krissinel 2010-2013.
 //
 //   This library is free software: you can redistribute it and/or
 //   modify it under the terms of the GNU Lesser General Public
@@ -22,16 +22,16 @@
 //
 //  =================================================================
 //
-//    11.03.10   <--  Date of Last Modification.
+//    03.02.14   <--  Date of Last Modification.
 //                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 //  -----------------------------------------------------------------
 //
 //  **** Module  :  mpfile_  <interface>
 //       ~~~~~~~~~
-//  **** Classes :  CMPFile  - multi-part file support
+//  **** Classes :  ccp4srs::MPFile  - multi-part file support
 //       ~~~~~~~~~
 //
-//  (C) E. Krissinel 2010
+//  (C) E. Krissinel 2010-2014
 //
 //  =================================================================
 //
@@ -39,62 +39,62 @@
 #ifndef  MPFILE_H
 #define  MPFILE_H
 
-#ifndef  __File__
-#include "mmdb/file_.h"
-#endif
-
-
-//  ===========================  CMPFile  ===========================
-
-DefineStructure(SMPFilePos);
-
-struct SMPFilePos  {
-  byte  chunkNo;   // file part number (1-254)
-  long  offset;    // offset in chunk
-  void Copy  ( RSMPFilePos dbf_pos );
-  void write ( RCFile f );
-  void read  ( RCFile f );
-};
-
-DefineClass(CMPFile);
-
-class CMPFile  {
-
-  public :
-    CMPFile ();
-    ~CMPFile();
-
-    void     assign  ( cpstr FName, Boolean UniB=True );
-    Boolean  reset   ( Boolean readOnly=False );
-    Boolean  rewrite ( long chunk_size=1000000000  );
-    Boolean  append  ( long chunk_size=1000000000  );
-
-    pstr     FileName    () { return fpath; }
-    void     getPosition ( RSMPFilePos MPFilePos );
-    Boolean  seek        ( RSMPFilePos MPFilePos );
-    Boolean  MPFileEnd   ();
-    Boolean  Success     ();
-    void     shut        ();
- 
-    PCFile   getChunkRead ();
-    PCFile   getChunkWrite();
-
-  protected :
-    PPCFile f;
-    pstr    fpath;
-    long    chunkSize;
-    byte    chunkNo;
-    Boolean uniBinary,readOnly;
-
-    pstr    getChunkPath  ();
-    Boolean getChunk      ( int toChunkNo, Boolean onRead );
-    Boolean checkChunkEnd ( Boolean onRead );
-
-  private :
-    pstr    chunkPath;
-    int     nchunks;
+#include "mmdb2/mmdb_io_file.h"
 
-};
+namespace ccp4srs  {
 
+  //  ===========================  MPFile  ===========================
+
+  DefineStructure(MPFilePos);
+
+  struct MPFilePos  {
+    mmdb::byte chunkNo;   // file part number (1-254)
+    long       offset;    // offset in chunk
+    void Copy  ( RMPFilePos dbf_pos );
+    void write ( mmdb::io::RFile f );
+    void read  ( mmdb::io::RFile f );
+  };
+
+  DefineClass(MPFile)
+
+  class MPFile  {
+
+    public :
+      MPFile ();
+      ~MPFile();
+
+      void  assign  ( mmdb::cpstr FName, bool UniB=true );
+      bool  reset   ( bool readOnly=false );
+      bool  rewrite ( long chunk_size=1000000000  );
+      bool  append  ( long chunk_size=1000000000  );
+
+      mmdb::pstr FileName    () { return fpath; }
+      void  getPosition ( RMPFilePos MPFilePos );
+      bool  seek        ( RMPFilePos MPFilePos );
+      bool  MPFileEnd   ();
+      bool  Success     ();
+      void  shut        ();
+
+      mmdb::io::PFile   getChunkRead ();
+      mmdb::io::PFile   getChunkWrite();
+
+    protected :
+      mmdb::io::PPFile f;
+      mmdb::pstr       fpath;
+      long             chunkSize;
+      mmdb::byte       chunkNo;
+      bool             uniBinary,readOnly;
+
+      mmdb::pstr getChunkPath  ();
+      bool getChunk      ( int toChunkNo, bool onRead );
+      bool checkChunkEnd ( bool onRead );
+
+    private :
+      mmdb::pstr chunkPath;
+      int        nchunks;
+
+  };
+
+}  // namespace ccp4srs
 
 #endif  //  MPFILE_H
diff -ruN ccp4srs-old/configure ccp4srs/configure
--- ccp4srs-old/configure	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/configure	2014-09-09 21:34:12.000000000 -0700
@@ -1,11 +1,9 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.68 for ccp4srs 1.0.0.
+# Generated by GNU Autoconf 2.69 for ccp4srs 1.0.0.
 #
 #
-# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
-# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software
-# Foundation, Inc.
+# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
 #
 #
 # This configure script is free software; the Free Software Foundation
@@ -134,6 +132,31 @@
 # CDPATH.
 (unset CDPATH) >/dev/null 2>&1 && unset CDPATH
 
+# Use a proper internal environment variable to ensure we don't fall
+  # into an infinite loop, continuously re-executing ourselves.
+  if test x"${_as_can_reexec}" != xno && test "x$CONFIG_SHELL" != x; then
+    _as_can_reexec=no; export _as_can_reexec;
+    # We cannot yet assume a decent shell, so we have to provide a
+# neutralization value for shells without unset; and this also
+# works around shells that cannot unset nonexistent variables.
+# Preserve -v and -x to the replacement shell.
+BASH_ENV=/dev/null
+ENV=/dev/null
+(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
+case $- in # ((((
+  *v*x* | *x*v* ) as_opts=-vx ;;
+  *v* ) as_opts=-v ;;
+  *x* ) as_opts=-x ;;
+  * ) as_opts= ;;
+esac
+exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"}
+# Admittedly, this is quite paranoid, since all the known shells bail
+# out after a failed `exec'.
+$as_echo "$0: could not re-execute with $CONFIG_SHELL" >&2
+as_fn_exit 255
+  fi
+  # We don't want this to propagate to other subprocesses.
+          { _as_can_reexec=; unset _as_can_reexec;}
 if test "x$CONFIG_SHELL" = x; then
   as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then :
   emulate sh
@@ -167,7 +190,8 @@
 else
   exitcode=1; echo positional parameters were not saved.
 fi
-test x\$exitcode = x0 || exit 1"
+test x\$exitcode = x0 || exit 1
+test -x / || exit 1"
   as_suggested="  as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO
   as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO
   eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" &&
@@ -220,21 +244,25 @@
 
 
       if test "x$CONFIG_SHELL" != x; then :
-  # We cannot yet assume a decent shell, so we have to provide a
-	# neutralization value for shells without unset; and this also
-	# works around shells that cannot unset nonexistent variables.
-	# Preserve -v and -x to the replacement shell.
-	BASH_ENV=/dev/null
-	ENV=/dev/null
-	(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
-	export CONFIG_SHELL
-	case $- in # ((((
-	  *v*x* | *x*v* ) as_opts=-vx ;;
-	  *v* ) as_opts=-v ;;
-	  *x* ) as_opts=-x ;;
-	  * ) as_opts= ;;
-	esac
-	exec "$CONFIG_SHELL" $as_opts "$as_myself" ${1+"$@"}
+  export CONFIG_SHELL
+             # We cannot yet assume a decent shell, so we have to provide a
+# neutralization value for shells without unset; and this also
+# works around shells that cannot unset nonexistent variables.
+# Preserve -v and -x to the replacement shell.
+BASH_ENV=/dev/null
+ENV=/dev/null
+(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
+case $- in # ((((
+  *v*x* | *x*v* ) as_opts=-vx ;;
+  *v* ) as_opts=-v ;;
+  *x* ) as_opts=-x ;;
+  * ) as_opts= ;;
+esac
+exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"}
+# Admittedly, this is quite paranoid, since all the known shells bail
+# out after a failed `exec'.
+$as_echo "$0: could not re-execute with $CONFIG_SHELL" >&2
+exit 255
 fi
 
     if test x$as_have_required = xno; then :
@@ -336,6 +364,14 @@
 
 
 } # as_fn_mkdir_p
+
+# as_fn_executable_p FILE
+# -----------------------
+# Test if FILE is an executable regular file.
+as_fn_executable_p ()
+{
+  test -f "$1" && test -x "$1"
+} # as_fn_executable_p
 # as_fn_append VAR VALUE
 # ----------------------
 # Append the text in VALUE to the end of the definition contained in VAR. Take
@@ -457,6 +493,10 @@
   chmod +x "$as_me.lineno" ||
     { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; }
 
+  # If we had to re-execute with $CONFIG_SHELL, we're ensured to have
+  # already done that, so ensure we don't try to do so again and fall
+  # in an infinite loop.  This has already happened in practice.
+  _as_can_reexec=no; export _as_can_reexec
   # Don't try to exec as it changes $[0], causing all sort of problems
   # (the dirname of $[0] is not the place where we might find the
   # original and so on.  Autoconf is especially sensitive to this).
@@ -491,16 +531,16 @@
     # ... but there are two gotchas:
     # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
     # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
-    # In both cases, we have to default to `cp -p'.
+    # In both cases, we have to default to `cp -pR'.
     ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
-      as_ln_s='cp -p'
+      as_ln_s='cp -pR'
   elif ln conf$$.file conf$$ 2>/dev/null; then
     as_ln_s=ln
   else
-    as_ln_s='cp -p'
+    as_ln_s='cp -pR'
   fi
 else
-  as_ln_s='cp -p'
+  as_ln_s='cp -pR'
 fi
 rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
 rmdir conf$$.dir 2>/dev/null
@@ -512,28 +552,8 @@
   as_mkdir_p=false
 fi
 
-if test -x / >/dev/null 2>&1; then
-  as_test_x='test -x'
-else
-  if ls -dL / >/dev/null 2>&1; then
-    as_ls_L_option=L
-  else
-    as_ls_L_option=
-  fi
-  as_test_x='
-    eval sh -c '\''
-      if test -d "$1"; then
-	test -d "$1/.";
-      else
-	case $1 in #(
-	-*)set "./$1";;
-	esac;
-	case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
-	???[sx]*):;;*)false;;esac;fi
-    '\'' sh
-  '
-fi
-as_executable_p=$as_test_x
+as_test_x='test -x'
+as_executable_p=as_fn_executable_p
 
 # Sed expression to map a string onto a valid CPP name.
 as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
@@ -631,8 +651,6 @@
 DSYMUTIL
 MANIFEST_TOOL
 RANLIB
-ac_ct_AR
-AR
 LN_S
 NM
 ac_ct_DUMPBIN
@@ -642,6 +660,18 @@
 EGREP
 GREP
 SED
+host_os
+host_vendor
+host_cpu
+host
+build_os
+build_vendor
+build_cpu
+build
+LIBTOOL
+OBJDUMP
+DLLTOOL
+AS
 am__fastdepCC_FALSE
 am__fastdepCC_TRUE
 CCDEPMODE
@@ -659,18 +689,8 @@
 LDFLAGS
 CFLAGS
 CC
-host_os
-host_vendor
-host_cpu
-host
-build_os
-build_vendor
-build_cpu
-build
-LIBTOOL
-OBJDUMP
-DLLTOOL
-AS
+ac_ct_AR
+AR
 AM_BACKSLASH
 AM_DEFAULT_VERBOSITY
 AM_DEFAULT_V
@@ -740,11 +760,11 @@
 ac_user_opts='
 enable_option_checking
 enable_silent_rules
+enable_dependency_tracking
 enable_shared
 enable_static
 with_pic
 enable_fast_install
-enable_dependency_tracking
 with_gnu_ld
 with_sysroot
 enable_libtool_lock
@@ -1218,8 +1238,6 @@
 if test "x$host_alias" != x; then
   if test "x$build_alias" = x; then
     cross_compiling=maybe
-    $as_echo "$as_me: WARNING: if you wanted to set the --build type, don't use --host.
-    If a cross compiler is detected then cross compile mode will be used" >&2
   elif test "x$build_alias" != "x$host_alias"; then
     cross_compiling=yes
   fi
@@ -1383,22 +1401,25 @@
   --disable-option-checking  ignore unrecognized --enable/--with options
   --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no)
   --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]
-  --enable-silent-rules          less verbose build output (undo: `make V=1')
-  --disable-silent-rules         verbose build output (undo: `make V=0')
+  --enable-silent-rules   less verbose build output (undo: "make V=1")
+  --disable-silent-rules  verbose build output (undo: "make V=0")
+  --enable-dependency-tracking
+                          do not reject slow dependency extractors
+  --disable-dependency-tracking
+                          speeds up one-time build
   --enable-shared[=PKGS]  build shared libraries [default=no]
   --enable-static[=PKGS]  build static libraries [default=yes]
   --enable-fast-install[=PKGS]
                           optimize for fast installation [default=yes]
-  --disable-dependency-tracking  speeds up one-time build
-  --enable-dependency-tracking   do not reject slow dependency extractors
   --disable-libtool-lock  avoid locking (might break parallel builds)
-  --enable-maintainer-mode  enable make rules and dependencies not useful
-			  (and sometimes confusing) to the casual installer
+  --enable-maintainer-mode
+                          enable make rules and dependencies not useful (and
+                          sometimes confusing) to the casual installer
 
 Optional Packages:
   --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
   --without-PACKAGE       do not use PACKAGE (same as --with-PACKAGE=no)
-  --with-pic              try to use only PIC/non-PIC objects [default=use
+  --with-pic[=PKGS]       try to use only PIC/non-PIC objects [default=use
                           both]
   --with-gnu-ld           assume the C compiler uses GNU ld [default=no]
   --with-sysroot=DIR Search for dependent libraries within DIR
@@ -1484,9 +1505,9 @@
 if $ac_init_version; then
   cat <<\_ACEOF
 ccp4srs configure 1.0.0
-generated by GNU Autoconf 2.68
+generated by GNU Autoconf 2.69
 
-Copyright (C) 2010 Free Software Foundation, Inc.
+Copyright (C) 2012 Free Software Foundation, Inc.
 This configure script is free software; the Free Software Foundation
 gives unlimited permission to copy, distribute and modify it.
 _ACEOF
@@ -1562,7 +1583,7 @@
 	 test ! -s conftest.err
        } && test -s conftest$ac_exeext && {
 	 test "$cross_compiling" = yes ||
-	 $as_test_x conftest$ac_exeext
+	 test -x conftest$ac_exeext
        }; then :
   ac_retval=0
 else
@@ -1860,7 +1881,7 @@
 	 test ! -s conftest.err
        } && test -s conftest$ac_exeext && {
 	 test "$cross_compiling" = yes ||
-	 $as_test_x conftest$ac_exeext
+	 test -x conftest$ac_exeext
        }; then :
   ac_retval=0
 else
@@ -2057,7 +2078,7 @@
 running configure, to aid debugging if configure makes a mistake.
 
 It was created by ccp4srs $as_me 1.0.0, which was
-generated by GNU Autoconf 2.68.  Invocation command line was
+generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
 
@@ -2438,7 +2459,7 @@
 
 ac_config_headers="$ac_config_headers config.h"
 
-am__api_version='1.11'
+am__api_version='1.13'
 
 # Find a good install program.  We prefer a C program (faster),
 # so one script is as good as another.  But avoid the broken or
@@ -2477,7 +2498,7 @@
     # by default.
     for ac_prog in ginstall scoinst install; do
       for ac_exec_ext in '' $ac_executable_extensions; do
-	if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then
+	if as_fn_executable_p "$as_dir/$ac_prog$ac_exec_ext"; then
 	  if test $ac_prog = install &&
 	    grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
 	    # AIX install.  It has an incompatible calling convention.
@@ -2535,9 +2556,6 @@
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether build environment is sane" >&5
 $as_echo_n "checking whether build environment is sane... " >&6; }
-# Just in case
-sleep 1
-echo timestamp > conftest.file
 # Reject unsafe characters in $srcdir or the absolute working directory
 # name.  Accept space and tab only in the latter.
 am_lf='
@@ -2548,32 +2566,40 @@
 esac
 case $srcdir in
   *[\\\"\#\$\&\'\`$am_lf\ \	]*)
-    as_fn_error $? "unsafe srcdir value: \`$srcdir'" "$LINENO" 5;;
+    as_fn_error $? "unsafe srcdir value: '$srcdir'" "$LINENO" 5;;
 esac
 
-# Do `set' in a subshell so we don't clobber the current shell's
+# Do 'set' in a subshell so we don't clobber the current shell's
 # arguments.  Must try -L first in case configure is actually a
 # symlink; some systems play weird games with the mod time of symlinks
 # (eg FreeBSD returns the mod time of the symlink's containing
 # directory).
 if (
-   set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
-   if test "$*" = "X"; then
-      # -L didn't work.
-      set X `ls -t "$srcdir/configure" conftest.file`
-   fi
-   rm -f conftest.file
-   if test "$*" != "X $srcdir/configure conftest.file" \
-      && test "$*" != "X conftest.file $srcdir/configure"; then
-
-      # If neither matched, then we have a broken ls.  This can happen
-      # if, for instance, CONFIG_SHELL is bash and it inherits a
-      # broken ls alias from the environment.  This has actually
-      # happened.  Such a system could not be considered "sane".
-      as_fn_error $? "ls -t appears to fail.  Make sure there is not a broken
-alias in your environment" "$LINENO" 5
-   fi
+   am_has_slept=no
+   for am_try in 1 2; do
+     echo "timestamp, slept: $am_has_slept" > conftest.file
+     set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
+     if test "$*" = "X"; then
+	# -L didn't work.
+	set X `ls -t "$srcdir/configure" conftest.file`
+     fi
+     if test "$*" != "X $srcdir/configure conftest.file" \
+	&& test "$*" != "X conftest.file $srcdir/configure"; then
 
+	# If neither matched, then we have a broken ls.  This can happen
+	# if, for instance, CONFIG_SHELL is bash and it inherits a
+	# broken ls alias from the environment.  This has actually
+	# happened.  Such a system could not be considered "sane".
+	as_fn_error $? "ls -t appears to fail.  Make sure there is not a broken
+  alias in your environment" "$LINENO" 5
+     fi
+     if test "$2" = conftest.file || test $am_try -eq 2; then
+       break
+     fi
+     # Just in case.
+     sleep 1
+     am_has_slept=yes
+   done
    test "$2" = conftest.file
    )
 then
@@ -2585,6 +2611,16 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
 $as_echo "yes" >&6; }
+# If we didn't sleep, we still need to ensure time stamps of config.status and
+# generated files are strictly newer.
+am_sleep_pid=
+if grep 'slept: no' conftest.file >/dev/null 2>&1; then
+  ( sleep 1 ) &
+  am_sleep_pid=$!
+fi
+
+rm -f conftest.file
+
 test "$program_prefix" != NONE &&
   program_transform_name="s&^&$program_prefix&;$program_transform_name"
 # Use a double $ so make ignores it.
@@ -2607,12 +2643,12 @@
   esac
 fi
 # Use eval to expand $SHELL
-if eval "$MISSING --run true"; then
-  am_missing_run="$MISSING --run "
+if eval "$MISSING --is-lightweight"; then
+  am_missing_run="$MISSING "
 else
   am_missing_run=
-  { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \`missing' script is too old or missing" >&5
-$as_echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;}
+  { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: 'missing' script is too old or missing" >&5
+$as_echo "$as_me: WARNING: 'missing' script is too old or missing" >&2;}
 fi
 
 if test x"${install_sh}" != xset; then
@@ -2624,10 +2660,10 @@
   esac
 fi
 
-# Installed binaries are usually stripped using `strip' when the user
-# run `make install-strip'.  However `strip' might not be the right
+# Installed binaries are usually stripped using 'strip' when the user
+# run "make install-strip".  However 'strip' might not be the right
 # tool to use in cross-compilation environments, therefore Automake
-# will honor the `STRIP' environment variable to overrule this program.
+# will honor the 'STRIP' environment variable to overrule this program.
 if test "$cross_compiling" != no; then
   if test -n "$ac_tool_prefix"; then
   # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
@@ -2646,7 +2682,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_STRIP="${ac_tool_prefix}strip"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -2686,7 +2722,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_STRIP="strip"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -2737,7 +2773,7 @@
   test -z "$as_dir" && as_dir=.
     for ac_prog in mkdir gmkdir; do
 	 for ac_exec_ext in '' $ac_executable_extensions; do
-	   { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; } || continue
+	   as_fn_executable_p "$as_dir/$ac_prog$ac_exec_ext" || continue
 	   case `"$as_dir/$ac_prog$ac_exec_ext" --version 2>&1` in #(
 	     'mkdir (GNU coreutils) '* | \
 	     'mkdir (coreutils) '* | \
@@ -2766,12 +2802,6 @@
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MKDIR_P" >&5
 $as_echo "$MKDIR_P" >&6; }
 
-mkdir_p="$MKDIR_P"
-case $mkdir_p in
-  [\\/$]* | ?:[\\/]*) ;;
-  */*) mkdir_p="\$(top_builddir)/$mkdir_p" ;;
-esac
-
 for ac_prog in gawk mawk nawk awk
 do
   # Extract the first word of "$ac_prog", so it can be a program name with args.
@@ -2790,7 +2820,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_AWK="$ac_prog"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -2859,10 +2889,10 @@
   enableval=$enable_silent_rules;
 fi
 
-case $enable_silent_rules in
-yes) AM_DEFAULT_VERBOSITY=0;;
-no)  AM_DEFAULT_VERBOSITY=1;;
-*)   AM_DEFAULT_VERBOSITY=1;;
+case $enable_silent_rules in # (((
+  yes) AM_DEFAULT_VERBOSITY=0;;
+   no) AM_DEFAULT_VERBOSITY=1;;
+    *) AM_DEFAULT_VERBOSITY=1;;
 esac
 am_make=${MAKE-make}
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $am_make supports nested variables" >&5
@@ -2943,177 +2973,23 @@
 
 MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
 
+# For better backward compatibility.  To be removed once Automake 1.9.x
+# dies out for good.  For more background, see:
+# <http://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
+# <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
+mkdir_p='$(MKDIR_P)'
+
 # We need awk for the "check" target.  The system "awk" is bad on
 # some platforms.
 # Always define AMTAR for backward compatibility.  Yes, it's still used
 # in the wild :-(  We should find a proper way to deprecate it ...
 AMTAR='$${TAR-tar}'
 
-am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'
-
-
-
-
-
-case `pwd` in
-  *\ * | *\	*)
-    { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: Libtool does not cope well with whitespace in \`pwd\`" >&5
-$as_echo "$as_me: WARNING: Libtool does not cope well with whitespace in \`pwd\`" >&2;} ;;
-esac
-
-
-
-macro_version='2.4.2'
-macro_revision='1.3337'
-
-
-
-
-
-
-
-
-
-
-
-
-
-ltmain="$ac_aux_dir/ltmain.sh"
-
-# Make sure we can run config.sub.
-$SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 ||
-  as_fn_error $? "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking build system type" >&5
-$as_echo_n "checking build system type... " >&6; }
-if ${ac_cv_build+:} false; then :
-  $as_echo_n "(cached) " >&6
-else
-  ac_build_alias=$build_alias
-test "x$ac_build_alias" = x &&
-  ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"`
-test "x$ac_build_alias" = x &&
-  as_fn_error $? "cannot guess build type; you must specify one" "$LINENO" 5
-ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` ||
-  as_fn_error $? "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5
-
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_build" >&5
-$as_echo "$ac_cv_build" >&6; }
-case $ac_cv_build in
-*-*-*) ;;
-*) as_fn_error $? "invalid value of canonical build" "$LINENO" 5;;
-esac
-build=$ac_cv_build
-ac_save_IFS=$IFS; IFS='-'
-set x $ac_cv_build
-shift
-build_cpu=$1
-build_vendor=$2
-shift; shift
-# Remember, the first character of IFS is used to create $*,
-# except with old shells:
-build_os=$*
-IFS=$ac_save_IFS
-case $build_os in *\ *) build_os=`echo "$build_os" | sed 's/ /-/g'`;; esac
-
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking host system type" >&5
-$as_echo_n "checking host system type... " >&6; }
-if ${ac_cv_host+:} false; then :
-  $as_echo_n "(cached) " >&6
-else
-  if test "x$host_alias" = x; then
-  ac_cv_host=$ac_cv_build
-else
-  ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` ||
-    as_fn_error $? "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5
-fi
-
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_host" >&5
-$as_echo "$ac_cv_host" >&6; }
-case $ac_cv_host in
-*-*-*) ;;
-*) as_fn_error $? "invalid value of canonical host" "$LINENO" 5;;
-esac
-host=$ac_cv_host
-ac_save_IFS=$IFS; IFS='-'
-set x $ac_cv_host
-shift
-host_cpu=$1
-host_vendor=$2
-shift; shift
-# Remember, the first character of IFS is used to create $*,
-# except with old shells:
-host_os=$*
-IFS=$ac_save_IFS
-case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac
-
-
-# Backslashify metacharacters that are still active within
-# double-quoted strings.
-sed_quote_subst='s/\(["`$\\]\)/\\\1/g'
-
-# Same as above, but do not quote variable references.
-double_quote_subst='s/\(["`\\]\)/\\\1/g'
-
-# Sed substitution to delay expansion of an escaped shell variable in a
-# double_quote_subst'ed string.
-delay_variable_subst='s/\\\\\\\\\\\$/\\\\\\$/g'
-
-# Sed substitution to delay expansion of an escaped single quote.
-delay_single_quote_subst='s/'\''/'\'\\\\\\\'\''/g'
-
-# Sed substitution to avoid accidental globbing in evaled expressions
-no_glob_subst='s/\*/\\\*/g'
-
-ECHO='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
-ECHO=$ECHO$ECHO$ECHO$ECHO$ECHO
-ECHO=$ECHO$ECHO$ECHO$ECHO$ECHO$ECHO
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to print strings" >&5
-$as_echo_n "checking how to print strings... " >&6; }
-# Test print first, because it will be a builtin if present.
-if test "X`( print -r -- -n ) 2>/dev/null`" = X-n && \
-   test "X`print -r -- $ECHO 2>/dev/null`" = "X$ECHO"; then
-  ECHO='print -r --'
-elif test "X`printf %s $ECHO 2>/dev/null`" = "X$ECHO"; then
-  ECHO='printf %s\n'
-else
-  # Use this function as a fallback that always works.
-  func_fallback_echo ()
-  {
-    eval 'cat <<_LTECHO_EOF
-$1
-_LTECHO_EOF'
-  }
-  ECHO='func_fallback_echo'
-fi
-
-# func_echo_all arg...
-# Invoke $ECHO with all args, space-separated.
-func_echo_all ()
-{
-    $ECHO ""
-}
-
-case "$ECHO" in
-  printf*) { $as_echo "$as_me:${as_lineno-$LINENO}: result: printf" >&5
-$as_echo "printf" >&6; } ;;
-  print*) { $as_echo "$as_me:${as_lineno-$LINENO}: result: print -r" >&5
-$as_echo "print -r" >&6; } ;;
-  *) { $as_echo "$as_me:${as_lineno-$LINENO}: result: cat" >&5
-$as_echo "cat" >&6; } ;;
-esac
-
-
-
-
-
-
 
+# We'll loop over all known methods to create a tar archive until one works.
+_am_tools='gnutar  pax cpio none'
 
+am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'
 
 
 
@@ -3139,7 +3015,7 @@
 _am_result=none
 # First try GNU make style include.
 echo "include confinc" > confmf
-# Ignore all kinds of additional output from `make'.
+# Ignore all kinds of additional output from 'make'.
 case `$am_make -s -f confmf 2> /dev/null` in #(
 *the\ am__doit\ target*)
   am__include=include
@@ -3205,7 +3081,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_CC="${ac_tool_prefix}gcc"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -3245,7 +3121,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_CC="gcc"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -3298,7 +3174,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_CC="${ac_tool_prefix}cc"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -3339,7 +3215,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then
        ac_prog_rejected=yes
        continue
@@ -3397,7 +3273,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -3441,7 +3317,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_CC="$ac_prog"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -3887,8 +3763,7 @@
 /* end confdefs.h.  */
 #include <stdarg.h>
 #include <stdio.h>
-#include <sys/types.h>
-#include <sys/stat.h>
+struct stat;
 /* Most of the following tests are stolen from RCS 5.7's src/conf.sh.  */
 struct buf { int x; };
 FILE * (*rcsopen) (struct buf *, struct stat *, int);
@@ -3922,183 +3797,509 @@
 #define FOO(x) 'x'
 int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1];
 
-int test (int i, double x);
-struct s1 {int (*f) (int a);};
-struct s2 {int (*f) (double a);};
-int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int);
-int argc;
-char **argv;
-int
-main ()
+int test (int i, double x);
+struct s1 {int (*f) (int a);};
+struct s2 {int (*f) (double a);};
+int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int);
+int argc;
+char **argv;
+int
+main ()
+{
+return f (e, argv, 0) != argv[0]  ||  f (e, argv, 1) != argv[1];
+  ;
+  return 0;
+}
+_ACEOF
+for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \
+	-Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__"
+do
+  CC="$ac_save_CC $ac_arg"
+  if ac_fn_c_try_compile "$LINENO"; then :
+  ac_cv_prog_cc_c89=$ac_arg
+fi
+rm -f core conftest.err conftest.$ac_objext
+  test "x$ac_cv_prog_cc_c89" != "xno" && break
+done
+rm -f conftest.$ac_ext
+CC=$ac_save_CC
+
+fi
+# AC_CACHE_VAL
+case "x$ac_cv_prog_cc_c89" in
+  x)
+    { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5
+$as_echo "none needed" >&6; } ;;
+  xno)
+    { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5
+$as_echo "unsupported" >&6; } ;;
+  *)
+    CC="$CC $ac_cv_prog_cc_c89"
+    { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5
+$as_echo "$ac_cv_prog_cc_c89" >&6; } ;;
+esac
+if test "x$ac_cv_prog_cc_c89" != xno; then :
+
+fi
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+depcc="$CC"   am_compiler_list=
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
+$as_echo_n "checking dependency style of $depcc... " >&6; }
+if ${am_cv_CC_dependencies_compiler_type+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+  # We make a subdir and do the tests there.  Otherwise we can end up
+  # making bogus files that we don't know about and never remove.  For
+  # instance it was reported that on HP-UX the gcc test will end up
+  # making a dummy file named 'D' -- because '-MD' means "put the output
+  # in D".
+  rm -rf conftest.dir
+  mkdir conftest.dir
+  # Copy depcomp to subdir because otherwise we won't find it if we're
+  # using a relative directory.
+  cp "$am_depcomp" conftest.dir
+  cd conftest.dir
+  # We will build objects and dependencies in a subdirectory because
+  # it helps to detect inapplicable dependency modes.  For instance
+  # both Tru64's cc and ICC support -MD to output dependencies as a
+  # side effect of compilation, but ICC will put the dependencies in
+  # the current directory while Tru64 will put them in the object
+  # directory.
+  mkdir sub
+
+  am_cv_CC_dependencies_compiler_type=none
+  if test "$am_compiler_list" = ""; then
+     am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+  fi
+  am__universal=false
+  case " $depcc " in #(
+     *\ -arch\ *\ -arch\ *) am__universal=true ;;
+     esac
+
+  for depmode in $am_compiler_list; do
+    # Setup a source with many dependencies, because some compilers
+    # like to wrap large dependency lists on column 80 (with \), and
+    # we should not choose a depcomp mode which is confused by this.
+    #
+    # We need to recreate these files for each test, as the compiler may
+    # overwrite some of them when testing with obscure command lines.
+    # This happens at least with the AIX C compiler.
+    : > sub/conftest.c
+    for i in 1 2 3 4 5 6; do
+      echo '#include "conftst'$i'.h"' >> sub/conftest.c
+      # Using ": > sub/conftst$i.h" creates only sub/conftst1.h with
+      # Solaris 10 /bin/sh.
+      echo '/* dummy */' > sub/conftst$i.h
+    done
+    echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+    # We check with '-c' and '-o' for the sake of the "dashmstdout"
+    # mode.  It turns out that the SunPro C++ compiler does not properly
+    # handle '-M -o', and we need to detect this.  Also, some Intel
+    # versions had trouble with output in subdirs.
+    am__obj=sub/conftest.${OBJEXT-o}
+    am__minus_obj="-o $am__obj"
+    case $depmode in
+    gcc)
+      # This depmode causes a compiler race in universal mode.
+      test "$am__universal" = false || continue
+      ;;
+    nosideeffect)
+      # After this tag, mechanisms are not by side-effect, so they'll
+      # only be used when explicitly requested.
+      if test "x$enable_dependency_tracking" = xyes; then
+	continue
+      else
+	break
+      fi
+      ;;
+    msvc7 | msvc7msys | msvisualcpp | msvcmsys)
+      # This compiler won't grok '-c -o', but also, the minuso test has
+      # not run yet.  These depmodes are late enough in the game, and
+      # so weak that their functioning should not be impacted.
+      am__obj=conftest.${OBJEXT-o}
+      am__minus_obj=
+      ;;
+    none) break ;;
+    esac
+    if depmode=$depmode \
+       source=sub/conftest.c object=$am__obj \
+       depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+       $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
+         >/dev/null 2>conftest.err &&
+       grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+       grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+       grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
+       ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+      # icc doesn't choke on unknown options, it will just issue warnings
+      # or remarks (even with -Werror).  So we grep stderr for any message
+      # that says an option was ignored or not supported.
+      # When given -MP, icc 7.0 and 7.1 complain thusly:
+      #   icc: Command line warning: ignoring option '-M'; no argument required
+      # The diagnosis changed in icc 8.0:
+      #   icc: Command line remark: option '-MP' not supported
+      if (grep 'ignoring option' conftest.err ||
+          grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+        am_cv_CC_dependencies_compiler_type=$depmode
+        break
+      fi
+    fi
+  done
+
+  cd ..
+  rm -rf conftest.dir
+else
+  am_cv_CC_dependencies_compiler_type=none
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CC_dependencies_compiler_type" >&5
+$as_echo "$am_cv_CC_dependencies_compiler_type" >&6; }
+CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type
+
+ if
+  test "x$enable_dependency_tracking" != xno \
+  && test "$am_cv_CC_dependencies_compiler_type" = gcc3; then
+  am__fastdepCC_TRUE=
+  am__fastdepCC_FALSE='#'
+else
+  am__fastdepCC_TRUE='#'
+  am__fastdepCC_FALSE=
+fi
+
+
+
+if test -n "$ac_tool_prefix"; then
+  for ac_prog in ar lib "link -lib"
+  do
+    # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_AR+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  if test -n "$AR"; then
+  ac_cv_prog_AR="$AR" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+    for ac_exec_ext in '' $ac_executable_extensions; do
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+    ac_cv_prog_AR="$ac_tool_prefix$ac_prog"
+    $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+  done
+IFS=$as_save_IFS
+
+fi
+fi
+AR=$ac_cv_prog_AR
+if test -n "$AR"; then
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AR" >&5
+$as_echo "$AR" >&6; }
+else
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+    test -n "$AR" && break
+  done
+fi
+if test -z "$AR"; then
+  ac_ct_AR=$AR
+  for ac_prog in ar lib "link -lib"
+do
+  # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_prog_ac_ct_AR+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  if test -n "$ac_ct_AR"; then
+  ac_cv_prog_ac_ct_AR="$ac_ct_AR" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+    for ac_exec_ext in '' $ac_executable_extensions; do
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+    ac_cv_prog_ac_ct_AR="$ac_prog"
+    $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+  done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_AR=$ac_cv_prog_ac_ct_AR
+if test -n "$ac_ct_AR"; then
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_AR" >&5
+$as_echo "$ac_ct_AR" >&6; }
+else
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+  test -n "$ac_ct_AR" && break
+done
+
+  if test "x$ac_ct_AR" = x; then
+    AR="false"
+  else
+    case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+    AR=$ac_ct_AR
+  fi
+fi
+
+: ${AR=ar}
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking the archiver ($AR) interface" >&5
+$as_echo_n "checking the archiver ($AR) interface... " >&6; }
+if ${am_cv_ar_interface+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  am_cv_ar_interface=ar
+   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+int some_variable = 0;
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+  am_ar_try='$AR cru libconftest.a conftest.$ac_objext >&5'
+      { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$am_ar_try\""; } >&5
+  (eval $am_ar_try) 2>&5
+  ac_status=$?
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; }
+      if test "$ac_status" -eq 0; then
+        am_cv_ar_interface=ar
+      else
+        am_ar_try='$AR -NOLOGO -OUT:conftest.lib conftest.$ac_objext >&5'
+        { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$am_ar_try\""; } >&5
+  (eval $am_ar_try) 2>&5
+  ac_status=$?
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; }
+        if test "$ac_status" -eq 0; then
+          am_cv_ar_interface=lib
+        else
+          am_cv_ar_interface=unknown
+        fi
+      fi
+      rm -f conftest.lib libconftest.a
+
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_ar_interface" >&5
+$as_echo "$am_cv_ar_interface" >&6; }
+
+case $am_cv_ar_interface in
+ar)
+  ;;
+lib)
+  # Microsoft lib, so override with the ar-lib wrapper script.
+  # FIXME: It is wrong to rewrite AR.
+  # But if we don't then we get into trouble of one sort or another.
+  # A longer-term fix would be to have automake use am__AR in this case,
+  # and then we could set am__AR="$am_aux_dir/ar-lib \$(AR)" or something
+  # similar.
+  AR="$am_aux_dir/ar-lib $AR"
+  ;;
+unknown)
+  as_fn_error $? "could not determine $AR interface" "$LINENO" 5
+  ;;
+esac
+
+case `pwd` in
+  *\ * | *\	*)
+    { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: Libtool does not cope well with whitespace in \`pwd\`" >&5
+$as_echo "$as_me: WARNING: Libtool does not cope well with whitespace in \`pwd\`" >&2;} ;;
+esac
+
+
+
+macro_version='2.4.2'
+macro_revision='1.3337'
+
+
+
+
+
+
+
+
+
+
+
+
+
+ltmain="$ac_aux_dir/ltmain.sh"
+
+# Make sure we can run config.sub.
+$SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 ||
+  as_fn_error $? "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking build system type" >&5
+$as_echo_n "checking build system type... " >&6; }
+if ${ac_cv_build+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  ac_build_alias=$build_alias
+test "x$ac_build_alias" = x &&
+  ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"`
+test "x$ac_build_alias" = x &&
+  as_fn_error $? "cannot guess build type; you must specify one" "$LINENO" 5
+ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` ||
+  as_fn_error $? "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_build" >&5
+$as_echo "$ac_cv_build" >&6; }
+case $ac_cv_build in
+*-*-*) ;;
+*) as_fn_error $? "invalid value of canonical build" "$LINENO" 5;;
+esac
+build=$ac_cv_build
+ac_save_IFS=$IFS; IFS='-'
+set x $ac_cv_build
+shift
+build_cpu=$1
+build_vendor=$2
+shift; shift
+# Remember, the first character of IFS is used to create $*,
+# except with old shells:
+build_os=$*
+IFS=$ac_save_IFS
+case $build_os in *\ *) build_os=`echo "$build_os" | sed 's/ /-/g'`;; esac
+
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking host system type" >&5
+$as_echo_n "checking host system type... " >&6; }
+if ${ac_cv_host+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  if test "x$host_alias" = x; then
+  ac_cv_host=$ac_cv_build
+else
+  ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` ||
+    as_fn_error $? "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5
+fi
+
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_host" >&5
+$as_echo "$ac_cv_host" >&6; }
+case $ac_cv_host in
+*-*-*) ;;
+*) as_fn_error $? "invalid value of canonical host" "$LINENO" 5;;
+esac
+host=$ac_cv_host
+ac_save_IFS=$IFS; IFS='-'
+set x $ac_cv_host
+shift
+host_cpu=$1
+host_vendor=$2
+shift; shift
+# Remember, the first character of IFS is used to create $*,
+# except with old shells:
+host_os=$*
+IFS=$ac_save_IFS
+case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac
+
+
+# Backslashify metacharacters that are still active within
+# double-quoted strings.
+sed_quote_subst='s/\(["`$\\]\)/\\\1/g'
+
+# Same as above, but do not quote variable references.
+double_quote_subst='s/\(["`\\]\)/\\\1/g'
+
+# Sed substitution to delay expansion of an escaped shell variable in a
+# double_quote_subst'ed string.
+delay_variable_subst='s/\\\\\\\\\\\$/\\\\\\$/g'
+
+# Sed substitution to delay expansion of an escaped single quote.
+delay_single_quote_subst='s/'\''/'\'\\\\\\\'\''/g'
+
+# Sed substitution to avoid accidental globbing in evaled expressions
+no_glob_subst='s/\*/\\\*/g'
+
+ECHO='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
+ECHO=$ECHO$ECHO$ECHO$ECHO$ECHO
+ECHO=$ECHO$ECHO$ECHO$ECHO$ECHO$ECHO
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to print strings" >&5
+$as_echo_n "checking how to print strings... " >&6; }
+# Test print first, because it will be a builtin if present.
+if test "X`( print -r -- -n ) 2>/dev/null`" = X-n && \
+   test "X`print -r -- $ECHO 2>/dev/null`" = "X$ECHO"; then
+  ECHO='print -r --'
+elif test "X`printf %s $ECHO 2>/dev/null`" = "X$ECHO"; then
+  ECHO='printf %s\n'
+else
+  # Use this function as a fallback that always works.
+  func_fallback_echo ()
+  {
+    eval 'cat <<_LTECHO_EOF
+$1
+_LTECHO_EOF'
+  }
+  ECHO='func_fallback_echo'
+fi
+
+# func_echo_all arg...
+# Invoke $ECHO with all args, space-separated.
+func_echo_all ()
 {
-return f (e, argv, 0) != argv[0]  ||  f (e, argv, 1) != argv[1];
-  ;
-  return 0;
+    $ECHO ""
 }
-_ACEOF
-for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \
-	-Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__"
-do
-  CC="$ac_save_CC $ac_arg"
-  if ac_fn_c_try_compile "$LINENO"; then :
-  ac_cv_prog_cc_c89=$ac_arg
-fi
-rm -f core conftest.err conftest.$ac_objext
-  test "x$ac_cv_prog_cc_c89" != "xno" && break
-done
-rm -f conftest.$ac_ext
-CC=$ac_save_CC
 
-fi
-# AC_CACHE_VAL
-case "x$ac_cv_prog_cc_c89" in
-  x)
-    { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5
-$as_echo "none needed" >&6; } ;;
-  xno)
-    { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5
-$as_echo "unsupported" >&6; } ;;
-  *)
-    CC="$CC $ac_cv_prog_cc_c89"
-    { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5
-$as_echo "$ac_cv_prog_cc_c89" >&6; } ;;
+case "$ECHO" in
+  printf*) { $as_echo "$as_me:${as_lineno-$LINENO}: result: printf" >&5
+$as_echo "printf" >&6; } ;;
+  print*) { $as_echo "$as_me:${as_lineno-$LINENO}: result: print -r" >&5
+$as_echo "print -r" >&6; } ;;
+  *) { $as_echo "$as_me:${as_lineno-$LINENO}: result: cat" >&5
+$as_echo "cat" >&6; } ;;
 esac
-if test "x$ac_cv_prog_cc_c89" != xno; then :
 
-fi
 
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
 
-depcc="$CC"   am_compiler_list=
 
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
-$as_echo_n "checking dependency style of $depcc... " >&6; }
-if ${am_cv_CC_dependencies_compiler_type+:} false; then :
-  $as_echo_n "(cached) " >&6
-else
-  if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
-  # We make a subdir and do the tests there.  Otherwise we can end up
-  # making bogus files that we don't know about and never remove.  For
-  # instance it was reported that on HP-UX the gcc test will end up
-  # making a dummy file named `D' -- because `-MD' means `put the output
-  # in D'.
-  rm -rf conftest.dir
-  mkdir conftest.dir
-  # Copy depcomp to subdir because otherwise we won't find it if we're
-  # using a relative directory.
-  cp "$am_depcomp" conftest.dir
-  cd conftest.dir
-  # We will build objects and dependencies in a subdirectory because
-  # it helps to detect inapplicable dependency modes.  For instance
-  # both Tru64's cc and ICC support -MD to output dependencies as a
-  # side effect of compilation, but ICC will put the dependencies in
-  # the current directory while Tru64 will put them in the object
-  # directory.
-  mkdir sub
 
-  am_cv_CC_dependencies_compiler_type=none
-  if test "$am_compiler_list" = ""; then
-     am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
-  fi
-  am__universal=false
-  case " $depcc " in #(
-     *\ -arch\ *\ -arch\ *) am__universal=true ;;
-     esac
 
-  for depmode in $am_compiler_list; do
-    # Setup a source with many dependencies, because some compilers
-    # like to wrap large dependency lists on column 80 (with \), and
-    # we should not choose a depcomp mode which is confused by this.
-    #
-    # We need to recreate these files for each test, as the compiler may
-    # overwrite some of them when testing with obscure command lines.
-    # This happens at least with the AIX C compiler.
-    : > sub/conftest.c
-    for i in 1 2 3 4 5 6; do
-      echo '#include "conftst'$i'.h"' >> sub/conftest.c
-      # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
-      # Solaris 8's {/usr,}/bin/sh.
-      touch sub/conftst$i.h
-    done
-    echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
 
-    # We check with `-c' and `-o' for the sake of the "dashmstdout"
-    # mode.  It turns out that the SunPro C++ compiler does not properly
-    # handle `-M -o', and we need to detect this.  Also, some Intel
-    # versions had trouble with output in subdirs
-    am__obj=sub/conftest.${OBJEXT-o}
-    am__minus_obj="-o $am__obj"
-    case $depmode in
-    gcc)
-      # This depmode causes a compiler race in universal mode.
-      test "$am__universal" = false || continue
-      ;;
-    nosideeffect)
-      # after this tag, mechanisms are not by side-effect, so they'll
-      # only be used when explicitly requested
-      if test "x$enable_dependency_tracking" = xyes; then
-	continue
-      else
-	break
-      fi
-      ;;
-    msvc7 | msvc7msys | msvisualcpp | msvcmsys)
-      # This compiler won't grok `-c -o', but also, the minuso test has
-      # not run yet.  These depmodes are late enough in the game, and
-      # so weak that their functioning should not be impacted.
-      am__obj=conftest.${OBJEXT-o}
-      am__minus_obj=
-      ;;
-    none) break ;;
-    esac
-    if depmode=$depmode \
-       source=sub/conftest.c object=$am__obj \
-       depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
-       $SHELL ./depcomp $depcc -c $am__minus_obj sub/conftest.c \
-         >/dev/null 2>conftest.err &&
-       grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
-       grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
-       grep $am__obj sub/conftest.Po > /dev/null 2>&1 &&
-       ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
-      # icc doesn't choke on unknown options, it will just issue warnings
-      # or remarks (even with -Werror).  So we grep stderr for any message
-      # that says an option was ignored or not supported.
-      # When given -MP, icc 7.0 and 7.1 complain thusly:
-      #   icc: Command line warning: ignoring option '-M'; no argument required
-      # The diagnosis changed in icc 8.0:
-      #   icc: Command line remark: option '-MP' not supported
-      if (grep 'ignoring option' conftest.err ||
-          grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
-        am_cv_CC_dependencies_compiler_type=$depmode
-        break
-      fi
-    fi
-  done
 
-  cd ..
-  rm -rf conftest.dir
-else
-  am_cv_CC_dependencies_compiler_type=none
-fi
 
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CC_dependencies_compiler_type" >&5
-$as_echo "$am_cv_CC_dependencies_compiler_type" >&6; }
-CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type
 
- if
-  test "x$enable_dependency_tracking" != xno \
-  && test "$am_cv_CC_dependencies_compiler_type" = gcc3; then
-  am__fastdepCC_TRUE=
-  am__fastdepCC_FALSE='#'
-else
-  am__fastdepCC_TRUE='#'
-  am__fastdepCC_FALSE=
-fi
+
+
 
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for a sed that does not truncate output" >&5
@@ -4123,7 +4324,7 @@
     for ac_prog in sed gsed; do
     for ac_exec_ext in '' $ac_executable_extensions; do
       ac_path_SED="$as_dir/$ac_prog$ac_exec_ext"
-      { test -f "$ac_path_SED" && $as_test_x "$ac_path_SED"; } || continue
+      as_fn_executable_p "$ac_path_SED" || continue
 # Check for GNU ac_path_SED and select it if it is found.
   # Check for GNU $ac_path_SED
 case `"$ac_path_SED" --version 2>&1` in
@@ -4199,7 +4400,7 @@
     for ac_prog in grep ggrep; do
     for ac_exec_ext in '' $ac_executable_extensions; do
       ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext"
-      { test -f "$ac_path_GREP" && $as_test_x "$ac_path_GREP"; } || continue
+      as_fn_executable_p "$ac_path_GREP" || continue
 # Check for GNU ac_path_GREP and select it if it is found.
   # Check for GNU $ac_path_GREP
 case `"$ac_path_GREP" --version 2>&1` in
@@ -4265,7 +4466,7 @@
     for ac_prog in egrep; do
     for ac_exec_ext in '' $ac_executable_extensions; do
       ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext"
-      { test -f "$ac_path_EGREP" && $as_test_x "$ac_path_EGREP"; } || continue
+      as_fn_executable_p "$ac_path_EGREP" || continue
 # Check for GNU ac_path_EGREP and select it if it is found.
   # Check for GNU $ac_path_EGREP
 case `"$ac_path_EGREP" --version 2>&1` in
@@ -4332,7 +4533,7 @@
     for ac_prog in fgrep; do
     for ac_exec_ext in '' $ac_executable_extensions; do
       ac_path_FGREP="$as_dir/$ac_prog$ac_exec_ext"
-      { test -f "$ac_path_FGREP" && $as_test_x "$ac_path_FGREP"; } || continue
+      as_fn_executable_p "$ac_path_FGREP" || continue
 # Check for GNU ac_path_FGREP and select it if it is found.
   # Check for GNU $ac_path_FGREP
 case `"$ac_path_FGREP" --version 2>&1` in
@@ -4588,7 +4789,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_DUMPBIN="$ac_tool_prefix$ac_prog"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -4632,7 +4833,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_DUMPBIN="$ac_prog"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -4790,6 +4991,11 @@
     lt_cv_sys_max_cmd_len=196608
     ;;
 
+  os2*)
+    # The test takes a long time on OS/2.
+    lt_cv_sys_max_cmd_len=8192
+    ;;
+
   osf*)
     # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure
     # due to this test when exec_disable_arg_limit is 1 on Tru64. It is not
@@ -4829,7 +5035,7 @@
       # If test is not a shell built-in, we'll probably end up computing a
       # maximum length that is only half of the actual maximum length, but
       # we can't tell.
-      while { test "X"`func_fallback_echo "$teststring$teststring" 2>/dev/null` \
+      while { test "X"`env echo "$teststring$teststring" 2>/dev/null` \
 	         = "X$teststring$teststring"; } >/dev/null 2>&1 &&
 	      test $i != 17 # 1/2 MB should be enough
       do
@@ -5051,7 +5257,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_OBJDUMP="${ac_tool_prefix}objdump"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -5091,7 +5297,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_OBJDUMP="objdump"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -5255,7 +5461,7 @@
   lt_cv_deplibs_check_method=pass_all
   ;;
 
-# This must be Linux ELF.
+# This must be glibc/ELF.
 linux* | k*bsd*-gnu | kopensolaris*-gnu)
   lt_cv_deplibs_check_method=pass_all
   ;;
@@ -5394,7 +5600,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_DLLTOOL="${ac_tool_prefix}dlltool"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -5434,7 +5640,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_DLLTOOL="dlltool"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -5515,7 +5721,6 @@
 
 
 
-
 if test -n "$ac_tool_prefix"; then
   for ac_prog in ar
   do
@@ -5535,7 +5740,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_AR="$ac_tool_prefix$ac_prog"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -5579,7 +5784,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_AR="$ac_prog"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -5704,7 +5909,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_STRIP="${ac_tool_prefix}strip"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -5744,7 +5949,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_STRIP="strip"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -5803,7 +6008,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -5843,7 +6048,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_RANLIB="ranlib"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -5893,13 +6098,13 @@
 if test -n "$RANLIB"; then
   case $host_os in
   openbsd*)
-    old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib"
+    old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$tool_oldlib"
     ;;
   *)
-    old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib"
+    old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$tool_oldlib"
     ;;
   esac
-  old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib"
+  old_archive_cmds="$old_archive_cmds~\$RANLIB \$tool_oldlib"
 fi
 
 case $host_os in
@@ -6046,6 +6251,7 @@
     # which start with @ or ?.
     lt_cv_sys_global_symbol_pipe="$AWK '"\
 "     {last_section=section; section=\$ 3};"\
+"     /^COFF SYMBOL TABLE/{for(i in hide) delete hide[i]};"\
 "     /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\
 "     \$ 0!~/External *\|/{next};"\
 "     / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\
@@ -6434,7 +6640,7 @@
     CFLAGS="$SAVE_CFLAGS"
   fi
   ;;
-sparc*-*solaris*)
+*-*solaris*)
   # Find out which ABI we are using.
   echo 'int i;' > conftest.$ac_ext
   if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
@@ -6445,7 +6651,20 @@
     case `/usr/bin/file conftest.o` in
     *64-bit*)
       case $lt_cv_prog_gnu_ld in
-      yes*) LD="${LD-ld} -m elf64_sparc" ;;
+      yes*)
+        case $host in
+        i?86-*-solaris*)
+          LD="${LD-ld} -m elf_x86_64"
+          ;;
+        sparc*-*-solaris*)
+          LD="${LD-ld} -m elf64_sparc"
+          ;;
+        esac
+        # GNU ld 2.21 introduced _sol2 emulations.  Use them if available.
+        if ${LD-ld} -V | grep _sol2 >/dev/null 2>&1; then
+          LD="${LD-ld}_sol2"
+        fi
+        ;;
       *)
 	if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then
 	  LD="${LD-ld} -64"
@@ -6478,7 +6697,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_MANIFEST_TOOL="${ac_tool_prefix}mt"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -6518,7 +6737,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_MANIFEST_TOOL="mt"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -6598,7 +6817,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_DSYMUTIL="${ac_tool_prefix}dsymutil"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -6638,7 +6857,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_DSYMUTIL="dsymutil"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -6690,7 +6909,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_NMEDIT="${ac_tool_prefix}nmedit"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -6730,7 +6949,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_NMEDIT="nmedit"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -6782,7 +7001,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_LIPO="${ac_tool_prefix}lipo"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -6822,7 +7041,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_LIPO="lipo"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -6874,7 +7093,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_OTOOL="${ac_tool_prefix}otool"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -6914,7 +7133,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_OTOOL="otool"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -6966,7 +7185,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_OTOOL64="${ac_tool_prefix}otool64"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -7006,7 +7225,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_OTOOL64="otool64"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -7085,7 +7304,13 @@
 	$LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \
 	  -dynamiclib -Wl,-single_module conftest.c 2>conftest.err
         _lt_result=$?
-	if test -f libconftest.dylib && test ! -s conftest.err && test $_lt_result = 0; then
+	# If there is a non-empty error log, and "single_module"
+	# appears in it, assume the flag caused a linker warning
+        if test -s conftest.err && $GREP single_module conftest.err; then
+	  cat conftest.err >&5
+	# Otherwise, if the output was created with a 0 exit code from
+	# the compiler, it worked.
+	elif test -f libconftest.dylib && test $_lt_result -eq 0; then
 	  lt_cv_apple_cc_single_mod=yes
 	else
 	  cat conftest.err >&5
@@ -7096,6 +7321,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_apple_cc_single_mod" >&5
 $as_echo "$lt_cv_apple_cc_single_mod" >&6; }
+
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for -exported_symbols_list linker flag" >&5
 $as_echo_n "checking for -exported_symbols_list linker flag... " >&6; }
 if ${lt_cv_ld_exported_symbols_list+:} false; then :
@@ -7128,6 +7354,7 @@
 fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_ld_exported_symbols_list" >&5
 $as_echo "$lt_cv_ld_exported_symbols_list" >&6; }
+
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking for -force_load linker flag" >&5
 $as_echo_n "checking for -force_load linker flag... " >&6; }
 if ${lt_cv_ld_force_load+:} false; then :
@@ -7149,7 +7376,9 @@
       echo "$LTCC $LTCFLAGS $LDFLAGS -o conftest conftest.c -Wl,-force_load,./libconftest.a" >&5
       $LTCC $LTCFLAGS $LDFLAGS -o conftest conftest.c -Wl,-force_load,./libconftest.a 2>conftest.err
       _lt_result=$?
-      if test -f conftest && test ! -s conftest.err && test $_lt_result = 0 && $GREP forced_load conftest 2>&1 >/dev/null; then
+      if test -s conftest.err && $GREP force_load conftest.err; then
+	cat conftest.err >&5
+      elif test -f conftest && test $_lt_result -eq 0 && $GREP forced_load conftest >/dev/null 2>&1 ; then
 	lt_cv_ld_force_load=yes
       else
 	cat conftest.err >&5
@@ -7530,7 +7759,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_AS="${ac_tool_prefix}as"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -7570,7 +7799,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_AS="as"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -7622,7 +7851,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_DLLTOOL="${ac_tool_prefix}dlltool"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -7662,7 +7891,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_DLLTOOL="dlltool"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -7714,7 +7943,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_OBJDUMP="${ac_tool_prefix}objdump"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -7754,7 +7983,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_OBJDUMP="objdump"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -7851,7 +8080,22 @@
 
 # Check whether --with-pic was given.
 if test "${with_pic+set}" = set; then :
-  withval=$with_pic; pic_mode="$withval"
+  withval=$with_pic; lt_p=${PACKAGE-default}
+    case $withval in
+    yes|no) pic_mode=$withval ;;
+    *)
+      pic_mode=default
+      # Look at the argument we got.  We use all the common list separators.
+      lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+      for lt_pkg in $withval; do
+	IFS="$lt_save_ifs"
+	if test "X$lt_pkg" = "X$lt_p"; then
+	  pic_mode=yes
+	fi
+      done
+      IFS="$lt_save_ifs"
+      ;;
+    esac
 else
   pic_mode=default
 fi
@@ -7929,6 +8173,10 @@
 
 
 
+
+
+
+
 test -z "$LN_S" && LN_S="ln -s"
 
 
@@ -8388,7 +8636,9 @@
     case $cc_basename in
     nvcc*) # Cuda Compiler Driver 2.2
       lt_prog_compiler_wl='-Xlinker '
-      lt_prog_compiler_pic='-Xcompiler -fPIC'
+      if test -n "$lt_prog_compiler_pic"; then
+        lt_prog_compiler_pic="-Xcompiler $lt_prog_compiler_pic"
+      fi
       ;;
     esac
   else
@@ -8479,18 +8729,33 @@
 	;;
       *)
 	case `$CC -V 2>&1 | sed 5q` in
-	*Sun\ F* | *Sun*Fortran*)
+	*Sun\ Ceres\ Fortran* | *Sun*Fortran*\ [1-7].* | *Sun*Fortran*\ 8.[0-3]*)
 	  # Sun Fortran 8.3 passes all unrecognized flags to the linker
 	  lt_prog_compiler_pic='-KPIC'
 	  lt_prog_compiler_static='-Bstatic'
 	  lt_prog_compiler_wl=''
 	  ;;
+	*Sun\ F* | *Sun*Fortran*)
+	  lt_prog_compiler_pic='-KPIC'
+	  lt_prog_compiler_static='-Bstatic'
+	  lt_prog_compiler_wl='-Qoption ld '
+	  ;;
 	*Sun\ C*)
 	  # Sun C 5.9
 	  lt_prog_compiler_pic='-KPIC'
 	  lt_prog_compiler_static='-Bstatic'
 	  lt_prog_compiler_wl='-Wl,'
 	  ;;
+        *Intel*\ [CF]*Compiler*)
+	  lt_prog_compiler_wl='-Wl,'
+	  lt_prog_compiler_pic='-fPIC'
+	  lt_prog_compiler_static='-static'
+	  ;;
+	*Portland\ Group*)
+	  lt_prog_compiler_wl='-Wl,'
+	  lt_prog_compiler_pic='-fpic'
+	  lt_prog_compiler_static='-Bstatic'
+	  ;;
 	esac
 	;;
       esac
@@ -8852,7 +9117,6 @@
   hardcode_direct=no
   hardcode_direct_absolute=no
   hardcode_libdir_flag_spec=
-  hardcode_libdir_flag_spec_ld=
   hardcode_libdir_separator=
   hardcode_minus_L=no
   hardcode_shlibpath_var=unsupported
@@ -9102,8 +9366,7 @@
 	xlf* | bgf* | bgxlf* | mpixlf*)
 	  # IBM XL Fortran 10.1 on PPC cannot create shared libs itself
 	  whole_archive_flag_spec='--whole-archive$convenience --no-whole-archive'
-	  hardcode_libdir_flag_spec=
-	  hardcode_libdir_flag_spec_ld='-rpath $libdir'
+	  hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
 	  archive_cmds='$LD -shared $libobjs $deplibs $linker_flags -soname $soname -o $lib'
 	  if test "x$supports_anon_versioning" = xyes; then
 	    archive_expsym_cmds='echo "{ global:" > $output_objdir/$libname.ver~
@@ -9482,6 +9745,7 @@
 	# The linker will not automatically build a static lib if we build a DLL.
 	# _LT_TAGVAR(old_archive_from_new_cmds, )='true'
 	enable_shared_with_static_runtimes=yes
+	exclude_expsyms='_NULL_IMPORT_DESCRIPTOR|_IMPORT_DESCRIPTOR_.*'
 	export_symbols_cmds='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS][ ]/s/.*[ ]\([^ ]*\)/\1,DATA/'\'' | $SED -e '\''/^[AITW][ ]/s/.*[ ]//'\'' | sort | uniq > $export_symbols'
 	# Don't use ranlib
 	old_postinstall_cmds='chmod 644 $oldlib'
@@ -9527,6 +9791,7 @@
   hardcode_shlibpath_var=unsupported
   if test "$lt_cv_ld_force_load" = "yes"; then
     whole_archive_flag_spec='`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience ${wl}-force_load,$conv\"; done; func_echo_all \"$new_convenience\"`'
+
   else
     whole_archive_flag_spec=''
   fi
@@ -9555,10 +9820,6 @@
       hardcode_shlibpath_var=no
       ;;
 
-    freebsd1*)
-      ld_shlibs=no
-      ;;
-
     # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor
     # support.  Future versions do this automatically, but an explicit c++rt0.o
     # does not break anything, and helps significantly (at the cost of a little
@@ -9571,7 +9832,7 @@
       ;;
 
     # Unfortunately, older versions of FreeBSD 2 do not have this feature.
-    freebsd2*)
+    freebsd2.*)
       archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
       hardcode_direct=yes
       hardcode_minus_L=yes
@@ -9610,7 +9871,6 @@
       fi
       if test "$with_gnu_ld" = no; then
 	hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir'
-	hardcode_libdir_flag_spec_ld='+b $libdir'
 	hardcode_libdir_separator=:
 	hardcode_direct=yes
 	hardcode_direct_absolute=yes
@@ -10234,11 +10494,6 @@
 
 
 
-
-
-
-
-
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking dynamic linker characteristics" >&5
 $as_echo_n "checking dynamic linker characteristics... " >&6; }
 
@@ -10328,7 +10583,7 @@
 
 case $host_os in
 aix3*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
   shlibpath_var=LIBPATH
 
@@ -10337,7 +10592,7 @@
   ;;
 
 aix[4-9]*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   hardcode_into_libs=yes
@@ -10402,7 +10657,7 @@
   ;;
 
 bsdi[45]*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_version=no
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
   soname_spec='${libname}${release}${shared_ext}$major'
@@ -10541,7 +10796,7 @@
   ;;
 
 dgux*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
@@ -10549,10 +10804,6 @@
   shlibpath_var=LD_LIBRARY_PATH
   ;;
 
-freebsd1*)
-  dynamic_linker=no
-  ;;
-
 freebsd* | dragonfly*)
   # DragonFly does not have aout.  When/if they implement a new
   # versioning mechanism, adjust this.
@@ -10560,7 +10811,7 @@
     objformat=`/usr/bin/objformat`
   else
     case $host_os in
-    freebsd[123]*) objformat=aout ;;
+    freebsd[23].*) objformat=aout ;;
     *) objformat=elf ;;
     esac
   fi
@@ -10578,7 +10829,7 @@
   esac
   shlibpath_var=LD_LIBRARY_PATH
   case $host_os in
-  freebsd2*)
+  freebsd2.*)
     shlibpath_overrides_runpath=yes
     ;;
   freebsd3.[01]* | freebsdelf3.[01]*)
@@ -10598,17 +10849,18 @@
   ;;
 
 gnu*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
   soname_spec='${libname}${release}${shared_ext}$major'
   shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=no
   hardcode_into_libs=yes
   ;;
 
 haiku*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   dynamic_linker="$host_os runtime_loader"
@@ -10669,7 +10921,7 @@
   ;;
 
 interix[3-9]*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
@@ -10685,7 +10937,7 @@
     nonstopux*) version_type=nonstopux ;;
     *)
 	if test "$lt_cv_prog_gnu_ld" = yes; then
-		version_type=linux
+		version_type=linux # correct to gnu/linux during the next big refactor
 	else
 		version_type=irix
 	fi ;;
@@ -10722,9 +10974,9 @@
   dynamic_linker=no
   ;;
 
-# This must be Linux ELF.
+# This must be glibc/ELF.
 linux* | k*bsd*-gnu | kopensolaris*-gnu)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
@@ -10772,14 +11024,10 @@
   # before this can be enabled.
   hardcode_into_libs=yes
 
-  # Add ABI-specific directories to the system library path.
-  sys_lib_dlsearch_path_spec="/lib64 /usr/lib64 /lib /usr/lib"
-
   # Append ld.so.conf contents to the search path
   if test -f /etc/ld.so.conf; then
     lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[	 ]*hwcap[	 ]/d;s/[:,	]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;s/"//g;/^$/d' | tr '\n' ' '`
-    sys_lib_dlsearch_path_spec="$sys_lib_dlsearch_path_spec $lt_ld_extra"
-
+    sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
   fi
 
   # We used to test for /lib/ld.so.1 and disable shared libraries on
@@ -10810,7 +11058,7 @@
   ;;
 
 newsos6)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
   shlibpath_var=LD_LIBRARY_PATH
   shlibpath_overrides_runpath=yes
@@ -10879,7 +11127,7 @@
   ;;
 
 solaris*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
@@ -10904,7 +11152,7 @@
   ;;
 
 sysv4 | sysv4.3*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
   soname_spec='${libname}${release}${shared_ext}$major'
   shlibpath_var=LD_LIBRARY_PATH
@@ -10928,7 +11176,7 @@
 
 sysv4*MP*)
   if test -d /usr/nec ;then
-    version_type=linux
+    version_type=linux # correct to gnu/linux during the next big refactor
     library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
     soname_spec='$libname${shared_ext}.$major'
     shlibpath_var=LD_LIBRARY_PATH
@@ -10959,7 +11207,7 @@
 
 tpf*)
   # TPF is a cross-target only.  Preferred cross-host = GNU/Linux.
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
@@ -10969,7 +11217,7 @@
   ;;
 
 uts4*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
   soname_spec='${libname}${release}${shared_ext}$major'
   shlibpath_var=LD_LIBRARY_PATH
@@ -11751,6 +11999,8 @@
 
 
 
+
+
         ac_config_commands="$ac_config_commands libtool"
 
 
@@ -11787,7 +12037,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_CXX="$ac_tool_prefix$ac_prog"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -11831,7 +12081,7 @@
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
     for ac_exec_ext in '' $ac_executable_extensions; do
-  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+  if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
     ac_cv_prog_ac_ct_CXX="$ac_prog"
     $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
     break 2
@@ -12027,8 +12277,8 @@
   # We make a subdir and do the tests there.  Otherwise we can end up
   # making bogus files that we don't know about and never remove.  For
   # instance it was reported that on HP-UX the gcc test will end up
-  # making a dummy file named `D' -- because `-MD' means `put the output
-  # in D'.
+  # making a dummy file named 'D' -- because '-MD' means "put the output
+  # in D".
   rm -rf conftest.dir
   mkdir conftest.dir
   # Copy depcomp to subdir because otherwise we won't find it if we're
@@ -12063,16 +12313,16 @@
     : > sub/conftest.c
     for i in 1 2 3 4 5 6; do
       echo '#include "conftst'$i'.h"' >> sub/conftest.c
-      # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
-      # Solaris 8's {/usr,}/bin/sh.
-      touch sub/conftst$i.h
+      # Using ": > sub/conftst$i.h" creates only sub/conftst1.h with
+      # Solaris 10 /bin/sh.
+      echo '/* dummy */' > sub/conftst$i.h
     done
     echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
 
-    # We check with `-c' and `-o' for the sake of the "dashmstdout"
+    # We check with '-c' and '-o' for the sake of the "dashmstdout"
     # mode.  It turns out that the SunPro C++ compiler does not properly
-    # handle `-M -o', and we need to detect this.  Also, some Intel
-    # versions had trouble with output in subdirs
+    # handle '-M -o', and we need to detect this.  Also, some Intel
+    # versions had trouble with output in subdirs.
     am__obj=sub/conftest.${OBJEXT-o}
     am__minus_obj="-o $am__obj"
     case $depmode in
@@ -12081,8 +12331,8 @@
       test "$am__universal" = false || continue
       ;;
     nosideeffect)
-      # after this tag, mechanisms are not by side-effect, so they'll
-      # only be used when explicitly requested
+      # After this tag, mechanisms are not by side-effect, so they'll
+      # only be used when explicitly requested.
       if test "x$enable_dependency_tracking" = xyes; then
 	continue
       else
@@ -12090,7 +12340,7 @@
       fi
       ;;
     msvc7 | msvc7msys | msvisualcpp | msvcmsys)
-      # This compiler won't grok `-c -o', but also, the minuso test has
+      # This compiler won't grok '-c -o', but also, the minuso test has
       # not run yet.  These depmodes are late enough in the game, and
       # so weak that their functioning should not be impacted.
       am__obj=conftest.${OBJEXT-o}
@@ -12309,7 +12559,6 @@
 hardcode_direct_CXX=no
 hardcode_direct_absolute_CXX=no
 hardcode_libdir_flag_spec_CXX=
-hardcode_libdir_flag_spec_ld_CXX=
 hardcode_libdir_separator_CXX=
 hardcode_minus_L_CXX=no
 hardcode_shlibpath_var_CXX=unsupported
@@ -12893,6 +13142,7 @@
   hardcode_shlibpath_var_CXX=unsupported
   if test "$lt_cv_ld_force_load" = "yes"; then
     whole_archive_flag_spec_CXX='`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience ${wl}-force_load,$conv\"; done; func_echo_all \"$new_convenience\"`'
+
   else
     whole_archive_flag_spec_CXX=''
   fi
@@ -12937,7 +13187,7 @@
         esac
         ;;
 
-      freebsd[12]*)
+      freebsd2.*)
         # C++ shared libraries reported to be fairly broken before
 	# switch to ELF
         ld_shlibs_CXX=no
@@ -13613,6 +13863,7 @@
 case "$CC $CFLAGS " in #(
 *\ -flto*\ *) CFLAGS="$CFLAGS -fno-lto" ;;
 *\ -fwhopr*\ *) CFLAGS="$CFLAGS -fno-whopr" ;;
+*\ -fuse-linker-plugin*\ *) CFLAGS="$CFLAGS -fno-use-linker-plugin" ;;
 esac
 
 if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
@@ -14402,7 +14653,9 @@
     ;;
   cygwin* | mingw* | cegcc*)
     case $cc_basename in
-    cl*) ;;
+    cl*)
+      exclude_expsyms_CXX='_NULL_IMPORT_DESCRIPTOR|_IMPORT_DESCRIPTOR_.*'
+      ;;
     *)
       export_symbols_cmds_CXX='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS][ ]/s/.*[ ]\([^ ]*\)/\1 DATA/;s/^.*[ ]__nm__\([^ ]*\)[ ][^ ]*/\1 DATA/;/^I[ ]/d;/^[AITW][ ]/s/.* //'\'' | sort | uniq > $export_symbols'
       exclude_expsyms_CXX='[_]+GLOBAL_OFFSET_TABLE_|[_]+GLOBAL__[FID]_.*|[_]+head_[A-Za-z0-9_]+_dll|[A-Za-z0-9_]+_dll_iname'
@@ -14555,8 +14808,6 @@
 
 
 
-
-
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking dynamic linker characteristics" >&5
 $as_echo_n "checking dynamic linker characteristics... " >&6; }
 
@@ -14582,7 +14833,7 @@
 
 case $host_os in
 aix3*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
   shlibpath_var=LIBPATH
 
@@ -14591,7 +14842,7 @@
   ;;
 
 aix[4-9]*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   hardcode_into_libs=yes
@@ -14656,7 +14907,7 @@
   ;;
 
 bsdi[45]*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_version=no
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
   soname_spec='${libname}${release}${shared_ext}$major'
@@ -14793,7 +15044,7 @@
   ;;
 
 dgux*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
@@ -14801,10 +15052,6 @@
   shlibpath_var=LD_LIBRARY_PATH
   ;;
 
-freebsd1*)
-  dynamic_linker=no
-  ;;
-
 freebsd* | dragonfly*)
   # DragonFly does not have aout.  When/if they implement a new
   # versioning mechanism, adjust this.
@@ -14812,7 +15059,7 @@
     objformat=`/usr/bin/objformat`
   else
     case $host_os in
-    freebsd[123]*) objformat=aout ;;
+    freebsd[23].*) objformat=aout ;;
     *) objformat=elf ;;
     esac
   fi
@@ -14830,7 +15077,7 @@
   esac
   shlibpath_var=LD_LIBRARY_PATH
   case $host_os in
-  freebsd2*)
+  freebsd2.*)
     shlibpath_overrides_runpath=yes
     ;;
   freebsd3.[01]* | freebsdelf3.[01]*)
@@ -14850,17 +15097,18 @@
   ;;
 
 gnu*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
   soname_spec='${libname}${release}${shared_ext}$major'
   shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=no
   hardcode_into_libs=yes
   ;;
 
 haiku*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   dynamic_linker="$host_os runtime_loader"
@@ -14921,7 +15169,7 @@
   ;;
 
 interix[3-9]*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
@@ -14937,7 +15185,7 @@
     nonstopux*) version_type=nonstopux ;;
     *)
 	if test "$lt_cv_prog_gnu_ld" = yes; then
-		version_type=linux
+		version_type=linux # correct to gnu/linux during the next big refactor
 	else
 		version_type=irix
 	fi ;;
@@ -14974,9 +15222,9 @@
   dynamic_linker=no
   ;;
 
-# This must be Linux ELF.
+# This must be glibc/ELF.
 linux* | k*bsd*-gnu | kopensolaris*-gnu)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
@@ -15024,14 +15272,10 @@
   # before this can be enabled.
   hardcode_into_libs=yes
 
-  # Add ABI-specific directories to the system library path.
-  sys_lib_dlsearch_path_spec="/lib64 /usr/lib64 /lib /usr/lib"
-
   # Append ld.so.conf contents to the search path
   if test -f /etc/ld.so.conf; then
     lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[	 ]*hwcap[	 ]/d;s/[:,	]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;s/"//g;/^$/d' | tr '\n' ' '`
-    sys_lib_dlsearch_path_spec="$sys_lib_dlsearch_path_spec $lt_ld_extra"
-
+    sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
   fi
 
   # We used to test for /lib/ld.so.1 and disable shared libraries on
@@ -15062,7 +15306,7 @@
   ;;
 
 newsos6)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
   shlibpath_var=LD_LIBRARY_PATH
   shlibpath_overrides_runpath=yes
@@ -15131,7 +15375,7 @@
   ;;
 
 solaris*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
@@ -15156,7 +15400,7 @@
   ;;
 
 sysv4 | sysv4.3*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
   soname_spec='${libname}${release}${shared_ext}$major'
   shlibpath_var=LD_LIBRARY_PATH
@@ -15180,7 +15424,7 @@
 
 sysv4*MP*)
   if test -d /usr/nec ;then
-    version_type=linux
+    version_type=linux # correct to gnu/linux during the next big refactor
     library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
     soname_spec='$libname${shared_ext}.$major'
     shlibpath_var=LD_LIBRARY_PATH
@@ -15211,7 +15455,7 @@
 
 tpf*)
   # TPF is a cross-target only.  Preferred cross-host = GNU/Linux.
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
@@ -15221,7 +15465,7 @@
   ;;
 
 uts4*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
   soname_spec='${libname}${release}${shared_ext}$major'
   shlibpath_var=LD_LIBRARY_PATH
@@ -15495,21 +15739,21 @@
 ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
 
 
-ac_fn_cxx_check_header_mongrel "$LINENO" "mmdb/mmdb_manager.h" "ac_cv_header_mmdb_mmdb_manager_h" "$ac_includes_default"
-if test "x$ac_cv_header_mmdb_mmdb_manager_h" = xyes; then :
+ac_fn_cxx_check_header_mongrel "$LINENO" "mmdb2/mmdb_manager.h" "ac_cv_header_mmdb2_mmdb_manager_h" "$ac_includes_default"
+if test "x$ac_cv_header_mmdb2_mmdb_manager_h" = xyes; then :
   :
 else
-  as_fn_error $? "mmdb headers not found." "$LINENO" 5
+  as_fn_error $? "mmdb2 headers not found." "$LINENO" 5
 fi
 
 
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for MMDB_CCIF_Init in -lmmdb" >&5
-$as_echo_n "checking for MMDB_CCIF_Init in -lmmdb... " >&6; }
-if ${ac_cv_lib_mmdb_MMDB_CCIF_Init+:} false; then :
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for MMDB_CCIF_Init in -lmmdb2" >&5
+$as_echo_n "checking for MMDB_CCIF_Init in -lmmdb2... " >&6; }
+if ${ac_cv_lib_mmdb2_MMDB_CCIF_Init+:} false; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
-LIBS="-lmmdb  $LIBS"
+LIBS="-lmmdb2  $LIBS"
 cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
 
@@ -15529,21 +15773,21 @@
 }
 _ACEOF
 if ac_fn_cxx_try_link "$LINENO"; then :
-  ac_cv_lib_mmdb_MMDB_CCIF_Init=yes
+  ac_cv_lib_mmdb2_MMDB_CCIF_Init=yes
 else
-  ac_cv_lib_mmdb_MMDB_CCIF_Init=no
+  ac_cv_lib_mmdb2_MMDB_CCIF_Init=no
 fi
 rm -f core conftest.err conftest.$ac_objext \
     conftest$ac_exeext conftest.$ac_ext
 LIBS=$ac_check_lib_save_LIBS
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_mmdb_MMDB_CCIF_Init" >&5
-$as_echo "$ac_cv_lib_mmdb_MMDB_CCIF_Init" >&6; }
-if test "x$ac_cv_lib_mmdb_MMDB_CCIF_Init" = xyes; then :
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_mmdb2_MMDB_CCIF_Init" >&5
+$as_echo "$ac_cv_lib_mmdb2_MMDB_CCIF_Init" >&6; }
+if test "x$ac_cv_lib_mmdb2_MMDB_CCIF_Init" = xyes; then :
   :
 else
-  { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: mmdb library not found." >&5
-$as_echo "$as_me: WARNING: mmdb library not found." >&2;}
+  { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: mmdb2 library not found." >&5
+$as_echo "$as_me: WARNING: mmdb2 library not found." >&2;}
 fi
 
 ac_ext=c
@@ -15664,6 +15908,14 @@
 LTLIBOBJS=$ac_ltlibobjs
 
 
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking that generated files are newer than configure" >&5
+$as_echo_n "checking that generated files are newer than configure... " >&6; }
+   if test -n "$am_sleep_pid"; then
+     # Hide warnings about reused PIDs.
+     wait $am_sleep_pid 2>/dev/null
+   fi
+   { $as_echo "$as_me:${as_lineno-$LINENO}: result: done" >&5
+$as_echo "done" >&6; }
  if test -n "$EXEEXT"; then
   am__EXEEXT_TRUE=
   am__EXEEXT_FALSE='#'
@@ -15986,16 +16238,16 @@
     # ... but there are two gotchas:
     # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
     # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
-    # In both cases, we have to default to `cp -p'.
+    # In both cases, we have to default to `cp -pR'.
     ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
-      as_ln_s='cp -p'
+      as_ln_s='cp -pR'
   elif ln conf$$.file conf$$ 2>/dev/null; then
     as_ln_s=ln
   else
-    as_ln_s='cp -p'
+    as_ln_s='cp -pR'
   fi
 else
-  as_ln_s='cp -p'
+  as_ln_s='cp -pR'
 fi
 rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
 rmdir conf$$.dir 2>/dev/null
@@ -16055,28 +16307,16 @@
   as_mkdir_p=false
 fi
 
-if test -x / >/dev/null 2>&1; then
-  as_test_x='test -x'
-else
-  if ls -dL / >/dev/null 2>&1; then
-    as_ls_L_option=L
-  else
-    as_ls_L_option=
-  fi
-  as_test_x='
-    eval sh -c '\''
-      if test -d "$1"; then
-	test -d "$1/.";
-      else
-	case $1 in #(
-	-*)set "./$1";;
-	esac;
-	case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
-	???[sx]*):;;*)false;;esac;fi
-    '\'' sh
-  '
-fi
-as_executable_p=$as_test_x
+
+# as_fn_executable_p FILE
+# -----------------------
+# Test if FILE is an executable regular file.
+as_fn_executable_p ()
+{
+  test -f "$1" && test -x "$1"
+} # as_fn_executable_p
+as_test_x='test -x'
+as_executable_p=as_fn_executable_p
 
 # Sed expression to map a string onto a valid CPP name.
 as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
@@ -16098,7 +16338,7 @@
 # values after options handling.
 ac_log="
 This file was extended by ccp4srs $as_me 1.0.0, which was
-generated by GNU Autoconf 2.68.  Invocation command line was
+generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
   CONFIG_HEADERS  = $CONFIG_HEADERS
@@ -16164,10 +16404,10 @@
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
 ccp4srs config.status 1.0.0
-configured by $0, generated by GNU Autoconf 2.68,
+configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 
-Copyright (C) 2010 Free Software Foundation, Inc.
+Copyright (C) 2012 Free Software Foundation, Inc.
 This config.status script is free software; the Free Software Foundation
 gives unlimited permission to copy, distribute and modify it."
 
@@ -16258,7 +16498,7 @@
 _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 if \$ac_cs_recheck; then
-  set X '$SHELL' '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
+  set X $SHELL '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
   shift
   \$as_echo "running CONFIG_SHELL=$SHELL \$*" >&6
   CONFIG_SHELL='$SHELL'
@@ -16303,6 +16543,7 @@
 enable_fast_install='`$ECHO "$enable_fast_install" | $SED "$delay_single_quote_subst"`'
 SHELL='`$ECHO "$SHELL" | $SED "$delay_single_quote_subst"`'
 ECHO='`$ECHO "$ECHO" | $SED "$delay_single_quote_subst"`'
+PATH_SEPARATOR='`$ECHO "$PATH_SEPARATOR" | $SED "$delay_single_quote_subst"`'
 host_alias='`$ECHO "$host_alias" | $SED "$delay_single_quote_subst"`'
 host='`$ECHO "$host" | $SED "$delay_single_quote_subst"`'
 host_os='`$ECHO "$host_os" | $SED "$delay_single_quote_subst"`'
@@ -16383,7 +16624,6 @@
 allow_undefined_flag='`$ECHO "$allow_undefined_flag" | $SED "$delay_single_quote_subst"`'
 no_undefined_flag='`$ECHO "$no_undefined_flag" | $SED "$delay_single_quote_subst"`'
 hardcode_libdir_flag_spec='`$ECHO "$hardcode_libdir_flag_spec" | $SED "$delay_single_quote_subst"`'
-hardcode_libdir_flag_spec_ld='`$ECHO "$hardcode_libdir_flag_spec_ld" | $SED "$delay_single_quote_subst"`'
 hardcode_libdir_separator='`$ECHO "$hardcode_libdir_separator" | $SED "$delay_single_quote_subst"`'
 hardcode_direct='`$ECHO "$hardcode_direct" | $SED "$delay_single_quote_subst"`'
 hardcode_direct_absolute='`$ECHO "$hardcode_direct_absolute" | $SED "$delay_single_quote_subst"`'
@@ -16455,7 +16695,6 @@
 allow_undefined_flag_CXX='`$ECHO "$allow_undefined_flag_CXX" | $SED "$delay_single_quote_subst"`'
 no_undefined_flag_CXX='`$ECHO "$no_undefined_flag_CXX" | $SED "$delay_single_quote_subst"`'
 hardcode_libdir_flag_spec_CXX='`$ECHO "$hardcode_libdir_flag_spec_CXX" | $SED "$delay_single_quote_subst"`'
-hardcode_libdir_flag_spec_ld_CXX='`$ECHO "$hardcode_libdir_flag_spec_ld_CXX" | $SED "$delay_single_quote_subst"`'
 hardcode_libdir_separator_CXX='`$ECHO "$hardcode_libdir_separator_CXX" | $SED "$delay_single_quote_subst"`'
 hardcode_direct_CXX='`$ECHO "$hardcode_direct_CXX" | $SED "$delay_single_quote_subst"`'
 hardcode_direct_absolute_CXX='`$ECHO "$hardcode_direct_absolute_CXX" | $SED "$delay_single_quote_subst"`'
@@ -16497,6 +16736,7 @@
 OBJDUMP \
 SHELL \
 ECHO \
+PATH_SEPARATOR \
 SED \
 GREP \
 EGREP \
@@ -16545,7 +16785,6 @@
 allow_undefined_flag \
 no_undefined_flag \
 hardcode_libdir_flag_spec \
-hardcode_libdir_flag_spec_ld \
 hardcode_libdir_separator \
 exclude_expsyms \
 include_expsyms \
@@ -16579,7 +16818,6 @@
 allow_undefined_flag_CXX \
 no_undefined_flag_CXX \
 hardcode_libdir_flag_spec_CXX \
-hardcode_libdir_flag_spec_ld_CXX \
 hardcode_libdir_separator_CXX \
 exclude_expsyms_CXX \
 include_expsyms_CXX \
@@ -17271,7 +17509,7 @@
 
   case $ac_file$ac_mode in
     "depfiles":C) test x"$AMDEP_TRUE" != x"" || {
-  # Autoconf 2.62 quotes --file arguments for eval, but not when files
+  # Older Autoconf quotes --file arguments for eval, but not when files
   # are listed without --file.  Let's play safe and only enable the eval
   # if we detect the quoting.
   case $CONFIG_FILES in
@@ -17284,7 +17522,7 @@
     # Strip MF so we end up with the name of the file.
     mf=`echo "$mf" | sed -e 's/:.*$//'`
     # Check whether this is an Automake generated Makefile or not.
-    # We used to match only the files named `Makefile.in', but
+    # We used to match only the files named 'Makefile.in', but
     # some people rename them; so instead we look at the file content.
     # Grep'ing the first line is not enough: some people post-process
     # each Makefile.in and add a new line on top of each file to say so.
@@ -17318,21 +17556,19 @@
       continue
     fi
     # Extract the definition of DEPDIR, am__include, and am__quote
-    # from the Makefile without running `make'.
+    # from the Makefile without running 'make'.
     DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
     test -z "$DEPDIR" && continue
     am__include=`sed -n 's/^am__include = //p' < "$mf"`
-    test -z "am__include" && continue
+    test -z "$am__include" && continue
     am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
-    # When using ansi2knr, U may be empty or an underscore; expand it
-    U=`sed -n 's/^U = //p' < "$mf"`
     # Find all dependency output files, they are included files with
     # $(DEPDIR) in their names.  We invoke sed twice because it is the
     # simplest approach to changing $(DEPDIR) to its actual value in the
     # expansion.
     for file in `sed -n "
       s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
-	 sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
+	 sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g'`; do
       # Make sure the directory exists.
       test -f "$dirpart/$file" && continue
       fdir=`$as_dirname -- "$file" ||
@@ -17386,8 +17622,8 @@
 # NOTE: Changes made to this file will be lost: look at ltmain.sh.
 #
 #   Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005,
-#                 2006, 2007, 2008, 2009, 2010 Free Software Foundation,
-#                 Inc.
+#                 2006, 2007, 2008, 2009, 2010, 2011 Free Software
+#                 Foundation, Inc.
 #   Written by Gordon Matzigkeit, 1996
 #
 #   This file is part of GNU Libtool.
@@ -17450,6 +17686,9 @@
 # An echo program that protects backslashes.
 ECHO=$lt_ECHO
 
+# The PATH separator for the build system.
+PATH_SEPARATOR=$lt_PATH_SEPARATOR
+
 # The host system.
 host_alias=$host_alias
 host=$host
@@ -17745,10 +17984,6 @@
 # This must work even if \$libdir does not exist
 hardcode_libdir_flag_spec=$lt_hardcode_libdir_flag_spec
 
-# If ld is used when linking, flag to hardcode \$libdir into a binary
-# during linking.  This must work even if \$libdir does not exist.
-hardcode_libdir_flag_spec_ld=$lt_hardcode_libdir_flag_spec_ld
-
 # Whether we need a single "-rpath" flag with a separated argument.
 hardcode_libdir_separator=$lt_hardcode_libdir_separator
 
@@ -18091,10 +18326,6 @@
 # This must work even if \$libdir does not exist
 hardcode_libdir_flag_spec=$lt_hardcode_libdir_flag_spec_CXX
 
-# If ld is used when linking, flag to hardcode \$libdir into a binary
-# during linking.  This must work even if \$libdir does not exist.
-hardcode_libdir_flag_spec_ld=$lt_hardcode_libdir_flag_spec_ld_CXX
-
 # Whether we need a single "-rpath" flag with a separated argument.
 hardcode_libdir_separator=$lt_hardcode_libdir_separator_CXX
 
diff -ruN ccp4srs-old/configure.ac ccp4srs/configure.ac
--- ccp4srs-old/configure.ac	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/configure.ac	2014-09-09 21:34:12.000000000 -0700
@@ -5,6 +5,7 @@
 AC_CONFIG_SRCDIR(ccp4srs/ccp4srs_angle.cpp)
 AC_CONFIG_HEADERS(config.h)
 AM_INIT_AUTOMAKE([1.11 foreign subdir-objects silent-rules -Wall])
+m4_ifdef([AM_PROG_AR], [AM_PROG_AR])
 LT_INIT([disable-shared win32-dll])
 AC_PROG_CXX
 AC_PROG_INSTALL
@@ -16,12 +17,12 @@
 AC_CHECK_HEADER(zlib.h, :, AC_MSG_ERROR(zlib.h header not found))
 
 AC_LANG_PUSH([C++])
-AC_CHECK_HEADER(mmdb/mmdb_manager.h, :,
-                AC_MSG_ERROR([mmdb headers not found.]))
+AC_CHECK_HEADER(mmdb2/mmdb_manager.h, :,
+                AC_MSG_ERROR([mmdb2 headers not found.]))
 dnl to make ccp4/configure script work, missing library at this stage
 dnl is not an error
-AC_CHECK_LIB(mmdb, MMDB_CCIF_Init, :,
-             AC_MSG_WARN([mmdb library not found.]))
+AC_CHECK_LIB(mmdb2, MMDB_CCIF_Init, :,
+             AC_MSG_WARN([mmdb2 library not found.]))
 AC_LANG_POP([C++])
 
 AC_OUTPUT([Makefile])
diff -ruN ccp4srs-old/doc-html/html/annotated.html ccp4srs/doc-html/html/annotated.html
--- ccp4srs-old/doc-html/html/annotated.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/annotated.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,94 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
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+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
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+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>Class List</h1>  </div>
+</div>
+<div class="contents">
+Here are the classes, structs, unions and interfaces with brief descriptions:<table>
+  <tr><td class="indexkey"><a class="el" href="classccp4srs_1_1_angle.html">ccp4srs::Angle</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey"><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey"><a class="el" href="structccp4srs_1_1_atom_pair.html">ccp4srs::AtomPair</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey"><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey"><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey"><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey"><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey"><a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container&lt; T &gt;</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey"><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html">ccp4srs::DASelHnds</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey"><a class="el" href="classccp4srs_1_1_entry.html">ccp4srs::Entry</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey"><a class="el" href="classccp4srs_1_1_index.html">ccp4srs::Index</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey"><a class="el" href="classccp4srs_1_1_manager.html">ccp4srs::Manager</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey"><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey"><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey"><a class="el" href="structccp4srs_1_1_m_p_file_pos.html">ccp4srs::MPFilePos</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey"><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey"><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey"><a class="el" href="classccp4srs_1_1_tree.html">ccp4srs::Tree</a></td><td class="indexvalue"></td></tr>
+</table>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
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+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
Binary files ccp4srs-old/doc-html/html/bc_s.png and ccp4srs/doc-html/html/bc_s.png differ
diff -ruN ccp4srs-old/doc-html/html/ccp4srs__angle_8cpp.html ccp4srs/doc-html/html/ccp4srs__angle_8cpp.html
--- ccp4srs-old/doc-html/html/ccp4srs__angle_8cpp.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__angle_8cpp.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,81 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/ccp4srs_angle.cpp File Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li class="current"><a href="files.html"><span>Files</span></a></li>
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+          <img id="MSearchSelect" src="search/mag_sel.png"
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+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
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+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="files.html"><span>File&#160;List</span></a></li>
+      <li><a href="globals.html"><span>File&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="summary">
+<a href="#namespaces">Namespaces</a>  </div>
+  <div class="headertitle">
+<h1>src/ccp4srs_angle.cpp File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &quot;<a class="el" href="ccp4srs__angle_8h_source.html">ccp4srs_angle.h</a>&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__defs_8h_source.html">ccp4srs_defs.h</a>&quot;</code><br/>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+</table>
+</div>
+<!--- window showing the filter options -->
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+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
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+
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+        name="MSearchResults" id="MSearchResults">
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__angle_8h.html ccp4srs/doc-html/html/ccp4srs__angle_8h.html
--- ccp4srs-old/doc-html/html/ccp4srs__angle_8h.html	1969-12-31 16:00:00.000000000 -0800
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+<h1>src/ccp4srs_angle.h File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &quot;<a class="el" href="ccp4srs__atom_8h_source.html">ccp4srs_atom.h</a>&quot;</code><br/>
+
+<p><a href="ccp4srs__angle_8h_source.html">Go to the source code of this file.</a></p>
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+<tr><td colspan="2"><h2><a name="nested-classes"></a>
+Classes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_angle.html">ccp4srs::Angle</a></td></tr>
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
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+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#afbb5df60616f08fcf36926a3585c185f">ccp4srs::DefineClass</a> (Angle)</td></tr>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__angle_8h_source.html ccp4srs/doc-html/html/ccp4srs__angle_8h_source.html
--- ccp4srs-old/doc-html/html/ccp4srs__angle_8h_source.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__angle_8h_source.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,155 @@
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+<h1>src/ccp4srs_angle.h</h1>  </div>
+</div>
+<div class="contents">
+<a href="ccp4srs__angle_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">//  $Id: ccp4srs_angle.h $</span>
+<a name="l00002"></a>00002 <span class="comment">//  =================================================================</span>
+<a name="l00003"></a>00003 <span class="comment">//</span>
+<a name="l00004"></a>00004 <span class="comment">//   CCP4 SRS Library: Storage, Retrieval and Search support for</span>
+<a name="l00005"></a>00005 <span class="comment">//   CCP4 ligand data.</span>
+<a name="l00006"></a>00006 <span class="comment">//</span>
+<a name="l00007"></a>00007 <span class="comment">//   Copyright (C) Eugene Krissinel 2010-2013.</span>
+<a name="l00008"></a>00008 <span class="comment">//</span>
+<a name="l00009"></a>00009 <span class="comment">//   This library is free software: you can redistribute it and/or</span>
+<a name="l00010"></a>00010 <span class="comment">//   modify it under the terms of the GNU Lesser General Public</span>
+<a name="l00011"></a>00011 <span class="comment">//   License version 3, modified in accordance with the provisions</span>
+<a name="l00012"></a>00012 <span class="comment">//   of the license to address the requirements of UK law.</span>
+<a name="l00013"></a>00013 <span class="comment">//</span>
+<a name="l00014"></a>00014 <span class="comment">//   You should have received a copy of the modified GNU Lesser</span>
+<a name="l00015"></a>00015 <span class="comment">//   General Public License along with this library. If not, copies</span>
+<a name="l00016"></a>00016 <span class="comment">//   may be downloaded from http://www.ccp4.ac.uk/ccp4license.php</span>
+<a name="l00017"></a>00017 <span class="comment">//</span>
+<a name="l00018"></a>00018 <span class="comment">//   This program is distributed in the hope that it will be useful,</span>
+<a name="l00019"></a>00019 <span class="comment">//   but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
+<a name="l00020"></a>00020 <span class="comment">//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
+<a name="l00021"></a>00021 <span class="comment">//   GNU Lesser General Public License for more details.</span>
+<a name="l00022"></a>00022 <span class="comment">//</span>
+<a name="l00023"></a>00023 <span class="comment">//  =================================================================</span>
+<a name="l00024"></a>00024 <span class="comment">//</span>
+<a name="l00025"></a>00025 <span class="comment">//    18.09.13   &lt;--  Date of Last Modification.</span>
+<a name="l00026"></a>00026 <span class="comment">//                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
+<a name="l00027"></a>00027 <span class="comment">//  -----------------------------------------------------------------</span>
+<a name="l00028"></a>00028 <span class="comment">//</span>
+<a name="l00029"></a>00029 <span class="comment">//  **** Module  :  ccp4srs_angle  &lt;interface&gt;</span>
+<a name="l00030"></a>00030 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00031"></a>00031 <span class="comment">//  **** Classes :  ccp4srs::Angle  - angle restraint class</span>
+<a name="l00032"></a>00032 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00033"></a>00033 <span class="comment">//</span>
+<a name="l00034"></a>00034 <span class="comment">//  (C) E. Krissinel 2010-2013</span>
+<a name="l00035"></a>00035 <span class="comment">//</span>
+<a name="l00036"></a>00036 <span class="comment">//  =================================================================</span>
+<a name="l00037"></a>00037 <span class="comment">//</span>
+<a name="l00038"></a>00038 
+<a name="l00039"></a>00039 <span class="preprocessor">#ifndef CCP4SRS_ANGLE_H</span>
+<a name="l00040"></a>00040 <span class="preprocessor"></span><span class="preprocessor">#define CCP4SRS_ANGLE_H</span>
+<a name="l00041"></a>00041 <span class="preprocessor"></span>
+<a name="l00042"></a>00042 <span class="preprocessor">#include &quot;<a class="code" href="ccp4srs__atom_8h.html">ccp4srs_atom.h</a>&quot;</span>
+<a name="l00043"></a>00043 
+<a name="l00044"></a>00044 <span class="keyword">namespace </span>ccp4srs  {
+<a name="l00045"></a>00045 
+<a name="l00046"></a>00046   <a class="code" href="namespaceccp4srs.html#afbb5df60616f08fcf36926a3585c185f">DefineClass</a>(Angle);
+<a name="l00047"></a>00047 
+<a name="l00048"></a><a class="code" href="classccp4srs_1_1_angle.html">00048</a>   <span class="keyword">class </span><a class="code" href="classccp4srs_1_1_angle.html">Angle</a>  {
+<a name="l00049"></a>00049 
+<a name="l00050"></a>00050     <span class="keyword">public</span>:
+<a name="l00051"></a>00051       <a class="code" href="classccp4srs_1_1_angle.html#a5ec6da380214e7100ff46e3e79898e15">Angle</a>();
+<a name="l00052"></a>00052       <span class="keyword">virtual</span> <a class="code" href="classccp4srs_1_1_angle.html#a8b6036ed3908589a9cee50f60f5e3806">~Angle</a>();
+<a name="l00053"></a>00053 
+<a name="l00054"></a><a class="code" href="classccp4srs_1_1_angle.html#a64770743097878619e8dccf787f93802">00054</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span>            <a class="code" href="classccp4srs_1_1_angle.html#a64770743097878619e8dccf787f93802">atom1</a>() { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_angle.html#ab59c639612d7dcae2b34213a647cdb45">atom_1</a>;    }
+<a name="l00055"></a><a class="code" href="classccp4srs_1_1_angle.html#a1be24203719da0b250775f7c0b5710ed">00055</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span>            <a class="code" href="classccp4srs_1_1_angle.html#a1be24203719da0b250775f7c0b5710ed">atom2</a>() { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_angle.html#a8a4fd7f9e6196f259b6ec0989b5cb64c">atom_2</a>;    }
+<a name="l00056"></a><a class="code" href="classccp4srs_1_1_angle.html#a6d62c8acfe549d3d439a061f2bbcada9">00056</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span>            <a class="code" href="classccp4srs_1_1_angle.html#a6d62c8acfe549d3d439a061f2bbcada9">atom3</a>() { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_angle.html#a545fb1039055e640aa938964b64c7d0a">atom_3</a>;    }
+<a name="l00057"></a><a class="code" href="classccp4srs_1_1_angle.html#a6ec0de44c0f607bcb5634a907fe9018a">00057</a>       <span class="keyword">inline</span> mmdb::realtype <a class="code" href="classccp4srs_1_1_angle.html#a6ec0de44c0f607bcb5634a907fe9018a">value</a>() { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_angle.html#abf55314566cb2fa1d3764d0485284113">angle</a>;     }
+<a name="l00058"></a><a class="code" href="classccp4srs_1_1_angle.html#a31b7030dec4dd77c0eefa3444c75901f">00058</a>       <span class="keyword">inline</span> mmdb::realtype <a class="code" href="classccp4srs_1_1_angle.html#a31b7030dec4dd77c0eefa3444c75901f">esd</a>  () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_angle.html#a39e05de948ddbf9c944bf0b14123caf8">angle_esd</a>; }
+<a name="l00059"></a>00059 
+<a name="l00060"></a>00060       <span class="keyword">static</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_angle.html#a257cefe6949d4371175d4c1573a1d40e">makeCIFTags</a> ( mmdb::mmcif::PLoop mmCIFLoop );
+<a name="l00061"></a>00061       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_angle.html#a9a366216e8c07f33829fd26db9df4f00">readFromCIF</a> ( mmdb::mmcif::PLoop mmCIFLoop, <span class="keywordtype">int</span> angleNo,
+<a name="l00062"></a>00062                          <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a> &amp; atoms );
+<a name="l00063"></a>00063       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_angle.html#a8a293c96f55ee3b13cc9b9db86d265cd">writeToCIF</a>  ( mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID,
+<a name="l00064"></a>00064                          <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a> &amp; atoms );
+<a name="l00065"></a>00065 
+<a name="l00066"></a>00066       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_angle.html#a5fcc085237045429dd4a946595c1488f">write_mem</a> ( PMemIO memIO, <span class="keywordtype">int</span> version );
+<a name="l00067"></a>00067       <span class="keywordtype">bool</span> <a class="code" href="classccp4srs_1_1_angle.html#a2f34c77527204676236a28c863f5adee">read_mem</a>  ( PMemIO memIO, <span class="keywordtype">int</span> version,
+<a name="l00068"></a>00068                           <span class="keywordtype">bool</span> * Ok = NULL );
+<a name="l00069"></a>00069 
+<a name="l00070"></a>00070       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_angle.html#a085c530866442b6b3dfb8c969de2bfe8">copy</a> ( PAngle ang, mmdb::ivector anmatch=NULL );
+<a name="l00071"></a>00071 
+<a name="l00072"></a>00072     <span class="keyword">protected</span>:
+<a name="l00073"></a><a class="code" href="classccp4srs_1_1_angle.html#a545fb1039055e640aa938964b64c7d0a">00073</a>       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_angle.html#ab59c639612d7dcae2b34213a647cdb45">atom_1</a>,<a class="code" href="classccp4srs_1_1_angle.html#a8a4fd7f9e6196f259b6ec0989b5cb64c">atom_2</a>,<a class="code" href="classccp4srs_1_1_angle.html#a545fb1039055e640aa938964b64c7d0a">atom_3</a>; <span class="comment">// ordinal numbers of of atoms</span>
+<a name="l00074"></a>00074                                  <span class="comment">//   that form the angle [0,1,...]</span>
+<a name="l00075"></a><a class="code" href="classccp4srs_1_1_angle.html#abf55314566cb2fa1d3764d0485284113">00075</a>       mmdb::realtype <a class="code" href="classccp4srs_1_1_angle.html#abf55314566cb2fa1d3764d0485284113">angle</a>;      <span class="comment">// angle in degrees</span>
+<a name="l00076"></a><a class="code" href="classccp4srs_1_1_angle.html#a39e05de948ddbf9c944bf0b14123caf8">00076</a>       mmdb::realtype <a class="code" href="classccp4srs_1_1_angle.html#a39e05de948ddbf9c944bf0b14123caf8">angle_esd</a>;  <span class="comment">// angle esd in degrees; set to 0.0</span>
+<a name="l00077"></a>00077                                  <span class="comment">// if not provided</span>
+<a name="l00078"></a>00078 
+<a name="l00079"></a>00079   };
+<a name="l00080"></a>00080 
+<a name="l00081"></a>00081 }  <span class="comment">// namespace ccp4srs</span>
+<a name="l00082"></a>00082 
+<a name="l00083"></a>00083 <span class="preprocessor">#endif // CCP4SRS_ANGLE_H</span>
+</pre></div></div>
+</div>
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+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
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+</html>
diff -ruN ccp4srs-old/doc-html/html/ccp4srs__atom_8cpp.html ccp4srs/doc-html/html/ccp4srs__atom_8cpp.html
--- ccp4srs-old/doc-html/html/ccp4srs__atom_8cpp.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__atom_8cpp.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,90 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/ccp4srs_atom.cpp File Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
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+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
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+      <li><a href="files.html"><span>File&#160;List</span></a></li>
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+<div class="header">
+  <div class="summary">
+<a href="#namespaces">Namespaces</a> &#124;
+<a href="#func-members">Functions</a>  </div>
+  <div class="headertitle">
+<h1>src/ccp4srs_atom.cpp File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &lt;string.h&gt;</code><br/>
+<code>#include &quot;mmdb/mmdb_tables.h&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__atom_8h_source.html">ccp4srs_atom.h</a>&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__types_8h_source.html">ccp4srs_types.h</a>&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__defs_8h_source.html">ccp4srs_defs.h</a>&quot;</code><br/>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+<tr><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#adead0e638933d7d2949df9bb7b44f910">ccp4srs::get_atom_from_cif</a> (int &amp;index, mmdb::mmcif::PLoop loop, mmdb::cpstr Tag, int row, Container&lt; Atom &gt; &amp;atoms, int &amp;rc)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a012e980439f3fcbb1844abf82ab2e95e">ccp4srs::get_atom_from_cif</a> (int &amp;index, mmdb::mmcif::PStruct mmCIFStruct, mmdb::cpstr Tag, Container&lt; Atom &gt; &amp;atoms, int &amp;rc)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#af3c63726e6eb75b06c5b1c33a3acb608">ccp4srs::add_atom_to_cif</a> (mmdb::mmcif::PLoop loop, int atom_no, Container&lt; Atom &gt; &amp;atoms)</td></tr>
+</table>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
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+<a href="http://www.doxygen.org/index.html">
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+</html>
diff -ruN ccp4srs-old/doc-html/html/ccp4srs__atom_8h.html ccp4srs/doc-html/html/ccp4srs__atom_8h.html
--- ccp4srs-old/doc-html/html/ccp4srs__atom_8h.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__atom_8h.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,97 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/ccp4srs_atom.h File Reference</title>
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+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
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+<body onload='searchBox.OnSelectItem(0);'>
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+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
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+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
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+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
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+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
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+      <li><a href="files.html"><span>File&#160;List</span></a></li>
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+<a href="#nested-classes">Classes</a> &#124;
+<a href="#namespaces">Namespaces</a> &#124;
+<a href="#func-members">Functions</a>  </div>
+  <div class="headertitle">
+<h1>src/ccp4srs_atom.h File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &quot;<a class="el" href="ccp4srs__container_8h_source.html">ccp4srs_container.h</a>&quot;</code><br/>
+<code>#include &quot;<a class="el" href="memio___8h_source.html">memio_.h</a>&quot;</code><br/>
+<code>#include &quot;mmdb/mmdb_atom.h&quot;</code><br/>
+<code>#include &quot;mmdb/mmdb_mmcif_.h&quot;</code><br/>
+<code>#include &quot;mmdb/mmdb_defs.h&quot;</code><br/>
+
+<p><a href="ccp4srs__atom_8h_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="nested-classes"></a>
+Classes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td></tr>
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+<tr><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#aaacc6a8b59c08ac1bbfd9305ee663a1b">ccp4srs::DefineClass</a> (Atom)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#adead0e638933d7d2949df9bb7b44f910">ccp4srs::get_atom_from_cif</a> (int &amp;index, mmdb::mmcif::PLoop loop, mmdb::cpstr Tag, int row, Container&lt; Atom &gt; &amp;atoms, int &amp;rc)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a012e980439f3fcbb1844abf82ab2e95e">ccp4srs::get_atom_from_cif</a> (int &amp;index, mmdb::mmcif::PStruct mmCIFStruct, mmdb::cpstr Tag, Container&lt; Atom &gt; &amp;atoms, int &amp;rc)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#af3c63726e6eb75b06c5b1c33a3acb608">ccp4srs::add_atom_to_cif</a> (mmdb::mmcif::PLoop loop, int atom_no, Container&lt; Atom &gt; &amp;atoms)</td></tr>
+</table>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
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+
+<!-- iframe showing the search results (closed by default) -->
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+        name="MSearchResults" id="MSearchResults">
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+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/ccp4srs__atom_8h_source.html ccp4srs/doc-html/html/ccp4srs__atom_8h_source.html
--- ccp4srs-old/doc-html/html/ccp4srs__atom_8h_source.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__atom_8h_source.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,243 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/ccp4srs_atom.h Source File</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
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+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
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+      <li><a href="annotated.html"><span>Classes</span></a></li>
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+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
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+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
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+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="files.html"><span>File&#160;List</span></a></li>
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+    </ul>
+  </div>
+<div class="header">
+  <div class="headertitle">
+<h1>src/ccp4srs_atom.h</h1>  </div>
+</div>
+<div class="contents">
+<a href="ccp4srs__atom_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">//  $Id: ccp4srs_atom.h $</span>
+<a name="l00002"></a>00002 <span class="comment">//  =================================================================</span>
+<a name="l00003"></a>00003 <span class="comment">//</span>
+<a name="l00004"></a>00004 <span class="comment">//   CCP4 SRS Library: Storage, Retrieval and Search support for</span>
+<a name="l00005"></a>00005 <span class="comment">//   CCP4 ligand data.</span>
+<a name="l00006"></a>00006 <span class="comment">//</span>
+<a name="l00007"></a>00007 <span class="comment">//   Copyright (C) Eugene Krissinel 2010-2013.</span>
+<a name="l00008"></a>00008 <span class="comment">//</span>
+<a name="l00009"></a>00009 <span class="comment">//   This library is free software: you can redistribute it and/or</span>
+<a name="l00010"></a>00010 <span class="comment">//   modify it under the terms of the GNU Lesser General Public</span>
+<a name="l00011"></a>00011 <span class="comment">//   License version 3, modified in accordance with the provisions</span>
+<a name="l00012"></a>00012 <span class="comment">//   of the license to address the requirements of UK law.</span>
+<a name="l00013"></a>00013 <span class="comment">//</span>
+<a name="l00014"></a>00014 <span class="comment">//   You should have received a copy of the modified GNU Lesser</span>
+<a name="l00015"></a>00015 <span class="comment">//   General Public License along with this library. If not, copies</span>
+<a name="l00016"></a>00016 <span class="comment">//   may be downloaded from http://www.ccp4.ac.uk/ccp4license.php</span>
+<a name="l00017"></a>00017 <span class="comment">//</span>
+<a name="l00018"></a>00018 <span class="comment">//   This program is distributed in the hope that it will be useful,</span>
+<a name="l00019"></a>00019 <span class="comment">//   but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
+<a name="l00020"></a>00020 <span class="comment">//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
+<a name="l00021"></a>00021 <span class="comment">//   GNU Lesser General Public License for more details.</span>
+<a name="l00022"></a>00022 <span class="comment">//</span>
+<a name="l00023"></a>00023 <span class="comment">//  =================================================================</span>
+<a name="l00024"></a>00024 <span class="comment">//</span>
+<a name="l00025"></a>00025 <span class="comment">//    18.09.13   &lt;--  Date of Last Modification.</span>
+<a name="l00026"></a>00026 <span class="comment">//                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
+<a name="l00027"></a>00027 <span class="comment">//  -----------------------------------------------------------------</span>
+<a name="l00028"></a>00028 <span class="comment">//</span>
+<a name="l00029"></a>00029 <span class="comment">//  **** Module  :  ccp4srs_atom  &lt;interface&gt;</span>
+<a name="l00030"></a>00030 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00031"></a>00031 <span class="comment">//  **** Classes :  ccp4srs::Atom  - atom description class</span>
+<a name="l00032"></a>00032 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00033"></a>00033 <span class="comment">//</span>
+<a name="l00034"></a>00034 <span class="comment">//  (C) E. Krissinel 2010-2013</span>
+<a name="l00035"></a>00035 <span class="comment">//</span>
+<a name="l00036"></a>00036 <span class="comment">//  =================================================================</span>
+<a name="l00037"></a>00037 <span class="comment">//</span>
+<a name="l00038"></a>00038 
+<a name="l00039"></a>00039 <span class="preprocessor">#ifndef CCP4SRS_ATOM_H</span>
+<a name="l00040"></a>00040 <span class="preprocessor"></span><span class="preprocessor">#define CCP4SRS_ATOM_H</span>
+<a name="l00041"></a>00041 <span class="preprocessor"></span>
+<a name="l00042"></a>00042 <span class="preprocessor">#include &quot;<a class="code" href="ccp4srs__container_8h.html">ccp4srs_container.h</a>&quot;</span>
+<a name="l00043"></a>00043 <span class="preprocessor">#include &quot;<a class="code" href="memio___8h.html">memio_.h</a>&quot;</span>
+<a name="l00044"></a>00044 
+<a name="l00045"></a>00045 <span class="preprocessor">#include &quot;mmdb/mmdb_atom.h&quot;</span>
+<a name="l00046"></a>00046 <span class="preprocessor">#include &quot;mmdb/mmdb_mmcif_.h&quot;</span>
+<a name="l00047"></a>00047 <span class="preprocessor">#include &quot;mmdb/mmdb_defs.h&quot;</span>
+<a name="l00048"></a>00048 
+<a name="l00049"></a>00049 <span class="keyword">namespace </span>ccp4srs  {
+<a name="l00050"></a>00050 
+<a name="l00051"></a>00051   <a class="code" href="namespaceccp4srs.html#afbb5df60616f08fcf36926a3585c185f">DefineClass</a>(Atom);
+<a name="l00052"></a>00052 
+<a name="l00053"></a><a class="code" href="classccp4srs_1_1_atom.html">00053</a>   <span class="keyword">class </span><a class="code" href="classccp4srs_1_1_atom.html">Atom</a>  {
+<a name="l00054"></a>00054 
+<a name="l00055"></a>00055     <span class="keyword">public</span>:
+<a name="l00056"></a>00056       <a class="code" href="classccp4srs_1_1_atom.html#a66084d9a746b51608e8f0f8e28138e9d">Atom</a>();
+<a name="l00057"></a>00057       <span class="keyword">virtual</span> <a class="code" href="classccp4srs_1_1_atom.html#a27de39105bac03d49c949780edda55fd">~Atom</a>();
+<a name="l00058"></a>00058 
+<a name="l00059"></a>00059       <span class="comment">// function for searches in containers</span>
+<a name="l00060"></a><a class="code" href="classccp4srs_1_1_atom.html#a276b8b3e31130e6f0116af498e3a7766">00060</a>       <span class="keyword">inline</span> mmdb::cpstr      <a class="code" href="classccp4srs_1_1_atom.html#a276b8b3e31130e6f0116af498e3a7766">id</a>         () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_atom.html#a75168bfe9aa3e0e24ba5f81854323039" title="atom name">atomName</a>;     }
+<a name="l00061"></a>00061 
+<a name="l00062"></a><a class="code" href="classccp4srs_1_1_atom.html#ad8288e82eeab398bf90da3f35ebe15c5">00062</a>       <span class="keyword">inline</span> mmdb::cpstr      <a class="code" href="classccp4srs_1_1_atom.html#ad8288e82eeab398bf90da3f35ebe15c5">name</a>       () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_atom.html#a75168bfe9aa3e0e24ba5f81854323039" title="atom name">atomName</a>;     }
+<a name="l00063"></a><a class="code" href="classccp4srs_1_1_atom.html#af0bbf72624e0f7de9900ec931b673410">00063</a>       <span class="keyword">inline</span> mmdb::cpstr      <a class="code" href="classccp4srs_1_1_atom.html#af0bbf72624e0f7de9900ec931b673410">rcsb_name</a>  () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_atom.html#a198154f097c4f42a4ae1dd73d5394734" title="alternative atom name">rcsbAtomName</a>; }
+<a name="l00064"></a><a class="code" href="classccp4srs_1_1_atom.html#acda740ae967221e50f1d383ce70d58d9">00064</a>       <span class="keyword">inline</span> mmdb::cpstr      <a class="code" href="classccp4srs_1_1_atom.html#acda740ae967221e50f1d383ce70d58d9">old_name</a>   () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_atom.html#a45682b942f2f9262bc8fa1b5316a702b" title="old atom name">oldAtomName</a>;  }
+<a name="l00065"></a><a class="code" href="classccp4srs_1_1_atom.html#a78344a993072c3e8918a54c3259d55d8">00065</a>       <span class="keyword">inline</span> mmdb::cpstr      <a class="code" href="classccp4srs_1_1_atom.html#a78344a993072c3e8918a54c3259d55d8">element</a>    () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_atom.html#a621e19772fdb901353b6f60288afdb70" title="chemical element name">chemElement</a>;  }
+<a name="l00066"></a><a class="code" href="classccp4srs_1_1_atom.html#af9d89db887cdbfc5523a79ece1c1e117">00066</a>       <span class="keyword">inline</span> mmdb::cpstr      <a class="code" href="classccp4srs_1_1_atom.html#af9d89db887cdbfc5523a79ece1c1e117">energy_type</a>() { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_atom.html#ac429b2d0c02fe21432c4b651ad181fdb" title="energy type">energyType</a>;   }
+<a name="l00067"></a><a class="code" href="classccp4srs_1_1_atom.html#a9af114ebe576f3a0af965579100da463">00067</a>       <span class="keyword">inline</span> mmdb::realtype   <a class="code" href="classccp4srs_1_1_atom.html#a9af114ebe576f3a0af965579100da463">x</a>          () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_atom.html#a49ff7aadab557a536541009606a2db12">pdb_x</a>;        }
+<a name="l00068"></a><a class="code" href="classccp4srs_1_1_atom.html#a10fc0f0f21af2cd5311c7d957b59f52b">00068</a>       <span class="keyword">inline</span> mmdb::realtype   <a class="code" href="classccp4srs_1_1_atom.html#a10fc0f0f21af2cd5311c7d957b59f52b">y</a>          () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_atom.html#a901c15656be6fa36e191df297d25521d">pdb_y</a>;        }
+<a name="l00069"></a><a class="code" href="classccp4srs_1_1_atom.html#a9d07e03f19613858142105d9f287466e">00069</a>       <span class="keyword">inline</span> mmdb::realtype   <a class="code" href="classccp4srs_1_1_atom.html#a9d07e03f19613858142105d9f287466e">z</a>          () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_atom.html#ae33b2033023270f96202151aed27a710" title="pdb cartesian coordinates">pdb_z</a>;        }
+<a name="l00070"></a><a class="code" href="classccp4srs_1_1_atom.html#ac0fc0e47750a53f2be7ab60efc604d3b">00070</a>       <span class="keyword">inline</span> mmdb::realtype   <a class="code" href="classccp4srs_1_1_atom.html#ac0fc0e47750a53f2be7ab60efc604d3b">x_pdbx</a>     () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_atom.html#aec57c2566b6a42361a8215d7b15a7e29">pdbx_x</a>;       }
+<a name="l00071"></a><a class="code" href="classccp4srs_1_1_atom.html#a65cdadf3090a0fa712b6c47040adb578">00071</a>       <span class="keyword">inline</span> mmdb::realtype   <a class="code" href="classccp4srs_1_1_atom.html#a65cdadf3090a0fa712b6c47040adb578">y_pdbx</a>     () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_atom.html#a1d138de5fa3e222554a95b796c246d40">pdbx_y</a>;       }
+<a name="l00072"></a><a class="code" href="classccp4srs_1_1_atom.html#aed837e19a61e89ce1e1eda0c35f10b2e">00072</a>       <span class="keyword">inline</span> mmdb::realtype   <a class="code" href="classccp4srs_1_1_atom.html#aed837e19a61e89ce1e1eda0c35f10b2e">z_pdbx</a>     () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_atom.html#a424a6001bc93ea1c8256f9f1fb48a585" title="pdbx cartesian coordinates">pdbx_z</a>;       }
+<a name="l00073"></a><a class="code" href="classccp4srs_1_1_atom.html#a7f9331955d7f98b1d2e869f8741a2188">00073</a>       <span class="keyword">inline</span> mmdb::realtype   <a class="code" href="classccp4srs_1_1_atom.html#a7f9331955d7f98b1d2e869f8741a2188">x_mlib</a>     () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_atom.html#a641d281e9661ff8ca51bc768b2db5628">mlib_x</a>;       }
+<a name="l00074"></a><a class="code" href="classccp4srs_1_1_atom.html#acc50ad679a297a2626a6662cd0b61d3e">00074</a>       <span class="keyword">inline</span> mmdb::realtype   <a class="code" href="classccp4srs_1_1_atom.html#acc50ad679a297a2626a6662cd0b61d3e">y_mlib</a>     () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_atom.html#a92043cd1d43d17069c0c8f96020218b9">mlib_y</a>;       }
+<a name="l00075"></a><a class="code" href="classccp4srs_1_1_atom.html#a73c4871fccf3ce91502449de659f835a">00075</a>       <span class="keyword">inline</span> mmdb::realtype   <a class="code" href="classccp4srs_1_1_atom.html#a73c4871fccf3ce91502449de659f835a">z_mlib</a>     () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_atom.html#a0b6c2ba6990da454ea672a64e285653f" title="m-lib cartesian coordinates">mlib_z</a>;       }
+<a name="l00076"></a><a class="code" href="classccp4srs_1_1_atom.html#a199caf3c186d47d5ca6e13e235471a84">00076</a>       <span class="keyword">inline</span> mmdb::realtype   <a class="code" href="classccp4srs_1_1_atom.html#a199caf3c186d47d5ca6e13e235471a84">charge</a>     () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_atom.html#a0e7a7e76f9fba1a8277dae436f900821" title="partial charge">atomCharge</a>;   }
+<a name="l00077"></a><a class="code" href="classccp4srs_1_1_atom.html#a4c6e0a23b45563f10657d839d4479961">00077</a>       <span class="keyword">inline</span> mmdb::realtype   <a class="code" href="classccp4srs_1_1_atom.html#a4c6e0a23b45563f10657d839d4479961">weight</a>     () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_atom.html#ac470c0fd96b775b2b1d979c353449ee4" title="atomic weight (in a.u.)">atomWeight</a>;   }
+<a name="l00078"></a><a class="code" href="classccp4srs_1_1_atom.html#a2c283b644afb507ec45667611a685827">00078</a>       <span class="keyword">inline</span> mmdb::realtype   <a class="code" href="classccp4srs_1_1_atom.html#a2c283b644afb507ec45667611a685827">vdw_radius</a> () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_atom.html#a74216b4c442b716656e5a55e908cea11" title="Van-Der-Waals radius.">vdwRadius</a>;    }
+<a name="l00079"></a><a class="code" href="classccp4srs_1_1_atom.html#a2a2e411586e9a0be619a5ab5c634169d">00079</a>       <span class="keyword">inline</span> mmdb::realtype   <a class="code" href="classccp4srs_1_1_atom.html#a2a2e411586e9a0be619a5ab5c634169d">vdwh_radius</a>() { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_atom.html#afd0adf07dd4f24e87acb6977335ff2ba" title="Van-Der-Waals radius with hydrogen.">vdwhRadius</a>;   }
+<a name="l00080"></a><a class="code" href="classccp4srs_1_1_atom.html#a4cbbb8a7a4d9f69eca5caadfffa6c956">00080</a>       <span class="keyword">inline</span> mmdb::realtype   <a class="code" href="classccp4srs_1_1_atom.html#a4cbbb8a7a4d9f69eca5caadfffa6c956">ion_radius</a> () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_atom.html#aeb773fbdd5b04c0311969ad498622185" title="ion radius">ionRadius</a>;    }
+<a name="l00081"></a><a class="code" href="classccp4srs_1_1_atom.html#a86606a9614641a62a9b477c0b90c3a87">00081</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span>              <a class="code" href="classccp4srs_1_1_atom.html#a86606a9614641a62a9b477c0b90c3a87">valency</a>    () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_atom.html#aeaa06e2eac23c671be3f49c0caaa7d12" title="valency">atomValency</a>;  }
+<a name="l00082"></a><a class="code" href="classccp4srs_1_1_atom.html#a9ae7f9281596f659071394247d484ffb">00082</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span>              <a class="code" href="classccp4srs_1_1_atom.html#a9ae7f9281596f659071394247d484ffb">sp</a>         () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_atom.html#acb4d50d536b22d4dd3f971072354f784" title="sp-hybridization">atomSP</a>;       }
+<a name="l00083"></a>00083 
+<a name="l00084"></a><a class="code" href="classccp4srs_1_1_atom.html#a1dc09ecc6dee155b93e5c3431d4c548e">00084</a>       <span class="keyword">inline</span> <span class="keywordtype">char</span> <a class="code" href="classccp4srs_1_1_atom.html#a1dc09ecc6dee155b93e5c3431d4c548e">rcsb_chirality</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> <span class="keyword">property</span>[0];  }
+<a name="l00085"></a><a class="code" href="classccp4srs_1_1_atom.html#ac0274e4727f43cedf27380121215cbfa">00085</a>       <span class="keyword">inline</span> <span class="keywordtype">char</span> <a class="code" href="classccp4srs_1_1_atom.html#ac0274e4727f43cedf27380121215cbfa">ccp4_chirality</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> <span class="keyword">property</span>[1];  }
+<a name="l00086"></a>00086       <span class="keywordtype">char</span> <a class="code" href="classccp4srs_1_1_atom.html#a88df4aee528a9e551c126e9e8adab2f3">chirality</a>() <span class="keyword">const</span>; <span class="comment">// ccp4&#39;s; if not set then rcsb&#39;s</span>
+<a name="l00087"></a><a class="code" href="classccp4srs_1_1_atom.html#ac7f1f1f474b56199e70bb0dcd364bb4b">00087</a>       <span class="keyword">inline</span> <span class="keywordtype">char</span> <a class="code" href="classccp4srs_1_1_atom.html#ac7f1f1f474b56199e70bb0dcd364bb4b">leaving</a>       ()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> <span class="keyword">property</span>[2];  }
+<a name="l00088"></a><a class="code" href="classccp4srs_1_1_atom.html#a7da89fae287dcf0c0838108fd442ec53">00088</a>       <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="classccp4srs_1_1_atom.html#a7da89fae287dcf0c0838108fd442ec53">isLeaving</a>     ()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> (<a class="code" href="classccp4srs_1_1_atom.html#aa363093b5746f782b8c4e60a73ec6438">property</a>[2]==<span class="charliteral">&#39;Y&#39;</span>); }
+<a name="l00089"></a><a class="code" href="classccp4srs_1_1_atom.html#ab45d65bdba2966ce382687548921cd56">00089</a>       <span class="keyword">inline</span> <span class="keywordtype">char</span> <a class="code" href="classccp4srs_1_1_atom.html#ab45d65bdba2966ce382687548921cd56">hb_type</a>       ()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> <span class="keyword">property</span>[3];  }
+<a name="l00090"></a>00090 
+<a name="l00091"></a>00091 
+<a name="l00092"></a>00092       mmdb::cpstr <a class="code" href="classccp4srs_1_1_atom.html#a357cfea9384684a64bb3220d02b3afa7">name_pdb</a>      ( mmdb::pstr aname );  <span class="comment">// with significant spacing</span>
+<a name="l00093"></a>00093       mmdb::cpstr <a class="code" href="classccp4srs_1_1_atom.html#ace51a15043535b0fef9b2816dba48cdb">rcsb_name_pdb</a> ( mmdb::pstr aname );  <span class="comment">// with significant spacing</span>
+<a name="l00094"></a>00094       mmdb::cpstr <a class="code" href="classccp4srs_1_1_atom.html#abd73ea1b813b1321048f850b88914982">old_name_pdb</a>  ( mmdb::pstr aname );  <span class="comment">// with significant spacing</span>
+<a name="l00095"></a>00095       mmdb::cpstr <a class="code" href="classccp4srs_1_1_atom.html#a8d78d445f18a9f9e83d82f66e715b274">element_pdb</a>   ( mmdb::pstr elem  );  <span class="comment">// with significant spacing</span>
+<a name="l00096"></a>00096 
+<a name="l00097"></a>00097       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_atom.html#abab85177d8d15e5dfc51e12ed9af4d69">set_energy_type</a> ( mmdb::cpstr etype );
+<a name="l00098"></a>00098       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_atom.html#a67142fe2e03f768fea4dc3334826ef2e">set_old_name</a>    ( mmdb::cpstr <a class="code" href="classccp4srs_1_1_atom.html#ad8288e82eeab398bf90da3f35ebe15c5">name</a>  );
+<a name="l00099"></a><a class="code" href="classccp4srs_1_1_atom.html#af46102bc6356f36610eda68ced6e9202">00099</a>       <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_atom.html#af46102bc6356f36610eda68ced6e9202">set_rcsb_chirality</a> ( <span class="keywordtype">char</span> c  )  { <span class="keyword">property</span>[0] = c; }
+<a name="l00100"></a><a class="code" href="classccp4srs_1_1_atom.html#a4839e285360f50dbe4dbfff765ece82c">00100</a>       <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_atom.html#a4839e285360f50dbe4dbfff765ece82c">set_chirality</a>      ( <span class="keywordtype">char</span> c  )  { <span class="keyword">property</span>[1] = c; }
+<a name="l00101"></a><a class="code" href="classccp4srs_1_1_atom.html#a983a276a7821c272f3952f4edfb826c6">00101</a>       <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_atom.html#a983a276a7821c272f3952f4edfb826c6">set_hb_type</a>        ( <span class="keywordtype">char</span> h  )  { <span class="keyword">property</span>[3] = h; }
+<a name="l00102"></a>00102 
+<a name="l00103"></a><a class="code" href="classccp4srs_1_1_atom.html#aa2c293fa289d7a24bc8858578dd3357e">00103</a>       <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_atom.html#aa2c293fa289d7a24bc8858578dd3357e">set_vdw_radius</a>  ( mmdb::realtype r )  { <a class="code" href="classccp4srs_1_1_atom.html#a74216b4c442b716656e5a55e908cea11" title="Van-Der-Waals radius.">vdwRadius</a>   = r; }
+<a name="l00104"></a><a class="code" href="classccp4srs_1_1_atom.html#a8912626b88300dcb9e736cf1b4369f82">00104</a>       <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_atom.html#a8912626b88300dcb9e736cf1b4369f82">set_vdwh_radius</a> ( mmdb::realtype r )  { <a class="code" href="classccp4srs_1_1_atom.html#afd0adf07dd4f24e87acb6977335ff2ba" title="Van-Der-Waals radius with hydrogen.">vdwhRadius</a>  = r; }
+<a name="l00105"></a><a class="code" href="classccp4srs_1_1_atom.html#a132fd6895be46a1afa96bb0529c0a6ba">00105</a>       <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_atom.html#a132fd6895be46a1afa96bb0529c0a6ba">set_ion_radius</a>  ( mmdb::realtype r )  { <a class="code" href="classccp4srs_1_1_atom.html#aeb773fbdd5b04c0311969ad498622185" title="ion radius">ionRadius</a>   = r; }
+<a name="l00106"></a><a class="code" href="classccp4srs_1_1_atom.html#af50fcb98ad0f4a42768079e985adec5b">00106</a>       <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_atom.html#af50fcb98ad0f4a42768079e985adec5b">set_valency</a>     ( <span class="keywordtype">int</span> v      )  { <a class="code" href="classccp4srs_1_1_atom.html#aeaa06e2eac23c671be3f49c0caaa7d12" title="valency">atomValency</a> = v; }
+<a name="l00107"></a><a class="code" href="classccp4srs_1_1_atom.html#aa9fe3297f6d6de92f1520a6631361861">00107</a>       <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_atom.html#aa9fe3297f6d6de92f1520a6631361861">set_sp</a>          ( <span class="keywordtype">int</span> s      )  { <a class="code" href="classccp4srs_1_1_atom.html#acb4d50d536b22d4dd3f971072354f784" title="sp-hybridization">atomSP</a>      = s; }
+<a name="l00108"></a>00108 
+<a name="l00109"></a>00109       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_atom.html#a2528b66c2480aa6e3db8d6cfba0c4586">makeAtom</a> ( mmdb::RPAtom a );
+<a name="l00110"></a>00110       mmdb::PAtom <a class="code" href="classccp4srs_1_1_atom.html#a2528b66c2480aa6e3db8d6cfba0c4586">makeAtom</a>();
+<a name="l00111"></a>00111 
+<a name="l00112"></a>00112       <span class="keyword">static</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_atom.html#ac1bcbe4ebfbf35c7d0369d41afa07714">makeCIFTags</a> ( mmdb::mmcif::PLoop mmCIFLoop );
+<a name="l00113"></a>00113       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_atom.html#a0e4f39d4293b8e1907b0295e215c4230">readFromCIF_ccp4</a> ( mmdb::mmcif::PLoop mmCIFLoop, <span class="keywordtype">int</span> atomNo );
+<a name="l00114"></a>00114       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_atom.html#a12b7ff09ff7aa0cc7581a55e89ac9e0e">readFromCIF_rcsb</a> ( mmdb::mmcif::PLoop mmCIFLoop, <span class="keywordtype">int</span> atomNo );
+<a name="l00115"></a>00115       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_atom.html#a94f5f81532b98126f3383f29c077473c">readFromCIF</a>      ( mmdb::mmcif::PStruct mmCIFStruct );
+<a name="l00116"></a>00116       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_atom.html#ac83667146ec86aeab8fdcce133c2fea0">writeToCIF</a>       ( mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID );
+<a name="l00117"></a>00117 
+<a name="l00118"></a>00118       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_atom.html#a5aa8172f59efa4ac90359b2be7424d92">copy</a>  ( PAtom atom );
+<a name="l00119"></a>00119       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_atom.html#af28439c95edf554364f29e988b47acd1">merge</a> ( PAtom atom );
+<a name="l00120"></a>00120 
+<a name="l00121"></a>00121       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_atom.html#adaebb2b3897e6758befc7c76d77c0420">write_mem</a> ( PMemIO memIO, <span class="keywordtype">int</span> version );
+<a name="l00122"></a>00122       <span class="keywordtype">bool</span> <a class="code" href="classccp4srs_1_1_atom.html#a150503215d6820dda3726b107e8e1bc7">read_mem</a>  ( PMemIO memIO, <span class="keywordtype">int</span> version, <span class="keywordtype">bool</span> * Ok = NULL );
+<a name="l00123"></a>00123 
+<a name="l00124"></a>00124     <span class="keyword">protected</span>:
+<a name="l00125"></a><a class="code" href="classccp4srs_1_1_atom.html#a75168bfe9aa3e0e24ba5f81854323039">00125</a>       mmdb::AtomName    <a class="code" href="classccp4srs_1_1_atom.html#a75168bfe9aa3e0e24ba5f81854323039" title="atom name">atomName</a>;     
+<a name="l00126"></a><a class="code" href="classccp4srs_1_1_atom.html#a198154f097c4f42a4ae1dd73d5394734">00126</a>       mmdb::AtomName    <a class="code" href="classccp4srs_1_1_atom.html#a198154f097c4f42a4ae1dd73d5394734" title="alternative atom name">rcsbAtomName</a>; 
+<a name="l00127"></a><a class="code" href="classccp4srs_1_1_atom.html#a45682b942f2f9262bc8fa1b5316a702b">00127</a>       mmdb::AtomName    <a class="code" href="classccp4srs_1_1_atom.html#a45682b942f2f9262bc8fa1b5316a702b" title="old atom name">oldAtomName</a>;  
+<a name="l00128"></a><a class="code" href="classccp4srs_1_1_atom.html#a621e19772fdb901353b6f60288afdb70">00128</a>       mmdb::Element     <a class="code" href="classccp4srs_1_1_atom.html#a621e19772fdb901353b6f60288afdb70" title="chemical element name">chemElement</a>;  
+<a name="l00129"></a><a class="code" href="classccp4srs_1_1_atom.html#ac429b2d0c02fe21432c4b651ad181fdb">00129</a>       mmdb::EnergyType  <a class="code" href="classccp4srs_1_1_atom.html#ac429b2d0c02fe21432c4b651ad181fdb" title="energy type">energyType</a>;   
+<a name="l00130"></a><a class="code" href="classccp4srs_1_1_atom.html#a0b6c2ba6990da454ea672a64e285653f">00130</a>       mmdb::realtype    <a class="code" href="classccp4srs_1_1_atom.html#a641d281e9661ff8ca51bc768b2db5628">mlib_x</a>,<a class="code" href="classccp4srs_1_1_atom.html#a92043cd1d43d17069c0c8f96020218b9">mlib_y</a>,<a class="code" href="classccp4srs_1_1_atom.html#a0b6c2ba6990da454ea672a64e285653f" title="m-lib cartesian coordinates">mlib_z</a>; 
+<a name="l00131"></a><a class="code" href="classccp4srs_1_1_atom.html#ae33b2033023270f96202151aed27a710">00131</a>       mmdb::realtype    <a class="code" href="classccp4srs_1_1_atom.html#a49ff7aadab557a536541009606a2db12">pdb_x</a> ,<a class="code" href="classccp4srs_1_1_atom.html#a901c15656be6fa36e191df297d25521d">pdb_y</a> ,<a class="code" href="classccp4srs_1_1_atom.html#ae33b2033023270f96202151aed27a710" title="pdb cartesian coordinates">pdb_z</a> ; 
+<a name="l00132"></a><a class="code" href="classccp4srs_1_1_atom.html#a424a6001bc93ea1c8256f9f1fb48a585">00132</a>       mmdb::realtype    <a class="code" href="classccp4srs_1_1_atom.html#aec57c2566b6a42361a8215d7b15a7e29">pdbx_x</a>,<a class="code" href="classccp4srs_1_1_atom.html#a1d138de5fa3e222554a95b796c246d40">pdbx_y</a>,<a class="code" href="classccp4srs_1_1_atom.html#a424a6001bc93ea1c8256f9f1fb48a585" title="pdbx cartesian coordinates">pdbx_z</a>; 
+<a name="l00133"></a><a class="code" href="classccp4srs_1_1_atom.html#a0e7a7e76f9fba1a8277dae436f900821">00133</a>       mmdb::realtype    <a class="code" href="classccp4srs_1_1_atom.html#a0e7a7e76f9fba1a8277dae436f900821" title="partial charge">atomCharge</a>;   
+<a name="l00134"></a><a class="code" href="classccp4srs_1_1_atom.html#ac470c0fd96b775b2b1d979c353449ee4">00134</a>       mmdb::realtype    <a class="code" href="classccp4srs_1_1_atom.html#ac470c0fd96b775b2b1d979c353449ee4" title="atomic weight (in a.u.)">atomWeight</a>;   
+<a name="l00135"></a><a class="code" href="classccp4srs_1_1_atom.html#a74216b4c442b716656e5a55e908cea11">00135</a>       mmdb::realtype    <a class="code" href="classccp4srs_1_1_atom.html#a74216b4c442b716656e5a55e908cea11" title="Van-Der-Waals radius.">vdwRadius</a>;    
+<a name="l00136"></a><a class="code" href="classccp4srs_1_1_atom.html#afd0adf07dd4f24e87acb6977335ff2ba">00136</a>       mmdb::realtype    <a class="code" href="classccp4srs_1_1_atom.html#afd0adf07dd4f24e87acb6977335ff2ba" title="Van-Der-Waals radius with hydrogen.">vdwhRadius</a>;   
+<a name="l00137"></a><a class="code" href="classccp4srs_1_1_atom.html#aeb773fbdd5b04c0311969ad498622185">00137</a>       mmdb::realtype    <a class="code" href="classccp4srs_1_1_atom.html#aeb773fbdd5b04c0311969ad498622185" title="ion radius">ionRadius</a>;    
+<a name="l00138"></a><a class="code" href="classccp4srs_1_1_atom.html#aeaa06e2eac23c671be3f49c0caaa7d12">00138</a>       <span class="keywordtype">int</span>               <a class="code" href="classccp4srs_1_1_atom.html#aeaa06e2eac23c671be3f49c0caaa7d12" title="valency">atomValency</a>;  
+<a name="l00139"></a><a class="code" href="classccp4srs_1_1_atom.html#acb4d50d536b22d4dd3f971072354f784">00139</a>       <span class="keywordtype">int</span>               <a class="code" href="classccp4srs_1_1_atom.html#acb4d50d536b22d4dd3f971072354f784" title="sp-hybridization">atomSP</a>;       
+<a name="l00140"></a><a class="code" href="classccp4srs_1_1_atom.html#aa363093b5746f782b8c4e60a73ec6438">00140</a>       <span class="keywordtype">char</span>              <span class="keyword">property</span>[4];  
+<a name="l00141"></a>00141 
+<a name="l00142"></a>00142 
+<a name="l00143"></a>00143 
+<a name="l00144"></a>00144 
+<a name="l00145"></a>00145 
+<a name="l00146"></a>00146 
+<a name="l00147"></a>00147 
+<a name="l00148"></a>00148 
+<a name="l00149"></a>00149 
+<a name="l00150"></a>00150 
+<a name="l00151"></a>00151       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_atom.html#ab6a22850541822e026c9d6a241079fd6">Init</a>();
+<a name="l00152"></a>00152 
+<a name="l00153"></a>00153   };
+<a name="l00154"></a>00154 
+<a name="l00155"></a>00155   <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="namespaceccp4srs.html#adead0e638933d7d2949df9bb7b44f910">get_atom_from_cif</a> ( <span class="keywordtype">int</span> &amp; index, mmdb::mmcif::PLoop loop,
+<a name="l00156"></a>00156                                   mmdb::cpstr Tag, <span class="keywordtype">int</span> row,
+<a name="l00157"></a>00157                                   <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a> &amp; atoms,
+<a name="l00158"></a>00158                                   <span class="keywordtype">int</span> &amp; rc );
+<a name="l00159"></a>00159 
+<a name="l00160"></a>00160   <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="namespaceccp4srs.html#adead0e638933d7d2949df9bb7b44f910">get_atom_from_cif</a> ( <span class="keywordtype">int</span> &amp; index, mmdb::mmcif::PStruct mmCIFStruct,
+<a name="l00161"></a>00161                                   mmdb::cpstr Tag,
+<a name="l00162"></a>00162                                   <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a> &amp; atoms,
+<a name="l00163"></a>00163                                   <span class="keywordtype">int</span> &amp; rc );
+<a name="l00164"></a>00164 
+<a name="l00165"></a>00165   <span class="keyword">extern</span> <span class="keywordtype">void</span> <a class="code" href="namespaceccp4srs.html#af3c63726e6eb75b06c5b1c33a3acb608">add_atom_to_cif</a>  ( mmdb::mmcif::PLoop loop, <span class="keywordtype">int</span> atom_no,
+<a name="l00166"></a>00166                                  <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a> &amp; atoms );
+<a name="l00167"></a>00167 
+<a name="l00168"></a>00168 } <span class="comment">// namespace ccp4srs</span>
+<a name="l00169"></a>00169 
+<a name="l00170"></a>00170 
+<a name="l00171"></a>00171 <span class="preprocessor">#endif // CCP4SRS_ATOM_H</span>
+</pre></div></div>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
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+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__base_8cpp.html ccp4srs/doc-html/html/ccp4srs__base_8cpp.html
--- ccp4srs-old/doc-html/html/ccp4srs__base_8cpp.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__base_8cpp.html	2014-09-09 21:34:12.000000000 -0700
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+<h1>src/ccp4srs_base.cpp File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &lt;string.h&gt;</code><br/>
+<code>#include &lt;stdlib.h&gt;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__base_8h_source.html">ccp4srs_base.h</a>&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__defs_8h_source.html">ccp4srs_defs.h</a>&quot;</code><br/>
+<code>#include &quot;mmdb/mmdb_tables.h&quot;</code><br/>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+<tr><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a99ea9b07a217ceb6c0645faaea831c82">ccp4srs::_makeChirInd</a> (char chirality)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#adf196969f21a33865d5f6c0f2f32cb7f">ccp4srs::_findName</a> (mmdb::PAtomName Nams, mmdb::cpstr N, int len)</td></tr>
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+<div class="contents">
+<code>#include &quot;<a class="el" href="ccp4srs__index_8h_source.html">ccp4srs_index.h</a>&quot;</code><br/>
+<code>#include &quot;mmdb/mmdb_math_graph.h&quot;</code><br/>
+
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+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a4c159612746fffa9c8740ead5f891bb4">ccp4srs::DefineClass</a> (Base)</td></tr>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__base_8h_source.html ccp4srs/doc-html/html/ccp4srs__base_8h_source.html
--- ccp4srs-old/doc-html/html/ccp4srs__base_8h_source.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__base_8h_source.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,270 @@
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+<h1>src/ccp4srs_base.h</h1>  </div>
+</div>
+<div class="contents">
+<a href="ccp4srs__base_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">//  $Id: ccp4srs_base.h $</span>
+<a name="l00002"></a>00002 <span class="comment">//  =================================================================</span>
+<a name="l00003"></a>00003 <span class="comment">//</span>
+<a name="l00004"></a>00004 <span class="comment">//   CCP4 SRS Library: Storage, Retrieval and Search support for</span>
+<a name="l00005"></a>00005 <span class="comment">//   CCP4 ligand data.</span>
+<a name="l00006"></a>00006 <span class="comment">//</span>
+<a name="l00007"></a>00007 <span class="comment">//   Copyright (C) Eugene Krissinel 2010-2013.</span>
+<a name="l00008"></a>00008 <span class="comment">//</span>
+<a name="l00009"></a>00009 <span class="comment">//   This library is free software: you can redistribute it and/or</span>
+<a name="l00010"></a>00010 <span class="comment">//   modify it under the terms of the GNU Lesser General Public</span>
+<a name="l00011"></a>00011 <span class="comment">//   License version 3, modified in accordance with the provisions</span>
+<a name="l00012"></a>00012 <span class="comment">//   of the license to address the requirements of UK law.</span>
+<a name="l00013"></a>00013 <span class="comment">//</span>
+<a name="l00014"></a>00014 <span class="comment">//   You should have received a copy of the modified GNU Lesser</span>
+<a name="l00015"></a>00015 <span class="comment">//   General Public License along with this library. If not, copies</span>
+<a name="l00016"></a>00016 <span class="comment">//   may be downloaded from http://www.ccp4.ac.uk/ccp4license.php</span>
+<a name="l00017"></a>00017 <span class="comment">//</span>
+<a name="l00018"></a>00018 <span class="comment">//   This program is distributed in the hope that it will be useful,</span>
+<a name="l00019"></a>00019 <span class="comment">//   but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
+<a name="l00020"></a>00020 <span class="comment">//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
+<a name="l00021"></a>00021 <span class="comment">//   GNU Lesser General Public License for more details.</span>
+<a name="l00022"></a>00022 <span class="comment">//</span>
+<a name="l00023"></a>00023 <span class="comment">//  =================================================================</span>
+<a name="l00024"></a>00024 <span class="comment">//</span>
+<a name="l00025"></a>00025 <span class="comment">//    18.09.13   &lt;--  Date of Last Modification.</span>
+<a name="l00026"></a>00026 <span class="comment">//                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
+<a name="l00027"></a>00027 <span class="comment">//  -----------------------------------------------------------------</span>
+<a name="l00028"></a>00028 <span class="comment">//</span>
+<a name="l00029"></a>00029 <span class="comment">//  **** Module  :  ccp4srs_base  &lt;interface&gt;</span>
+<a name="l00030"></a>00030 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00031"></a>00031 <span class="comment">//  **** Classes :  ccp4srs::Base - SRS base manager class</span>
+<a name="l00032"></a>00032 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00033"></a>00033 <span class="comment">//</span>
+<a name="l00034"></a>00034 <span class="comment">//  (C) E. Krissinel 2010-2013</span>
+<a name="l00035"></a>00035 <span class="comment">//</span>
+<a name="l00036"></a>00036 <span class="comment">//  =================================================================</span>
+<a name="l00037"></a>00037 <span class="comment">//</span>
+<a name="l00038"></a>00038 
+<a name="l00039"></a>00039 <span class="preprocessor">#ifndef CCP4SRS_BASE_H</span>
+<a name="l00040"></a>00040 <span class="preprocessor"></span><span class="preprocessor">#define CCP4SRS_BASE_H</span>
+<a name="l00041"></a>00041 <span class="preprocessor"></span>
+<a name="l00042"></a>00042 <span class="preprocessor">#include &quot;<a class="code" href="ccp4srs__index_8h.html">ccp4srs_index.h</a>&quot;</span>
+<a name="l00043"></a>00043 <span class="preprocessor">#include &quot;mmdb/mmdb_math_graph.h&quot;</span>
+<a name="l00044"></a>00044 
+<a name="l00045"></a>00045 <span class="keyword">namespace </span>ccp4srs  {
+<a name="l00046"></a>00046 
+<a name="l00047"></a>00047   <span class="comment">// ==================================================================</span>
+<a name="l00048"></a>00048 
+<a name="l00049"></a>00049   <a class="code" href="namespaceccp4srs.html#afbb5df60616f08fcf36926a3585c185f">DefineClass</a>(Base);
+<a name="l00050"></a>00050 
+<a name="l00051"></a><a class="code" href="classccp4srs_1_1_base.html">00051</a>   <span class="keyword">class </span><a class="code" href="classccp4srs_1_1_base.html">Base</a>  {
+<a name="l00052"></a>00052 
+<a name="l00053"></a>00053     <span class="keyword">public</span>:
+<a name="l00054"></a>00054 
+<a name="l00055"></a>00055       <a class="code" href="classccp4srs_1_1_base.html#a0c37b44fe77e9f171d5f40281a6e82ae" title="Constructor.">Base</a> ();  
+<a name="l00056"></a>00056       <a class="code" href="classccp4srs_1_1_base.html#a2c46b036cb9701ac6a2d22fcec3fbdcf" title="Destructor.">~Base</a>();  
+<a name="l00057"></a>00057 
+<a name="l00058"></a>00058       <span class="comment">//   LoadIndex() loads index of the structural database. &#39;srsPath&#39;</span>
+<a name="l00059"></a>00059       <span class="comment">// must point on the directory containing the database files.</span>
+<a name="l00060"></a>00060       <span class="comment">// The index must be loaded once before retrieving any</span>
+<a name="l00061"></a>00061       <span class="comment">// information from the database.</span>
+<a name="l00062"></a>00062       <span class="comment">//   LoadIndex() may return either CCP4SRS_Ok, CCP4SRS_CorruptIndex</span>
+<a name="l00063"></a>00063       <span class="comment">// or CCP4SRS_FileNotFound.</span>
+<a name="l00064"></a>00064       <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_base.html#ae95af9ff2fb5c9d0edb437be3bcbe016">loadIndex</a> ( mmdb::cpstr srsPath );
+<a name="l00065"></a>00065 
+<a name="l00066"></a>00066       <span class="comment">//   LoadStructure(..) reads structure from *.srs files and</span>
+<a name="l00067"></a>00067       <span class="comment">// stores it in RAM for faster access. There is no special</span>
+<a name="l00068"></a>00068       <span class="comment">// functions to access loaded structures, all requests to</span>
+<a name="l00069"></a>00069       <span class="comment">// *.sbase files and RAM-storage are dispatched automatically.</span>
+<a name="l00070"></a>00070       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_base.html#a663ef26d53b80f6c8b1f9c9cdeb70d2c">loadStructure</a>   ( mmdb::cpstr entryID );
+<a name="l00071"></a>00071 
+<a name="l00072"></a>00072       PIndex <a class="code" href="classccp4srs_1_1_base.html#affa058db2078bc7835e9c78ca3bdde81">getIndex</a> ( mmdb::cpstr entryID );
+<a name="l00073"></a>00073       PIndex <a class="code" href="classccp4srs_1_1_base.html#affa058db2078bc7835e9c78ca3bdde81">getIndex</a> ( <span class="keywordtype">int</span> n         );
+<a name="l00074"></a>00074 
+<a name="l00075"></a>00075       <span class="comment">//   UnloadStructure(..) deletes strtucture from RAM and releases</span>
+<a name="l00076"></a>00076       <span class="comment">// its memory. The structure is then accessible in the normal</span>
+<a name="l00077"></a>00077       <span class="comment">// way from *.srs files, which is slower.</span>
+<a name="l00078"></a>00078       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_base.html#a6d15803597f5a515c19848a5e8dbe164">unloadStructure</a> ( mmdb::cpstr entryID );
+<a name="l00079"></a>00079 
+<a name="l00080"></a>00080       <span class="comment">//   GetPath() returns full path to a file with file name FName</span>
+<a name="l00081"></a>00081       <span class="comment">// in the database directory.  Length of S should suffice for</span>
+<a name="l00082"></a>00082       <span class="comment">// accomodating the path. The function returns S.</span>
+<a name="l00083"></a>00083       <span class="comment">//   GetPath() will work only after loading the database index.</span>
+<a name="l00084"></a>00084       mmdb::pstr <a class="code" href="classccp4srs_1_1_base.html#ac5481a8eeeb26ead06d7df61f605dac9">getPath</a> ( mmdb::pstr &amp; S, mmdb::cpstr FName );
+<a name="l00085"></a>00085 
+<a name="l00086"></a>00086       <span class="comment">//   GetStructFile() creates and opens the database structure</span>
+<a name="l00087"></a>00087       <span class="comment">// file and returns its pointer. In the case of errors returns</span>
+<a name="l00088"></a>00088       <span class="comment">// NULL. Application is responsible for deleting this class.</span>
+<a name="l00089"></a>00089       mmdb::io::PFile <a class="code" href="classccp4srs_1_1_base.html#a03eac100b52d1f2d2d13981799f928bb">getStructFile</a>();
+<a name="l00090"></a>00090 
+<a name="l00091"></a>00091       <span class="comment">//   GetGraphFile() creates and opens the database graph</span>
+<a name="l00092"></a>00092       <span class="comment">// file and returns its pointer. In the case of errors returns</span>
+<a name="l00093"></a>00093       <span class="comment">// NULL. Application is responsible for deleting this class.</span>
+<a name="l00094"></a>00094       mmdb::io::PFile <a class="code" href="classccp4srs_1_1_base.html#a656b776b70ead2f8346b352b3bd1311e">getGraphFile</a>();
+<a name="l00095"></a>00095 
+<a name="l00096"></a>00096       <span class="comment">//   n_entries() returns number of entries in the database index.</span>
+<a name="l00097"></a><a class="code" href="classccp4srs_1_1_base.html#aeb551e05e822e5eb3673aba1fa85bda6">00097</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_base.html#aeb551e05e822e5eb3673aba1fa85bda6">n_entries</a>() { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_base.html#a863fd5090d78f3bada7f351dd2f33859">nEntries</a>; }
+<a name="l00098"></a>00098 
+<a name="l00099"></a>00099       <span class="comment">//   getEntryNo() returns position of the structure with</span>
+<a name="l00100"></a>00100       <span class="comment">// (3-letter) name &#39;name&#39; as found in the database index.</span>
+<a name="l00101"></a>00101       <span class="comment">//   Non-negative return means success, otherwise</span>
+<a name="l00102"></a>00102       <span class="comment">// CCP4SRS_EntryNotFound indicates that the requested structure</span>
+<a name="l00103"></a>00103       <span class="comment">// was not found in the database index.</span>
+<a name="l00104"></a>00104       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_base.html#a57b706684f3e84c741099ff904e01152">getEntryNo</a> ( mmdb::cpstr entryID );
+<a name="l00105"></a>00105 
+<a name="l00106"></a>00106       <span class="comment">//   getMonomer returns pointer to the monomer structure</span>
+<a name="l00107"></a>00107       <span class="comment">// identified by 3-letter entryID. If such structure is not</span>
+<a name="l00108"></a>00108       <span class="comment">// found, the function returns NULL.</span>
+<a name="l00109"></a>00109       <span class="comment">//   The function returns a pointer to a private copy of the</span>
+<a name="l00110"></a>00110       <span class="comment">// structure. Modifying it will not change data in the structural</span>
+<a name="l00111"></a>00111       <span class="comment">// database. The application is responsible for deallocating</span>
+<a name="l00112"></a>00112       <span class="comment">// the structure after use (simply use delete).</span>
+<a name="l00113"></a>00113       <span class="comment">//   See description of CCP4SRSMonomer for the explanation of</span>
+<a name="l00114"></a>00114       <span class="comment">// its fields.</span>
+<a name="l00115"></a>00115       PMonomer <a class="code" href="classccp4srs_1_1_base.html#a339033984c68dd221cd6db184b734694">getMonomer</a> ( mmdb::cpstr entryID );
+<a name="l00116"></a>00116 
+<a name="l00117"></a>00117       <span class="comment">//   Another form of getMonomer(..) uses an open structure</span>
+<a name="l00118"></a>00118       <span class="comment">// file, which allows to save on opening/closing file if</span>
+<a name="l00119"></a>00119       <span class="comment">// multiple access to SRS structures is required.</span>
+<a name="l00120"></a>00120       PMonomer <a class="code" href="classccp4srs_1_1_base.html#a339033984c68dd221cd6db184b734694">getMonomer</a> ( <span class="keywordtype">int</span> entryNo,  <span class="comment">// 0...nEntries-1</span>
+<a name="l00121"></a>00121                             mmdb::io::PFile structFile );
+<a name="l00122"></a>00122       PMonomer <a class="code" href="classccp4srs_1_1_base.html#a339033984c68dd221cd6db184b734694">getMonomer</a> ( mmdb::cpstr entryID,
+<a name="l00123"></a>00123                             mmdb::io::PFile structFile );
+<a name="l00124"></a>00124 
+<a name="l00125"></a>00125 
+<a name="l00131"></a>00131       <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_base.html#a646d2c4349be4a740f2121dfd2091150" title="Returns the number of atoms in the references monomer.">getNofAtoms</a> ( mmdb::cpstr entryID );
+<a name="l00132"></a>00132 
+<a name="l00138"></a>00138       <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_base.html#a646d2c4349be4a740f2121dfd2091150" title="Returns the number of atoms in the references monomer.">getNofAtoms</a> ( <span class="keywordtype">int</span> entryNo );
+<a name="l00139"></a>00139 
+<a name="l00146"></a>00146       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_base.html#a646d2c4349be4a740f2121dfd2091150" title="Returns the number of atoms in the references monomer.">getNofAtoms</a> ( <span class="keywordtype">int</span> entryNo, <span class="keywordtype">int</span> &amp; nNonHAtoms, <span class="keywordtype">int</span> &amp; nHAtoms );
+<a name="l00147"></a>00147 
+<a name="l00157"></a>00157       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_base.html#af9a1789b20b43e97a8eb6a56b4ef32c4" title="Returns atom names, total number of atoms and number of hydrogens (nH) for referenced monomer...">getAtNames</a> ( <span class="keywordtype">int</span>  entryNo, mmdb::PAtomName AtName,
+<a name="l00158"></a>00158                         <span class="keywordtype">int</span> &amp; nAtoms, <span class="keywordtype">int</span> &amp; nH );
+<a name="l00159"></a>00159 
+<a name="l00170"></a>00170       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_base.html#af9a1789b20b43e97a8eb6a56b4ef32c4" title="Returns atom names, total number of atoms and number of hydrogens (nH) for referenced monomer...">getAtNames</a>  ( mmdb::io::PFile structFile, <span class="keywordtype">int</span> entryNo,
+<a name="l00171"></a>00171                          mmdb::PAtomName  AtName, <span class="keywordtype">int</span> &amp; nAtoms, <span class="keywordtype">int</span> &amp; nH  );
+<a name="l00172"></a>00172 
+<a name="l00187"></a>00187       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_base.html#a7e47408dacc9bd80de046504e235cc06" title="Retrieves various atom properties for referenced structure.">getAtoms</a> ( mmdb::cpstr entryID,
+<a name="l00188"></a>00188                       <span class="keywordtype">int</span> &amp; nNonHAtoms, mmdb::PAtomName NonHAtName,
+<a name="l00189"></a>00189                       <span class="keywordtype">int</span> &amp; nHAtoms,    mmdb::PAtomName HAtName,
+<a name="l00190"></a>00190                       mmdb::ivector Hconnect, mmdb::ivector Elem,
+<a name="l00191"></a>00191                       mmdb::ivector Chiral );
+<a name="l00192"></a>00192 
+<a name="l00203"></a>00203       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_base.html#a8bb61486d7dd2df0566b8e3a1c7f1c89" title="Retrieves bonds for referenced structure.">getBonds</a> ( mmdb::cpstr   entryID,
+<a name="l00204"></a>00204                       mmdb::ivector nBonds, mmdb::imatrix bondPair,
+<a name="l00205"></a>00205                       <span class="keywordtype">int</span> &amp;   nAtoms, <span class="keywordtype">int</span> maxNAtoms,
+<a name="l00206"></a>00206                       <span class="keywordtype">int</span>     maxNBonds );
+<a name="l00207"></a>00207 
+<a name="l00208"></a>00208       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_base.html#a88c88924e247250d08cc4795b345c66a">getHetInfo</a> ( mmdb::cpstr       entryID,
+<a name="l00209"></a>00209                         mmdb::pstr        Formula,
+<a name="l00210"></a>00210                         mmdb::pstr        Hname,
+<a name="l00211"></a>00211                         mmdb::pstr        Hsynonym,
+<a name="l00212"></a>00212                         mmdb::pstr        Hcharge,
+<a name="l00213"></a>00213                         mmdb::PAtomName &amp; ClinkAtom,  <span class="comment">// will</span>
+<a name="l00214"></a>00214                         mmdb::PElement  &amp; ClinkEle,   <span class="comment">//   be</span>
+<a name="l00215"></a>00215                         mmdb::PAtomName &amp; SlinkAtom,  <span class="comment">//     allocated</span>
+<a name="l00216"></a>00216                         mmdb::PElement  &amp; SlinkEle,   <span class="comment">//       or NULL</span>
+<a name="l00217"></a>00217                         <span class="keywordtype">int</span>             &amp; nLeavingAtoms );
+<a name="l00218"></a>00218 
+<a name="l00219"></a>00219       <span class="comment">//   getGraph(..) retrieves data for chemical structure number</span>
+<a name="l00220"></a>00220       <span class="comment">// entryNo (as in Index) from graph file graphFile, then</span>
+<a name="l00221"></a>00221       <span class="comment">// allocates and builds the corresponding graph, which is</span>
+<a name="l00222"></a>00222       <span class="comment">// returned in G.</span>
+<a name="l00223"></a>00223       <span class="comment">//   If Hflag is set &gt;= 1, all hydrogens are removed from</span>
+<a name="l00224"></a>00224       <span class="comment">// the graph. If Hflag is set to 2, element types of atoms,</span>
+<a name="l00225"></a>00225       <span class="comment">// to which hydrogens are bonded, are modified with flag</span>
+<a name="l00226"></a>00226       <span class="comment">// HYDROGEN_BOND.</span>
+<a name="l00227"></a>00227       <span class="comment">//   Returns CCP4SRS_Ok in case of success. Other return code are</span>
+<a name="l00228"></a>00228       <span class="comment">// CCP4SRS_WrongIndex and CCP4SRS_ReadError.</span>
+<a name="l00229"></a>00229       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_base.html#a17b78139832b00d7025236171ab31b7e">getGraph</a> ( mmdb::io::PFile graphFile, mmdb::math::RPGraph G );
+<a name="l00230"></a>00230       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_base.html#a17b78139832b00d7025236171ab31b7e">getGraph</a> ( mmdb::io::PFile graphFile, <span class="keywordtype">int</span> entryNo,
+<a name="l00231"></a>00231                       mmdb::math::RPGraph G, <span class="keywordtype">int</span> Hflag );
+<a name="l00232"></a>00232       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_base.html#a17b78139832b00d7025236171ab31b7e">getGraph</a> ( mmdb::io::PFile graphFile, mmdb::math::RPGraph G,
+<a name="l00233"></a>00233                       <span class="keywordtype">int</span> Hflag );
+<a name="l00234"></a>00234       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_base.html#a17b78139832b00d7025236171ab31b7e">getGraph</a> ( <span class="keywordtype">int</span>    entryNo, mmdb::math::RPGraph G, <span class="keywordtype">int</span> Hflag );
+<a name="l00235"></a>00235       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_base.html#a17b78139832b00d7025236171ab31b7e">getGraph</a> ( mmdb::cpstr entryID, mmdb::math::RPGraph G,
+<a name="l00236"></a>00236                       <span class="keywordtype">int</span> Hflag );
+<a name="l00237"></a>00237 
+<a name="l00238"></a>00238 
+<a name="l00239"></a>00239     <span class="keyword">protected</span>:
+<a name="l00240"></a><a class="code" href="classccp4srs_1_1_base.html#adf128b2adae954f6b25463c70ede5a58">00240</a>       <a class="code" href="classccp4srs_1_1_mem_i_o.html">MemIO</a>      <a class="code" href="classccp4srs_1_1_base.html#adf128b2adae954f6b25463c70ede5a58">memIO</a>;
+<a name="l00241"></a><a class="code" href="classccp4srs_1_1_base.html#ada41928311fa3ba94bcb48a1ebf4b4df">00241</a>       PPIndex    <a class="code" href="classccp4srs_1_1_base.html#ada41928311fa3ba94bcb48a1ebf4b4df">index</a>;
+<a name="l00242"></a><a class="code" href="classccp4srs_1_1_base.html#af3caa0403ce8a1c4489948fa4fc62b0c">00242</a>       mmdb::pstr <a class="code" href="classccp4srs_1_1_base.html#af3caa0403ce8a1c4489948fa4fc62b0c">srsDir</a>;
+<a name="l00243"></a><a class="code" href="classccp4srs_1_1_base.html#ad18087156761086530c1f01f3078f869">00243</a>       <span class="keywordtype">int</span>        <a class="code" href="classccp4srs_1_1_base.html#ad18087156761086530c1f01f3078f869">srsVersion</a>;
+<a name="l00244"></a><a class="code" href="classccp4srs_1_1_base.html#a863fd5090d78f3bada7f351dd2f33859">00244</a>       <span class="keywordtype">int</span>        <a class="code" href="classccp4srs_1_1_base.html#a863fd5090d78f3bada7f351dd2f33859">nEntries</a>;
+<a name="l00245"></a>00245 
+<a name="l00246"></a>00246       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_base.html#a9fb463b8df4034fefb6e136ab56d135b">init_base</a> ();
+<a name="l00247"></a>00247       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_base.html#ab67f138edc7ae19791be69dde485c719">freeMemory</a>();
+<a name="l00248"></a>00248 
+<a name="l00249"></a>00249     <span class="keyword">private</span>:
+<a name="l00250"></a>00250       <span class="keywordtype">int</span> index_alloc;
+<a name="l00251"></a>00251 
+<a name="l00252"></a>00252   };
+<a name="l00253"></a>00253 
+<a name="l00254"></a>00254 } <span class="comment">// namespace ccp4srs</span>
+<a name="l00255"></a>00255 
+<a name="l00256"></a>00256 
+<a name="l00257"></a>00257 <span class="preprocessor">#endif // CCP4SRS_BASE_H</span>
+</pre></div></div>
+</div>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__bond_8cpp.html ccp4srs/doc-html/html/ccp4srs__bond_8cpp.html
--- ccp4srs-old/doc-html/html/ccp4srs__bond_8cpp.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__bond_8cpp.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,90 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<a href="#namespaces">Namespaces</a> &#124;
+<a href="#func-members">Functions</a>  </div>
+  <div class="headertitle">
+<h1>src/ccp4srs_bond.cpp File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &lt;string.h&gt;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__bond_8h_source.html">ccp4srs_bond.h</a>&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__types_8h_source.html">ccp4srs_types.h</a>&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__defs_8h_source.html">ccp4srs_defs.h</a>&quot;</code><br/>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+<tr><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a134be7dad55bde913e9bbb02825064e0">ccp4srs::get_bond_type_from_cif_ccp4</a> (int &amp;type, mmdb::mmcif::PLoop loop, mmdb::cpstr Tag, int row, int &amp;rc)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a2fc315dbfb7012f8e39ff3a2f440a5d6">ccp4srs::get_bond_type_from_cif_rcsb</a> (int &amp;type, mmdb::mmcif::PLoop loop, mmdb::cpstr Tag, int row, int &amp;rc)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a66b5a7cbf87409e898be86c84505275a">ccp4srs::get_bond_type_from_cif</a> (int &amp;type, mmdb::mmcif::PStruct mmCIFStruct, mmdb::cpstr Tag, int &amp;rc)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#aaf4dd7dc419cfe6ae4f5a162bf528bf3">ccp4srs::add_bond_type_to_cif</a> (mmdb::mmcif::PLoop loop, int type)</td></tr>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__bond_8h.html ccp4srs/doc-html/html/ccp4srs__bond_8h.html
--- ccp4srs-old/doc-html/html/ccp4srs__bond_8h.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__bond_8h.html	2014-09-09 21:34:12.000000000 -0700
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+<h1>src/ccp4srs_bond.h File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &quot;<a class="el" href="ccp4srs__atom_8h_source.html">ccp4srs_atom.h</a>&quot;</code><br/>
+
+<p><a href="ccp4srs__bond_8h_source.html">Go to the source code of this file.</a></p>
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+Classes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td></tr>
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+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
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+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a156f31d96da750c94e75880a12fd5523">ccp4srs::DefineClass</a> (Bond)</td></tr>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__bond_8h_source.html ccp4srs/doc-html/html/ccp4srs__bond_8h_source.html
--- ccp4srs-old/doc-html/html/ccp4srs__bond_8h_source.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__bond_8h_source.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,170 @@
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+<h1>src/ccp4srs_bond.h</h1>  </div>
+</div>
+<div class="contents">
+<a href="ccp4srs__bond_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">//  $Id: ccp4srs_bond.h $</span>
+<a name="l00002"></a>00002 <span class="comment">//  =================================================================</span>
+<a name="l00003"></a>00003 <span class="comment">//</span>
+<a name="l00004"></a>00004 <span class="comment">//   CCP4 SRS Library: Storage, Retrieval and Search support for</span>
+<a name="l00005"></a>00005 <span class="comment">//   CCP4 ligand data.</span>
+<a name="l00006"></a>00006 <span class="comment">//</span>
+<a name="l00007"></a>00007 <span class="comment">//   Copyright (C) Eugene Krissinel 2010-2013.</span>
+<a name="l00008"></a>00008 <span class="comment">//</span>
+<a name="l00009"></a>00009 <span class="comment">//   This library is free software: you can redistribute it and/or</span>
+<a name="l00010"></a>00010 <span class="comment">//   modify it under the terms of the GNU Lesser General Public</span>
+<a name="l00011"></a>00011 <span class="comment">//   License version 3, modified in accordance with the provisions</span>
+<a name="l00012"></a>00012 <span class="comment">//   of the license to address the requirements of UK law.</span>
+<a name="l00013"></a>00013 <span class="comment">//</span>
+<a name="l00014"></a>00014 <span class="comment">//   You should have received a copy of the modified GNU Lesser</span>
+<a name="l00015"></a>00015 <span class="comment">//   General Public License along with this library. If not, copies</span>
+<a name="l00016"></a>00016 <span class="comment">//   may be downloaded from http://www.ccp4.ac.uk/ccp4license.php</span>
+<a name="l00017"></a>00017 <span class="comment">//</span>
+<a name="l00018"></a>00018 <span class="comment">//   This program is distributed in the hope that it will be useful,</span>
+<a name="l00019"></a>00019 <span class="comment">//   but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
+<a name="l00020"></a>00020 <span class="comment">//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
+<a name="l00021"></a>00021 <span class="comment">//   GNU Lesser General Public License for more details.</span>
+<a name="l00022"></a>00022 <span class="comment">//</span>
+<a name="l00023"></a>00023 <span class="comment">//  =================================================================</span>
+<a name="l00024"></a>00024 <span class="comment">//</span>
+<a name="l00025"></a>00025 <span class="comment">//    18.09.13   &lt;--  Date of Last Modification.</span>
+<a name="l00026"></a>00026 <span class="comment">//                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
+<a name="l00027"></a>00027 <span class="comment">//  -----------------------------------------------------------------</span>
+<a name="l00028"></a>00028 <span class="comment">//</span>
+<a name="l00029"></a>00029 <span class="comment">//  **** Module  :  ccp4srs_bond  &lt;interface&gt;</span>
+<a name="l00030"></a>00030 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00031"></a>00031 <span class="comment">//  **** Classes :  ccp4srs::Bond  - atom description class</span>
+<a name="l00032"></a>00032 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00033"></a>00033 <span class="comment">//</span>
+<a name="l00034"></a>00034 <span class="comment">//  (C) E. Krissinel 2010-2013</span>
+<a name="l00035"></a>00035 <span class="comment">//</span>
+<a name="l00036"></a>00036 <span class="comment">//  =================================================================</span>
+<a name="l00037"></a>00037 <span class="comment">//</span>
+<a name="l00038"></a>00038 
+<a name="l00039"></a>00039 <span class="preprocessor">#ifndef CCP4SRS_BOND_H</span>
+<a name="l00040"></a>00040 <span class="preprocessor"></span><span class="preprocessor">#define CCP4SRS_BOND_H</span>
+<a name="l00041"></a>00041 <span class="preprocessor"></span>
+<a name="l00042"></a>00042 <span class="preprocessor">#include &quot;<a class="code" href="ccp4srs__atom_8h.html">ccp4srs_atom.h</a>&quot;</span>
+<a name="l00043"></a>00043 
+<a name="l00044"></a>00044 <span class="keyword">namespace </span>ccp4srs  {
+<a name="l00045"></a>00045 
+<a name="l00046"></a>00046   <a class="code" href="namespaceccp4srs.html#afbb5df60616f08fcf36926a3585c185f">DefineClass</a>(Bond);
+<a name="l00047"></a>00047 
+<a name="l00048"></a><a class="code" href="classccp4srs_1_1_bond.html">00048</a>   <span class="keyword">class </span><a class="code" href="classccp4srs_1_1_bond.html">Bond</a>  {
+<a name="l00049"></a>00049 
+<a name="l00050"></a>00050     <span class="keyword">public</span>:
+<a name="l00051"></a>00051 
+<a name="l00052"></a>00052       <span class="comment">//  bond orders</span>
+<a name="l00053"></a><a class="code" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795baf6c5cfdf98463c48cd5772a18e49ad6f">00053</a>       <span class="keyword">enum</span> {<a class="code" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba3a534360bb854109f0ad2d34f1858997">noOrder</a>,<a class="code" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba338d16bbed971e9a0c912ff78efed793">Single</a>,<a class="code" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba1511fd16010981add30c1e054980f193">Aromatic</a>,<a class="code" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba0311fe9d41fd3830910b1e4f93d9a83a">Double</a>,<a class="code" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795baf6c5cfdf98463c48cd5772a18e49ad6f">Triple</a>,<a class="code" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba3e459a041fa6b33d363df5a335413e13">Deloc</a>,<a class="code" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795babaf2bbca3b364f84e83bbc9927b45e39">Covalent</a>,<a class="code" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba1be67f1d82568ea8bb92f456440e7f01">Metal</a>};
+<a name="l00054"></a>00054 
+<a name="l00055"></a>00055       <a class="code" href="classccp4srs_1_1_bond.html#acd3c055b0b0827de95e44ca9a9ac972a">Bond</a>();
+<a name="l00056"></a>00056       <span class="keyword">virtual</span> <a class="code" href="classccp4srs_1_1_bond.html#a695a8236689b60df2ad108c7cc55eb1a">~Bond</a>();
+<a name="l00057"></a>00057 
+<a name="l00058"></a><a class="code" href="classccp4srs_1_1_bond.html#a6ec052956ddec875a707d7e375ce0748">00058</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span>      <a class="code" href="classccp4srs_1_1_bond.html#a6ec052956ddec875a707d7e375ce0748">atom1</a>     () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_bond.html#ad359689c475101246c6c3061d31c2541">atom_1</a>;          }
+<a name="l00059"></a><a class="code" href="classccp4srs_1_1_bond.html#a364bc6a611e192c07d0bf5236a3503b9">00059</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span>      <a class="code" href="classccp4srs_1_1_bond.html#a364bc6a611e192c07d0bf5236a3503b9">atom2</a>     () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_bond.html#a277aee984c745dcdfd338f19e7df1e48" title="ordinal numbers of bonded atoms [0,1,.">atom_2</a>;          }
+<a name="l00060"></a><a class="code" href="classccp4srs_1_1_bond.html#ae18a9e08399e96910028f01a376d41f0">00060</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span>      <a class="code" href="classccp4srs_1_1_bond.html#ae18a9e08399e96910028f01a376d41f0">order</a>     () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_bond.html#ac6365bacbc07dd7cf914b6c7ad6cd5d7" title="bond order">bond_order</a>;      }
+<a name="l00061"></a><a class="code" href="classccp4srs_1_1_bond.html#a3ebb971fa0af7886f076da460b4875e9">00061</a>       <span class="keyword">inline</span> mmdb::realtype <a class="code" href="classccp4srs_1_1_bond.html#a3ebb971fa0af7886f076da460b4875e9">length</a>    () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_bond.html#a43513fb523b43f7f5f407a0bae151a95">bond_length</a>;     }
+<a name="l00062"></a><a class="code" href="classccp4srs_1_1_bond.html#a28f3638c15b007dddaab637362635009">00062</a>       <span class="keyword">inline</span> mmdb::realtype <a class="code" href="classccp4srs_1_1_bond.html#a28f3638c15b007dddaab637362635009">length_esd</a>() { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_bond.html#af438937a89d3cb3c7f2342ca6f38301c">bond_length_esd</a>; }
+<a name="l00063"></a>00063 
+<a name="l00064"></a>00064       <span class="keyword">static</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_bond.html#a781542dae98140ea687a5d83a3e02e8e">makeCIFTags</a> ( mmdb::mmcif::PLoop mmCIFLoop );
+<a name="l00065"></a>00065       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_bond.html#ac6a267f1cb4e7553d746537cf36e5ea3">readFromCIF_ccp4</a> ( mmdb::mmcif::PLoop mmCIFLoop, <span class="keywordtype">int</span> bondNo,
+<a name="l00066"></a>00066                               <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a> &amp; atoms );
+<a name="l00067"></a>00067       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_bond.html#a54c6291defa953cc5f5750b0f116719c">readFromCIF_rcsb</a> ( mmdb::mmcif::PLoop mmCIFLoop, <span class="keywordtype">int</span> bondNo,
+<a name="l00068"></a>00068                               <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a> &amp; atoms );
+<a name="l00069"></a>00069       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_bond.html#a24976c4962050d858ca00fa6f72684e2">readFromCIF</a> ( mmdb::mmcif::PStruct mmCIFStruct,
+<a name="l00070"></a>00070                          <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a> &amp; atoms );
+<a name="l00071"></a>00071       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_bond.html#a89214f5f730f603bdd8dacea6317428f">writeToCIF</a>  ( mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID,
+<a name="l00072"></a>00072                          <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a> &amp; atoms );
+<a name="l00073"></a>00073 
+<a name="l00074"></a>00074       <span class="keywordtype">bool</span> <a class="code" href="classccp4srs_1_1_bond.html#acefa794143d2ab128897441895cdf562">compare</a> ( <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a> &amp; atoms, PBond bond,
+<a name="l00075"></a>00075                      <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a> &amp; bond_atoms );
+<a name="l00076"></a>00076 
+<a name="l00077"></a>00077       <span class="keywordtype">bool</span> <a class="code" href="classccp4srs_1_1_bond.html#a4bb135bfcd9ee6078a2770fe9f15319c">copy</a>    ( <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a> &amp; atoms, PBond bond,
+<a name="l00078"></a>00078                      <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a> &amp; bond_atoms );
+<a name="l00079"></a>00079 
+<a name="l00080"></a>00080       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_bond.html#aa44d448aa0181e6d51048beda35052f4">write_mem</a> ( PMemIO memIO, <span class="keywordtype">int</span> version );
+<a name="l00081"></a>00081       <span class="keywordtype">bool</span> <a class="code" href="classccp4srs_1_1_bond.html#a47ad8a18d4c0363dc1f04f3cfbc670ec">read_mem</a>  ( PMemIO memIO, <span class="keywordtype">int</span> version,
+<a name="l00082"></a>00082                           <span class="keywordtype">bool</span> * Ok = NULL );
+<a name="l00083"></a>00083 
+<a name="l00084"></a>00084       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_bond.html#a4bb135bfcd9ee6078a2770fe9f15319c">copy</a>  ( PBond bond, mmdb::ivector anmatch=NULL );
+<a name="l00085"></a>00085 
+<a name="l00086"></a>00086     <span class="keyword">protected</span>:
+<a name="l00087"></a><a class="code" href="classccp4srs_1_1_bond.html#a277aee984c745dcdfd338f19e7df1e48">00087</a>       <span class="keywordtype">int</span>            <a class="code" href="classccp4srs_1_1_bond.html#ad359689c475101246c6c3061d31c2541">atom_1</a>,<a class="code" href="classccp4srs_1_1_bond.html#a277aee984c745dcdfd338f19e7df1e48" title="ordinal numbers of bonded atoms [0,1,.">atom_2</a>;   
+<a name="l00088"></a><a class="code" href="classccp4srs_1_1_bond.html#ac6365bacbc07dd7cf914b6c7ad6cd5d7">00088</a>       <span class="keywordtype">int</span>            <a class="code" href="classccp4srs_1_1_bond.html#ac6365bacbc07dd7cf914b6c7ad6cd5d7" title="bond order">bond_order</a>;      
+<a name="l00089"></a><a class="code" href="classccp4srs_1_1_bond.html#a43513fb523b43f7f5f407a0bae151a95">00089</a>       mmdb::realtype <a class="code" href="classccp4srs_1_1_bond.html#a43513fb523b43f7f5f407a0bae151a95">bond_length</a>;     
+<a name="l00090"></a>00090 
+<a name="l00091"></a><a class="code" href="classccp4srs_1_1_bond.html#af438937a89d3cb3c7f2342ca6f38301c">00091</a>       mmdb::realtype <a class="code" href="classccp4srs_1_1_bond.html#af438937a89d3cb3c7f2342ca6f38301c">bond_length_esd</a>; 
+<a name="l00092"></a>00092 
+<a name="l00093"></a>00093 
+<a name="l00094"></a>00094   };
+<a name="l00095"></a>00095 
+<a name="l00096"></a>00096 }  <span class="comment">// namespace ccp4srs</span>
+<a name="l00097"></a>00097 
+<a name="l00098"></a>00098 <span class="preprocessor">#endif // CCP4SRS_BOND_H</span>
+</pre></div></div>
+</div>
+<!--- window showing the filter options -->
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__chem_8cpp.html ccp4srs/doc-html/html/ccp4srs__chem_8cpp.html
--- ccp4srs-old/doc-html/html/ccp4srs__chem_8cpp.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__chem_8cpp.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,86 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/ccp4srs_chem.cpp File Reference</title>
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+<a href="#namespaces">Namespaces</a> &#124;
+<a href="#func-members">Functions</a>  </div>
+  <div class="headertitle">
+<h1>src/ccp4srs_chem.cpp File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &lt;string.h&gt;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__chem_8h_source.html">ccp4srs_chem.h</a>&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__defs_8h_source.html">ccp4srs_defs.h</a>&quot;</code><br/>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+<tr><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a50bab1a74a6f5ebde0253478a4964b24">ccp4srs::_addAtomPair</a> (mmdb::PAtom a1, mmdb::PAtom a2, PAtomPair &amp;Pair, int &amp;nPairs, int &amp;nPAlloc)</td></tr>
+</table>
+</div>
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+<a href="http://www.doxygen.org/index.html">
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+</html>
diff -ruN ccp4srs-old/doc-html/html/ccp4srs__chem_8h.html ccp4srs/doc-html/html/ccp4srs__chem_8h.html
--- ccp4srs-old/doc-html/html/ccp4srs__chem_8h.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__chem_8h.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,91 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/ccp4srs_chem.h File Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
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+<body onload='searchBox.OnSelectItem(0);'>
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+var searchBox = new SearchBox("searchBox", "search",false,'Search');
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+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
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+<a href="#nested-classes">Classes</a> &#124;
+<a href="#namespaces">Namespaces</a> &#124;
+<a href="#func-members">Functions</a>  </div>
+  <div class="headertitle">
+<h1>src/ccp4srs_chem.h File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &quot;<a class="el" href="ccp4srs__base_8h_source.html">ccp4srs_base.h</a>&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__types_8h_source.html">ccp4srs_types.h</a>&quot;</code><br/>
+
+<p><a href="ccp4srs__chem_8h_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="nested-classes"></a>
+Classes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td></tr>
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+<tr><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#abe82012e7a8178ae1069f381769da72d">ccp4srs::DefineClass</a> (Chem)</td></tr>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__chem_8h_source.html ccp4srs/doc-html/html/ccp4srs__chem_8h_source.html
--- ccp4srs-old/doc-html/html/ccp4srs__chem_8h_source.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__chem_8h_source.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,259 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/ccp4srs_chem.h Source File</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
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+      <li><a href="files.html"><span>File&#160;List</span></a></li>
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+    </ul>
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+<div class="header">
+  <div class="headertitle">
+<h1>src/ccp4srs_chem.h</h1>  </div>
+</div>
+<div class="contents">
+<a href="ccp4srs__chem_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">//  $Id: ccp4srs_chem.h $</span>
+<a name="l00002"></a>00002 <span class="comment">//  =================================================================</span>
+<a name="l00003"></a>00003 <span class="comment">//</span>
+<a name="l00004"></a>00004 <span class="comment">//   CCP4 SRS Library: Storage, Retrieval and Search support for</span>
+<a name="l00005"></a>00005 <span class="comment">//   CCP4 ligand data.</span>
+<a name="l00006"></a>00006 <span class="comment">//</span>
+<a name="l00007"></a>00007 <span class="comment">//   Copyright (C) Eugene Krissinel 2010-2013.</span>
+<a name="l00008"></a>00008 <span class="comment">//</span>
+<a name="l00009"></a>00009 <span class="comment">//   This library is free software: you can redistribute it and/or</span>
+<a name="l00010"></a>00010 <span class="comment">//   modify it under the terms of the GNU Lesser General Public</span>
+<a name="l00011"></a>00011 <span class="comment">//   License version 3, modified in accordance with the provisions</span>
+<a name="l00012"></a>00012 <span class="comment">//   of the license to address the requirements of UK law.</span>
+<a name="l00013"></a>00013 <span class="comment">//</span>
+<a name="l00014"></a>00014 <span class="comment">//   You should have received a copy of the modified GNU Lesser</span>
+<a name="l00015"></a>00015 <span class="comment">//   General Public License along with this library. If not, copies</span>
+<a name="l00016"></a>00016 <span class="comment">//   may be downloaded from http://www.ccp4.ac.uk/ccp4license.php</span>
+<a name="l00017"></a>00017 <span class="comment">//</span>
+<a name="l00018"></a>00018 <span class="comment">//   This program is distributed in the hope that it will be useful,</span>
+<a name="l00019"></a>00019 <span class="comment">//   but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
+<a name="l00020"></a>00020 <span class="comment">//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
+<a name="l00021"></a>00021 <span class="comment">//   GNU Lesser General Public License for more details.</span>
+<a name="l00022"></a>00022 <span class="comment">//</span>
+<a name="l00023"></a>00023 <span class="comment">//  =================================================================</span>
+<a name="l00024"></a>00024 <span class="comment">//</span>
+<a name="l00025"></a>00025 <span class="comment">//    18.09.13   &lt;--  Date of Last Modification.</span>
+<a name="l00026"></a>00026 <span class="comment">//                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
+<a name="l00027"></a>00027 <span class="comment">//  -----------------------------------------------------------------</span>
+<a name="l00028"></a>00028 <span class="comment">//</span>
+<a name="l00029"></a>00029 <span class="comment">//  **** Module  :  ccp4srs_chem  &lt;interface&gt;</span>
+<a name="l00030"></a>00030 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00031"></a>00031 <span class="comment">//  **** Classes :  ccp4srs::Chem - SRS chemistry manager class</span>
+<a name="l00032"></a>00032 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00033"></a>00033 <span class="comment">//</span>
+<a name="l00034"></a>00034 <span class="comment">//  (C) E. Krissinel 2010-2013</span>
+<a name="l00035"></a>00035 <span class="comment">//</span>
+<a name="l00036"></a>00036 <span class="comment">//  =================================================================</span>
+<a name="l00037"></a>00037 <span class="comment">//</span>
+<a name="l00038"></a>00038 
+<a name="l00039"></a>00039 <span class="preprocessor">#ifndef CCP4SRS_CHEM_H</span>
+<a name="l00040"></a>00040 <span class="preprocessor"></span><span class="preprocessor">#define CCP4SRS_CHEM_H</span>
+<a name="l00041"></a>00041 <span class="preprocessor"></span>
+<a name="l00042"></a>00042 <span class="preprocessor">#include &quot;<a class="code" href="ccp4srs__base_8h.html">ccp4srs_base.h</a>&quot;</span>
+<a name="l00043"></a>00043 <span class="preprocessor">#include &quot;<a class="code" href="ccp4srs__types_8h.html">ccp4srs_types.h</a>&quot;</span>
+<a name="l00044"></a>00044 
+<a name="l00045"></a>00045 <span class="keyword">namespace </span>ccp4srs  {
+<a name="l00046"></a>00046 
+<a name="l00047"></a>00047   <span class="comment">// ==================================================================</span>
+<a name="l00048"></a>00048 
+<a name="l00049"></a>00049   <a class="code" href="namespaceccp4srs.html#afbb5df60616f08fcf36926a3585c185f">DefineClass</a>(Chem);
+<a name="l00050"></a>00050 
+<a name="l00051"></a><a class="code" href="classccp4srs_1_1_chem.html">00051</a>   <span class="keyword">class </span><a class="code" href="classccp4srs_1_1_chem.html">Chem</a> : <span class="keyword">public</span> <a class="code" href="classccp4srs_1_1_base.html">Base</a>  {
+<a name="l00052"></a>00052 
+<a name="l00053"></a>00053     <span class="keyword">public</span>:
+<a name="l00054"></a>00054       <a class="code" href="classccp4srs_1_1_chem.html#a6ca2d1c22ede07e88978645ab6a5887e">Chem</a> ();
+<a name="l00055"></a>00055       <a class="code" href="classccp4srs_1_1_chem.html#a939cae4367e5e32664e60c725fabafbe">~Chem</a>();
+<a name="l00056"></a>00056 
+<a name="l00057"></a>00057       <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">CCP4SRS_RC</a> <a class="code" href="classccp4srs_1_1_chem.html#a301341ad4a91bf6cc4e7641efeb56309">getEnergyTypes</a> ( mmdb::PResidue  R,
+<a name="l00058"></a>00058                                   mmdb::io::PFile structFile );
+<a name="l00059"></a>00059       <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">CCP4SRS_RC</a> <a class="code" href="classccp4srs_1_1_chem.html#a301341ad4a91bf6cc4e7641efeb56309">getEnergyTypes</a> ( mmdb::PPResidue R, <span class="keywordtype">int</span> nRes,
+<a name="l00060"></a>00060                                   mmdb::io::PFile structFile );
+<a name="l00061"></a>00061       <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">CCP4SRS_RC</a> <a class="code" href="classccp4srs_1_1_chem.html#a301341ad4a91bf6cc4e7641efeb56309">getEnergyTypes</a> ( mmdb::PChain  chain,
+<a name="l00062"></a>00062                                   mmdb::io::PFile structFile );
+<a name="l00063"></a>00063       <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">CCP4SRS_RC</a> <a class="code" href="classccp4srs_1_1_chem.html#a301341ad4a91bf6cc4e7641efeb56309">getEnergyTypes</a> ( mmdb::PModel  model,
+<a name="l00064"></a>00064                                   mmdb::io::PFile structFile );
+<a name="l00065"></a>00065       <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">CCP4SRS_RC</a> <a class="code" href="classccp4srs_1_1_chem.html#a301341ad4a91bf6cc4e7641efeb56309">getEnergyTypes</a> ( mmdb::PManager MMDB,
+<a name="l00066"></a>00066                                   mmdb::io::PFile structFile );
+<a name="l00067"></a>00067 
+<a name="l00068"></a>00068       <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">CCP4SRS_RC</a> <a class="code" href="classccp4srs_1_1_chem.html#acada705ca803ac2b68bb2c787a83fcb1">addHydrogens</a>   ( mmdb::PResidue    R,
+<a name="l00069"></a>00069                                   mmdb::io::PFile structFile );
+<a name="l00070"></a>00070       <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">CCP4SRS_RC</a> <a class="code" href="classccp4srs_1_1_chem.html#acada705ca803ac2b68bb2c787a83fcb1">addHydrogens</a>   ( mmdb::PChain  chain,
+<a name="l00071"></a>00071                                   mmdb::io::PFile structFile );
+<a name="l00072"></a>00072       <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">CCP4SRS_RC</a> <a class="code" href="classccp4srs_1_1_chem.html#acada705ca803ac2b68bb2c787a83fcb1">addHydrogens</a>   ( mmdb::PModel  model,
+<a name="l00073"></a>00073                                   mmdb::io::PFile structFile );
+<a name="l00074"></a>00074       <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">CCP4SRS_RC</a> <a class="code" href="classccp4srs_1_1_chem.html#acada705ca803ac2b68bb2c787a83fcb1">addHydrogens</a>   ( mmdb::PManager MMDB,
+<a name="l00075"></a>00075                                   mmdb::io::PFile structFile );
+<a name="l00076"></a>00076 
+<a name="l00077"></a>00077 
+<a name="l00078"></a>00078       <span class="comment">//   MakeBonds(..) makes bonds between atoms in MMDB&#39;s residue R</span>
+<a name="l00079"></a>00079       <span class="comment">// from data found in SBase. Residue R must be associated with</span>
+<a name="l00080"></a>00080       <span class="comment">// coordinate hierarchy. Data is retrieved from SBase on the basis</span>
+<a name="l00081"></a>00081       <span class="comment">// of residue name only. In case of multiple conformations, if</span>
+<a name="l00082"></a>00082       <span class="comment">// altLoc:</span>
+<a name="l00083"></a>00083       <span class="comment">//    NULL  - the highest occupancy atom will be taken</span>
+<a name="l00084"></a>00084       <span class="comment">//            if all occupancies are equal then atom with</span>
+<a name="l00085"></a>00085       <span class="comment">//            first altLoc taken</span>
+<a name="l00086"></a>00086       <span class="comment">//    other - atoms with given altLoc are taken. If such</span>
+<a name="l00087"></a>00087       <span class="comment">//            altLoc is not found, the function does as if</span>
+<a name="l00088"></a>00088       <span class="comment">//            NULL value for altLoc is given.</span>
+<a name="l00089"></a>00089       <span class="comment">//   If selHandles is not NULL, the function also selects atoms</span>
+<a name="l00090"></a>00090       <span class="comment">// in the residue according to their hydrogen bond attributes.</span>
+<a name="l00091"></a>00091       <span class="comment">// This is a special option for hydrogen bond calculations</span>
+<a name="l00092"></a>00092       <span class="comment">//   If ignoreNegSigOcc is set True then the function will ignore</span>
+<a name="l00093"></a>00093       <span class="comment">// atoms with negative occupancy standard deviation. Such atoms</span>
+<a name="l00094"></a>00094       <span class="comment">// may be hydrogens added by CSBase0::AddHydrogen(..) function,</span>
+<a name="l00095"></a>00095       <span class="comment">// in general any atoms added by CSBAtom::MakeCAtom(..) function.</span>
+<a name="l00096"></a>00096       <span class="comment">// Added hydrogens may be ignored if MakeBonds is used in</span>
+<a name="l00097"></a>00097       <span class="comment">// CSbase::CalcHBonds(..) function.</span>
+<a name="l00098"></a>00098       <span class="comment">//   Return:</span>
+<a name="l00099"></a>00099       <span class="comment">//     SBASE_Ok             success</span>
+<a name="l00100"></a>00100       <span class="comment">//     SBASE_FileNotFound   non-initiated SBase</span>
+<a name="l00101"></a>00101       <span class="comment">//     SBASE_StructNotFound the residue&#39;s name is not found</span>
+<a name="l00102"></a>00102       <span class="comment">//                          in SBase</span>
+<a name="l00103"></a>00103       <span class="comment">//     SBASE_EmptyResidue   residue R does not contain atoms</span>
+<a name="l00104"></a>00104       <span class="comment">//     SBASE_NoAtomsFound   SBase entry does not contain atoms</span>
+<a name="l00105"></a>00105       <span class="comment">//     SBASE_BrokenBonds    some bonds could not be set up because</span>
+<a name="l00106"></a>00106       <span class="comment">//                          of missing atoms in R. This could be</span>
+<a name="l00107"></a>00107       <span class="comment">//                          a result of residue R named wrongly.</span>
+<a name="l00108"></a>00108       <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">CCP4SRS_RC</a> <a class="code" href="classccp4srs_1_1_chem.html#ad60a617bc151e054eb306e8c6bf592f4">makeBonds</a> ( mmdb::PResidue  R,
+<a name="l00109"></a>00109                              mmdb::pstr      altLoc,
+<a name="l00110"></a>00110                              mmdb::io::PFile structFile,
+<a name="l00111"></a>00111                              PDASelHnds      selHandles,
+<a name="l00112"></a>00112                              <span class="keywordtype">bool</span>            ignoreNegSigOcc );
+<a name="l00113"></a>00113 
+<a name="l00114"></a>00114       <span class="comment">//   CalcHBonds(..) calculates hydrogen bonds and salt bridges</span>
+<a name="l00115"></a>00115       <span class="comment">// between atoms of residues given in Res1[0..nres1-1] and</span>
+<a name="l00116"></a>00116       <span class="comment">// Res2[0..nres2-1]. H-bonds are returned in HBond[0..nHBonds-1]</span>
+<a name="l00117"></a>00117       <span class="comment">// and salt bridges are returned in SBridge[0..nSBridges-1].</span>
+<a name="l00118"></a>00118       <span class="comment">//</span>
+<a name="l00119"></a>00119       <span class="comment">//   On input:</span>
+<a name="l00120"></a>00120       <span class="comment">//     Res1, Res2         must belong to the same MMDB</span>
+<a name="l00121"></a>00121       <span class="comment">//     HBond, SBridge     should be set NULL, otherwise the</span>
+<a name="l00122"></a>00122       <span class="comment">//                        function attempts to deallocate them</span>
+<a name="l00123"></a>00123       <span class="comment">//     nHBonds, nSBridges ignored</span>
+<a name="l00124"></a>00124       <span class="comment">//     structFile         may be a pointer to open SBase stucture</span>
+<a name="l00125"></a>00125       <span class="comment">//                        file in order to save on file open</span>
+<a name="l00126"></a>00126       <span class="comment">//                        operation. If structFile is set NULL,</span>
+<a name="l00127"></a>00127       <span class="comment">//                        the function will open the SBase</span>
+<a name="l00128"></a>00128       <span class="comment">//                        structure file by itself</span>
+<a name="l00129"></a>00129       <span class="comment">//     altLoc             specifies the alternative location for</span>
+<a name="l00130"></a>00130       <span class="comment">//                        donors and acceptors.</span>
+<a name="l00131"></a>00131       <span class="comment">//                          altLoc==NULL  the highest occupancy</span>
+<a name="l00132"></a>00132       <span class="comment">//                                        atoms are taken. If all</span>
+<a name="l00133"></a>00133       <span class="comment">//                                        occupancies are equal</span>
+<a name="l00134"></a>00134       <span class="comment">//                                        equal then atom with</span>
+<a name="l00135"></a>00135       <span class="comment">//                                        first altLoc taken</span>
+<a name="l00136"></a>00136       <span class="comment">//                          altLoc!=NULL  atoms with given altLoc</span>
+<a name="l00137"></a>00137       <span class="comment">//                                        are taken. If such</span>
+<a name="l00138"></a>00138       <span class="comment">//                                        altLoc is not found,</span>
+<a name="l00139"></a>00139       <span class="comment">//                                        the function acts as</span>
+<a name="l00140"></a>00140       <span class="comment">//                                        if NULL value for altLoc</span>
+<a name="l00141"></a>00141       <span class="comment">//                                        were given.</span>
+<a name="l00142"></a>00142       <span class="comment">//     ignoreNegSigOcc    if it is set True, then the function</span>
+<a name="l00143"></a>00143       <span class="comment">//                        ignores atoms with negative occupancy</span>
+<a name="l00144"></a>00144       <span class="comment">//                        standard deviation. Such atoms may be</span>
+<a name="l00145"></a>00145       <span class="comment">//                        hydrogens added by addHydrogen(..)</span>
+<a name="l00146"></a>00146       <span class="comment">//                        function, or, in general, any atoms added</span>
+<a name="l00147"></a>00147       <span class="comment">//                        by CCP4SRSAtom::MakeCAtom(..) function.</span>
+<a name="l00148"></a>00148       <span class="comment">//                        Such added hydrogens are not guaranteed to</span>
+<a name="l00149"></a>00149       <span class="comment">//                        be in correct place, therefore the</span>
+<a name="l00150"></a>00150       <span class="comment">//                        function may mistake on some hydrogen</span>
+<a name="l00151"></a>00151       <span class="comment">//                        bonds if they are not neglected.</span>
+<a name="l00152"></a>00152       <span class="comment">//</span>
+<a name="l00153"></a>00153       <span class="comment">//   On output:</span>
+<a name="l00154"></a>00154       <span class="comment">//     Allocated arrays HBond[0..nHBonds-1] and</span>
+<a name="l00155"></a>00155       <span class="comment">//     SBridge[0..nSBridges-1]. If no bonds/bridges were found,</span>
+<a name="l00156"></a>00156       <span class="comment">//     the corresponding array is not allocated and set NULL.</span>
+<a name="l00157"></a>00157       <span class="comment">//     Application is responsible for deallocation of the arrays,</span>
+<a name="l00158"></a>00158       <span class="comment">//     when not needed, using statements</span>
+<a name="l00159"></a>00159       <span class="comment">//       if (HBond)    delete[] HBond;</span>
+<a name="l00160"></a>00160       <span class="comment">//       if (SBridge)  delete[] SBridge;</span>
+<a name="l00161"></a>00161       <span class="comment">//     HBond[i].a1, SBridge[i].a1 always refer atom from Res1[],</span>
+<a name="l00162"></a>00162       <span class="comment">//     and HBond[i].a2, SBridge[i].a2 always refer atom from</span>
+<a name="l00163"></a>00163       <span class="comment">//     Res2[].</span>
+<a name="l00164"></a>00164       <span class="comment">//</span>
+<a name="l00165"></a>00165       <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">CCP4SRS_RC</a> <a class="code" href="classccp4srs_1_1_chem.html#ab5d4ff0f43b6785dc2c3cec72d4b8eec">CalcHBonds</a> ( mmdb::PPResidue Res1, <span class="keywordtype">int</span> nres1,
+<a name="l00166"></a>00166                               mmdb::PPResidue Res2, <span class="keywordtype">int</span> nres2,
+<a name="l00167"></a>00167                               RPAtomPair     HBond, <span class="keywordtype">int</span> &amp; nHBonds,
+<a name="l00168"></a>00168                               RPAtomPair   SBridge, <span class="keywordtype">int</span> &amp; nSBridges,
+<a name="l00169"></a>00169                               mmdb::io::PFile structFile=NULL,
+<a name="l00170"></a>00170                               mmdb::pstr      altLoc=NULL,
+<a name="l00171"></a>00171                               <span class="keywordtype">bool</span> ignoreNegSigOcc=<span class="keyword">false</span> );
+<a name="l00172"></a>00172 
+<a name="l00173"></a>00173     <span class="keyword">protected</span>:
+<a name="l00174"></a>00174       <span class="comment">// Geometry parameters for H-bond calculations</span>
+<a name="l00175"></a><a class="code" href="classccp4srs_1_1_chem.html#a2e63b74dcf71dbf8583a64342de3848c">00175</a>       mmdb::realtype <a class="code" href="classccp4srs_1_1_chem.html#a2e63b74dcf71dbf8583a64342de3848c">minDAdist</a>,<a class="code" href="classccp4srs_1_1_chem.html#aeeb0e6bc6cc2e1a3f5ce78d59d8b496d">maxSBdist</a>,<a class="code" href="classccp4srs_1_1_chem.html#a6655092e23b55ff3d6465a60101c135d">maxDAdist</a>,<a class="code" href="classccp4srs_1_1_chem.html#ada14781ad5390841304d35f262705c57">maxHAdist2</a>;
+<a name="l00176"></a><a class="code" href="classccp4srs_1_1_chem.html#a71cea07257deb2795443e04e07ee4bed">00176</a>       mmdb::realtype <a class="code" href="classccp4srs_1_1_chem.html#a7408580f10d8868ae368f3faa1253577">maxDHAcos</a>,<a class="code" href="classccp4srs_1_1_chem.html#a71cea07257deb2795443e04e07ee4bed">maxHAAcos</a>,<a class="code" href="classccp4srs_1_1_chem.html#aa32277562470e13dfe292f01bc269c17">maxDAAcos</a>,<a class="code" href="classccp4srs_1_1_chem.html#aa5d2547bfa92f55c755aa57fce717a65">maxDDAcos</a>;
+<a name="l00177"></a>00177 
+<a name="l00178"></a>00178       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_chem.html#a7ed4ac373981270bc1af2b8cc99b461d">init_chem</a>();
+<a name="l00179"></a>00179 
+<a name="l00180"></a>00180     <span class="keyword">private</span>:
+<a name="l00181"></a>00181       <span class="keywordtype">int</span> index_alloc;
+<a name="l00182"></a>00182 
+<a name="l00183"></a>00183   };
+<a name="l00184"></a>00184 
+<a name="l00185"></a>00185 }  <span class="comment">// namespace ccp4srs</span>
+<a name="l00186"></a>00186 
+<a name="l00187"></a>00187 <span class="preprocessor">#endif // CCP4SRS_CHEM_H</span>
+</pre></div></div>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
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+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__chicenter_8cpp.html ccp4srs/doc-html/html/ccp4srs__chicenter_8cpp.html
--- ccp4srs-old/doc-html/html/ccp4srs__chicenter_8cpp.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__chicenter_8cpp.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,128 @@
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+<a href="#namespaces">Namespaces</a> &#124;
+<a href="#define-members">Defines</a>  </div>
+  <div class="headertitle">
+<h1>src/ccp4srs_chicenter.cpp File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &lt;string.h&gt;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__chicenter_8h_source.html">ccp4srs_chicenter.h</a>&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__defs_8h_source.html">ccp4srs_defs.h</a>&quot;</code><br/>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+<tr><td colspan="2"><h2><a name="define-members"></a>
+Defines</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__chicenter_8cpp.html#ab5d2d0dcd4a9adac0699b5e37132fcae">VOLUME_SIGN_POSITIVE</a>&#160;&#160;&#160;&quot;positiv&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__chicenter_8cpp.html#a5e50b082b9f721d74d142b1a564358c8">VOLUME_SIGN_NEGATIVE</a>&#160;&#160;&#160;&quot;negativ&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__chicenter_8cpp.html#a0876b7b066ef447a65ca374d8dc86417">VOLUME_SIGN_BOTH</a>&#160;&#160;&#160;&quot;both&quot;</td></tr>
+</table>
+<hr/><h2>Define Documentation</h2>
+<a class="anchor" id="a0876b7b066ef447a65ca374d8dc86417"></a><!-- doxytag: member="ccp4srs_chicenter.cpp::VOLUME_SIGN_BOTH" ref="a0876b7b066ef447a65ca374d8dc86417" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define VOLUME_SIGN_BOTH&#160;&#160;&#160;&quot;both&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a5e50b082b9f721d74d142b1a564358c8"></a><!-- doxytag: member="ccp4srs_chicenter.cpp::VOLUME_SIGN_NEGATIVE" ref="a5e50b082b9f721d74d142b1a564358c8" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define VOLUME_SIGN_NEGATIVE&#160;&#160;&#160;&quot;negativ&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ab5d2d0dcd4a9adac0699b5e37132fcae"></a><!-- doxytag: member="ccp4srs_chicenter.cpp::VOLUME_SIGN_POSITIVE" ref="ab5d2d0dcd4a9adac0699b5e37132fcae" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define VOLUME_SIGN_POSITIVE&#160;&#160;&#160;&quot;positiv&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__chicenter_8h.html ccp4srs/doc-html/html/ccp4srs__chicenter_8h.html
--- ccp4srs-old/doc-html/html/ccp4srs__chicenter_8h.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__chicenter_8h.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,94 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<a href="#typedef-members">Typedefs</a> &#124;
+<a href="#func-members">Functions</a>  </div>
+  <div class="headertitle">
+<h1>src/ccp4srs_chicenter.h File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &quot;<a class="el" href="ccp4srs__atom_8h_source.html">ccp4srs_atom.h</a>&quot;</code><br/>
+
+<p><a href="ccp4srs__chicenter_8h_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="nested-classes"></a>
+Classes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td></tr>
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+<tr><td colspan="2"><h2><a name="typedef-members"></a>
+Typedefs</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">typedef char&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#ae91f970060d687d02ccfb78cbd6222bb">ccp4srs::ChiCenterID</a> [20]</td></tr>
+<tr><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#aed1b87fee568c115c3bbdb07ad9a5bd7">ccp4srs::DefineClass</a> (ChiCenter)</td></tr>
+</table>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__chicenter_8h_source.html ccp4srs/doc-html/html/ccp4srs__chicenter_8h_source.html
--- ccp4srs-old/doc-html/html/ccp4srs__chicenter_8h_source.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__chicenter_8h_source.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,162 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<link href="search/search.css" rel="stylesheet" type="text/css"/>
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+      <li><a href="files.html"><span>File&#160;List</span></a></li>
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+<div class="header">
+  <div class="headertitle">
+<h1>src/ccp4srs_chicenter.h</h1>  </div>
+</div>
+<div class="contents">
+<a href="ccp4srs__chicenter_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">//  $Id: ccp4srs_chicenter.h $</span>
+<a name="l00002"></a>00002 <span class="comment">//  =================================================================</span>
+<a name="l00003"></a>00003 <span class="comment">//</span>
+<a name="l00004"></a>00004 <span class="comment">//   CCP4 SRS Library: Storage, Retrieval and Search support for</span>
+<a name="l00005"></a>00005 <span class="comment">//   CCP4 ligand data.</span>
+<a name="l00006"></a>00006 <span class="comment">//</span>
+<a name="l00007"></a>00007 <span class="comment">//   Copyright (C) Eugene Krissinel 2010-2013.</span>
+<a name="l00008"></a>00008 <span class="comment">//</span>
+<a name="l00009"></a>00009 <span class="comment">//   This library is free software: you can redistribute it and/or</span>
+<a name="l00010"></a>00010 <span class="comment">//   modify it under the terms of the GNU Lesser General Public</span>
+<a name="l00011"></a>00011 <span class="comment">//   License version 3, modified in accordance with the provisions</span>
+<a name="l00012"></a>00012 <span class="comment">//   of the license to address the requirements of UK law.</span>
+<a name="l00013"></a>00013 <span class="comment">//</span>
+<a name="l00014"></a>00014 <span class="comment">//   You should have received a copy of the modified GNU Lesser</span>
+<a name="l00015"></a>00015 <span class="comment">//   General Public License along with this library. If not, copies</span>
+<a name="l00016"></a>00016 <span class="comment">//   may be downloaded from http://www.ccp4.ac.uk/ccp4license.php</span>
+<a name="l00017"></a>00017 <span class="comment">//</span>
+<a name="l00018"></a>00018 <span class="comment">//   This program is distributed in the hope that it will be useful,</span>
+<a name="l00019"></a>00019 <span class="comment">//   but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
+<a name="l00020"></a>00020 <span class="comment">//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
+<a name="l00021"></a>00021 <span class="comment">//   GNU Lesser General Public License for more details.</span>
+<a name="l00022"></a>00022 <span class="comment">//</span>
+<a name="l00023"></a>00023 <span class="comment">//  =================================================================</span>
+<a name="l00024"></a>00024 <span class="comment">//</span>
+<a name="l00025"></a>00025 <span class="comment">//    18.09.13   &lt;--  Date of Last Modification.</span>
+<a name="l00026"></a>00026 <span class="comment">//                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
+<a name="l00027"></a>00027 <span class="comment">//  -----------------------------------------------------------------</span>
+<a name="l00028"></a>00028 <span class="comment">//</span>
+<a name="l00029"></a>00029 <span class="comment">//  **** Module  :  ccp4srs_chicenter  &lt;interface&gt;</span>
+<a name="l00030"></a>00030 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00031"></a>00031 <span class="comment">//  **** Classes :  ccp4srs::ChiCenter - chiral center class</span>
+<a name="l00032"></a>00032 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00033"></a>00033 <span class="comment">//</span>
+<a name="l00034"></a>00034 <span class="comment">//  (C) E. Krissinel 2010-2013</span>
+<a name="l00035"></a>00035 <span class="comment">//</span>
+<a name="l00036"></a>00036 <span class="comment">//  =================================================================</span>
+<a name="l00037"></a>00037 <span class="comment">//</span>
+<a name="l00038"></a>00038 
+<a name="l00039"></a>00039 <span class="preprocessor">#ifndef CCP4SRS_CHICENTER_H</span>
+<a name="l00040"></a>00040 <span class="preprocessor"></span><span class="preprocessor">#define CCP4SRS_CHICENTER_H</span>
+<a name="l00041"></a>00041 <span class="preprocessor"></span>
+<a name="l00042"></a>00042 <span class="preprocessor">#include &quot;<a class="code" href="ccp4srs__atom_8h.html">ccp4srs_atom.h</a>&quot;</span>
+<a name="l00043"></a>00043 
+<a name="l00044"></a>00044 <span class="keyword">namespace </span>ccp4srs  {
+<a name="l00045"></a>00045 
+<a name="l00046"></a>00046   <a class="code" href="namespaceccp4srs.html#afbb5df60616f08fcf36926a3585c185f">DefineClass</a>(ChiCenter);
+<a name="l00047"></a>00047 
+<a name="l00048"></a><a class="code" href="namespaceccp4srs.html#ae91f970060d687d02ccfb78cbd6222bb">00048</a>   <span class="keyword">typedef</span> <span class="keywordtype">char</span> <a class="code" href="namespaceccp4srs.html#ae91f970060d687d02ccfb78cbd6222bb">ChiCenterID</a>[20];
+<a name="l00049"></a>00049 
+<a name="l00050"></a><a class="code" href="classccp4srs_1_1_chi_center.html">00050</a>   <span class="keyword">class </span><a class="code" href="classccp4srs_1_1_chi_center.html">ChiCenter</a>  {
+<a name="l00051"></a>00051 
+<a name="l00052"></a>00052     <span class="comment">// Chiral center signs</span>
+<a name="l00053"></a>00053     <span class="keyword">enum</span>  {noSign,Positive,Negative,Both};
+<a name="l00054"></a>00054 
+<a name="l00055"></a>00055     <span class="keyword">public</span>:
+<a name="l00056"></a>00056       <a class="code" href="classccp4srs_1_1_chi_center.html#a536462552b25777be443867ec6a28b48">ChiCenter</a>();
+<a name="l00057"></a>00057       <span class="keyword">virtual</span> <a class="code" href="classccp4srs_1_1_chi_center.html#a051ae00e2cdb590a2dd7f4899c264cb9">~ChiCenter</a>();
+<a name="l00058"></a>00058 
+<a name="l00059"></a><a class="code" href="classccp4srs_1_1_chi_center.html#a9bd5958f4cb3519a6a745d1db16b135b">00059</a>       <span class="keyword">inline</span> mmdb::cpstr <a class="code" href="classccp4srs_1_1_chi_center.html#a9bd5958f4cb3519a6a745d1db16b135b">id</a>    () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_chi_center.html#ac2387dc7a46c0c4451bcd08e23b25ae5" title="chiral center id">chicenter_id</a>; }
+<a name="l00060"></a><a class="code" href="classccp4srs_1_1_chi_center.html#a0264f7a5c26c795bda84de7b233e70ab">00060</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span>         <a class="code" href="classccp4srs_1_1_chi_center.html#a0264f7a5c26c795bda84de7b233e70ab">center</a>() { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_chi_center.html#a5fe75db982419a5d7f3c3ff8b2e41f46" title="chiral center atom [0,1,...]">atom_center</a>;  }
+<a name="l00061"></a><a class="code" href="classccp4srs_1_1_chi_center.html#ae27490ac46e2f3904ee230fe0c5b80af">00061</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span>         <a class="code" href="classccp4srs_1_1_chi_center.html#ae27490ac46e2f3904ee230fe0c5b80af">atom1</a> () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_chi_center.html#a246c77c96df7921a1d1c989de4a50f8f">atom_1</a>;       }
+<a name="l00062"></a><a class="code" href="classccp4srs_1_1_chi_center.html#a5e1600b63a2e92494176dc328c6fc8a6">00062</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span>         <a class="code" href="classccp4srs_1_1_chi_center.html#a5e1600b63a2e92494176dc328c6fc8a6">atom2</a> () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_chi_center.html#aa80d6d7fbec0a8497b62af13b16e2a12" title="ordinal numbers of atoms that">atom_2</a>;       }
+<a name="l00063"></a><a class="code" href="classccp4srs_1_1_chi_center.html#ac668dea1c66f203a26e46a1c87b37760">00063</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span>         <a class="code" href="classccp4srs_1_1_chi_center.html#ac668dea1c66f203a26e46a1c87b37760">atom3</a> () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_chi_center.html#a2b249cab1cc7c2ea80ea9259914fcd34" title="form the center [0,1,...]">atom_3</a>;       }
+<a name="l00064"></a><a class="code" href="classccp4srs_1_1_chi_center.html#a17574c6830e27efde72575acdf154d80">00064</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span>         <a class="code" href="classccp4srs_1_1_chi_center.html#a17574c6830e27efde72575acdf154d80">sign</a>  () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_chi_center.html#a6fc568ab5bcd12bc56b58d6b9f2933a1" title="chirality">volume_sign</a>;  }
+<a name="l00065"></a>00065 
+<a name="l00066"></a>00066       <span class="keywordtype">char</span> <a class="code" href="classccp4srs_1_1_chi_center.html#a1aa5ee605cdc3756abcb075279eeb8af">get_chirality</a>();
+<a name="l00067"></a>00067 
+<a name="l00068"></a>00068       <span class="keyword">static</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_chi_center.html#a93d09528c86718358137aaf48c1a8ce1">makeCIFTags</a> ( mmdb::mmcif::PLoop mmCIFLoop );
+<a name="l00069"></a>00069       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_chi_center.html#a8c038c3d35ef4effbe5e02db4cdf9f88">readFromCIF</a> ( mmdb::mmcif::PLoop mmCIFLoop, <span class="keywordtype">int</span> chiNo,
+<a name="l00070"></a>00070                          <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a> &amp; atoms );
+<a name="l00071"></a>00071       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_chi_center.html#a04b85d396a4ebc8d5163d3184206329d">writeToCIF</a>  ( mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID,
+<a name="l00072"></a>00072                          <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a> &amp; atoms );
+<a name="l00073"></a>00073 
+<a name="l00074"></a>00074       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_chi_center.html#ac36306727683e319c2282b936bd11d37">write_mem</a> ( PMemIO memIO, <span class="keywordtype">int</span> version );
+<a name="l00075"></a>00075       <span class="keywordtype">bool</span> <a class="code" href="classccp4srs_1_1_chi_center.html#a64588b20c5010e22ad5d571343a7e6d0">read_mem</a>  ( PMemIO memIO, <span class="keywordtype">int</span> version, <span class="keywordtype">bool</span> * Ok = NULL );
+<a name="l00076"></a>00076 
+<a name="l00077"></a>00077       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_chi_center.html#ab3dc0fe1813d51055e829586a27ddd15">copy</a> ( PChiCenter chicenter, mmdb::ivector anmatch=NULL );
+<a name="l00078"></a>00078 
+<a name="l00079"></a>00079     <span class="keyword">protected</span>:
+<a name="l00080"></a><a class="code" href="classccp4srs_1_1_chi_center.html#ac2387dc7a46c0c4451bcd08e23b25ae5">00080</a>       <a class="code" href="namespaceccp4srs.html#ae91f970060d687d02ccfb78cbd6222bb">ChiCenterID</a> <a class="code" href="classccp4srs_1_1_chi_center.html#ac2387dc7a46c0c4451bcd08e23b25ae5" title="chiral center id">chicenter_id</a>;    
+<a name="l00081"></a><a class="code" href="classccp4srs_1_1_chi_center.html#a5fe75db982419a5d7f3c3ff8b2e41f46">00081</a>       <span class="keywordtype">int</span>         <a class="code" href="classccp4srs_1_1_chi_center.html#a5fe75db982419a5d7f3c3ff8b2e41f46" title="chiral center atom [0,1,...]">atom_center</a>;     
+<a name="l00082"></a><a class="code" href="classccp4srs_1_1_chi_center.html#aa80d6d7fbec0a8497b62af13b16e2a12">00082</a>       <span class="keywordtype">int</span>         <a class="code" href="classccp4srs_1_1_chi_center.html#a246c77c96df7921a1d1c989de4a50f8f">atom_1</a>,<a class="code" href="classccp4srs_1_1_chi_center.html#aa80d6d7fbec0a8497b62af13b16e2a12" title="ordinal numbers of atoms that">atom_2</a>;   
+<a name="l00083"></a><a class="code" href="classccp4srs_1_1_chi_center.html#a2b249cab1cc7c2ea80ea9259914fcd34">00083</a>       <span class="keywordtype">int</span>         <a class="code" href="classccp4srs_1_1_chi_center.html#a2b249cab1cc7c2ea80ea9259914fcd34" title="form the center [0,1,...]">atom_3</a>;          
+<a name="l00084"></a><a class="code" href="classccp4srs_1_1_chi_center.html#a6fc568ab5bcd12bc56b58d6b9f2933a1">00084</a>       <span class="keywordtype">int</span>         <a class="code" href="classccp4srs_1_1_chi_center.html#a6fc568ab5bcd12bc56b58d6b9f2933a1" title="chirality">volume_sign</a>;     
+<a name="l00085"></a>00085 
+<a name="l00086"></a>00086   };
+<a name="l00087"></a>00087 
+<a name="l00088"></a>00088 }  <span class="comment">// namespace ccp4srs</span>
+<a name="l00089"></a>00089 
+<a name="l00090"></a>00090 <span class="preprocessor">#endif // CCP4SRS_CHICENTER_H</span>
+</pre></div></div>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__container_8cpp.html ccp4srs/doc-html/html/ccp4srs__container_8cpp.html
--- ccp4srs-old/doc-html/html/ccp4srs__container_8cpp.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__container_8cpp.html	2014-09-09 21:34:12.000000000 -0700
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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__container_8h.html ccp4srs/doc-html/html/ccp4srs__container_8h.html
--- ccp4srs-old/doc-html/html/ccp4srs__container_8h.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__container_8h.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,86 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/ccp4srs_container.h File Reference</title>
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+<link href="search/search.css" rel="stylesheet" type="text/css"/>
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+<code>#include &quot;<a class="el" href="memio___8h_source.html">memio_.h</a>&quot;</code><br/>
+
+<p><a href="ccp4srs__container_8h_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="nested-classes"></a>
+Classes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container&lt; T &gt;</a></td></tr>
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__container_8h_source.html ccp4srs/doc-html/html/ccp4srs__container_8h_source.html
--- ccp4srs-old/doc-html/html/ccp4srs__container_8h_source.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__container_8h_source.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,212 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+  </div>
+<div class="header">
+  <div class="headertitle">
+<h1>src/ccp4srs_container.h</h1>  </div>
+</div>
+<div class="contents">
+<a href="ccp4srs__container_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">//  $Id: ccp4srs_container.h $</span>
+<a name="l00002"></a>00002 <span class="comment">//  =================================================================</span>
+<a name="l00003"></a>00003 <span class="comment">//</span>
+<a name="l00004"></a>00004 <span class="comment">//   CCP4 SRS Library: Storage, Retrieval and Search support for</span>
+<a name="l00005"></a>00005 <span class="comment">//   CCP4 ligand data.</span>
+<a name="l00006"></a>00006 <span class="comment">//</span>
+<a name="l00007"></a>00007 <span class="comment">//   Copyright (C) Eugene Krissinel 2010-2013.</span>
+<a name="l00008"></a>00008 <span class="comment">//</span>
+<a name="l00009"></a>00009 <span class="comment">//   This library is free software: you can redistribute it and/or</span>
+<a name="l00010"></a>00010 <span class="comment">//   modify it under the terms of the GNU Lesser General Public</span>
+<a name="l00011"></a>00011 <span class="comment">//   License version 3, modified in accordance with the provisions</span>
+<a name="l00012"></a>00012 <span class="comment">//   of the license to address the requirements of UK law.</span>
+<a name="l00013"></a>00013 <span class="comment">//</span>
+<a name="l00014"></a>00014 <span class="comment">//   You should have received a copy of the modified GNU Lesser</span>
+<a name="l00015"></a>00015 <span class="comment">//   General Public License along with this library. If not, copies</span>
+<a name="l00016"></a>00016 <span class="comment">//   may be downloaded from http://www.ccp4.ac.uk/ccp4license.php</span>
+<a name="l00017"></a>00017 <span class="comment">//</span>
+<a name="l00018"></a>00018 <span class="comment">//   This program is distributed in the hope that it will be useful,</span>
+<a name="l00019"></a>00019 <span class="comment">//   but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
+<a name="l00020"></a>00020 <span class="comment">//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
+<a name="l00021"></a>00021 <span class="comment">//   GNU Lesser General Public License for more details.</span>
+<a name="l00022"></a>00022 <span class="comment">//</span>
+<a name="l00023"></a>00023 <span class="comment">//  =================================================================</span>
+<a name="l00024"></a>00024 <span class="comment">//</span>
+<a name="l00025"></a>00025 <span class="comment">//    18.09.13   &lt;--  Date of Last Modification.</span>
+<a name="l00026"></a>00026 <span class="comment">//                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
+<a name="l00027"></a>00027 <span class="comment">//  -----------------------------------------------------------------</span>
+<a name="l00028"></a>00028 <span class="comment">//</span>
+<a name="l00029"></a>00029 <span class="comment">//  **** Module  :  ccp4srs_container  &lt;interface&gt;</span>
+<a name="l00030"></a>00030 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00031"></a>00031 <span class="comment">//  **** Classes :  ccp4srs::Container  - template container class</span>
+<a name="l00032"></a>00032 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00033"></a>00033 <span class="comment">//</span>
+<a name="l00034"></a>00034 <span class="comment">//  (C) E. Krissinel 2010-2013</span>
+<a name="l00035"></a>00035 <span class="comment">//</span>
+<a name="l00036"></a>00036 <span class="comment">//  =================================================================</span>
+<a name="l00037"></a>00037 <span class="comment">//</span>
+<a name="l00038"></a>00038 
+<a name="l00039"></a>00039 <span class="preprocessor">#ifndef CCP4SRS_CONTAINER_H</span>
+<a name="l00040"></a>00040 <span class="preprocessor"></span><span class="preprocessor">#define CCP4SRS_CONTAINER_H</span>
+<a name="l00041"></a>00041 <span class="preprocessor"></span>
+<a name="l00042"></a>00042 <span class="preprocessor">#include &quot;<a class="code" href="memio___8h.html">memio_.h</a>&quot;</span>
+<a name="l00043"></a>00043 
+<a name="l00044"></a>00044 <span class="keyword">namespace </span>ccp4srs  {
+<a name="l00045"></a>00045 
+<a name="l00046"></a>00046   <span class="keyword">template</span> &lt;<span class="keyword">class</span> T&gt;
+<a name="l00047"></a>00047 
+<a name="l00048"></a><a class="code" href="classccp4srs_1_1_container.html">00048</a>   <span class="keyword">class </span><a class="code" href="classccp4srs_1_1_container.html">Container</a>  {
+<a name="l00049"></a>00049 
+<a name="l00050"></a>00050     <span class="keyword">protected</span>:
+<a name="l00051"></a><a class="code" href="classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748">00051</a>       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748">n_objects</a>;
+<a name="l00052"></a><a class="code" href="classccp4srs_1_1_container.html#a25a4ad3660f2ef6760c949be2c1372a8">00052</a>       T  **<a class="code" href="classccp4srs_1_1_container.html#a25a4ad3660f2ef6760c949be2c1372a8">object</a>;
+<a name="l00053"></a>00053 
+<a name="l00054"></a>00054     <span class="keyword">private</span>:
+<a name="l00055"></a>00055       <span class="keywordtype">int</span>  n_alloc;
+<a name="l00056"></a>00056 
+<a name="l00057"></a>00057     <span class="keyword">public</span>:
+<a name="l00058"></a>00058 
+<a name="l00059"></a><a class="code" href="classccp4srs_1_1_container.html#acdff89dd6d441d731b517565021e3881">00059</a>       <a class="code" href="classccp4srs_1_1_container.html#acdff89dd6d441d731b517565021e3881">Container</a>()  {
+<a name="l00060"></a>00060         <span class="keywordtype">object</span>    = NULL;
+<a name="l00061"></a>00061         <a class="code" href="classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748">n_objects</a> = 0;
+<a name="l00062"></a>00062         n_alloc   = 0;
+<a name="l00063"></a>00063       }
+<a name="l00064"></a>00064 
+<a name="l00065"></a><a class="code" href="classccp4srs_1_1_container.html#a831fc7371918ff96de32b96c35fe31a2">00065</a>       <span class="keyword">virtual</span> <a class="code" href="classccp4srs_1_1_container.html#a831fc7371918ff96de32b96c35fe31a2">~Container</a>()  {
+<a name="l00066"></a>00066         <a class="code" href="classccp4srs_1_1_container.html#aeed888e25348f83a53021beaa21a0b1e">empty</a>();
+<a name="l00067"></a>00067       }
+<a name="l00068"></a>00068 
+<a name="l00069"></a><a class="code" href="classccp4srs_1_1_container.html#aeed888e25348f83a53021beaa21a0b1e">00069</a>       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_container.html#aeed888e25348f83a53021beaa21a0b1e">empty</a>()  {
+<a name="l00070"></a>00070       <span class="keywordtype">int</span> i;
+<a name="l00071"></a>00071         <span class="keywordflow">if</span> (<span class="keywordtype">object</span>)  {
+<a name="l00072"></a>00072           <span class="keywordflow">for</span> (i=0;i&lt;n_alloc;i++)
+<a name="l00073"></a>00073             <span class="keywordflow">if</span> (<span class="keywordtype">object</span>[i])  <span class="keyword">delete</span> <span class="keywordtype">object</span>[i];
+<a name="l00074"></a>00074           <span class="keyword">delete</span>[] <a class="code" href="classccp4srs_1_1_container.html#a25a4ad3660f2ef6760c949be2c1372a8">object</a>;
+<a name="l00075"></a>00075           <span class="keywordtype">object</span> = NULL;
+<a name="l00076"></a>00076         }
+<a name="l00077"></a>00077         <a class="code" href="classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748">n_objects</a> = 0;
+<a name="l00078"></a>00078         n_alloc   = 0;
+<a name="l00079"></a>00079       }
+<a name="l00080"></a>00080 
+<a name="l00081"></a><a class="code" href="classccp4srs_1_1_container.html#abbc5e6eeb9ea4d37b8d2025892ebd9ff">00081</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_container.html#abbc5e6eeb9ea4d37b8d2025892ebd9ff">numberOf</a>()      { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748">n_objects</a>;   }
+<a name="l00082"></a><a class="code" href="classccp4srs_1_1_container.html#ae9929d576289dd2313aaf4b2d9c377e9">00082</a>       <span class="keyword">inline</span> T*  <a class="code" href="classccp4srs_1_1_container.html#ae9929d576289dd2313aaf4b2d9c377e9">at</a> ( <span class="keywordtype">int</span> pos )  { <span class="keywordflow">return</span> <span class="keywordtype">object</span>[pos]; }
+<a name="l00083"></a>00083 
+<a name="l00084"></a><a class="code" href="classccp4srs_1_1_container.html#a6afe8d51f68e07697d7362464e433cac">00084</a>       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_container.html#a6afe8d51f68e07697d7362464e433cac">index</a> ( mmdb::cpstr <span class="keywordtype">id</span> )  {
+<a name="l00085"></a>00085       <span class="keywordtype">int</span>  i,k;
+<a name="l00086"></a>00086         k = -1;
+<a name="l00087"></a>00087         <span class="keywordflow">if</span> (<span class="keywordtype">id</span>)  {
+<a name="l00088"></a>00088           <span class="keywordflow">for</span> (i=0;(i&lt;<a class="code" href="classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748">n_objects</a>) &amp;&amp; (k&lt;0);i++)
+<a name="l00089"></a>00089             <span class="keywordflow">if</span> (!strcmp(<span class="keywordtype">id</span>,<span class="keywordtype">object</span>[i]-&gt;<span class="keywordtype">id</span>()))  k = i;
+<a name="l00090"></a>00090         }
+<a name="l00091"></a>00091         <span class="keywordflow">return</span> k;
+<a name="l00092"></a>00092       }
+<a name="l00093"></a>00093 
+<a name="l00094"></a><a class="code" href="classccp4srs_1_1_container.html#a6caf1893b780f2cf196c85ee141baf18">00094</a>       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_container.html#a6caf1893b780f2cf196c85ee141baf18">add</a> ( T* obj )  {
+<a name="l00095"></a>00095       T**  tobject;
+<a name="l00096"></a>00096       <span class="keywordtype">int</span>  i;
+<a name="l00097"></a>00097         <span class="keywordflow">if</span> (<a class="code" href="classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748">n_objects</a>&gt;=n_alloc)  {
+<a name="l00098"></a>00098           n_alloc = <a class="code" href="classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748">n_objects</a>+10;
+<a name="l00099"></a>00099           tobject = <span class="keyword">new</span> T*[n_alloc];
+<a name="l00100"></a>00100           <span class="keywordflow">for</span> (i=0;i&lt;<a class="code" href="classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748">n_objects</a>;i++)
+<a name="l00101"></a>00101             tobject[i] = <span class="keywordtype">object</span>[i];
+<a name="l00102"></a>00102           <span class="keywordflow">for</span> (i=n_objects;i&lt;n_alloc;i++)
+<a name="l00103"></a>00103             tobject[i] = NULL;
+<a name="l00104"></a>00104           <span class="keyword">delete</span>[] <a class="code" href="classccp4srs_1_1_container.html#a25a4ad3660f2ef6760c949be2c1372a8">object</a>;
+<a name="l00105"></a>00105           <span class="keywordtype">object</span> = tobject;
+<a name="l00106"></a>00106         }
+<a name="l00107"></a>00107         <span class="keywordtype">object</span>[<a class="code" href="classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748">n_objects</a>++] = obj;
+<a name="l00108"></a>00108       }
+<a name="l00109"></a>00109 
+<a name="l00110"></a><a class="code" href="classccp4srs_1_1_container.html#ae3d1a80023e670f0828814b887af5dc8">00110</a>       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_container.html#ae3d1a80023e670f0828814b887af5dc8">write_mem</a> ( PMemIO memIO, <span class="keywordtype">int</span> version )  {
+<a name="l00111"></a>00111       <span class="keywordtype">int</span> i;
+<a name="l00112"></a>00112         memIO-&gt;put_integer ( <a class="code" href="classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748">n_objects</a> );
+<a name="l00113"></a>00113         <span class="keywordflow">for</span> (i=0;i&lt;<a class="code" href="classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748">n_objects</a>;i++)
+<a name="l00114"></a>00114           <span class="keywordtype">object</span>[i]-&gt;<a class="code" href="classccp4srs_1_1_container.html#ae3d1a80023e670f0828814b887af5dc8">write_mem</a> ( memIO,version );
+<a name="l00115"></a>00115       }
+<a name="l00116"></a>00116 
+<a name="l00117"></a><a class="code" href="classccp4srs_1_1_container.html#a9f42bc8ec160490ba2dd8d7a8eeae15e">00117</a>       <span class="keywordtype">bool</span> <a class="code" href="classccp4srs_1_1_container.html#a9f42bc8ec160490ba2dd8d7a8eeae15e">read_mem</a> ( PMemIO memIO, <span class="keywordtype">int</span> version, <span class="keywordtype">bool</span> * Ok )  {
+<a name="l00118"></a>00118       <span class="keywordtype">int</span>  i;
+<a name="l00119"></a>00119       <span class="keywordtype">bool</span> success;
+<a name="l00120"></a>00120         <a class="code" href="classccp4srs_1_1_container.html#aeed888e25348f83a53021beaa21a0b1e">empty</a>();
+<a name="l00121"></a>00121         <span class="keywordflow">if</span> (Ok)  success = *Ok;
+<a name="l00122"></a>00122            <span class="keywordflow">else</span>  success = <span class="keyword">true</span>;
+<a name="l00123"></a>00123         memIO-&gt;get_integer ( <a class="code" href="classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748">n_objects</a>,&amp;success );
+<a name="l00124"></a>00124         n_alloc = <a class="code" href="classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748">n_objects</a>;
+<a name="l00125"></a>00125         <span class="keywordflow">if</span> (<a class="code" href="classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748">n_objects</a>&gt;0)  {
+<a name="l00126"></a>00126           <span class="keywordtype">object</span> = <span class="keyword">new</span> T*[n_alloc];
+<a name="l00127"></a>00127           <span class="keywordflow">for</span> (i=0;i&lt;<a class="code" href="classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748">n_objects</a>;i++)  {
+<a name="l00128"></a>00128             <span class="keywordtype">object</span>[i] = <span class="keyword">new</span> T();
+<a name="l00129"></a>00129             <span class="keywordtype">object</span>[i]-&gt;read_mem ( memIO,version,&amp;success );
+<a name="l00130"></a>00130           }
+<a name="l00131"></a>00131         }
+<a name="l00132"></a>00132         <span class="keywordflow">if</span> (Ok)  *Ok = success;
+<a name="l00133"></a>00133         <span class="keywordflow">return</span> success;
+<a name="l00134"></a>00134       }
+<a name="l00135"></a>00135 
+<a name="l00136"></a>00136   };
+<a name="l00137"></a>00137 
+<a name="l00138"></a>00138 }  <span class="comment">// namespace ccp4srs</span>
+<a name="l00139"></a>00139 
+<a name="l00140"></a>00140 <span class="preprocessor">#endif // CCP4SRS_CONTAINER_H</span>
+</pre></div></div>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
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+        name="MSearchResults" id="MSearchResults">
+</iframe>
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+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/ccp4srs__defs_8cpp.html ccp4srs/doc-html/html/ccp4srs__defs_8cpp.html
--- ccp4srs-old/doc-html/html/ccp4srs__defs_8cpp.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__defs_8cpp.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,131 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/ccp4srs_defs.cpp File Reference</title>
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+  <div class="summary">
+<a href="#namespaces">Namespaces</a> &#124;
+<a href="#var-members">Variables</a>  </div>
+  <div class="headertitle">
+<h1>src/ccp4srs_defs.cpp File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &quot;<a class="el" href="ccp4srs__defs_8h_source.html">ccp4srs_defs.h</a>&quot;</code><br/>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+<tr><td colspan="2"><h2><a name="var-members"></a>
+Variables</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">const int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a4938160ce6172269adc59b8077014f7c">ccp4srs::CCP4SRS_file_version</a> = 2</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a3f27798432992515be969c17425412d3">ccp4srs::srsIndexFile</a> = &quot;index.srs&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a4132afa4ce21fdcd2ff268bf6e980cfc">ccp4srs::srsGraphFile</a> = &quot;graph.srs&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#af51e5a096118e643d5fcf5490d44c6db">ccp4srs::srsStructFile</a> = &quot;struct.srs&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">const int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#aa44a92ce883cd1c525381111cd1a4ab3">ccp4srs::AtomID_NA</a> = -10000</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a734401576e443c1364c97e3cf2b87620">ccp4srs::MMCIF_COMP</a> = &quot;comp_&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a895ac2dc79a4b49f80535ab27f84a813">ccp4srs::MMCIF_TAG_Name</a> = &quot;name&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a9fa66c69223316c62033120393337021">ccp4srs::MMCIF_TAG_Type</a> = &quot;type&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#ae88d641023482ccc3b61ad9283c5b36a">ccp4srs::MMCIF_TAG_Formula</a> = &quot;formula&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a5a6a67536a849a8a9918e80d45786e6c">ccp4srs::MMCIF_STRUCT_CHEM_COMP</a> = &quot;_chem_comp&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#acb29038a62c97dc90cdf0e2781762fd9">ccp4srs::MMCIF_LOOP_CHEM_COMP_ATOM</a> = &quot;_chem_comp_atom&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#acc74aa86c0bd13e205ea231687c59385">ccp4srs::MMCIF_TAG_COMP_ID</a> = &quot;comp_id&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a7a00a2c248bef6dc887855f022b74dac">ccp4srs::MMCIF_TAG_ATOM_ID</a> = &quot;atom_id&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a4eca0339da86cab6e8df4fd7f2d83bc7">ccp4srs::MMCIF_TAG_ALT_ATOM_ID</a> = &quot;alt_atom_id&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a8c8658465186581211c239565271885f">ccp4srs::MMCIF_TAG_TYPE_SYMBOL</a> = &quot;type_symbol&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#aa9aa8bf64e9e09c8f2c26b8b1658ca08">ccp4srs::MMCIF_TAG_TYPE_ENERGY</a> = &quot;type_energy&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a108c265a420b97ec1dd94a0f1ac57b91">ccp4srs::MMCIF_TAG_PARTIAL_CHARGE</a> = &quot;partial_charge&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#ad80ada9589e78e474ff4454a5bebf112">ccp4srs::MMCIF_TAG_X</a> = &quot;x&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a231de8e82b046b216056111da3e55f48">ccp4srs::MMCIF_TAG_Y</a> = &quot;y&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a01ba67da4b786c837c153db23dad5a8a">ccp4srs::MMCIF_TAG_Z</a> = &quot;z&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#afdb327819ed02075a3232832a6f4a045">ccp4srs::MMCIF_TAG_MODEL_CARTN_X</a> = &quot;model_Cartn_x&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a533f7a722584cf3cf9ef6df2a273824e">ccp4srs::MMCIF_TAG_MODEL_CARTN_Y</a> = &quot;model_Cartn_y&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a3264c62259388f92af22de46973b9a7b">ccp4srs::MMCIF_TAG_MODEL_CARTN_Z</a> = &quot;model_Cartn_z&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a5962191d6f9befcf2091f3dcc4de19f9">ccp4srs::MMCIF_TAG_PDBX_MODEL_CARTN_X</a> = &quot;pdbx_model_Cartn_x&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#ab6bf3c65a9a75276e8eda6d417722b9d">ccp4srs::MMCIF_TAG_PDBX_MODEL_CARTN_Y</a> = &quot;pdbx_model_Cartn_y&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#aa9a13777348bab4aa6b96a018483ebe7">ccp4srs::MMCIF_TAG_PDBX_MODEL_CARTN_Z</a> = &quot;pdbx_model_Cartn_z&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#ab2e4db5f470fc4b644e7cade055d9ccb">ccp4srs::MMCIF_TAG_PDBX_STEREO_CONFIG</a> = &quot;pdbx_stereo_config&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a6cb1789c079414b694d826d55e5204f9">ccp4srs::MMCIF_TAG_PDBX_LEAVING_ATOM_FLAG</a> = &quot;pdbx_leaving_atom_flag&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#ad1ecee6e860abb6b1143d12b9cc501d7">ccp4srs::MMCIF_TAG_PDBX_AROMATIC_FLAG</a> = &quot;pdbx_aromatic_flag&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a88132b72d6e025fc7d9e1916bd2f45a5">ccp4srs::MMCIF_TAG_VALUE_ORDER</a> = &quot;value_order&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a8dd52287fe52b415ab2d437017c80509">ccp4srs::MMCIF_LOOP_CHEM_COMP_TREE</a> = &quot;_chem_comp_tree&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#acddd884d876108e5793eac0dfdc7e77f">ccp4srs::MMCIF_TAG_ATOM_BACK</a> = &quot;atom_back&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a6bd10c965fd9353204236160a1a135e5">ccp4srs::MMCIF_TAG_ATOM_FORWARD</a> = &quot;atom_forward&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#aa0d0ce5d2deeba363ef05b52867584dc">ccp4srs::MMCIF_TAG_CONNECT_TYPE</a> = &quot;connect_type&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a4fdbe7b8b6f8b358b46f9ee0a898fd8b">ccp4srs::MMCIF_LOOP_CHEM_COMP_BOND</a> = &quot;_chem_comp_bond&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a172156c75469fcbe0db9dede959d54c5">ccp4srs::MMCIF_TAG_ATOM_ID_1</a> = &quot;atom_id_1&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#adfdabe1fe7abb5ffa30f353c118dfae3">ccp4srs::MMCIF_TAG_ATOM_ID_2</a> = &quot;atom_id_2&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a7d5e9bdb717c1f37f76ec33c75ce79f5">ccp4srs::MMCIF_TAG_TYPE</a> = &quot;type&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a1f39896726a564431238e11c98d8a9a0">ccp4srs::MMCIF_TAG_VALUE_DIST</a> = &quot;value_dist&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a829c6927cef2307072a4ab445cf227d6">ccp4srs::MMCIF_TAG_VALUE_DIST_ESD</a> = &quot;value_dist_esd&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a1aa056bdc67a5e6da564c08676e0a337">ccp4srs::MMCIF_LOOP_CHEM_COMP_ANGLE</a> = &quot;_chem_comp_angle&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#aec7e041a1b79b4afe090ca5ea3868d34">ccp4srs::MMCIF_TAG_ATOM_ID_3</a> = &quot;atom_id_3&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#acd0f8fb4dd60bf62bb514b366ce68b7c">ccp4srs::MMCIF_TAG_VALUE_ANGLE</a> = &quot;value_angle&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a2ca234394606056dbfec79c27e713839">ccp4srs::MMCIF_TAG_VALUE_ANGLE_ESD</a> = &quot;value_angle_esd&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a5becf461bc6db4ede6142e4efe5cf9ac">ccp4srs::MMCIF_LOOP_CHEM_COMP_CHIR</a> = &quot;_chem_comp_chir&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#aecf31bb82d1ecbb25c380a7498fd8ead">ccp4srs::MMCIF_TAG_ID</a> = &quot;id&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a32ea98265079426127b2b32d8228d438">ccp4srs::MMCIF_TAG_ATOM_ID_CENTRE</a> = &quot;atom_id_centre&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a15628f583622fc075a2f4fddc8848e70">ccp4srs::MMCIF_TAG_VOLUME_SIGN</a> = &quot;volume_sign&quot;</td></tr>
+</table>
+</div>
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+        name="MSearchResults" id="MSearchResults">
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+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 18 2013 15:19:52 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__defs_8h.html ccp4srs/doc-html/html/ccp4srs__defs_8h.html
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/ccp4srs_defs.h File Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
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+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li class="current"><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
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+  <div class="tabs2">
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+      <li><a href="files.html"><span>File&#160;List</span></a></li>
+      <li><a href="globals.html"><span>File&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="summary">
+<a href="#define-members">Defines</a>  </div>
+  <div class="headertitle">
+<h1>src/ccp4srs_defs.h File Reference</h1>  </div>
+</div>
+<div class="contents">
+
+<p><a href="ccp4srs__defs_8h_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="define-members"></a>
+Defines</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#aefbf24090a7fbe6109d4e58390f1aae4">MMCIF_COMP</a>&#160;&#160;&#160;&quot;comp_&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a0f3964efb8ec1746a152fa5aac689273">MMCIF_TAG_Name</a>&#160;&#160;&#160;&quot;name&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a20179e20def570d67ea892e8cd3bd666">MMCIF_TAG_Type</a>&#160;&#160;&#160;&quot;type&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a5cf744094676b0bd89430c485933f6fb">MMCIF_TAG_Formula</a>&#160;&#160;&#160;&quot;formula&quot;</td></tr>
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+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a96f3d7ae6d26ccb1b693b687f85ff382">MMCIF_LOOP_CHEM_COMP_ATOM</a>&#160;&#160;&#160;&quot;_chem_comp_atom&quot;</td></tr>
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+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a2b31545950368db39b67371d64cbbef7">MMCIF_TAG_PARTIAL_CHARGE</a>&#160;&#160;&#160;&quot;partial_charge&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#ae9e78e9a02868061bee6c1a6b45453ca">MMCIF_TAG_X</a>&#160;&#160;&#160;&quot;x&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#ac08945b8f7b2dabe39335c716edc8266">MMCIF_TAG_Y</a>&#160;&#160;&#160;&quot;y&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#ab3af4414a670e8553431994f5ba24aab">MMCIF_TAG_Z</a>&#160;&#160;&#160;&quot;z&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a84559f7c12aa9f1a387b8f530264ab16">MMCIF_TAG_MODEL_CARTN_X</a>&#160;&#160;&#160;&quot;model_Cartn_x&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#af0b16d01af53acaed091894e08162b54">MMCIF_TAG_MODEL_CARTN_Y</a>&#160;&#160;&#160;&quot;model_Cartn_y&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a252481f6fc180b9d746ef063c9a3609c">MMCIF_TAG_MODEL_CARTN_Z</a>&#160;&#160;&#160;&quot;model_Cartn_z&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a0993df52ba1ecc98ca2591a8392ffee6">MMCIF_TAG_PDBX_MODEL_CARTN_X</a>&#160;&#160;&#160;&quot;pdbx_model_Cartn_x&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a56fcc86c982c756f3573ecd213c149d9">MMCIF_TAG_PDBX_MODEL_CARTN_Y</a>&#160;&#160;&#160;&quot;pdbx_model_Cartn_y&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a5cbd04910c2725cdc0c72531dfd38cac">MMCIF_TAG_PDBX_MODEL_CARTN_Z</a>&#160;&#160;&#160;&quot;pdbx_model_Cartn_z&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#ad753a24e5bb150fc4cc1161dcc31111a">MMCIF_TAG_PDBX_STEREO_CONFIG</a>&#160;&#160;&#160;&quot;pdbx_stereo_config&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a3a906be28069a81e9429b36c1cfc2edc">MMCIF_TAG_PDBX_LEAVING_ATOM_FLAG</a>&#160;&#160;&#160;&quot;pdbx_leaving_atom_flag&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a9207204b4fac4b0f5587e33a56d6aca5">MMCIF_TAG_PDBX_AROMATIC_FLAG</a>&#160;&#160;&#160;&quot;pdbx_aromatic_flag&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a7b962f3e20a4c60f50b720aaaf483080">MMCIF_TAG_VALUE_ORDER</a>&#160;&#160;&#160;&quot;value_order&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#ab82eb4b740280944b8fbe74362121d2f">MMCIF_LOOP_CHEM_COMP_TREE</a>&#160;&#160;&#160;&quot;_chem_comp_tree&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a2fc723c8a3cb4d9aecd670de41e006e5">MMCIF_TAG_ATOM_BACK</a>&#160;&#160;&#160;&quot;atom_back&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a07c7f15b018109563b8dde9b59484568">MMCIF_TAG_ATOM_FORWARD</a>&#160;&#160;&#160;&quot;atom_forward&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#aaf8c20eee68a9718052502c7ddb35c16">MMCIF_TAG_CONNECT_TYPE</a>&#160;&#160;&#160;&quot;connect_type&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a442e6c574a7a90cf6955d1ca8e4cf18f">MMCIF_LOOP_CHEM_COMP_BOND</a>&#160;&#160;&#160;&quot;_chem_comp_bond&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a379e5bcb509192bb36b833265f32ff9b">MMCIF_TAG_ATOM_ID_1</a>&#160;&#160;&#160;&quot;atom_id_1&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#ac01791d945ab084eecb5cb33e9d0232c">MMCIF_TAG_ATOM_ID_2</a>&#160;&#160;&#160;&quot;atom_id_2&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#af5de8de3a7e69bd50f9c8ee2a7c9c53a">MMCIF_TAG_TYPE</a>&#160;&#160;&#160;&quot;type&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a36bc56204ef3bc3ab0b33754e8e791fb">MMCIF_TAG_VALUE_DIST</a>&#160;&#160;&#160;&quot;value_dist&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a773a38551554ef102c997ba5e391c101">MMCIF_TAG_VALUE_DIST_ESD</a>&#160;&#160;&#160;&quot;value_dist_esd&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#ad95350f455f90a8b546d688a1b7604d2">MMCIF_LOOP_CHEM_COMP_ANGLE</a>&#160;&#160;&#160;&quot;_chem_comp_angle&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a5a61b6835d1309e469feb356e2695388">MMCIF_TAG_ATOM_ID_3</a>&#160;&#160;&#160;&quot;atom_id_3&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#ac8d6aed8f4893094ad1dac7790505a30">MMCIF_TAG_VALUE_ANGLE</a>&#160;&#160;&#160;&quot;value_angle&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a63fccdc102c24817b6dcef20a4135187">MMCIF_TAG_VALUE_ANGLE_ESD</a>&#160;&#160;&#160;&quot;value_angle_esd&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a745441f40029534d9996304227bc0d5c">MMCIF_LOOP_CHEM_COMP_CHIR</a>&#160;&#160;&#160;&quot;_chem_comp_chir&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#acb2e2c33e267f4d67aa3550454a6400c">MMCIF_TAG_ID</a>&#160;&#160;&#160;&quot;id&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a20c0ca81595c8d02438d80c53033f99d">MMCIF_TAG_ATOM_ID_CENTRE</a>&#160;&#160;&#160;&quot;atom_id_centre&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#ace32f1cd1f6052d3cd1d78c18835016c">MMCIF_TAG_VOLUME_SIGN</a>&#160;&#160;&#160;&quot;volume_sign&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#aed5250676b70b953e859e148a46d26b2">MMCIF_LOOP_CHEM_COMP_TOR</a>&#160;&#160;&#160;&quot;_chem_comp_tor&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a0c93c9f5f166a7c389a0d6a6be3fd3b4">MMCIF_TAG_ATOM_ID_4</a>&#160;&#160;&#160;&quot;atom_id_4&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#ad7d263713c3571c9b1597ac2ffdceb8c">MMCIF_TAG_PERIOD</a>&#160;&#160;&#160;&quot;period&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a66aec28ad11df2c52c17f89e854d3717">MMCIF_LOOP_CHEM_COMP_PLANE_ATOM</a>&#160;&#160;&#160;&quot;_chem_comp_plane_atom&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a727023c5a08af92c674e88a97d3361f1">MMCIF_TAG_PLANE_ID</a>&#160;&#160;&#160;&quot;plane_id&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="ccp4srs__defs_8h.html#a410537d70cb039747f3bd8a36a52f553">MMCIF_TAG_DIST_ESD</a>&#160;&#160;&#160;&quot;dist_esd&quot;</td></tr>
+</table>
+<hr/><h2>Define Documentation</h2>
+<a class="anchor" id="aefbf24090a7fbe6109d4e58390f1aae4"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_COMP" ref="aefbf24090a7fbe6109d4e58390f1aae4" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_COMP&#160;&#160;&#160;&quot;comp_&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ad95350f455f90a8b546d688a1b7604d2"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_LOOP_CHEM_COMP_ANGLE" ref="ad95350f455f90a8b546d688a1b7604d2" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_LOOP_CHEM_COMP_ANGLE&#160;&#160;&#160;&quot;_chem_comp_angle&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a96f3d7ae6d26ccb1b693b687f85ff382"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_LOOP_CHEM_COMP_ATOM" ref="a96f3d7ae6d26ccb1b693b687f85ff382" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_LOOP_CHEM_COMP_ATOM&#160;&#160;&#160;&quot;_chem_comp_atom&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a442e6c574a7a90cf6955d1ca8e4cf18f"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_LOOP_CHEM_COMP_BOND" ref="a442e6c574a7a90cf6955d1ca8e4cf18f" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_LOOP_CHEM_COMP_BOND&#160;&#160;&#160;&quot;_chem_comp_bond&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a745441f40029534d9996304227bc0d5c"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_LOOP_CHEM_COMP_CHIR" ref="a745441f40029534d9996304227bc0d5c" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_LOOP_CHEM_COMP_CHIR&#160;&#160;&#160;&quot;_chem_comp_chir&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a66aec28ad11df2c52c17f89e854d3717"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_LOOP_CHEM_COMP_PLANE_ATOM" ref="a66aec28ad11df2c52c17f89e854d3717" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_LOOP_CHEM_COMP_PLANE_ATOM&#160;&#160;&#160;&quot;_chem_comp_plane_atom&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aed5250676b70b953e859e148a46d26b2"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_LOOP_CHEM_COMP_TOR" ref="aed5250676b70b953e859e148a46d26b2" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_LOOP_CHEM_COMP_TOR&#160;&#160;&#160;&quot;_chem_comp_tor&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ab82eb4b740280944b8fbe74362121d2f"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_LOOP_CHEM_COMP_TREE" ref="ab82eb4b740280944b8fbe74362121d2f" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_LOOP_CHEM_COMP_TREE&#160;&#160;&#160;&quot;_chem_comp_tree&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ae071049f6b4c72d884d50a7fb00c796b"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_STRUCT_CHEM_COMP" ref="ae071049f6b4c72d884d50a7fb00c796b" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_STRUCT_CHEM_COMP&#160;&#160;&#160;&quot;_chem_comp&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="abf103686dc23d212a4dd43ebe9883f36"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_ALT_ATOM_ID" ref="abf103686dc23d212a4dd43ebe9883f36" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_ALT_ATOM_ID&#160;&#160;&#160;&quot;alt_atom_id&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a2fc723c8a3cb4d9aecd670de41e006e5"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_ATOM_BACK" ref="a2fc723c8a3cb4d9aecd670de41e006e5" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_ATOM_BACK&#160;&#160;&#160;&quot;atom_back&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a07c7f15b018109563b8dde9b59484568"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_ATOM_FORWARD" ref="a07c7f15b018109563b8dde9b59484568" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_ATOM_FORWARD&#160;&#160;&#160;&quot;atom_forward&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a0063d4d4b2407acb4c5e962e937d987c"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_ATOM_ID" ref="a0063d4d4b2407acb4c5e962e937d987c" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_ATOM_ID&#160;&#160;&#160;&quot;atom_id&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a379e5bcb509192bb36b833265f32ff9b"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_ATOM_ID_1" ref="a379e5bcb509192bb36b833265f32ff9b" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_ATOM_ID_1&#160;&#160;&#160;&quot;atom_id_1&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ac01791d945ab084eecb5cb33e9d0232c"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_ATOM_ID_2" ref="ac01791d945ab084eecb5cb33e9d0232c" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_ATOM_ID_2&#160;&#160;&#160;&quot;atom_id_2&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a5a61b6835d1309e469feb356e2695388"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_ATOM_ID_3" ref="a5a61b6835d1309e469feb356e2695388" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_ATOM_ID_3&#160;&#160;&#160;&quot;atom_id_3&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a0c93c9f5f166a7c389a0d6a6be3fd3b4"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_ATOM_ID_4" ref="a0c93c9f5f166a7c389a0d6a6be3fd3b4" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_ATOM_ID_4&#160;&#160;&#160;&quot;atom_id_4&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a20c0ca81595c8d02438d80c53033f99d"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_ATOM_ID_CENTRE" ref="a20c0ca81595c8d02438d80c53033f99d" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_ATOM_ID_CENTRE&#160;&#160;&#160;&quot;atom_id_centre&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a70bb9ac01714d5ddf96f030e39fc925d"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_COMP_ID" ref="a70bb9ac01714d5ddf96f030e39fc925d" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_COMP_ID&#160;&#160;&#160;&quot;comp_id&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aaf8c20eee68a9718052502c7ddb35c16"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_CONNECT_TYPE" ref="aaf8c20eee68a9718052502c7ddb35c16" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_CONNECT_TYPE&#160;&#160;&#160;&quot;connect_type&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a410537d70cb039747f3bd8a36a52f553"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_DIST_ESD" ref="a410537d70cb039747f3bd8a36a52f553" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_DIST_ESD&#160;&#160;&#160;&quot;dist_esd&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a5cf744094676b0bd89430c485933f6fb"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_Formula" ref="a5cf744094676b0bd89430c485933f6fb" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_Formula&#160;&#160;&#160;&quot;formula&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="acb2e2c33e267f4d67aa3550454a6400c"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_ID" ref="acb2e2c33e267f4d67aa3550454a6400c" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_ID&#160;&#160;&#160;&quot;id&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a84559f7c12aa9f1a387b8f530264ab16"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_MODEL_CARTN_X" ref="a84559f7c12aa9f1a387b8f530264ab16" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_MODEL_CARTN_X&#160;&#160;&#160;&quot;model_Cartn_x&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="af0b16d01af53acaed091894e08162b54"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_MODEL_CARTN_Y" ref="af0b16d01af53acaed091894e08162b54" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_MODEL_CARTN_Y&#160;&#160;&#160;&quot;model_Cartn_y&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a252481f6fc180b9d746ef063c9a3609c"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_MODEL_CARTN_Z" ref="a252481f6fc180b9d746ef063c9a3609c" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_MODEL_CARTN_Z&#160;&#160;&#160;&quot;model_Cartn_z&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a0f3964efb8ec1746a152fa5aac689273"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_Name" ref="a0f3964efb8ec1746a152fa5aac689273" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_Name&#160;&#160;&#160;&quot;name&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a2b31545950368db39b67371d64cbbef7"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_PARTIAL_CHARGE" ref="a2b31545950368db39b67371d64cbbef7" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_PARTIAL_CHARGE&#160;&#160;&#160;&quot;partial_charge&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a9207204b4fac4b0f5587e33a56d6aca5"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_PDBX_AROMATIC_FLAG" ref="a9207204b4fac4b0f5587e33a56d6aca5" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_PDBX_AROMATIC_FLAG&#160;&#160;&#160;&quot;pdbx_aromatic_flag&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a3a906be28069a81e9429b36c1cfc2edc"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_PDBX_LEAVING_ATOM_FLAG" ref="a3a906be28069a81e9429b36c1cfc2edc" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_PDBX_LEAVING_ATOM_FLAG&#160;&#160;&#160;&quot;pdbx_leaving_atom_flag&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a0993df52ba1ecc98ca2591a8392ffee6"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_PDBX_MODEL_CARTN_X" ref="a0993df52ba1ecc98ca2591a8392ffee6" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_PDBX_MODEL_CARTN_X&#160;&#160;&#160;&quot;pdbx_model_Cartn_x&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a56fcc86c982c756f3573ecd213c149d9"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_PDBX_MODEL_CARTN_Y" ref="a56fcc86c982c756f3573ecd213c149d9" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_PDBX_MODEL_CARTN_Y&#160;&#160;&#160;&quot;pdbx_model_Cartn_y&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a5cbd04910c2725cdc0c72531dfd38cac"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_PDBX_MODEL_CARTN_Z" ref="a5cbd04910c2725cdc0c72531dfd38cac" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_PDBX_MODEL_CARTN_Z&#160;&#160;&#160;&quot;pdbx_model_Cartn_z&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ad753a24e5bb150fc4cc1161dcc31111a"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_PDBX_STEREO_CONFIG" ref="ad753a24e5bb150fc4cc1161dcc31111a" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_PDBX_STEREO_CONFIG&#160;&#160;&#160;&quot;pdbx_stereo_config&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ad7d263713c3571c9b1597ac2ffdceb8c"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_PERIOD" ref="ad7d263713c3571c9b1597ac2ffdceb8c" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_PERIOD&#160;&#160;&#160;&quot;period&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a727023c5a08af92c674e88a97d3361f1"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_PLANE_ID" ref="a727023c5a08af92c674e88a97d3361f1" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_PLANE_ID&#160;&#160;&#160;&quot;plane_id&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="af5de8de3a7e69bd50f9c8ee2a7c9c53a"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_TYPE" ref="af5de8de3a7e69bd50f9c8ee2a7c9c53a" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_TYPE&#160;&#160;&#160;&quot;type&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a20179e20def570d67ea892e8cd3bd666"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_Type" ref="a20179e20def570d67ea892e8cd3bd666" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_Type&#160;&#160;&#160;&quot;type&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a9e64e930d30f442af1eb427927297fad"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_TYPE_ENERGY" ref="a9e64e930d30f442af1eb427927297fad" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_TYPE_ENERGY&#160;&#160;&#160;&quot;type_energy&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a681fa0489227ecf64eee279db3a2f21b"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_TYPE_SYMBOL" ref="a681fa0489227ecf64eee279db3a2f21b" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_TYPE_SYMBOL&#160;&#160;&#160;&quot;type_symbol&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ac8d6aed8f4893094ad1dac7790505a30"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_VALUE_ANGLE" ref="ac8d6aed8f4893094ad1dac7790505a30" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_VALUE_ANGLE&#160;&#160;&#160;&quot;value_angle&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a63fccdc102c24817b6dcef20a4135187"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_VALUE_ANGLE_ESD" ref="a63fccdc102c24817b6dcef20a4135187" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_VALUE_ANGLE_ESD&#160;&#160;&#160;&quot;value_angle_esd&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a36bc56204ef3bc3ab0b33754e8e791fb"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_VALUE_DIST" ref="a36bc56204ef3bc3ab0b33754e8e791fb" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_VALUE_DIST&#160;&#160;&#160;&quot;value_dist&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a773a38551554ef102c997ba5e391c101"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_VALUE_DIST_ESD" ref="a773a38551554ef102c997ba5e391c101" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_VALUE_DIST_ESD&#160;&#160;&#160;&quot;value_dist_esd&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a7b962f3e20a4c60f50b720aaaf483080"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_VALUE_ORDER" ref="a7b962f3e20a4c60f50b720aaaf483080" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_VALUE_ORDER&#160;&#160;&#160;&quot;value_order&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ace32f1cd1f6052d3cd1d78c18835016c"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_VOLUME_SIGN" ref="ace32f1cd1f6052d3cd1d78c18835016c" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_VOLUME_SIGN&#160;&#160;&#160;&quot;volume_sign&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ae9e78e9a02868061bee6c1a6b45453ca"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_X" ref="ae9e78e9a02868061bee6c1a6b45453ca" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_X&#160;&#160;&#160;&quot;x&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ac08945b8f7b2dabe39335c716edc8266"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_Y" ref="ac08945b8f7b2dabe39335c716edc8266" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_Y&#160;&#160;&#160;&quot;y&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ab3af4414a670e8553431994f5ba24aab"></a><!-- doxytag: member="ccp4srs_defs.h::MMCIF_TAG_Z" ref="ab3af4414a670e8553431994f5ba24aab" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">#define MMCIF_TAG_Z&#160;&#160;&#160;&quot;z&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
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+<h1>src/ccp4srs_defs.h</h1>  </div>
+</div>
+<div class="contents">
+<a href="ccp4srs__defs_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">//  $Id: ccp4srs_defs.h $</span>
+<a name="l00002"></a>00002 <span class="comment">//  =================================================================</span>
+<a name="l00003"></a>00003 <span class="comment">//</span>
+<a name="l00004"></a>00004 <span class="comment">//   CCP4 SRS Library: Storage, Retrievak and Search support for</span>
+<a name="l00005"></a>00005 <span class="comment">//   CCP4 ligand data.</span>
+<a name="l00006"></a>00006 <span class="comment">//</span>
+<a name="l00007"></a>00007 <span class="comment">//   Copyright (C) Eugene Krissinel 2010-2013.</span>
+<a name="l00008"></a>00008 <span class="comment">//</span>
+<a name="l00009"></a>00009 <span class="comment">//   This library is free software: you can redistribute it and/or</span>
+<a name="l00010"></a>00010 <span class="comment">//   modify it under the terms of the GNU Lesser General Public</span>
+<a name="l00011"></a>00011 <span class="comment">//   License version 3, modified in accordance with the provisions</span>
+<a name="l00012"></a>00012 <span class="comment">//   of the license to address the requirements of UK law.</span>
+<a name="l00013"></a>00013 <span class="comment">//</span>
+<a name="l00014"></a>00014 <span class="comment">//   You should have received a copy of the modified GNU Lesser</span>
+<a name="l00015"></a>00015 <span class="comment">//   General Public License along with this library. If not, copies</span>
+<a name="l00016"></a>00016 <span class="comment">//   may be downloaded from http://www.ccp4.ac.uk/ccp4license.php</span>
+<a name="l00017"></a>00017 <span class="comment">//</span>
+<a name="l00018"></a>00018 <span class="comment">//   This program is distributed in the hope that it will be useful,</span>
+<a name="l00019"></a>00019 <span class="comment">//   but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
+<a name="l00020"></a>00020 <span class="comment">//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
+<a name="l00021"></a>00021 <span class="comment">//   GNU Lesser General Public License for more details.</span>
+<a name="l00022"></a>00022 <span class="comment">//</span>
+<a name="l00023"></a>00023 <span class="comment">//  =================================================================</span>
+<a name="l00024"></a>00024 <span class="comment">//</span>
+<a name="l00025"></a>00025 <span class="comment">//    18.09.13   &lt;--  Date of Last Modification.</span>
+<a name="l00026"></a>00026 <span class="comment">//                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
+<a name="l00027"></a>00027 <span class="comment">//  -----------------------------------------------------------------</span>
+<a name="l00028"></a>00028 <span class="comment">//</span>
+<a name="l00029"></a>00029 <span class="comment">//  **** Module  :  ccp4srs_defs  &lt;interface&gt;</span>
+<a name="l00030"></a>00030 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00031"></a>00031 <span class="comment">//  **** Content :  CCP4 SRS definitions</span>
+<a name="l00032"></a>00032 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00033"></a>00033 <span class="comment">//</span>
+<a name="l00034"></a>00034 <span class="comment">//  (C) E. Krissinel 2010-2013</span>
+<a name="l00035"></a>00035 <span class="comment">//</span>
+<a name="l00036"></a>00036 <span class="comment">//  =================================================================</span>
+<a name="l00037"></a>00037 <span class="comment">//</span>
+<a name="l00038"></a>00038 
+<a name="l00039"></a>00039 <span class="preprocessor">#ifndef CCP4SRS_DEFS_H</span>
+<a name="l00040"></a>00040 <span class="preprocessor"></span><span class="preprocessor">#define CCP4SRS_DEFS_H</span>
+<a name="l00041"></a>00041 <span class="preprocessor"></span>
+<a name="l00042"></a>00042 <span class="comment">// THIS FILE SHOULD BE NEVER UNCLUDED IN HEADERS. USE CCP4SRS_TYPES.H</span>
+<a name="l00043"></a>00043 <span class="comment">// INSTEAD</span>
+<a name="l00044"></a>00044 
+<a name="l00045"></a>00045 <span class="comment">//  mmCIF tags</span>
+<a name="l00046"></a><a class="code" href="ccp4srs__defs_8h.html#aefbf24090a7fbe6109d4e58390f1aae4">00046</a> <span class="preprocessor">#define MMCIF_COMP                   &quot;comp_&quot;</span>
+<a name="l00047"></a><a class="code" href="ccp4srs__defs_8h.html#a0f3964efb8ec1746a152fa5aac689273">00047</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_Name               &quot;name&quot;</span>
+<a name="l00048"></a><a class="code" href="ccp4srs__defs_8h.html#a20179e20def570d67ea892e8cd3bd666">00048</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_Type               &quot;type&quot;</span>
+<a name="l00049"></a><a class="code" href="ccp4srs__defs_8h.html#a5cf744094676b0bd89430c485933f6fb">00049</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_Formula            &quot;formula&quot;</span>
+<a name="l00050"></a>00050 <span class="preprocessor"></span>
+<a name="l00051"></a><a class="code" href="ccp4srs__defs_8h.html#ae071049f6b4c72d884d50a7fb00c796b">00051</a> <span class="preprocessor">#define MMCIF_STRUCT_CHEM_COMP       &quot;_chem_comp&quot;</span>
+<a name="l00052"></a>00052 <span class="preprocessor"></span>
+<a name="l00053"></a><a class="code" href="ccp4srs__defs_8h.html#a96f3d7ae6d26ccb1b693b687f85ff382">00053</a> <span class="preprocessor">#define MMCIF_LOOP_CHEM_COMP_ATOM    &quot;_chem_comp_atom&quot;</span>
+<a name="l00054"></a><a class="code" href="ccp4srs__defs_8h.html#a70bb9ac01714d5ddf96f030e39fc925d">00054</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_COMP_ID            &quot;comp_id&quot;</span>
+<a name="l00055"></a><a class="code" href="ccp4srs__defs_8h.html#a0063d4d4b2407acb4c5e962e937d987c">00055</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_ATOM_ID            &quot;atom_id&quot;</span>
+<a name="l00056"></a><a class="code" href="ccp4srs__defs_8h.html#abf103686dc23d212a4dd43ebe9883f36">00056</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_ALT_ATOM_ID        &quot;alt_atom_id&quot;</span>
+<a name="l00057"></a><a class="code" href="ccp4srs__defs_8h.html#a681fa0489227ecf64eee279db3a2f21b">00057</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_TYPE_SYMBOL        &quot;type_symbol&quot;</span>
+<a name="l00058"></a><a class="code" href="ccp4srs__defs_8h.html#a9e64e930d30f442af1eb427927297fad">00058</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_TYPE_ENERGY        &quot;type_energy&quot;</span>
+<a name="l00059"></a><a class="code" href="ccp4srs__defs_8h.html#a2b31545950368db39b67371d64cbbef7">00059</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_PARTIAL_CHARGE     &quot;partial_charge&quot;</span>
+<a name="l00060"></a><a class="code" href="ccp4srs__defs_8h.html#ae9e78e9a02868061bee6c1a6b45453ca">00060</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_X                  &quot;x&quot;</span>
+<a name="l00061"></a><a class="code" href="ccp4srs__defs_8h.html#ac08945b8f7b2dabe39335c716edc8266">00061</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_Y                  &quot;y&quot;</span>
+<a name="l00062"></a><a class="code" href="ccp4srs__defs_8h.html#ab3af4414a670e8553431994f5ba24aab">00062</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_Z                  &quot;z&quot;</span>
+<a name="l00063"></a><a class="code" href="ccp4srs__defs_8h.html#a84559f7c12aa9f1a387b8f530264ab16">00063</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_MODEL_CARTN_X      &quot;model_Cartn_x&quot;</span>
+<a name="l00064"></a><a class="code" href="ccp4srs__defs_8h.html#af0b16d01af53acaed091894e08162b54">00064</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_MODEL_CARTN_Y      &quot;model_Cartn_y&quot;</span>
+<a name="l00065"></a><a class="code" href="ccp4srs__defs_8h.html#a252481f6fc180b9d746ef063c9a3609c">00065</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_MODEL_CARTN_Z      &quot;model_Cartn_z&quot;</span>
+<a name="l00066"></a><a class="code" href="ccp4srs__defs_8h.html#a0993df52ba1ecc98ca2591a8392ffee6">00066</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_PDBX_MODEL_CARTN_X &quot;pdbx_model_Cartn_x&quot;</span>
+<a name="l00067"></a><a class="code" href="ccp4srs__defs_8h.html#a56fcc86c982c756f3573ecd213c149d9">00067</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_PDBX_MODEL_CARTN_Y &quot;pdbx_model_Cartn_y&quot;</span>
+<a name="l00068"></a><a class="code" href="ccp4srs__defs_8h.html#a5cbd04910c2725cdc0c72531dfd38cac">00068</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_PDBX_MODEL_CARTN_Z &quot;pdbx_model_Cartn_z&quot;</span>
+<a name="l00069"></a>00069 <span class="preprocessor"></span>
+<a name="l00070"></a><a class="code" href="ccp4srs__defs_8h.html#ad753a24e5bb150fc4cc1161dcc31111a">00070</a> <span class="preprocessor">#define MMCIF_TAG_PDBX_STEREO_CONFIG     &quot;pdbx_stereo_config&quot;</span>
+<a name="l00071"></a><a class="code" href="ccp4srs__defs_8h.html#a3a906be28069a81e9429b36c1cfc2edc">00071</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_PDBX_LEAVING_ATOM_FLAG &quot;pdbx_leaving_atom_flag&quot;</span>
+<a name="l00072"></a><a class="code" href="ccp4srs__defs_8h.html#a9207204b4fac4b0f5587e33a56d6aca5">00072</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_PDBX_AROMATIC_FLAG     &quot;pdbx_aromatic_flag&quot;</span>
+<a name="l00073"></a><a class="code" href="ccp4srs__defs_8h.html#a7b962f3e20a4c60f50b720aaaf483080">00073</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_VALUE_ORDER            &quot;value_order&quot;</span>
+<a name="l00074"></a>00074 <span class="preprocessor"></span>
+<a name="l00075"></a><a class="code" href="ccp4srs__defs_8h.html#ab82eb4b740280944b8fbe74362121d2f">00075</a> <span class="preprocessor">#define MMCIF_LOOP_CHEM_COMP_TREE   &quot;_chem_comp_tree&quot;</span>
+<a name="l00076"></a><a class="code" href="ccp4srs__defs_8h.html#a2fc723c8a3cb4d9aecd670de41e006e5">00076</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_ATOM_BACK         &quot;atom_back&quot;</span>
+<a name="l00077"></a><a class="code" href="ccp4srs__defs_8h.html#a07c7f15b018109563b8dde9b59484568">00077</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_ATOM_FORWARD      &quot;atom_forward&quot;</span>
+<a name="l00078"></a><a class="code" href="ccp4srs__defs_8h.html#aaf8c20eee68a9718052502c7ddb35c16">00078</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_CONNECT_TYPE      &quot;connect_type&quot;</span>
+<a name="l00079"></a>00079 <span class="preprocessor"></span>
+<a name="l00080"></a><a class="code" href="ccp4srs__defs_8h.html#a442e6c574a7a90cf6955d1ca8e4cf18f">00080</a> <span class="preprocessor">#define MMCIF_LOOP_CHEM_COMP_BOND   &quot;_chem_comp_bond&quot;</span>
+<a name="l00081"></a><a class="code" href="ccp4srs__defs_8h.html#a379e5bcb509192bb36b833265f32ff9b">00081</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_ATOM_ID_1          &quot;atom_id_1&quot;</span>
+<a name="l00082"></a><a class="code" href="ccp4srs__defs_8h.html#ac01791d945ab084eecb5cb33e9d0232c">00082</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_ATOM_ID_2          &quot;atom_id_2&quot;</span>
+<a name="l00083"></a><a class="code" href="ccp4srs__defs_8h.html#af5de8de3a7e69bd50f9c8ee2a7c9c53a">00083</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_TYPE               &quot;type&quot;</span>
+<a name="l00084"></a><a class="code" href="ccp4srs__defs_8h.html#a36bc56204ef3bc3ab0b33754e8e791fb">00084</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_VALUE_DIST         &quot;value_dist&quot;</span>
+<a name="l00085"></a><a class="code" href="ccp4srs__defs_8h.html#a773a38551554ef102c997ba5e391c101">00085</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_VALUE_DIST_ESD     &quot;value_dist_esd&quot;</span>
+<a name="l00086"></a>00086 <span class="preprocessor"></span>
+<a name="l00087"></a><a class="code" href="ccp4srs__defs_8h.html#ad95350f455f90a8b546d688a1b7604d2">00087</a> <span class="preprocessor">#define MMCIF_LOOP_CHEM_COMP_ANGLE   &quot;_chem_comp_angle&quot;</span>
+<a name="l00088"></a><a class="code" href="ccp4srs__defs_8h.html#a5a61b6835d1309e469feb356e2695388">00088</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_ATOM_ID_3          &quot;atom_id_3&quot;</span>
+<a name="l00089"></a><a class="code" href="ccp4srs__defs_8h.html#ac8d6aed8f4893094ad1dac7790505a30">00089</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_VALUE_ANGLE        &quot;value_angle&quot;</span>
+<a name="l00090"></a><a class="code" href="ccp4srs__defs_8h.html#a63fccdc102c24817b6dcef20a4135187">00090</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_VALUE_ANGLE_ESD    &quot;value_angle_esd&quot;</span>
+<a name="l00091"></a>00091 <span class="preprocessor"></span>
+<a name="l00092"></a><a class="code" href="ccp4srs__defs_8h.html#a745441f40029534d9996304227bc0d5c">00092</a> <span class="preprocessor">#define MMCIF_LOOP_CHEM_COMP_CHIR    &quot;_chem_comp_chir&quot;</span>
+<a name="l00093"></a><a class="code" href="ccp4srs__defs_8h.html#acb2e2c33e267f4d67aa3550454a6400c">00093</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_ID                 &quot;id&quot;</span>
+<a name="l00094"></a><a class="code" href="ccp4srs__defs_8h.html#a20c0ca81595c8d02438d80c53033f99d">00094</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_ATOM_ID_CENTRE     &quot;atom_id_centre&quot;</span>
+<a name="l00095"></a><a class="code" href="ccp4srs__defs_8h.html#ace32f1cd1f6052d3cd1d78c18835016c">00095</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_VOLUME_SIGN        &quot;volume_sign&quot;</span>
+<a name="l00096"></a>00096 <span class="preprocessor"></span>
+<a name="l00097"></a><a class="code" href="ccp4srs__defs_8h.html#aed5250676b70b953e859e148a46d26b2">00097</a> <span class="preprocessor">#define MMCIF_LOOP_CHEM_COMP_TOR     &quot;_chem_comp_tor&quot;</span>
+<a name="l00098"></a><a class="code" href="ccp4srs__defs_8h.html#a0c93c9f5f166a7c389a0d6a6be3fd3b4">00098</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_ATOM_ID_4          &quot;atom_id_4&quot;</span>
+<a name="l00099"></a><a class="code" href="ccp4srs__defs_8h.html#ad7d263713c3571c9b1597ac2ffdceb8c">00099</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_PERIOD             &quot;period&quot;</span>
+<a name="l00100"></a>00100 <span class="preprocessor"></span>
+<a name="l00101"></a><a class="code" href="ccp4srs__defs_8h.html#a66aec28ad11df2c52c17f89e854d3717">00101</a> <span class="preprocessor">#define MMCIF_LOOP_CHEM_COMP_PLANE_ATOM  &quot;_chem_comp_plane_atom&quot;</span>
+<a name="l00102"></a><a class="code" href="ccp4srs__defs_8h.html#a727023c5a08af92c674e88a97d3361f1">00102</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_PLANE_ID               &quot;plane_id&quot;</span>
+<a name="l00103"></a><a class="code" href="ccp4srs__defs_8h.html#a410537d70cb039747f3bd8a36a52f553">00103</a> <span class="preprocessor"></span><span class="preprocessor">#define MMCIF_TAG_DIST_ESD               &quot;dist_esd&quot;</span>
+<a name="l00104"></a>00104 <span class="preprocessor"></span>
+<a name="l00105"></a>00105 
+<a name="l00106"></a>00106 <span class="comment">//   Entry types</span>
+<a name="l00107"></a>00107 <span class="comment">/*</span>
+<a name="l00108"></a>00108 <span class="comment">#define CCP4SRS_Entry_None        0x00</span>
+<a name="l00109"></a>00109 <span class="comment">#define CCP4SRS_Entry_Structure   0x01</span>
+<a name="l00110"></a>00110 <span class="comment">#define CCP4SRS_Entry_Link        0x02</span>
+<a name="l00111"></a>00111 <span class="comment">*/</span>
+<a name="l00112"></a>00112 
+<a name="l00113"></a>00113 <span class="preprocessor">#endif // CCP4SRS_DEFS_H</span>
+</pre></div></div>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__entry_8cpp.html ccp4srs/doc-html/html/ccp4srs__entry_8cpp.html
--- ccp4srs-old/doc-html/html/ccp4srs__entry_8cpp.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__entry_8cpp.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,81 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/ccp4srs_entry.cpp File Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
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+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
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+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
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+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="files.html"><span>File&#160;List</span></a></li>
+      <li><a href="globals.html"><span>File&#160;Members</span></a></li>
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+<a href="#namespaces">Namespaces</a>  </div>
+  <div class="headertitle">
+<h1>src/ccp4srs_entry.cpp File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &quot;<a class="el" href="ccp4srs__entry_8h_source.html">ccp4srs_entry.h</a>&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__defs_8h_source.html">ccp4srs_defs.h</a>&quot;</code><br/>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
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+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
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+</html>
diff -ruN ccp4srs-old/doc-html/html/ccp4srs__entry_8h.html ccp4srs/doc-html/html/ccp4srs__entry_8h.html
--- ccp4srs-old/doc-html/html/ccp4srs__entry_8h.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__entry_8h.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,90 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/ccp4srs_entry.h File Reference</title>
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+<link href="search/search.css" rel="stylesheet" type="text/css"/>
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+      <li><a href="files.html"><span>File&#160;List</span></a></li>
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+<a href="#func-members">Functions</a>  </div>
+  <div class="headertitle">
+<h1>src/ccp4srs_entry.h File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &quot;<a class="el" href="memio___8h_source.html">memio_.h</a>&quot;</code><br/>
+
+<p><a href="ccp4srs__entry_8h_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="nested-classes"></a>
+Classes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_entry.html">ccp4srs::Entry</a></td></tr>
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+<tr><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#aa72ee17a81ce821f1c37483a10153ae7">ccp4srs::DefineClass</a> (Entry)</td></tr>
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+
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+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
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+</html>
diff -ruN ccp4srs-old/doc-html/html/ccp4srs__entry_8h_source.html ccp4srs/doc-html/html/ccp4srs__entry_8h_source.html
--- ccp4srs-old/doc-html/html/ccp4srs__entry_8h_source.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__entry_8h_source.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,146 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/ccp4srs_entry.h Source File</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
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+          <img id="MSearchSelect" src="search/mag_sel.png"
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+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
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+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="files.html"><span>File&#160;List</span></a></li>
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+    </ul>
+  </div>
+<div class="header">
+  <div class="headertitle">
+<h1>src/ccp4srs_entry.h</h1>  </div>
+</div>
+<div class="contents">
+<a href="ccp4srs__entry_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">//  $Id: ccp4srs_entry.h $</span>
+<a name="l00002"></a>00002 <span class="comment">//  =================================================================</span>
+<a name="l00003"></a>00003 <span class="comment">//</span>
+<a name="l00004"></a>00004 <span class="comment">//   CCP4 SRS Library: Storage, Retrieval and Search support for</span>
+<a name="l00005"></a>00005 <span class="comment">//   CCP4 ligand data.</span>
+<a name="l00006"></a>00006 <span class="comment">//</span>
+<a name="l00007"></a>00007 <span class="comment">//   Copyright (C) Eugene Krissinel 2010-2013.</span>
+<a name="l00008"></a>00008 <span class="comment">//</span>
+<a name="l00009"></a>00009 <span class="comment">//   This library is free software: you can redistribute it and/or</span>
+<a name="l00010"></a>00010 <span class="comment">//   modify it under the terms of the GNU Lesser General Public</span>
+<a name="l00011"></a>00011 <span class="comment">//   License version 3, modified in accordance with the provisions</span>
+<a name="l00012"></a>00012 <span class="comment">//   of the license to address the requirements of UK law.</span>
+<a name="l00013"></a>00013 <span class="comment">//</span>
+<a name="l00014"></a>00014 <span class="comment">//   You should have received a copy of the modified GNU Lesser</span>
+<a name="l00015"></a>00015 <span class="comment">//   General Public License along with this library. If not, copies</span>
+<a name="l00016"></a>00016 <span class="comment">//   may be downloaded from http://www.ccp4.ac.uk/ccp4license.php</span>
+<a name="l00017"></a>00017 <span class="comment">//</span>
+<a name="l00018"></a>00018 <span class="comment">//   This program is distributed in the hope that it will be useful,</span>
+<a name="l00019"></a>00019 <span class="comment">//   but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
+<a name="l00020"></a>00020 <span class="comment">//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
+<a name="l00021"></a>00021 <span class="comment">//   GNU Lesser General Public License for more details.</span>
+<a name="l00022"></a>00022 <span class="comment">//</span>
+<a name="l00023"></a>00023 <span class="comment">//  =================================================================</span>
+<a name="l00024"></a>00024 <span class="comment">//</span>
+<a name="l00025"></a>00025 <span class="comment">//    18.09.13   &lt;--  Date of Last Modification.</span>
+<a name="l00026"></a>00026 <span class="comment">//                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
+<a name="l00027"></a>00027 <span class="comment">//  -----------------------------------------------------------------</span>
+<a name="l00028"></a>00028 <span class="comment">//</span>
+<a name="l00029"></a>00029 <span class="comment">//  **** Module  :  ccp4srs_entry  &lt;interface&gt;</span>
+<a name="l00030"></a>00030 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00031"></a>00031 <span class="comment">//  **** Classes :  ccp4srs::Entry  - base class for all SRS entries</span>
+<a name="l00032"></a>00032 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00033"></a>00033 <span class="comment">//</span>
+<a name="l00034"></a>00034 <span class="comment">//  (C) E. Krissinel 2010-2013</span>
+<a name="l00035"></a>00035 <span class="comment">//</span>
+<a name="l00036"></a>00036 <span class="comment">//  =================================================================</span>
+<a name="l00037"></a>00037 <span class="comment">//</span>
+<a name="l00038"></a>00038 
+<a name="l00039"></a>00039 <span class="preprocessor">#ifndef CCP4SRS_ENTRY_H</span>
+<a name="l00040"></a>00040 <span class="preprocessor"></span><span class="preprocessor">#define CCP4SRS_ENTRY_H</span>
+<a name="l00041"></a>00041 <span class="preprocessor"></span>
+<a name="l00042"></a>00042 <span class="preprocessor">#include &quot;<a class="code" href="memio___8h.html">memio_.h</a>&quot;</span>
+<a name="l00043"></a>00043 
+<a name="l00044"></a>00044 <span class="keyword">namespace </span>ccp4srs  {
+<a name="l00045"></a>00045 
+<a name="l00046"></a>00046   <a class="code" href="namespaceccp4srs.html#afbb5df60616f08fcf36926a3585c185f">DefineClass</a>(Entry);
+<a name="l00047"></a>00047 
+<a name="l00048"></a><a class="code" href="classccp4srs_1_1_entry.html">00048</a>   <span class="keyword">class </span><a class="code" href="classccp4srs_1_1_entry.html">Entry</a>  {
+<a name="l00049"></a>00049 
+<a name="l00050"></a>00050     <span class="keyword">public</span>:
+<a name="l00051"></a>00051 
+<a name="l00052"></a>00052       <span class="comment">// entry types</span>
+<a name="l00053"></a><a class="code" href="classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88ca616c951330c4d0b080622857146e2457">00053</a>       <span class="keyword">enum</span> {<a class="code" href="classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88ca616c951330c4d0b080622857146e2457">None</a>,<a class="code" href="classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88ca447bc9153594c5d2b79e47041f4982b6">Monomer</a>,<a class="code" href="classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88cae7d526eebfeb15c8370f473885073095">Link</a>};
+<a name="l00054"></a>00054 
+<a name="l00055"></a>00055       <a class="code" href="classccp4srs_1_1_entry.html#aa72cb70c4f1c115a2134e2da80b9bc34">Entry</a>();
+<a name="l00056"></a>00056       <span class="keyword">virtual</span> <a class="code" href="classccp4srs_1_1_entry.html#a191661efae468b8e2a62b69a247bcd3a">~Entry</a>();
+<a name="l00057"></a>00057 
+<a name="l00058"></a><a class="code" href="classccp4srs_1_1_entry.html#a401d0e96699c34bef6b408e054f14540">00058</a>       <span class="keyword">virtual</span> <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_entry.html#a401d0e96699c34bef6b408e054f14540">type</a>()  { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88ca616c951330c4d0b080622857146e2457">Entry::None</a>; }
+<a name="l00059"></a>00059 
+<a name="l00060"></a>00060       <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_entry.html#a46d1eaa50c45f6e40ff054b30b93790d">write</a> ( mmdb::io::RFile f, <span class="keywordtype">int</span> version, PMemIO memIO=NULL );
+<a name="l00061"></a>00061       <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_entry.html#a262e2814d9a1bc35fbbfd75e46397343">read</a>  ( mmdb::io::RFile f, <span class="keywordtype">int</span> version, PMemIO memIO=NULL );
+<a name="l00062"></a>00062 
+<a name="l00063"></a>00063     <span class="keyword">protected</span>:
+<a name="l00064"></a>00064 
+<a name="l00065"></a>00065       <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_entry.html#a817f6f566baf41280c5cee0fc3507871">write_mem</a> ( PMemIO memIO, <span class="keywordtype">int</span> version );
+<a name="l00066"></a>00066       <span class="keyword">virtual</span> <span class="keywordtype">bool</span> <a class="code" href="classccp4srs_1_1_entry.html#a2d3193b4e34c21b286526931e2e5b62d">read_mem</a>  ( PMemIO memIO, <span class="keywordtype">int</span> version,
+<a name="l00067"></a>00067                                <span class="keywordtype">bool</span> * Ok = NULL );
+<a name="l00068"></a>00068 
+<a name="l00069"></a>00069   };
+<a name="l00070"></a>00070 
+<a name="l00071"></a>00071 }  <span class="comment">// namespace ccp4srs</span>
+<a name="l00072"></a>00072 
+<a name="l00073"></a>00073 
+<a name="l00074"></a>00074 <span class="preprocessor">#endif // CCP4SRS_ENTRY_H</span>
+</pre></div></div>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__index_8cpp.html ccp4srs/doc-html/html/ccp4srs__index_8cpp.html
--- ccp4srs-old/doc-html/html/ccp4srs__index_8cpp.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__index_8cpp.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,82 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/ccp4srs_index.cpp File Reference</title>
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+<link href="search/search.css" rel="stylesheet" type="text/css"/>
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+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
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+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
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+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="files.html"><span>File&#160;List</span></a></li>
+      <li><a href="globals.html"><span>File&#160;Members</span></a></li>
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+<a href="#namespaces">Namespaces</a>  </div>
+  <div class="headertitle">
+<h1>src/ccp4srs_index.cpp File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &lt;string.h&gt;</code><br/>
+<code>#include &quot;mmdb/mmdb_tables.h&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__index_8h_source.html">ccp4srs_index.h</a>&quot;</code><br/>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+</table>
+</div>
+<!--- window showing the filter options -->
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+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/ccp4srs__index_8h.html ccp4srs/doc-html/html/ccp4srs__index_8h.html
--- ccp4srs-old/doc-html/html/ccp4srs__index_8h.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__index_8h.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,90 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/ccp4srs_index.h File Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
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+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
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+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
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+               onfocus="searchBox.OnSearchFieldFocus(true)" 
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+    <ul class="tablist">
+      <li><a href="files.html"><span>File&#160;List</span></a></li>
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+<a href="#nested-classes">Classes</a> &#124;
+<a href="#namespaces">Namespaces</a> &#124;
+<a href="#func-members">Functions</a>  </div>
+  <div class="headertitle">
+<h1>src/ccp4srs_index.h File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &quot;<a class="el" href="ccp4srs__monomer_8h_source.html">ccp4srs_monomer.h</a>&quot;</code><br/>
+
+<p><a href="ccp4srs__index_8h_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="nested-classes"></a>
+Classes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_index.html">ccp4srs::Index</a></td></tr>
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+<tr><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#afeba477403b4f346ef1c74ab27c0a797">ccp4srs::DefineClass</a> (Index)</td></tr>
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+
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+<a href="http://www.doxygen.org/index.html">
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__index_8h_source.html ccp4srs/doc-html/html/ccp4srs__index_8h_source.html
--- ccp4srs-old/doc-html/html/ccp4srs__index_8h_source.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__index_8h_source.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,153 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/ccp4srs_index.h Source File</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
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+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
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+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
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+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
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+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="files.html"><span>File&#160;List</span></a></li>
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+    </ul>
+  </div>
+<div class="header">
+  <div class="headertitle">
+<h1>src/ccp4srs_index.h</h1>  </div>
+</div>
+<div class="contents">
+<a href="ccp4srs__index_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">//  $Id: ccp4srs_index.h $</span>
+<a name="l00002"></a>00002 <span class="comment">//  =================================================================</span>
+<a name="l00003"></a>00003 <span class="comment">//</span>
+<a name="l00004"></a>00004 <span class="comment">//   CCP4 SRS Library: Storage, Retrieval and Search support for</span>
+<a name="l00005"></a>00005 <span class="comment">//   CCP4 ligand data.</span>
+<a name="l00006"></a>00006 <span class="comment">//</span>
+<a name="l00007"></a>00007 <span class="comment">//   Copyright (C) Eugene Krissinel 2010-2013.</span>
+<a name="l00008"></a>00008 <span class="comment">//</span>
+<a name="l00009"></a>00009 <span class="comment">//   This library is free software: you can redistribute it and/or</span>
+<a name="l00010"></a>00010 <span class="comment">//   modify it under the terms of the GNU Lesser General Public</span>
+<a name="l00011"></a>00011 <span class="comment">//   License version 3, modified in accordance with the provisions</span>
+<a name="l00012"></a>00012 <span class="comment">//   of the license to address the requirements of UK law.</span>
+<a name="l00013"></a>00013 <span class="comment">//</span>
+<a name="l00014"></a>00014 <span class="comment">//   You should have received a copy of the modified GNU Lesser</span>
+<a name="l00015"></a>00015 <span class="comment">//   General Public License along with this library. If not, copies</span>
+<a name="l00016"></a>00016 <span class="comment">//   may be downloaded from http://www.ccp4.ac.uk/ccp4license.php</span>
+<a name="l00017"></a>00017 <span class="comment">//</span>
+<a name="l00018"></a>00018 <span class="comment">//   This program is distributed in the hope that it will be useful,</span>
+<a name="l00019"></a>00019 <span class="comment">//   but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
+<a name="l00020"></a>00020 <span class="comment">//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
+<a name="l00021"></a>00021 <span class="comment">//   GNU Lesser General Public License for more details.</span>
+<a name="l00022"></a>00022 <span class="comment">//</span>
+<a name="l00023"></a>00023 <span class="comment">//  =================================================================</span>
+<a name="l00024"></a>00024 <span class="comment">//</span>
+<a name="l00025"></a>00025 <span class="comment">//    18.09.13   &lt;--  Date of Last Modification.</span>
+<a name="l00026"></a>00026 <span class="comment">//                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
+<a name="l00027"></a>00027 <span class="comment">//  -----------------------------------------------------------------</span>
+<a name="l00028"></a>00028 <span class="comment">//</span>
+<a name="l00029"></a>00029 <span class="comment">//  **** Module  :  ccp4srs_index  &lt;interface&gt;</span>
+<a name="l00030"></a>00030 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00031"></a>00031 <span class="comment">//  **** Classes :  ccp4srs::Index - SRS data index class</span>
+<a name="l00032"></a>00032 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00033"></a>00033 <span class="comment">//</span>
+<a name="l00034"></a>00034 <span class="comment">//  (C) E. Krissinel 2010-2013</span>
+<a name="l00035"></a>00035 <span class="comment">//</span>
+<a name="l00036"></a>00036 <span class="comment">//  =================================================================</span>
+<a name="l00037"></a>00037 <span class="comment">//</span>
+<a name="l00038"></a>00038 
+<a name="l00039"></a>00039 <span class="preprocessor">#ifndef CCP4SRS_INDEX_H</span>
+<a name="l00040"></a>00040 <span class="preprocessor"></span><span class="preprocessor">#define CCP4SRS_INDEX_H</span>
+<a name="l00041"></a>00041 <span class="preprocessor"></span>
+<a name="l00042"></a>00042 <span class="preprocessor">#include &quot;<a class="code" href="ccp4srs__monomer_8h.html">ccp4srs_monomer.h</a>&quot;</span>
+<a name="l00043"></a>00043 
+<a name="l00044"></a>00044 <span class="keyword">namespace </span>ccp4srs  {
+<a name="l00045"></a>00045 
+<a name="l00046"></a>00046   <a class="code" href="namespaceccp4srs.html#afbb5df60616f08fcf36926a3585c185f">DefineClass</a>(Index);
+<a name="l00047"></a>00047 
+<a name="l00048"></a><a class="code" href="classccp4srs_1_1_index.html">00048</a>   <span class="keyword">class </span><a class="code" href="classccp4srs_1_1_index.html">Index</a>  {
+<a name="l00049"></a>00049 
+<a name="l00050"></a>00050     <span class="keyword">public</span> :
+<a name="l00051"></a><a class="code" href="classccp4srs_1_1_index.html#a0bd1aedcf3b32bdd48d0de5cd2cc563e">00051</a>       mmdb::ResName <a class="code" href="classccp4srs_1_1_index.html#a0bd1aedcf3b32bdd48d0de5cd2cc563e" title="monomer or link ID">entryID</a>;    
+<a name="l00052"></a><a class="code" href="classccp4srs_1_1_index.html#abba65d2d400f004fa3815a06101ac478">00052</a>       <span class="keywordtype">int</span>           <a class="code" href="classccp4srs_1_1_index.html#abba65d2d400f004fa3815a06101ac478" title="number of atoms in the entry">nAtoms</a>;     
+<a name="l00053"></a><a class="code" href="classccp4srs_1_1_index.html#aa97eb5251314eeb77e5acd2af72ce1aa">00053</a>       <span class="keywordtype">int</span>           <a class="code" href="classccp4srs_1_1_index.html#aa97eb5251314eeb77e5acd2af72ce1aa" title="number of non-hydrogen atoms in the entry">nNonHAtoms</a>; 
+<a name="l00054"></a><a class="code" href="classccp4srs_1_1_index.html#a5906658999e6e4e095589e0cdffabf11">00054</a>       <span class="keywordtype">int</span>           <a class="code" href="classccp4srs_1_1_index.html#a5906658999e6e4e095589e0cdffabf11" title="number of bonds in the entry">nBonds</a>;     
+<a name="l00055"></a><a class="code" href="classccp4srs_1_1_index.html#a3be74bae1c6afc52ea36690b45ec5b96">00055</a>       <span class="keywordtype">long</span>          <a class="code" href="classccp4srs_1_1_index.html#a3be74bae1c6afc52ea36690b45ec5b96" title="file offset for CGraph">fGraphPos</a>;  
+<a name="l00056"></a><a class="code" href="classccp4srs_1_1_index.html#a21a1eddc77e99baf8df0b7450dee548b">00056</a>       <span class="keywordtype">long</span>          <a class="code" href="classccp4srs_1_1_index.html#a21a1eddc77e99baf8df0b7450dee548b" title="file offset for CCP4SRSMonomer">fStructPos</a>; 
+<a name="l00057"></a><a class="code" href="classccp4srs_1_1_index.html#af2a41a666517311e8877a3ec9e288916">00057</a>       mmdb::pstr    <a class="code" href="classccp4srs_1_1_index.html#af2a41a666517311e8877a3ec9e288916" title="composition string">Comp1</a>;      
+<a name="l00058"></a><a class="code" href="classccp4srs_1_1_index.html#af4ce5b42fe2cf6364f9916d0a42f08b2">00058</a>       mmdb::pstr    <a class="code" href="classccp4srs_1_1_index.html#af4ce5b42fe2cf6364f9916d0a42f08b2" title="composition string with leaving atom">Comp2</a>;      
+<a name="l00059"></a>00059 
+<a name="l00060"></a>00060       <a class="code" href="classccp4srs_1_1_index.html#aaff51df26ae81aff0425bda97d6f7030">Index</a> ();
+<a name="l00061"></a>00061       <span class="keyword">virtual</span> <a class="code" href="classccp4srs_1_1_index.html#a5a0d5db83db471eae5aa87dcfa6a151c">~Index</a>();
+<a name="l00062"></a>00062 
+<a name="l00063"></a>00063       <span class="keywordtype">int</span>   <a class="code" href="classccp4srs_1_1_index.html#afda5436941f171c791be43b9d28f43a5">MakeCompositions</a> ( PMonomer monomer );
+<a name="l00064"></a>00064 
+<a name="l00065"></a>00065       <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_index.html#a2d6f487a5a3e945f92b90fc6f034f08b">write</a> ( mmdb::io::RFile f, <span class="keywordtype">int</span> version, PMemIO memIO=NULL );
+<a name="l00066"></a>00066       <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_index.html#a17c3250780def030676fef212a19731c">read</a>  ( mmdb::io::RFile f, <span class="keywordtype">int</span> version, PMemIO memIO=NULL );
+<a name="l00067"></a>00067 
+<a name="l00068"></a>00068     <span class="keyword">protected</span>:
+<a name="l00069"></a>00069 
+<a name="l00070"></a>00070       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_index.html#aedec88e9928356d4f7c913d449ca0d3e">IndexInit</a>();
+<a name="l00071"></a>00071 
+<a name="l00072"></a>00072       <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_index.html#a5591c13f7296928d053492322b8bd02b">write_mem</a> ( PMemIO memIO, <span class="keywordtype">int</span> version );
+<a name="l00073"></a>00073       <span class="keyword">virtual</span> <span class="keywordtype">bool</span> <a class="code" href="classccp4srs_1_1_index.html#a06b50353c15a21a56688b3e00aad2e2d">read_mem</a>  ( PMemIO memIO, <span class="keywordtype">int</span> version,
+<a name="l00074"></a>00074                                <span class="keywordtype">bool</span> * Ok = NULL );
+<a name="l00075"></a>00075 
+<a name="l00076"></a>00076   };
+<a name="l00077"></a>00077 
+<a name="l00078"></a>00078 }  <span class="comment">// namespace ccp4srs</span>
+<a name="l00079"></a>00079 
+<a name="l00080"></a>00080 
+<a name="l00081"></a>00081 <span class="preprocessor">#endif // CCP4SRS_INDEX_H</span>
+</pre></div></div>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__manager_8cpp.html ccp4srs/doc-html/html/ccp4srs__manager_8cpp.html
--- ccp4srs-old/doc-html/html/ccp4srs__manager_8cpp.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__manager_8cpp.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,81 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/ccp4srs_manager.cpp File Reference</title>
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+  <div class="headertitle">
+<h1>src/ccp4srs_manager.cpp File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &lt;string.h&gt;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__manager_8h_source.html">ccp4srs_manager.h</a>&quot;</code><br/>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__manager_8h.html ccp4srs/doc-html/html/ccp4srs__manager_8h.html
--- ccp4srs-old/doc-html/html/ccp4srs__manager_8h.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__manager_8h.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,90 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
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+<a href="#func-members">Functions</a>  </div>
+  <div class="headertitle">
+<h1>src/ccp4srs_manager.h File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &quot;<a class="el" href="ccp4srs__chem_8h_source.html">ccp4srs_chem.h</a>&quot;</code><br/>
+
+<p><a href="ccp4srs__manager_8h_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="nested-classes"></a>
+Classes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_manager.html">ccp4srs::Manager</a></td></tr>
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+<tr><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a8c36728a6d09c1cb65fe3168735979cb">ccp4srs::DefineClass</a> (Manager)</td></tr>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__manager_8h_source.html ccp4srs/doc-html/html/ccp4srs__manager_8h_source.html
--- ccp4srs-old/doc-html/html/ccp4srs__manager_8h_source.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__manager_8h_source.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,132 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<h1>src/ccp4srs_manager.h</h1>  </div>
+</div>
+<div class="contents">
+<a href="ccp4srs__manager_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">//  $Id: ccp4srs_manager.h $</span>
+<a name="l00002"></a>00002 <span class="comment">//  =================================================================</span>
+<a name="l00003"></a>00003 <span class="comment">//</span>
+<a name="l00004"></a>00004 <span class="comment">//   CCP4 SRS Library: Storage, Retrieval and Search support for</span>
+<a name="l00005"></a>00005 <span class="comment">//   CCP4 ligand data.</span>
+<a name="l00006"></a>00006 <span class="comment">//</span>
+<a name="l00007"></a>00007 <span class="comment">//   Copyright (C) Eugene Krissinel 2010-2013.</span>
+<a name="l00008"></a>00008 <span class="comment">//</span>
+<a name="l00009"></a>00009 <span class="comment">//   This library is free software: you can redistribute it and/or</span>
+<a name="l00010"></a>00010 <span class="comment">//   modify it under the terms of the GNU Lesser General Public</span>
+<a name="l00011"></a>00011 <span class="comment">//   License version 3, modified in accordance with the provisions</span>
+<a name="l00012"></a>00012 <span class="comment">//   of the license to address the requirements of UK law.</span>
+<a name="l00013"></a>00013 <span class="comment">//</span>
+<a name="l00014"></a>00014 <span class="comment">//   You should have received a copy of the modified GNU Lesser</span>
+<a name="l00015"></a>00015 <span class="comment">//   General Public License along with this library. If not, copies</span>
+<a name="l00016"></a>00016 <span class="comment">//   may be downloaded from http://www.ccp4.ac.uk/ccp4license.php</span>
+<a name="l00017"></a>00017 <span class="comment">//</span>
+<a name="l00018"></a>00018 <span class="comment">//   This program is distributed in the hope that it will be useful,</span>
+<a name="l00019"></a>00019 <span class="comment">//   but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
+<a name="l00020"></a>00020 <span class="comment">//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
+<a name="l00021"></a>00021 <span class="comment">//   GNU Lesser General Public License for more details.</span>
+<a name="l00022"></a>00022 <span class="comment">//</span>
+<a name="l00023"></a>00023 <span class="comment">//  =================================================================</span>
+<a name="l00024"></a>00024 <span class="comment">//</span>
+<a name="l00025"></a>00025 <span class="comment">//    18.09.13   &lt;--  Date of Last Modification.</span>
+<a name="l00026"></a>00026 <span class="comment">//                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
+<a name="l00027"></a>00027 <span class="comment">//  -----------------------------------------------------------------</span>
+<a name="l00028"></a>00028 <span class="comment">//</span>
+<a name="l00029"></a>00029 <span class="comment">//  **** Module  :  ccp4srs_manager  &lt;interface&gt;</span>
+<a name="l00030"></a>00030 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00031"></a>00031 <span class="comment">//  **** Classes :  ccp4srs::Manager - SRS general manager class</span>
+<a name="l00032"></a>00032 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00033"></a>00033 <span class="comment">//</span>
+<a name="l00034"></a>00034 <span class="comment">//  (C) E. Krissinel 2010-2013</span>
+<a name="l00035"></a>00035 <span class="comment">//</span>
+<a name="l00036"></a>00036 <span class="comment">//  =================================================================</span>
+<a name="l00037"></a>00037 <span class="comment">//</span>
+<a name="l00038"></a>00038 
+<a name="l00039"></a>00039 <span class="preprocessor">#ifndef CCP4SRS_MANAGER_H</span>
+<a name="l00040"></a>00040 <span class="preprocessor"></span><span class="preprocessor">#define CCP4SRS_MANAGER_H</span>
+<a name="l00041"></a>00041 <span class="preprocessor"></span>
+<a name="l00042"></a>00042 <span class="preprocessor">#include &quot;<a class="code" href="ccp4srs__chem_8h.html">ccp4srs_chem.h</a>&quot;</span>
+<a name="l00043"></a>00043 
+<a name="l00044"></a>00044 <span class="keyword">namespace </span>ccp4srs  {
+<a name="l00045"></a>00045 
+<a name="l00046"></a>00046   <span class="comment">// ==================================================================</span>
+<a name="l00047"></a>00047 
+<a name="l00048"></a>00048   <a class="code" href="namespaceccp4srs.html#afbb5df60616f08fcf36926a3585c185f">DefineClass</a>(Manager);
+<a name="l00049"></a>00049 
+<a name="l00050"></a><a class="code" href="classccp4srs_1_1_manager.html">00050</a>   <span class="keyword">class </span><a class="code" href="classccp4srs_1_1_manager.html">Manager</a> : <span class="keyword">public</span> <a class="code" href="classccp4srs_1_1_chem.html">Chem</a> {
+<a name="l00051"></a>00051 
+<a name="l00052"></a>00052     <span class="keyword">public</span>:
+<a name="l00053"></a>00053       <a class="code" href="classccp4srs_1_1_manager.html#a7b1bcc6f68308560b402c5b3f8533158">Manager</a> ();
+<a name="l00054"></a>00054       <a class="code" href="classccp4srs_1_1_manager.html#ac6d91d47cb19b9f6ea6c7b64a7f69bb5">~Manager</a>();
+<a name="l00055"></a>00055 
+<a name="l00056"></a>00056   };
+<a name="l00057"></a>00057 
+<a name="l00058"></a>00058 }  <span class="comment">// namespace ccp4srs</span>
+<a name="l00059"></a>00059 
+<a name="l00060"></a>00060 <span class="preprocessor">#endif // CCP4SRS_MANAGER_H</span>
+</pre></div></div>
+</div>
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+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__monomer_8cpp.html ccp4srs/doc-html/html/ccp4srs__monomer_8cpp.html
--- ccp4srs-old/doc-html/html/ccp4srs__monomer_8cpp.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__monomer_8cpp.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,89 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/ccp4srs_monomer.cpp File Reference</title>
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+<link href="search/search.css" rel="stylesheet" type="text/css"/>
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+<a href="#namespaces">Namespaces</a> &#124;
+<a href="#func-members">Functions</a>  </div>
+  <div class="headertitle">
+<h1>src/ccp4srs_monomer.cpp File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &lt;string.h&gt;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__monomer_8h_source.html">ccp4srs_monomer.h</a>&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__defs_8h_source.html">ccp4srs_defs.h</a>&quot;</code><br/>
+<code>#include &quot;mmdb/mmdb_math_linalg.h&quot;</code><br/>
+<code>#include &quot;mmdb/mmdb_tables.h&quot;</code><br/>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+<tr><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#ab9a709bd669d7de2cf530774f80905c7">ccp4srs::superpose_atoms</a> (mmdb::mat44 &amp;T, PPAtom A1, mmdb::PPAtom A2, int nAtoms, mmdb::rmatrix &amp;A, mmdb::rmatrix &amp;U, mmdb::rmatrix &amp;V, mmdb::rvector &amp;W, mmdb::rvector &amp;RV1)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a8b4dcaee4f20949271ceaadfb7b5a96f">ccp4srs::makeElementType</a> (int ElType, char chirality)</td></tr>
+</table>
+</div>
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+     onmouseover="return searchBox.OnSearchSelectShow()"
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+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
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+</html>
diff -ruN ccp4srs-old/doc-html/html/ccp4srs__monomer_8h.html ccp4srs/doc-html/html/ccp4srs__monomer_8h.html
--- ccp4srs-old/doc-html/html/ccp4srs__monomer_8h.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__monomer_8h.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,99 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/ccp4srs_monomer.h File Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
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+--></script>
+<div class="navigation" id="top">
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+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
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+<a href="#func-members">Functions</a>  </div>
+  <div class="headertitle">
+<h1>src/ccp4srs_monomer.h File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &quot;mmdb/mmdb_mmcif_.h&quot;</code><br/>
+<code>#include &quot;mmdb/mmdb_math_graph.h&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__entry_8h_source.html">ccp4srs_entry.h</a>&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__bond_8h_source.html">ccp4srs_bond.h</a>&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__angle_8h_source.html">ccp4srs_angle.h</a>&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__torsion_8h_source.html">ccp4srs_torsion.h</a>&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__chicenter_8h_source.html">ccp4srs_chicenter.h</a>&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__plane_8h_source.html">ccp4srs_plane.h</a>&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__tree_8h_source.html">ccp4srs_tree.h</a>&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__types_8h_source.html">ccp4srs_types.h</a>&quot;</code><br/>
+
+<p><a href="ccp4srs__monomer_8h_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="nested-classes"></a>
+Classes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td></tr>
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+<tr><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#aea118bfa214275496e94e42beca05c35">ccp4srs::DefineClass</a> (Monomer)</td></tr>
+</table>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__monomer_8h_source.html ccp4srs/doc-html/html/ccp4srs__monomer_8h_source.html
--- ccp4srs-old/doc-html/html/ccp4srs__monomer_8h_source.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__monomer_8h_source.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,259 @@
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+<h1>src/ccp4srs_monomer.h</h1>  </div>
+</div>
+<div class="contents">
+<a href="ccp4srs__monomer_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">//  $Id: ccp4srs_monomer.h $</span>
+<a name="l00002"></a>00002 <span class="comment">//  =================================================================</span>
+<a name="l00003"></a>00003 <span class="comment">//</span>
+<a name="l00004"></a>00004 <span class="comment">//   CCP4 SRS Library: Storage, Retrieval and Search support for</span>
+<a name="l00005"></a>00005 <span class="comment">//   CCP4 ligand data.</span>
+<a name="l00006"></a>00006 <span class="comment">//</span>
+<a name="l00007"></a>00007 <span class="comment">//   Copyright (C) Eugene Krissinel 2010-2013.</span>
+<a name="l00008"></a>00008 <span class="comment">//</span>
+<a name="l00009"></a>00009 <span class="comment">//   This library is free software: you can redistribute it and/or</span>
+<a name="l00010"></a>00010 <span class="comment">//   modify it under the terms of the GNU Lesser General Public</span>
+<a name="l00011"></a>00011 <span class="comment">//   License version 3, modified in accordance with the provisions</span>
+<a name="l00012"></a>00012 <span class="comment">//   of the license to address the requirements of UK law.</span>
+<a name="l00013"></a>00013 <span class="comment">//</span>
+<a name="l00014"></a>00014 <span class="comment">//   You should have received a copy of the modified GNU Lesser</span>
+<a name="l00015"></a>00015 <span class="comment">//   General Public License along with this library. If not, copies</span>
+<a name="l00016"></a>00016 <span class="comment">//   may be downloaded from http://www.ccp4.ac.uk/ccp4license.php</span>
+<a name="l00017"></a>00017 <span class="comment">//</span>
+<a name="l00018"></a>00018 <span class="comment">//   This program is distributed in the hope that it will be useful,</span>
+<a name="l00019"></a>00019 <span class="comment">//   but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
+<a name="l00020"></a>00020 <span class="comment">//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
+<a name="l00021"></a>00021 <span class="comment">//   GNU Lesser General Public License for more details.</span>
+<a name="l00022"></a>00022 <span class="comment">//</span>
+<a name="l00023"></a>00023 <span class="comment">//  =================================================================</span>
+<a name="l00024"></a>00024 <span class="comment">//</span>
+<a name="l00025"></a>00025 <span class="comment">//    18.09.13   &lt;--  Date of Last Modification.</span>
+<a name="l00026"></a>00026 <span class="comment">//                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
+<a name="l00027"></a>00027 <span class="comment">//  -----------------------------------------------------------------</span>
+<a name="l00028"></a>00028 <span class="comment">//</span>
+<a name="l00029"></a>00029 <span class="comment">//  **** Module  :  ccp4srs_monomer  &lt;interface&gt;</span>
+<a name="l00030"></a>00030 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00031"></a>00031 <span class="comment">//  **** Classes :  ccp4srs::Monomer  - monomer structure</span>
+<a name="l00032"></a>00032 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00033"></a>00033 <span class="comment">//</span>
+<a name="l00034"></a>00034 <span class="comment">//  (C) E. Krissinel 2010-2013</span>
+<a name="l00035"></a>00035 <span class="comment">//</span>
+<a name="l00036"></a>00036 <span class="comment">//  =================================================================</span>
+<a name="l00037"></a>00037 <span class="comment">//</span>
+<a name="l00038"></a>00038 
+<a name="l00039"></a>00039 <span class="preprocessor">#ifndef CCP4SRS_MONOMER_H</span>
+<a name="l00040"></a>00040 <span class="preprocessor"></span><span class="preprocessor">#define CCP4SRS_MONOMER_H</span>
+<a name="l00041"></a>00041 <span class="preprocessor"></span>
+<a name="l00042"></a>00042 <span class="preprocessor">#include &quot;mmdb/mmdb_mmcif_.h&quot;</span>
+<a name="l00043"></a>00043 <span class="preprocessor">#include &quot;mmdb/mmdb_math_graph.h&quot;</span>
+<a name="l00044"></a>00044 
+<a name="l00045"></a>00045 <span class="preprocessor">#include &quot;<a class="code" href="ccp4srs__entry_8h.html">ccp4srs_entry.h</a>&quot;</span>
+<a name="l00046"></a>00046 <span class="preprocessor">#include &quot;<a class="code" href="ccp4srs__bond_8h.html">ccp4srs_bond.h</a>&quot;</span>
+<a name="l00047"></a>00047 <span class="preprocessor">#include &quot;<a class="code" href="ccp4srs__angle_8h.html">ccp4srs_angle.h</a>&quot;</span>
+<a name="l00048"></a>00048 <span class="preprocessor">#include &quot;<a class="code" href="ccp4srs__torsion_8h.html">ccp4srs_torsion.h</a>&quot;</span>
+<a name="l00049"></a>00049 <span class="preprocessor">#include &quot;<a class="code" href="ccp4srs__chicenter_8h.html">ccp4srs_chicenter.h</a>&quot;</span>
+<a name="l00050"></a>00050 <span class="preprocessor">#include &quot;<a class="code" href="ccp4srs__plane_8h.html">ccp4srs_plane.h</a>&quot;</span>
+<a name="l00051"></a>00051 <span class="preprocessor">#include &quot;<a class="code" href="ccp4srs__tree_8h.html">ccp4srs_tree.h</a>&quot;</span>
+<a name="l00052"></a>00052 <span class="preprocessor">#include &quot;<a class="code" href="ccp4srs__types_8h.html">ccp4srs_types.h</a>&quot;</span>
+<a name="l00053"></a>00053 
+<a name="l00054"></a>00054 <span class="keyword">namespace </span>ccp4srs  {
+<a name="l00055"></a>00055 
+<a name="l00056"></a>00056   <a class="code" href="namespaceccp4srs.html#afbb5df60616f08fcf36926a3585c185f">DefineClass</a>(Monomer);
+<a name="l00057"></a>00057 
+<a name="l00058"></a><a class="code" href="classccp4srs_1_1_monomer.html">00058</a>   <span class="keyword">class </span><a class="code" href="classccp4srs_1_1_monomer.html">Monomer</a> : <span class="keyword">public</span> <a class="code" href="classccp4srs_1_1_entry.html">Entry</a>  {
+<a name="l00059"></a>00059 
+<a name="l00060"></a>00060     <span class="keyword">public</span>:
+<a name="l00061"></a>00061       <a class="code" href="classccp4srs_1_1_monomer.html#abd3a6efc83918f121e3e83165681ccd5">Monomer</a>();
+<a name="l00062"></a>00062       <a class="code" href="classccp4srs_1_1_monomer.html#a33207c3c799fe120851007002464e2e2">~Monomer</a>();
+<a name="l00063"></a>00063 
+<a name="l00064"></a><a class="code" href="classccp4srs_1_1_monomer.html#a01201fb01a7ed370e593563b129c74af">00064</a>       <span class="keyword">virtual</span> <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_monomer.html#a01201fb01a7ed370e593563b129c74af">type</a>()  { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_monomer.html#abd3a6efc83918f121e3e83165681ccd5">Entry::Monomer</a>; }
+<a name="l00065"></a>00065 
+<a name="l00066"></a>00066       <span class="keywordtype">void</span>   <a class="code" href="classccp4srs_1_1_monomer.html#a42598d1f669c5e539cb024bb023e0551">reset</a>();  <span class="comment">// deletes all data</span>
+<a name="l00067"></a>00067 
+<a name="l00068"></a><a class="code" href="classccp4srs_1_1_monomer.html#a1eca7f4a9537bddf81de26df20984183">00068</a>       <span class="keyword">inline</span> mmdb::cpstr <a class="code" href="classccp4srs_1_1_monomer.html#a1eca7f4a9537bddf81de26df20984183">ID</a>   ()  { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_monomer.html#a34240535a6e703495662936dba863026">monID</a>;    }
+<a name="l00069"></a><a class="code" href="classccp4srs_1_1_monomer.html#a271e6aaeed7ace67e36f2c5fea626d70">00069</a>       <span class="keyword">inline</span> mmdb::cpstr <a class="code" href="classccp4srs_1_1_monomer.html#a271e6aaeed7ace67e36f2c5fea626d70">oldID</a>()  { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_monomer.html#a896cc0c3979b65913de25be2c2f75ec9">oldMonID</a>; }
+<a name="l00070"></a>00070       <span class="keywordtype">void</span>   <a class="code" href="classccp4srs_1_1_monomer.html#a3d9cd816f0e032e64e0d47ed7673ec63">setOldID</a>   ( mmdb::cpstr <a class="code" href="classccp4srs_1_1_monomer.html#a271e6aaeed7ace67e36f2c5fea626d70">oldID</a> );
+<a name="l00071"></a>00071 
+<a name="l00072"></a>00072       mmdb::cpstr  <a class="code" href="classccp4srs_1_1_monomer.html#ab5a8d9361def2e547d1e65bf180f3252">chem_name</a>   ();
+<a name="l00073"></a>00073       mmdb::cpstr  <a class="code" href="classccp4srs_1_1_monomer.html#a37432cca1867e01cd9af6d4569c2326a">chem_type</a>   ();
+<a name="l00074"></a>00074       mmdb::cpstr  <a class="code" href="classccp4srs_1_1_monomer.html#a6bbfc74c882e403c57984d7310d4fb98">chem_formula</a>();
+<a name="l00075"></a>00075 
+<a name="l00076"></a><a class="code" href="classccp4srs_1_1_monomer.html#a3e3e771e2d60581384b1169648b4d751">00076</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_monomer.html#a3e3e771e2d60581384b1169648b4d751">n_atoms</a>     () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_monomer.html#abd7decc2129038a1416f324fee53afa1">atoms</a>     .<a class="code" href="classccp4srs_1_1_container.html#abbc5e6eeb9ea4d37b8d2025892ebd9ff">numberOf</a>(); }
+<a name="l00077"></a><a class="code" href="classccp4srs_1_1_monomer.html#a6a6e470c174fd570667bf43f95757c0d">00077</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_monomer.html#a6a6e470c174fd570667bf43f95757c0d">n_bonds</a>     () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_monomer.html#a19495bb3c7e8d1c27f12f06729979d9e">bonds</a>     .<a class="code" href="classccp4srs_1_1_container.html#abbc5e6eeb9ea4d37b8d2025892ebd9ff">numberOf</a>(); }
+<a name="l00078"></a><a class="code" href="classccp4srs_1_1_monomer.html#a832521f11b1adb4a0deb9fd92b4bc725">00078</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_monomer.html#a832521f11b1adb4a0deb9fd92b4bc725">n_angles</a>    () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_monomer.html#a9177ec12ea5aeaa59228831d4127e592">angles</a>    .<a class="code" href="classccp4srs_1_1_container.html#abbc5e6eeb9ea4d37b8d2025892ebd9ff">numberOf</a>(); }
+<a name="l00079"></a><a class="code" href="classccp4srs_1_1_monomer.html#a0bf10d776d5d992424b99d88d884f101">00079</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_monomer.html#a0bf10d776d5d992424b99d88d884f101">n_torsions</a>  () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_monomer.html#a70123373bff5c842e122856fb75634ab">torsions</a>  .<a class="code" href="classccp4srs_1_1_container.html#abbc5e6eeb9ea4d37b8d2025892ebd9ff">numberOf</a>(); }
+<a name="l00080"></a><a class="code" href="classccp4srs_1_1_monomer.html#a047ec20b44f73aa0027fdd071aa265d6">00080</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_monomer.html#a047ec20b44f73aa0027fdd071aa265d6">n_chicenters</a>() { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_monomer.html#a96a126d39760ce281f8bf04186e29c13">chicenters</a>.<a class="code" href="classccp4srs_1_1_container.html#abbc5e6eeb9ea4d37b8d2025892ebd9ff">numberOf</a>(); }
+<a name="l00081"></a><a class="code" href="classccp4srs_1_1_monomer.html#a123cf02246e052730361055de3f0d477">00081</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_monomer.html#a123cf02246e052730361055de3f0d477">n_planes</a>    () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_monomer.html#a2f927ab2a3e517f9fe6cba6e89954cfe">planes</a>    .<a class="code" href="classccp4srs_1_1_container.html#abbc5e6eeb9ea4d37b8d2025892ebd9ff">numberOf</a>(); }
+<a name="l00082"></a>00082 
+<a name="l00083"></a><a class="code" href="classccp4srs_1_1_monomer.html#ac3492a092c5436d182acae9b6712da7f">00083</a>       <span class="keyword">inline</span> PAtom  <a class="code" href="classccp4srs_1_1_monomer.html#ac3492a092c5436d182acae9b6712da7f">atom</a>  ( <span class="keywordtype">int</span> n ) { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_monomer.html#abd7decc2129038a1416f324fee53afa1">atoms</a>   .<a class="code" href="classccp4srs_1_1_container.html#ae9929d576289dd2313aaf4b2d9c377e9">at</a>(n); }
+<a name="l00084"></a><a class="code" href="classccp4srs_1_1_monomer.html#a6b01e3fa4cb59dc507460ea0715823fa">00084</a>       <span class="keyword">inline</span> PBond  <a class="code" href="classccp4srs_1_1_monomer.html#a6b01e3fa4cb59dc507460ea0715823fa">bond</a>  ( <span class="keywordtype">int</span> n ) { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_monomer.html#a19495bb3c7e8d1c27f12f06729979d9e">bonds</a>   .<a class="code" href="classccp4srs_1_1_container.html#ae9929d576289dd2313aaf4b2d9c377e9">at</a>(n); }
+<a name="l00085"></a><a class="code" href="classccp4srs_1_1_monomer.html#a61b179edff80a9d168997038093cc92f">00085</a>       <span class="keyword">inline</span> PAngle <a class="code" href="classccp4srs_1_1_monomer.html#a61b179edff80a9d168997038093cc92f">angle</a> ( <span class="keywordtype">int</span> n ) { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_monomer.html#a9177ec12ea5aeaa59228831d4127e592">angles</a>  .<a class="code" href="classccp4srs_1_1_container.html#ae9929d576289dd2313aaf4b2d9c377e9">at</a>(n); }
+<a name="l00086"></a><a class="code" href="classccp4srs_1_1_monomer.html#afdebf230f6aa9bf2692a82b919d59918">00086</a>       <span class="keyword">inline</span> PPlane <a class="code" href="classccp4srs_1_1_monomer.html#afdebf230f6aa9bf2692a82b919d59918">plane</a> ( <span class="keywordtype">int</span> n ) { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_monomer.html#a2f927ab2a3e517f9fe6cba6e89954cfe">planes</a>  .<a class="code" href="classccp4srs_1_1_container.html#ae9929d576289dd2313aaf4b2d9c377e9">at</a>(n); }
+<a name="l00087"></a><a class="code" href="classccp4srs_1_1_monomer.html#a79a4445aa7279951aa8426dc79114ebf">00087</a>       <span class="keyword">inline</span> PTree  <a class="code" href="classccp4srs_1_1_monomer.html#a79a4445aa7279951aa8426dc79114ebf">tree</a>  ()        { <span class="keywordflow">return</span> &amp;<a class="code" href="classccp4srs_1_1_monomer.html#aef8794097a333f1e4e20dd3d876f1432">struct_tree</a>;   }
+<a name="l00088"></a><a class="code" href="classccp4srs_1_1_monomer.html#a1fdc6bd34cea4b7ea59d5399a8367f70">00088</a>       <span class="keyword">inline</span> PTorsion <a class="code" href="classccp4srs_1_1_monomer.html#a1fdc6bd34cea4b7ea59d5399a8367f70">torsion</a> ( <span class="keywordtype">int</span> n )
+<a name="l00089"></a>00089                                            { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_monomer.html#a70123373bff5c842e122856fb75634ab">torsions</a>.<a class="code" href="classccp4srs_1_1_container.html#ae9929d576289dd2313aaf4b2d9c377e9">at</a>(n); }
+<a name="l00090"></a><a class="code" href="classccp4srs_1_1_monomer.html#a3c1ea4e271769745f01c8dc4146c683e">00090</a>       <span class="keyword">inline</span> PChiCenter <a class="code" href="classccp4srs_1_1_monomer.html#a3c1ea4e271769745f01c8dc4146c683e">chicenter</a> ( <span class="keywordtype">int</span> n )
+<a name="l00091"></a>00091                                          { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_monomer.html#a96a126d39760ce281f8bf04186e29c13">chicenters</a>.<a class="code" href="classccp4srs_1_1_container.html#ae9929d576289dd2313aaf4b2d9c377e9">at</a>(n); }
+<a name="l00092"></a>00092 
+<a name="l00093"></a><a class="code" href="classccp4srs_1_1_monomer.html#ae1c9221ebd49b62830621cd40524d215">00093</a>       <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_monomer.html#ae1c9221ebd49b62830621cd40524d215">add</a> ( PAtom  <a class="code" href="classccp4srs_1_1_monomer.html#ac3492a092c5436d182acae9b6712da7f">atom</a>    ) { <a class="code" href="classccp4srs_1_1_monomer.html#abd7decc2129038a1416f324fee53afa1">atoms</a> .<a class="code" href="classccp4srs_1_1_container.html#a6caf1893b780f2cf196c85ee141baf18">add</a>(atom ); }
+<a name="l00094"></a><a class="code" href="classccp4srs_1_1_monomer.html#a88d4f2d1f97364930fed4bf349b23cb1">00094</a>       <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_monomer.html#a88d4f2d1f97364930fed4bf349b23cb1">add</a> ( PBond  <a class="code" href="classccp4srs_1_1_monomer.html#a6b01e3fa4cb59dc507460ea0715823fa">bond</a>    ) { <a class="code" href="classccp4srs_1_1_monomer.html#a19495bb3c7e8d1c27f12f06729979d9e">bonds</a> .<a class="code" href="classccp4srs_1_1_container.html#a6caf1893b780f2cf196c85ee141baf18">add</a>(bond ); }
+<a name="l00095"></a><a class="code" href="classccp4srs_1_1_monomer.html#a3eab75471f83c2c92834a1e30400642e">00095</a>       <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_monomer.html#a3eab75471f83c2c92834a1e30400642e">add</a> ( PAngle <a class="code" href="classccp4srs_1_1_monomer.html#a61b179edff80a9d168997038093cc92f">angle</a>   ) { <a class="code" href="classccp4srs_1_1_monomer.html#a9177ec12ea5aeaa59228831d4127e592">angles</a>.<a class="code" href="classccp4srs_1_1_container.html#a6caf1893b780f2cf196c85ee141baf18">add</a>(angle); }
+<a name="l00096"></a><a class="code" href="classccp4srs_1_1_monomer.html#a394b2b32b99cd3c6e0b3654593436a2f">00096</a>       <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_monomer.html#a394b2b32b99cd3c6e0b3654593436a2f">add</a> ( PPlane <a class="code" href="classccp4srs_1_1_monomer.html#afdebf230f6aa9bf2692a82b919d59918">plane</a>   ) { <a class="code" href="classccp4srs_1_1_monomer.html#a2f927ab2a3e517f9fe6cba6e89954cfe">planes</a>.<a class="code" href="classccp4srs_1_1_container.html#a6caf1893b780f2cf196c85ee141baf18">add</a>(plane); }
+<a name="l00097"></a><a class="code" href="classccp4srs_1_1_monomer.html#acdfa8628139cfb914f2aecdb1e2f37d2">00097</a>       <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_monomer.html#acdfa8628139cfb914f2aecdb1e2f37d2">add</a> ( PTree  stree   ) { <a class="code" href="classccp4srs_1_1_monomer.html#aef8794097a333f1e4e20dd3d876f1432">struct_tree</a>.<a class="code" href="classccp4srs_1_1_tree.html#acfc010d5d168bb288379e6b6721fb9fa">copy</a>(stree); }
+<a name="l00098"></a><a class="code" href="classccp4srs_1_1_monomer.html#a555cba2de4ecd6d3d7c192a52a9d44a3">00098</a>       <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_monomer.html#ae1c9221ebd49b62830621cd40524d215">add</a> ( PTorsion <a class="code" href="classccp4srs_1_1_monomer.html#a1fdc6bd34cea4b7ea59d5399a8367f70">torsion</a> )
+<a name="l00099"></a>00099                                             { <a class="code" href="classccp4srs_1_1_monomer.html#a70123373bff5c842e122856fb75634ab">torsions</a>.<a class="code" href="classccp4srs_1_1_container.html#a6caf1893b780f2cf196c85ee141baf18">add</a>(torsion); }
+<a name="l00100"></a><a class="code" href="classccp4srs_1_1_monomer.html#a1820529a0bee358372e53ea0fb0c0a56">00100</a>       <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_monomer.html#ae1c9221ebd49b62830621cd40524d215">add</a> ( PChiCenter <a class="code" href="classccp4srs_1_1_monomer.html#a3c1ea4e271769745f01c8dc4146c683e">chicenter</a> )
+<a name="l00101"></a>00101                                         { <a class="code" href="classccp4srs_1_1_monomer.html#a96a126d39760ce281f8bf04186e29c13">chicenters</a>.<a class="code" href="classccp4srs_1_1_container.html#a6caf1893b780f2cf196c85ee141baf18">add</a>(chicenter); }
+<a name="l00102"></a>00102 
+<a name="l00103"></a><a class="code" href="classccp4srs_1_1_monomer.html#a1ca9838123fea51260be3c44abd6771f">00103</a>       <span class="keyword">inline</span> <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a>    *<a class="code" href="classccp4srs_1_1_monomer.html#a1ca9838123fea51260be3c44abd6771f">get_atoms</a>   () { <span class="keywordflow">return</span> &amp;<a class="code" href="classccp4srs_1_1_monomer.html#abd7decc2129038a1416f324fee53afa1">atoms</a>;      }
+<a name="l00104"></a><a class="code" href="classccp4srs_1_1_monomer.html#af36aeb36b83f49d3b4fc28d4737b5efd">00104</a>       <span class="keyword">inline</span> <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Bond&gt;</a>    *<a class="code" href="classccp4srs_1_1_monomer.html#af36aeb36b83f49d3b4fc28d4737b5efd">get_bonds</a>   () { <span class="keywordflow">return</span> &amp;<a class="code" href="classccp4srs_1_1_monomer.html#a19495bb3c7e8d1c27f12f06729979d9e">bonds</a>;      }
+<a name="l00105"></a><a class="code" href="classccp4srs_1_1_monomer.html#a8d4b4084ca5c0e0fa42075f59eaf3e08">00105</a>       <span class="keyword">inline</span> <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Angle&gt;</a>   *<a class="code" href="classccp4srs_1_1_monomer.html#a8d4b4084ca5c0e0fa42075f59eaf3e08">get_angles</a>  () { <span class="keywordflow">return</span> &amp;<a class="code" href="classccp4srs_1_1_monomer.html#a9177ec12ea5aeaa59228831d4127e592">angles</a>;     }
+<a name="l00106"></a><a class="code" href="classccp4srs_1_1_monomer.html#a7b31b6675690c2edc0baa0e070d349ad">00106</a>       <span class="keyword">inline</span> <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Torsion&gt;</a> *<a class="code" href="classccp4srs_1_1_monomer.html#a7b31b6675690c2edc0baa0e070d349ad">get_torsions</a>() { <span class="keywordflow">return</span> &amp;<a class="code" href="classccp4srs_1_1_monomer.html#a70123373bff5c842e122856fb75634ab">torsions</a>;   }
+<a name="l00107"></a><a class="code" href="classccp4srs_1_1_monomer.html#a591d5f8275f5b5756442d96221039ef3">00107</a>       <span class="keyword">inline</span> <a class="code" href="classccp4srs_1_1_container.html">Container&lt;ChiCenter&gt;</a> *<a class="code" href="classccp4srs_1_1_monomer.html#a591d5f8275f5b5756442d96221039ef3">get_chicenters</a>() { <span class="keywordflow">return</span> &amp;<a class="code" href="classccp4srs_1_1_monomer.html#a96a126d39760ce281f8bf04186e29c13">chicenters</a>; }
+<a name="l00108"></a><a class="code" href="classccp4srs_1_1_monomer.html#aa454ac38a87c19006580a42bc38958fc">00108</a>       <span class="keyword">inline</span> <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Plane&gt;</a>   *<a class="code" href="classccp4srs_1_1_monomer.html#aa454ac38a87c19006580a42bc38958fc">get_planes</a>  () { <span class="keywordflow">return</span> &amp;<a class="code" href="classccp4srs_1_1_monomer.html#a2f927ab2a3e517f9fe6cba6e89954cfe">planes</a>;     }
+<a name="l00109"></a><a class="code" href="classccp4srs_1_1_monomer.html#a351a18b323af41b74d1b415fcd1df640">00109</a>       <span class="keyword">inline</span> <a class="code" href="classccp4srs_1_1_tree.html">Tree</a> *<a class="code" href="classccp4srs_1_1_monomer.html#a351a18b323af41b74d1b415fcd1df640">get_tree</a>() { <span class="keywordflow">return</span> &amp;<a class="code" href="classccp4srs_1_1_monomer.html#aef8794097a333f1e4e20dd3d876f1432">struct_tree</a>; }
+<a name="l00110"></a>00110 
+<a name="l00111"></a>00111       <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_monomer.html#a9ac9e9e610a1a0450130d5e5c4242d34">atom_no</a>   ( mmdb::cpstr aname );
+<a name="l00112"></a>00112       <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_monomer.html#a7b6acc92258007c15351989930e8672f">get_bound</a> ( <span class="keywordtype">int</span>  atomNo, mmdb::cpstr elem, <span class="keywordtype">int</span> serNo );
+<a name="l00113"></a>00113       <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_monomer.html#a7b6acc92258007c15351989930e8672f">get_bound</a> ( <span class="keywordtype">int</span>  atomNo, <span class="keywordtype">int</span> n );
+<a name="l00114"></a>00114       <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_monomer.html#a7b6acc92258007c15351989930e8672f">get_bound</a> ( mmdb::cpstr aname, <span class="keywordtype">int</span> n );
+<a name="l00115"></a>00115 
+<a name="l00116"></a>00116       <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">CCP4SRS_RC</a> <a class="code" href="classccp4srs_1_1_monomer.html#a67a965eb782472588f1a5f4e693c509e">addHydrogens</a> ( mmdb::PResidue R );
+<a name="l00117"></a>00117 
+<a name="l00118"></a>00118       <span class="comment">//  getAtomNameMatch(..) returns anmatch[i], i=0..nAtoms-1, equal</span>
+<a name="l00119"></a>00119       <span class="comment">// to j such that name(Atom[i])==name(A[j]). Note that atom names</span>
+<a name="l00120"></a>00120       <span class="comment">// are similarly aligned and space-padded in MMDB, but not in SRS.</span>
+<a name="l00121"></a>00121       <span class="comment">// However, the proper alignment is done on fly. If ith atom in</span>
+<a name="l00122"></a>00122       <span class="comment">// the structue is not found in A, anmatch[i] is set -1.</span>
+<a name="l00123"></a>00123       <span class="comment">//   If array A contains atoms in different alternative</span>
+<a name="l00124"></a>00124       <span class="comment">// conformations, the the value of altLoc is interpreted as</span>
+<a name="l00125"></a>00125       <span class="comment">// follows:</span>
+<a name="l00126"></a>00126       <span class="comment">//    NULL  - the highest occupancy atom will be taken</span>
+<a name="l00127"></a>00127       <span class="comment">//            if all occupancies are equal then atom with</span>
+<a name="l00128"></a>00128       <span class="comment">//            first altLoc taken</span>
+<a name="l00129"></a>00129       <span class="comment">//    other - atoms with given altLoc are taken. If such</span>
+<a name="l00130"></a>00130       <span class="comment">//            altLoc is not found, the function does as if</span>
+<a name="l00131"></a>00131       <span class="comment">//            NULL value for altLoc is given.</span>
+<a name="l00132"></a>00132       <span class="comment">//   A clean PDB file is anticipated, so that atoms with</span>
+<a name="l00133"></a>00133       <span class="comment">// alternative conformations are grouped together.</span>
+<a name="l00134"></a>00134       <span class="comment">//   It is Ok to have NULL pointers in A.</span>
+<a name="l00135"></a>00135       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_monomer.html#abb514ab63af7e9dbb68f59bc13551618">getAtomNameMatch</a> ( mmdb::PPAtom A, <span class="keywordtype">int</span> nat, mmdb::pstr altLoc,
+<a name="l00136"></a>00136                               mmdb::ivector anmatch );
+<a name="l00137"></a>00137 
+<a name="l00147"></a>00147       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_monomer.html#abb514ab63af7e9dbb68f59bc13551618">getAtomNameMatch</a> ( <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a> *A, mmdb::ivector anmatch );
+<a name="l00148"></a>00148 
+<a name="l00149"></a>00149       mmdb::math::PGraph <a class="code" href="classccp4srs_1_1_monomer.html#a9d1a2b0facb208344413158d74446755">getGraph</a> ( <span class="keywordtype">int</span> *retCode );
+<a name="l00150"></a>00150 
+<a name="l00151"></a>00151       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_monomer.html#a6c3ad68f13fb779921605d0e696add1c">getLeavingAtoms</a> ( <span class="keywordtype">int</span> &amp; nLeavingAtoms,
+<a name="l00152"></a>00152                              mmdb::ivector &amp; leavingAtom,
+<a name="l00153"></a>00153                              mmdb::ivector &amp; bondedAtom );
+<a name="l00154"></a>00154 
+<a name="l00155"></a>00155       <span class="comment">// Return code:</span>
+<a name="l00156"></a>00156       <span class="comment">//     CCP4SRS_Ok    success</span>
+<a name="l00157"></a>00157       <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_monomer.html#aa9b0a99023e890070aec088182f8a65b">readFromCIF</a> ( mmdb::mmcif::PData mmCIFData,
+<a name="l00158"></a>00158                         mmdb::pstr error_desc = NULL );
+<a name="l00159"></a>00159 
+<a name="l00160"></a>00160       mmdb::mmcif::PData <a class="code" href="classccp4srs_1_1_monomer.html#a5e3fb1e64eab3e764cc83ff1e6c61fa3">makeCIF</a>();  <span class="comment">// return to be deleted by application</span>
+<a name="l00161"></a>00161 
+<a name="l00162"></a>00162       <span class="comment">// service function</span>
+<a name="l00163"></a>00163       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_monomer.html#a6453406b0256cf9fbf74177a7db8770b">merge</a> ( PMonomer monomer );
+<a name="l00164"></a>00164 
+<a name="l00165"></a>00165     <span class="keyword">protected</span>:
+<a name="l00166"></a><a class="code" href="classccp4srs_1_1_monomer.html#a34240535a6e703495662936dba863026">00166</a>       mmdb::ResName        <a class="code" href="classccp4srs_1_1_monomer.html#a34240535a6e703495662936dba863026">monID</a>;
+<a name="l00167"></a><a class="code" href="classccp4srs_1_1_monomer.html#a896cc0c3979b65913de25be2c2f75ec9">00167</a>       mmdb::ResName        <a class="code" href="classccp4srs_1_1_monomer.html#a896cc0c3979b65913de25be2c2f75ec9">oldMonID</a>;
+<a name="l00168"></a><a class="code" href="classccp4srs_1_1_monomer.html#a53b8d5232f3b2085d531eca33fb7c55a">00168</a>       mmdb::pstr           <a class="code" href="classccp4srs_1_1_monomer.html#a53b8d5232f3b2085d531eca33fb7c55a">monName</a>;
+<a name="l00169"></a><a class="code" href="classccp4srs_1_1_monomer.html#af0a573429afbbea61647c9851f0deba7">00169</a>       mmdb::pstr           <a class="code" href="classccp4srs_1_1_monomer.html#af0a573429afbbea61647c9851f0deba7">monType</a>;
+<a name="l00170"></a><a class="code" href="classccp4srs_1_1_monomer.html#aeb6bee62372a765e8aca0c1496689b3a">00170</a>       mmdb::pstr           <a class="code" href="classccp4srs_1_1_monomer.html#aeb6bee62372a765e8aca0c1496689b3a">monFormula</a>;
+<a name="l00171"></a><a class="code" href="classccp4srs_1_1_monomer.html#abd7decc2129038a1416f324fee53afa1">00171</a>       <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a>      <a class="code" href="classccp4srs_1_1_monomer.html#abd7decc2129038a1416f324fee53afa1">atoms</a>;
+<a name="l00172"></a><a class="code" href="classccp4srs_1_1_monomer.html#a19495bb3c7e8d1c27f12f06729979d9e">00172</a>       <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Bond&gt;</a>      <a class="code" href="classccp4srs_1_1_monomer.html#a19495bb3c7e8d1c27f12f06729979d9e">bonds</a>;
+<a name="l00173"></a><a class="code" href="classccp4srs_1_1_monomer.html#a9177ec12ea5aeaa59228831d4127e592">00173</a>       <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Angle&gt;</a>     <a class="code" href="classccp4srs_1_1_monomer.html#a9177ec12ea5aeaa59228831d4127e592">angles</a>;
+<a name="l00174"></a><a class="code" href="classccp4srs_1_1_monomer.html#a70123373bff5c842e122856fb75634ab">00174</a>       <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Torsion&gt;</a>   <a class="code" href="classccp4srs_1_1_monomer.html#a70123373bff5c842e122856fb75634ab">torsions</a>;
+<a name="l00175"></a><a class="code" href="classccp4srs_1_1_monomer.html#a96a126d39760ce281f8bf04186e29c13">00175</a>       <a class="code" href="classccp4srs_1_1_container.html">Container&lt;ChiCenter&gt;</a> <a class="code" href="classccp4srs_1_1_monomer.html#a96a126d39760ce281f8bf04186e29c13">chicenters</a>;
+<a name="l00176"></a><a class="code" href="classccp4srs_1_1_monomer.html#a2f927ab2a3e517f9fe6cba6e89954cfe">00176</a>       <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Plane&gt;</a>     <a class="code" href="classccp4srs_1_1_monomer.html#a2f927ab2a3e517f9fe6cba6e89954cfe">planes</a>;
+<a name="l00177"></a><a class="code" href="classccp4srs_1_1_monomer.html#aef8794097a333f1e4e20dd3d876f1432">00177</a>       <a class="code" href="classccp4srs_1_1_tree.html">Tree</a>                 <a class="code" href="classccp4srs_1_1_monomer.html#aef8794097a333f1e4e20dd3d876f1432">struct_tree</a>;
+<a name="l00178"></a>00178 
+<a name="l00179"></a>00179       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_monomer.html#a6a50cfb8d8e87162309106c66f5fc155">Init</a>();
+<a name="l00180"></a>00180 
+<a name="l00181"></a>00181       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_monomer.html#a4e12236b18de645dabd1afe57b46ebc0">readMonIDFromCIF</a> ( mmdb::mmcif::PLoop   loop );
+<a name="l00182"></a>00182       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_monomer.html#a4e12236b18de645dabd1afe57b46ebc0">readMonIDFromCIF</a> ( mmdb::mmcif::PStruct mmCIFStruct );
+<a name="l00183"></a>00183       <span class="keywordtype">int</span>   <a class="code" href="classccp4srs_1_1_monomer.html#a9e457d3f7633b79b598b66f382fa5c5c">readFromCIF_ccp4</a> ( mmdb::mmcif::PData   mmCIFData,
+<a name="l00184"></a>00184                                mmdb::pstr error_desc );
+<a name="l00185"></a>00185       <span class="keywordtype">int</span>   <a class="code" href="classccp4srs_1_1_monomer.html#aaaec1b93dd1dcfe0e20484fd4bbc2a72">readFromCIF_rcsb</a> ( mmdb::mmcif::PData   mmCIFData,
+<a name="l00186"></a>00186                                mmdb::pstr error_desc );
+<a name="l00187"></a>00187 
+<a name="l00188"></a>00188       <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_monomer.html#ac0eb44f5d4ec3da57994cd741c8d6b0b">write_mem</a> ( PMemIO memIO, <span class="keywordtype">int</span> version );
+<a name="l00189"></a>00189       <span class="keyword">virtual</span> <span class="keywordtype">bool</span> <a class="code" href="classccp4srs_1_1_monomer.html#ac12b93e766cfbcfd4288512df739a56e">read_mem</a>  ( PMemIO memIO, <span class="keywordtype">int</span> version,
+<a name="l00190"></a>00190                                <span class="keywordtype">bool</span> * Ok = NULL );
+<a name="l00191"></a>00191 
+<a name="l00192"></a>00192   };
+<a name="l00193"></a>00193 
+<a name="l00194"></a>00194 }  <span class="comment">// namespace ccp4srs</span>
+<a name="l00195"></a>00195 
+<a name="l00196"></a>00196 <span class="preprocessor">#endif // CCP4SRS_MONOMER_H</span>
+</pre></div></div>
+</div>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__plane_8cpp.html ccp4srs/doc-html/html/ccp4srs__plane_8cpp.html
--- ccp4srs-old/doc-html/html/ccp4srs__plane_8cpp.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__plane_8cpp.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,82 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+  <div class="headertitle">
+<h1>src/ccp4srs_plane.cpp File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &lt;string.h&gt;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__plane_8h_source.html">ccp4srs_plane.h</a>&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__defs_8h_source.html">ccp4srs_defs.h</a>&quot;</code><br/>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
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+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__plane_8h.html ccp4srs/doc-html/html/ccp4srs__plane_8h.html
--- ccp4srs-old/doc-html/html/ccp4srs__plane_8h.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__plane_8h.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,94 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+  <div class="headertitle">
+<h1>src/ccp4srs_plane.h File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &quot;<a class="el" href="ccp4srs__atom_8h_source.html">ccp4srs_atom.h</a>&quot;</code><br/>
+
+<p><a href="ccp4srs__plane_8h_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="nested-classes"></a>
+Classes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td></tr>
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+<tr><td colspan="2"><h2><a name="typedef-members"></a>
+Typedefs</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">typedef char&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#ac768cc62149be89b81a30d88a09f0166">ccp4srs::PlaneID</a> [20]</td></tr>
+<tr><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a299f5fc0ddc551524a80fe756cf2525d">ccp4srs::DefineClass</a> (Plane)</td></tr>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__plane_8h_source.html ccp4srs/doc-html/html/ccp4srs__plane_8h_source.html
--- ccp4srs-old/doc-html/html/ccp4srs__plane_8h_source.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__plane_8h_source.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,161 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<h1>src/ccp4srs_plane.h</h1>  </div>
+</div>
+<div class="contents">
+<a href="ccp4srs__plane_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">//  $Id: ccp4srs_plane.h $</span>
+<a name="l00002"></a>00002 <span class="comment">//  =================================================================</span>
+<a name="l00003"></a>00003 <span class="comment">//</span>
+<a name="l00004"></a>00004 <span class="comment">//   CCP4 SRS Library: Storage, Retrieval and Search support for</span>
+<a name="l00005"></a>00005 <span class="comment">//   CCP4 ligand data.</span>
+<a name="l00006"></a>00006 <span class="comment">//</span>
+<a name="l00007"></a>00007 <span class="comment">//   Copyright (C) Eugene Krissinel 2010-2013.</span>
+<a name="l00008"></a>00008 <span class="comment">//</span>
+<a name="l00009"></a>00009 <span class="comment">//   This library is free software: you can redistribute it and/or</span>
+<a name="l00010"></a>00010 <span class="comment">//   modify it under the terms of the GNU Lesser General Public</span>
+<a name="l00011"></a>00011 <span class="comment">//   License version 3, modified in accordance with the provisions</span>
+<a name="l00012"></a>00012 <span class="comment">//   of the license to address the requirements of UK law.</span>
+<a name="l00013"></a>00013 <span class="comment">//</span>
+<a name="l00014"></a>00014 <span class="comment">//   You should have received a copy of the modified GNU Lesser</span>
+<a name="l00015"></a>00015 <span class="comment">//   General Public License along with this library. If not, copies</span>
+<a name="l00016"></a>00016 <span class="comment">//   may be downloaded from http://www.ccp4.ac.uk/ccp4license.php</span>
+<a name="l00017"></a>00017 <span class="comment">//</span>
+<a name="l00018"></a>00018 <span class="comment">//   This program is distributed in the hope that it will be useful,</span>
+<a name="l00019"></a>00019 <span class="comment">//   but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
+<a name="l00020"></a>00020 <span class="comment">//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
+<a name="l00021"></a>00021 <span class="comment">//   GNU Lesser General Public License for more details.</span>
+<a name="l00022"></a>00022 <span class="comment">//</span>
+<a name="l00023"></a>00023 <span class="comment">//  =================================================================</span>
+<a name="l00024"></a>00024 <span class="comment">//</span>
+<a name="l00025"></a>00025 <span class="comment">//    18.09.13   &lt;--  Date of Last Modification.</span>
+<a name="l00026"></a>00026 <span class="comment">//                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
+<a name="l00027"></a>00027 <span class="comment">//  -----------------------------------------------------------------</span>
+<a name="l00028"></a>00028 <span class="comment">//</span>
+<a name="l00029"></a>00029 <span class="comment">//  **** Module  :  ccp4srs_plane  &lt;interface&gt;</span>
+<a name="l00030"></a>00030 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00031"></a>00031 <span class="comment">//  **** Classes :  ccp4srs::Plane  - plain group of atoms</span>
+<a name="l00032"></a>00032 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00033"></a>00033 <span class="comment">//</span>
+<a name="l00034"></a>00034 <span class="comment">//  (C) E. Krissinel 2010-2013</span>
+<a name="l00035"></a>00035 <span class="comment">//</span>
+<a name="l00036"></a>00036 <span class="comment">//  =================================================================</span>
+<a name="l00037"></a>00037 <span class="comment">//</span>
+<a name="l00038"></a>00038 
+<a name="l00039"></a>00039 <span class="preprocessor">#ifndef CCP4SRS_PLANE_H</span>
+<a name="l00040"></a>00040 <span class="preprocessor"></span><span class="preprocessor">#define CCP4SRS_PLANE_H</span>
+<a name="l00041"></a>00041 <span class="preprocessor"></span>
+<a name="l00042"></a>00042 <span class="preprocessor">#include &quot;<a class="code" href="ccp4srs__atom_8h.html">ccp4srs_atom.h</a>&quot;</span>
+<a name="l00043"></a>00043 
+<a name="l00044"></a>00044 <span class="keyword">namespace </span>ccp4srs  {
+<a name="l00045"></a>00045 
+<a name="l00046"></a>00046   <a class="code" href="namespaceccp4srs.html#afbb5df60616f08fcf36926a3585c185f">DefineClass</a>(Plane);
+<a name="l00047"></a>00047 
+<a name="l00048"></a><a class="code" href="namespaceccp4srs.html#ac768cc62149be89b81a30d88a09f0166">00048</a>   <span class="keyword">typedef</span> <span class="keywordtype">char</span> <a class="code" href="namespaceccp4srs.html#ac768cc62149be89b81a30d88a09f0166">PlaneID</a>[20];
+<a name="l00049"></a>00049 
+<a name="l00050"></a><a class="code" href="classccp4srs_1_1_plane.html">00050</a>   <span class="keyword">class </span><a class="code" href="classccp4srs_1_1_plane.html">Plane</a>  {
+<a name="l00051"></a>00051 
+<a name="l00052"></a>00052     <span class="keyword">public</span>:
+<a name="l00053"></a>00053 
+<a name="l00054"></a><a class="code" href="classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5edae47dd3ee9591c478c387ddbe09f7ef34">00054</a>       <span class="keyword">enum</span> { <a class="code" href="classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5edae47dd3ee9591c478c387ddbe09f7ef34">Ok</a>=0,<a class="code" href="classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5edad0a61a72f29321313e1bc19920df40f9">EmptyLoop</a>=-11111,<a class="code" href="classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5eda95f4f7898a15589a3db43827444d2692">NoMorePlanes</a>=-11112 };
+<a name="l00055"></a>00055 
+<a name="l00056"></a>00056       <a class="code" href="classccp4srs_1_1_plane.html#ab45260579cf6dd22ecdaa93ad3b5c183">Plane</a>();
+<a name="l00057"></a>00057       <span class="keyword">virtual</span> <a class="code" href="classccp4srs_1_1_plane.html#a521911d044ea2aa8ca4e769b9d8d4e58">~Plane</a>();
+<a name="l00058"></a>00058 
+<a name="l00059"></a><a class="code" href="classccp4srs_1_1_plane.html#ac47f99cd6bf3190767da8fc85d01dc18">00059</a>       <span class="keyword">inline</span> mmdb::cpstr    <a class="code" href="classccp4srs_1_1_plane.html#ac47f99cd6bf3190767da8fc85d01dc18">id</a>   () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_plane.html#afdfdff5528e19537d834061022c2b2bf" title="plane id">plane_id</a>;    }
+<a name="l00060"></a><a class="code" href="classccp4srs_1_1_plane.html#a61ab65ef97a61c79d1190673a5a1b8e3">00060</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span>            <a class="code" href="classccp4srs_1_1_plane.html#a61ab65ef97a61c79d1190673a5a1b8e3">size</a> () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_plane.html#aa76a845ff6abce3d2c8f40db13717842" title="plane size">n_atoms</a>;     }
+<a name="l00061"></a><a class="code" href="classccp4srs_1_1_plane.html#a91e4f55f473565e42c27b6aab5311222">00061</a>       <span class="keyword">inline</span> mmdb::ivector  <a class="code" href="classccp4srs_1_1_plane.html#a91e4f55f473565e42c27b6aab5311222">atoms</a>() { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_plane.html#a4c8155332953ddb6cf79acf018c98c85" title="vector of plain&amp;#39;s atom names">plane_atoms</a>; }
+<a name="l00062"></a><a class="code" href="classccp4srs_1_1_plane.html#a4fd16b46609257ebe87c7b7347597b2b">00062</a>       <span class="keyword">inline</span> mmdb::rvector  <a class="code" href="classccp4srs_1_1_plane.html#a4fd16b46609257ebe87c7b7347597b2b">esds</a> () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_plane.html#a5837e387b59c8d350271fd11a644ee8d" title="vector of distance esds from the plane">dist_esd</a>;    }
+<a name="l00063"></a><a class="code" href="classccp4srs_1_1_plane.html#ad1e544c70729b5a17dba23301ba6ca7e">00063</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span>            <a class="code" href="classccp4srs_1_1_plane.html#ad1e544c70729b5a17dba23301ba6ca7e">atom</a> ( <span class="keywordtype">int</span> atomNo ) { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_plane.html#a4c8155332953ddb6cf79acf018c98c85" title="vector of plain&amp;#39;s atom names">plane_atoms</a>[atomNo]; }
+<a name="l00064"></a><a class="code" href="classccp4srs_1_1_plane.html#ad9f1d004296b308a0955997695277ff4">00064</a>       <span class="keyword">inline</span> mmdb::realtype <a class="code" href="classccp4srs_1_1_plane.html#ad9f1d004296b308a0955997695277ff4">esd</a>  ( <span class="keywordtype">int</span> atomNo ) { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_plane.html#a5837e387b59c8d350271fd11a644ee8d" title="vector of distance esds from the plane">dist_esd</a>   [atomNo]; }
+<a name="l00065"></a>00065 
+<a name="l00066"></a>00066       <span class="keyword">static</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_plane.html#a1ac0cfa095deac2bd97e99ce2b30de96">makeCIFTags</a> ( mmdb::mmcif::PLoop mmCIFLoop );
+<a name="l00067"></a>00067       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_plane.html#a656a93b833de401dcac75db47b5bcf57">readFromCIF</a> ( mmdb::mmcif::PLoop mmCIFLoop, <span class="keywordtype">int</span> planeNo,
+<a name="l00068"></a>00068                          <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a> &amp; <a class="code" href="classccp4srs_1_1_plane.html#a91e4f55f473565e42c27b6aab5311222">atoms</a> );
+<a name="l00069"></a>00069       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_plane.html#abd5b6df5e6d2bdafdd064a04974cf82a">writeToCIF</a>  ( mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID,
+<a name="l00070"></a>00070                          <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a> &amp; <a class="code" href="classccp4srs_1_1_plane.html#a91e4f55f473565e42c27b6aab5311222">atoms</a> );
+<a name="l00071"></a>00071 
+<a name="l00072"></a>00072       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_plane.html#a759255f2b21b770caa535f129e5f60bb">write_mem</a> ( PMemIO memIO, <span class="keywordtype">int</span> version );
+<a name="l00073"></a>00073       <span class="keywordtype">bool</span> <a class="code" href="classccp4srs_1_1_plane.html#a148162145438f6f97414eee0aa72275a">read_mem</a>  ( PMemIO memIO, <span class="keywordtype">int</span> version, <span class="keywordtype">bool</span> * <a class="code" href="classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5edae47dd3ee9591c478c387ddbe09f7ef34">Ok</a> = NULL );
+<a name="l00074"></a>00074 
+<a name="l00075"></a>00075       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_plane.html#a9db264baa4154922dfac882f4f437d34">copy</a> ( PPlane plane, mmdb::ivector anmatch=NULL );
+<a name="l00076"></a>00076 
+<a name="l00077"></a>00077     <span class="keyword">protected</span>:
+<a name="l00078"></a><a class="code" href="classccp4srs_1_1_plane.html#afdfdff5528e19537d834061022c2b2bf">00078</a>       <a class="code" href="namespaceccp4srs.html#ac768cc62149be89b81a30d88a09f0166">PlaneID</a>       <a class="code" href="classccp4srs_1_1_plane.html#afdfdff5528e19537d834061022c2b2bf" title="plane id">plane_id</a>;     
+<a name="l00079"></a><a class="code" href="classccp4srs_1_1_plane.html#aa76a845ff6abce3d2c8f40db13717842">00079</a>       <span class="keywordtype">int</span>           <a class="code" href="classccp4srs_1_1_plane.html#aa76a845ff6abce3d2c8f40db13717842" title="plane size">n_atoms</a>;      
+<a name="l00080"></a><a class="code" href="classccp4srs_1_1_plane.html#a4c8155332953ddb6cf79acf018c98c85">00080</a>       mmdb::ivector <a class="code" href="classccp4srs_1_1_plane.html#a4c8155332953ddb6cf79acf018c98c85" title="vector of plain&amp;#39;s atom names">plane_atoms</a>;  
+<a name="l00081"></a><a class="code" href="classccp4srs_1_1_plane.html#a5837e387b59c8d350271fd11a644ee8d">00081</a>       mmdb::rvector <a class="code" href="classccp4srs_1_1_plane.html#a5837e387b59c8d350271fd11a644ee8d" title="vector of distance esds from the plane">dist_esd</a>;     
+<a name="l00082"></a>00082 
+<a name="l00083"></a>00083       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_plane.html#a8da6c13ce79682d5f17e23f7c3e84849">empty</a>();
+<a name="l00084"></a>00084 
+<a name="l00085"></a>00085   };
+<a name="l00086"></a>00086 
+<a name="l00087"></a>00087 }  <span class="comment">// namespace ccp4srs</span>
+<a name="l00088"></a>00088 
+<a name="l00089"></a>00089 <span class="preprocessor">#endif // CCP4SRS_PLANE_H</span>
+</pre></div></div>
+</div>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__torsion_8cpp.html ccp4srs/doc-html/html/ccp4srs__torsion_8cpp.html
--- ccp4srs-old/doc-html/html/ccp4srs__torsion_8cpp.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__torsion_8cpp.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,82 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+  <div class="headertitle">
+<h1>src/ccp4srs_torsion.cpp File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &lt;string.h&gt;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__torsion_8h_source.html">ccp4srs_torsion.h</a>&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__defs_8h_source.html">ccp4srs_defs.h</a>&quot;</code><br/>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__torsion_8h.html ccp4srs/doc-html/html/ccp4srs__torsion_8h.html
--- ccp4srs-old/doc-html/html/ccp4srs__torsion_8h.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__torsion_8h.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,94 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<a href="#func-members">Functions</a>  </div>
+  <div class="headertitle">
+<h1>src/ccp4srs_torsion.h File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &quot;<a class="el" href="ccp4srs__atom_8h_source.html">ccp4srs_atom.h</a>&quot;</code><br/>
+
+<p><a href="ccp4srs__torsion_8h_source.html">Go to the source code of this file.</a></p>
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+<tr><td class="memItemLeft" align="right" valign="top">typedef char&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a192f47d1deb71790866bce922f50bba1">ccp4srs::TorsionID</a> [20]</td></tr>
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+<h1>src/ccp4srs_torsion.h</h1>  </div>
+</div>
+<div class="contents">
+<a href="ccp4srs__torsion_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">//  $Id: ccp4srs_torsion.h $</span>
+<a name="l00002"></a>00002 <span class="comment">//  =================================================================</span>
+<a name="l00003"></a>00003 <span class="comment">//</span>
+<a name="l00004"></a>00004 <span class="comment">//   CCP4 SRS Library: Storage, Retrieval and Search support for</span>
+<a name="l00005"></a>00005 <span class="comment">//   CCP4 ligand data.</span>
+<a name="l00006"></a>00006 <span class="comment">//</span>
+<a name="l00007"></a>00007 <span class="comment">//   Copyright (C) Eugene Krissinel 2010-2013.</span>
+<a name="l00008"></a>00008 <span class="comment">//</span>
+<a name="l00009"></a>00009 <span class="comment">//   This library is free software: you can redistribute it and/or</span>
+<a name="l00010"></a>00010 <span class="comment">//   modify it under the terms of the GNU Lesser General Public</span>
+<a name="l00011"></a>00011 <span class="comment">//   License version 3, modified in accordance with the provisions</span>
+<a name="l00012"></a>00012 <span class="comment">//   of the license to address the requirements of UK law.</span>
+<a name="l00013"></a>00013 <span class="comment">//</span>
+<a name="l00014"></a>00014 <span class="comment">//   You should have received a copy of the modified GNU Lesser</span>
+<a name="l00015"></a>00015 <span class="comment">//   General Public License along with this library. If not, copies</span>
+<a name="l00016"></a>00016 <span class="comment">//   may be downloaded from http://www.ccp4.ac.uk/ccp4license.php</span>
+<a name="l00017"></a>00017 <span class="comment">//</span>
+<a name="l00018"></a>00018 <span class="comment">//   This program is distributed in the hope that it will be useful,</span>
+<a name="l00019"></a>00019 <span class="comment">//   but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
+<a name="l00020"></a>00020 <span class="comment">//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
+<a name="l00021"></a>00021 <span class="comment">//   GNU Lesser General Public License for more details.</span>
+<a name="l00022"></a>00022 <span class="comment">//</span>
+<a name="l00023"></a>00023 <span class="comment">//  =================================================================</span>
+<a name="l00024"></a>00024 <span class="comment">//</span>
+<a name="l00025"></a>00025 <span class="comment">//    18.09.13   &lt;--  Date of Last Modification.</span>
+<a name="l00026"></a>00026 <span class="comment">//                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
+<a name="l00027"></a>00027 <span class="comment">//  -----------------------------------------------------------------</span>
+<a name="l00028"></a>00028 <span class="comment">//</span>
+<a name="l00029"></a>00029 <span class="comment">//  **** Module  :  ccp4srs_torsion  &lt;interface&gt;</span>
+<a name="l00030"></a>00030 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00031"></a>00031 <span class="comment">//  **** Classes :  ccp4srs::Torsion  - torsion angle restraint class</span>
+<a name="l00032"></a>00032 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00033"></a>00033 <span class="comment">//</span>
+<a name="l00034"></a>00034 <span class="comment">//  (C) E. Krissinel 2010-2013</span>
+<a name="l00035"></a>00035 <span class="comment">//</span>
+<a name="l00036"></a>00036 <span class="comment">//  =================================================================</span>
+<a name="l00037"></a>00037 <span class="comment">//</span>
+<a name="l00038"></a>00038 
+<a name="l00039"></a>00039 <span class="preprocessor">#ifndef CCP4SRS_TORSION_H</span>
+<a name="l00040"></a>00040 <span class="preprocessor"></span><span class="preprocessor">#define CCP4SRS_TORSION_H</span>
+<a name="l00041"></a>00041 <span class="preprocessor"></span>
+<a name="l00042"></a>00042 <span class="preprocessor">#include &quot;<a class="code" href="ccp4srs__atom_8h.html">ccp4srs_atom.h</a>&quot;</span>
+<a name="l00043"></a>00043 
+<a name="l00044"></a>00044 <span class="keyword">namespace </span>ccp4srs  {
+<a name="l00045"></a>00045 
+<a name="l00046"></a>00046   <a class="code" href="namespaceccp4srs.html#afbb5df60616f08fcf36926a3585c185f">DefineClass</a>(Torsion);
+<a name="l00047"></a>00047 
+<a name="l00048"></a><a class="code" href="namespaceccp4srs.html#a192f47d1deb71790866bce922f50bba1">00048</a>   <span class="keyword">typedef</span> <span class="keywordtype">char</span> <a class="code" href="namespaceccp4srs.html#a192f47d1deb71790866bce922f50bba1">TorsionID</a>[20];
+<a name="l00049"></a>00049 
+<a name="l00050"></a><a class="code" href="classccp4srs_1_1_torsion.html">00050</a>   <span class="keyword">class </span><a class="code" href="classccp4srs_1_1_torsion.html">Torsion</a> {
+<a name="l00051"></a>00051 
+<a name="l00052"></a>00052     <span class="keyword">public</span>:
+<a name="l00053"></a>00053       <a class="code" href="classccp4srs_1_1_torsion.html#a1939dda0f4d9e56c3762acade101e938">Torsion</a>();
+<a name="l00054"></a>00054       <span class="keyword">virtual</span> <a class="code" href="classccp4srs_1_1_torsion.html#a45434048948cdf6fc5f01a6e3ca149a8">~Torsion</a>();
+<a name="l00055"></a>00055 
+<a name="l00056"></a><a class="code" href="classccp4srs_1_1_torsion.html#a63cbef738a4be2da8a46367802f83e3d">00056</a>       <span class="keyword">inline</span> mmdb::cpstr    <a class="code" href="classccp4srs_1_1_torsion.html#a63cbef738a4be2da8a46367802f83e3d">id</a>    () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_torsion.html#ab82fe72dc4fb966139befa1636f0c4bd" title="torsion angle id">torsion_id</a>;     }
+<a name="l00057"></a><a class="code" href="classccp4srs_1_1_torsion.html#af30f2e612259dedd1e569db13ff583fd">00057</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span>            <a class="code" href="classccp4srs_1_1_torsion.html#af30f2e612259dedd1e569db13ff583fd">atom1</a> () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_torsion.html#ae6bb750e2ebd67defafc5bd38515e923">atom_1</a>;         }
+<a name="l00058"></a><a class="code" href="classccp4srs_1_1_torsion.html#ae34ef1ddabf50dd732bf66336bb4a2eb">00058</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span>            <a class="code" href="classccp4srs_1_1_torsion.html#ae34ef1ddabf50dd732bf66336bb4a2eb">atom2</a> () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_torsion.html#aae803284861c24535f6ea3cab02f00b8" title="ordinal numbers of atoms">atom_2</a>;         }
+<a name="l00059"></a><a class="code" href="classccp4srs_1_1_torsion.html#a37c594eb8a06aa962efd46c8d5c0e1b9">00059</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span>            <a class="code" href="classccp4srs_1_1_torsion.html#a37c594eb8a06aa962efd46c8d5c0e1b9">atom3</a> () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_torsion.html#a16456310c79412ef19e6b3dd22baf3b3">atom_3</a>;         }
+<a name="l00060"></a><a class="code" href="classccp4srs_1_1_torsion.html#afb752f1836193a0af5befba252e16703">00060</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span>            <a class="code" href="classccp4srs_1_1_torsion.html#afb752f1836193a0af5befba252e16703">atom4</a> () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_torsion.html#a73c5cc1a3f37ac0998b1316beb35c579">atom_4</a>;         }
+<a name="l00061"></a><a class="code" href="classccp4srs_1_1_torsion.html#a8fd30d637a8002a46ff4c50cadc8d34f">00061</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span>            <a class="code" href="classccp4srs_1_1_torsion.html#a8fd30d637a8002a46ff4c50cadc8d34f">period</a>() { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_torsion.html#a681cd0d538d13fa8d30dee2eb0c7df20" title="that form the angle [0,1,...]">torsion_period</a>; }
+<a name="l00062"></a><a class="code" href="classccp4srs_1_1_torsion.html#a001451fd28649a8df65416d7e551b7a9">00062</a>       <span class="keyword">inline</span> mmdb::realtype <a class="code" href="classccp4srs_1_1_torsion.html#a001451fd28649a8df65416d7e551b7a9">value</a> () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_torsion.html#a68b1d2a3529f1b153db01830a6cde818" title="torsion angle in degrees">torsion</a>;        }
+<a name="l00063"></a><a class="code" href="classccp4srs_1_1_torsion.html#a44095b8e5025c92a4b443a8715beceee">00063</a>       <span class="keyword">inline</span> mmdb::realtype <a class="code" href="classccp4srs_1_1_torsion.html#a44095b8e5025c92a4b443a8715beceee">esd</a>   () { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_torsion.html#a34011e29f9c0faa8bc15a31274dd27c3">torsion_esd</a>;    }
+<a name="l00064"></a>00064 
+<a name="l00065"></a>00065       <span class="keyword">static</span> <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_torsion.html#ae33b6fc8d12fdbd48a299cf488e16f0e">makeCIFTags</a> ( mmdb::mmcif::PLoop mmCIFLoop );
+<a name="l00066"></a>00066       <span class="keywordtype">int</span>  <a class="code" href="classccp4srs_1_1_torsion.html#aaf9375ff9aeb22a2a148763276ec80d1">readFromCIF</a> ( mmdb::mmcif::PLoop mmCIFLoop, <span class="keywordtype">int</span> angleNo,
+<a name="l00067"></a>00067                          <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a> &amp; atoms );
+<a name="l00068"></a>00068       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_torsion.html#ae53494ec218062be243d5e7b36f43dd0">writeToCIF</a>  ( mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID,
+<a name="l00069"></a>00069                          <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a> &amp; atoms );
+<a name="l00070"></a>00070 
+<a name="l00071"></a>00071       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_torsion.html#a9b4f1d2c543776a8e0412eae4c7db651">write_mem</a> ( PMemIO memIO, <span class="keywordtype">int</span> version );
+<a name="l00072"></a>00072       <span class="keywordtype">bool</span> <a class="code" href="classccp4srs_1_1_torsion.html#af65ef2e18a3b6494070300afec0099e1">read_mem</a>  ( PMemIO memIO, <span class="keywordtype">int</span> version, <span class="keywordtype">bool</span> * Ok = NULL );
+<a name="l00073"></a>00073 
+<a name="l00074"></a>00074       <span class="keywordtype">void</span> <a class="code" href="classccp4srs_1_1_torsion.html#a2a6ff05c37b9ce514fe557ab3817a072">copy</a> ( PTorsion trs, mmdb::ivector anmatch=NULL );
+<a name="l00075"></a>00075 
+<a name="l00076"></a>00076     <span class="keyword">protected</span>:
+<a name="l00077"></a><a class="code" href="classccp4srs_1_1_torsion.html#ab82fe72dc4fb966139befa1636f0c4bd">00077</a>       <a class="code" href="namespaceccp4srs.html#a192f47d1deb71790866bce922f50bba1">TorsionID</a>   <a class="code" href="classccp4srs_1_1_torsion.html#ab82fe72dc4fb966139befa1636f0c4bd" title="torsion angle id">torsion_id</a>;     
+<a name="l00078"></a><a class="code" href="classccp4srs_1_1_torsion.html#aae803284861c24535f6ea3cab02f00b8">00078</a>       <span class="keywordtype">int</span>         <a class="code" href="classccp4srs_1_1_torsion.html#ae6bb750e2ebd67defafc5bd38515e923">atom_1</a>,<a class="code" href="classccp4srs_1_1_torsion.html#aae803284861c24535f6ea3cab02f00b8" title="ordinal numbers of atoms">atom_2</a>;  
+<a name="l00079"></a><a class="code" href="classccp4srs_1_1_torsion.html#a73c5cc1a3f37ac0998b1316beb35c579">00079</a>       <span class="keywordtype">int</span>         <a class="code" href="classccp4srs_1_1_torsion.html#a16456310c79412ef19e6b3dd22baf3b3">atom_3</a>,<a class="code" href="classccp4srs_1_1_torsion.html#a73c5cc1a3f37ac0998b1316beb35c579">atom_4</a>;  
+<a name="l00080"></a><a class="code" href="classccp4srs_1_1_torsion.html#a681cd0d538d13fa8d30dee2eb0c7df20">00080</a>       <span class="keywordtype">int</span>         <a class="code" href="classccp4srs_1_1_torsion.html#a681cd0d538d13fa8d30dee2eb0c7df20" title="that form the angle [0,1,...]">torsion_period</a>; 
+<a name="l00081"></a><a class="code" href="classccp4srs_1_1_torsion.html#a68b1d2a3529f1b153db01830a6cde818">00081</a>       mmdb::realtype <a class="code" href="classccp4srs_1_1_torsion.html#a68b1d2a3529f1b153db01830a6cde818" title="torsion angle in degrees">torsion</a>;     
+<a name="l00082"></a><a class="code" href="classccp4srs_1_1_torsion.html#a34011e29f9c0faa8bc15a31274dd27c3">00082</a>       mmdb::realtype <a class="code" href="classccp4srs_1_1_torsion.html#a34011e29f9c0faa8bc15a31274dd27c3">torsion_esd</a>; 
+<a name="l00083"></a>00083 
+<a name="l00084"></a>00084 
+<a name="l00085"></a>00085   };
+<a name="l00086"></a>00086 
+<a name="l00087"></a>00087 }  <span class="comment">// namespace ccp4srs</span>
+<a name="l00088"></a>00088 
+<a name="l00089"></a>00089 <span class="preprocessor">#endif // CCP4SRS_TORSION_H</span>
+</pre></div></div>
+</div>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__tree_8cpp.html ccp4srs/doc-html/html/ccp4srs__tree_8cpp.html
--- ccp4srs-old/doc-html/html/ccp4srs__tree_8cpp.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__tree_8cpp.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,82 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+  <div class="headertitle">
+<h1>src/ccp4srs_tree.cpp File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &lt;string.h&gt;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__tree_8h_source.html">ccp4srs_tree.h</a>&quot;</code><br/>
+<code>#include &quot;<a class="el" href="ccp4srs__defs_8h_source.html">ccp4srs_defs.h</a>&quot;</code><br/>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__tree_8h.html ccp4srs/doc-html/html/ccp4srs__tree_8h.html
--- ccp4srs-old/doc-html/html/ccp4srs__tree_8h.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__tree_8h.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,90 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
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+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
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+<a href="#func-members">Functions</a>  </div>
+  <div class="headertitle">
+<h1>src/ccp4srs_tree.h File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &quot;<a class="el" href="ccp4srs__atom_8h_source.html">ccp4srs_atom.h</a>&quot;</code><br/>
+
+<p><a href="ccp4srs__tree_8h_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="nested-classes"></a>
+Classes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_tree.html">ccp4srs::Tree</a></td></tr>
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+<tr><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a6d1229e1b71f24fdb95a8700d402c6f8">ccp4srs::DefineClass</a> (Tree)</td></tr>
+</table>
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diff -ruN ccp4srs-old/doc-html/html/ccp4srs__tree_8h_source.html ccp4srs/doc-html/html/ccp4srs__tree_8h_source.html
--- ccp4srs-old/doc-html/html/ccp4srs__tree_8h_source.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__tree_8h_source.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,160 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/ccp4srs_tree.h Source File</title>
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+<link href="search/search.css" rel="stylesheet" type="text/css"/>
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+<div class="header">
+  <div class="headertitle">
+<h1>src/ccp4srs_tree.h</h1>  </div>
+</div>
+<div class="contents">
+<a href="ccp4srs__tree_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">//  $Id: ccp4srs_tree.h $</span>
+<a name="l00002"></a>00002 <span class="comment">//  =================================================================</span>
+<a name="l00003"></a>00003 <span class="comment">//</span>
+<a name="l00004"></a>00004 <span class="comment">//   CCP4 SRS Library: Storage, Retrieval and Search support for</span>
+<a name="l00005"></a>00005 <span class="comment">//   CCP4 ligand data.</span>
+<a name="l00006"></a>00006 <span class="comment">//</span>
+<a name="l00007"></a>00007 <span class="comment">//   Copyright (C) Eugene Krissinel 2010-2013.</span>
+<a name="l00008"></a>00008 <span class="comment">//</span>
+<a name="l00009"></a>00009 <span class="comment">//   This library is free software: you can redistribute it and/or</span>
+<a name="l00010"></a>00010 <span class="comment">//   modify it under the terms of the GNU Lesser General Public</span>
+<a name="l00011"></a>00011 <span class="comment">//   License version 3, modified in accordance with the provisions</span>
+<a name="l00012"></a>00012 <span class="comment">//   of the license to address the requirements of UK law.</span>
+<a name="l00013"></a>00013 <span class="comment">//</span>
+<a name="l00014"></a>00014 <span class="comment">//   You should have received a copy of the modified GNU Lesser</span>
+<a name="l00015"></a>00015 <span class="comment">//   General Public License along with this library. If not, copies</span>
+<a name="l00016"></a>00016 <span class="comment">//   may be downloaded from http://www.ccp4.ac.uk/ccp4license.php</span>
+<a name="l00017"></a>00017 <span class="comment">//</span>
+<a name="l00018"></a>00018 <span class="comment">//   This program is distributed in the hope that it will be useful,</span>
+<a name="l00019"></a>00019 <span class="comment">//   but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
+<a name="l00020"></a>00020 <span class="comment">//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
+<a name="l00021"></a>00021 <span class="comment">//   GNU Lesser General Public License for more details.</span>
+<a name="l00022"></a>00022 <span class="comment">//</span>
+<a name="l00023"></a>00023 <span class="comment">//  =================================================================</span>
+<a name="l00024"></a>00024 <span class="comment">//</span>
+<a name="l00025"></a>00025 <span class="comment">//    18.09.13   &lt;--  Date of Last Modification.</span>
+<a name="l00026"></a>00026 <span class="comment">//                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
+<a name="l00027"></a>00027 <span class="comment">//  -----------------------------------------------------------------</span>
+<a name="l00028"></a>00028 <span class="comment">//</span>
+<a name="l00029"></a>00029 <span class="comment">//  **** Module  :  ccp4srs_tree  &lt;interface&gt;</span>
+<a name="l00030"></a>00030 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00031"></a>00031 <span class="comment">//  **** Classes :  ccp4srs::Tree  - structure tree</span>
+<a name="l00032"></a>00032 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00033"></a>00033 <span class="comment">//</span>
+<a name="l00034"></a>00034 <span class="comment">//  (C) E. Krissinel 2010-2013</span>
+<a name="l00035"></a>00035 <span class="comment">//</span>
+<a name="l00036"></a>00036 <span class="comment">//  =================================================================</span>
+<a name="l00037"></a>00037 <span class="comment">//</span>
+<a name="l00038"></a>00038 
+<a name="l00039"></a>00039 <span class="preprocessor">#ifndef CCP4SRS_TREE_H</span>
+<a name="l00040"></a>00040 <span class="preprocessor"></span><span class="preprocessor">#define CCP4SRS_TREE_H</span>
+<a name="l00041"></a>00041 <span class="preprocessor"></span>
+<a name="l00042"></a>00042 <span class="preprocessor">#include &quot;<a class="code" href="ccp4srs__atom_8h.html">ccp4srs_atom.h</a>&quot;</span>
+<a name="l00043"></a>00043 
+<a name="l00044"></a>00044 <span class="keyword">namespace </span>ccp4srs  {
+<a name="l00045"></a>00045 
+<a name="l00046"></a>00046   <a class="code" href="namespaceccp4srs.html#afbb5df60616f08fcf36926a3585c185f">DefineClass</a>(Tree);
+<a name="l00047"></a>00047 
+<a name="l00048"></a><a class="code" href="classccp4srs_1_1_tree.html">00048</a>   <span class="keyword">class </span><a class="code" href="classccp4srs_1_1_tree.html">Tree</a>  {
+<a name="l00049"></a>00049 
+<a name="l00050"></a>00050     <span class="comment">// atom connectivity types</span>
+<a name="l00051"></a>00051     <span class="keyword">enum</span>  {None,Start,End,Add};
+<a name="l00052"></a>00052 
+<a name="l00053"></a>00053     <span class="keyword">public</span>:
+<a name="l00054"></a>00054       <a class="code" href="classccp4srs_1_1_tree.html#a342a1de215612310580d0cd6a06262cb">Tree</a>();
+<a name="l00055"></a>00055       <span class="keyword">virtual</span> <a class="code" href="classccp4srs_1_1_tree.html#ab5a113a9574397dbb5e7679211ee3c24">~Tree</a>();
+<a name="l00056"></a>00056 
+<a name="l00057"></a>00057       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_tree.html#a5f5e595cfdb5623cc59c0651ff7a25d3">empty</a>();
+<a name="l00058"></a>00058 
+<a name="l00059"></a><a class="code" href="classccp4srs_1_1_tree.html#a308ddfce7a902729218e39356db92cc0">00059</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_tree.html#a308ddfce7a902729218e39356db92cc0">size</a>() { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_tree.html#a4056f0bb5ef8add5a55133eb8166c639" title="number of sections">n_sections</a>;    }
+<a name="l00060"></a><a class="code" href="classccp4srs_1_1_tree.html#aa05e210175e281b0b975b22040cbf45d">00060</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_tree.html#aa05e210175e281b0b975b22040cbf45d">atom</a>     ( <span class="keywordtype">int</span> secNo ) { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_tree.html#a27d256081e9d371ff22a6644d9ee8a91" title="tree atom name">atom_tree</a>    [secNo]; }
+<a name="l00061"></a><a class="code" href="classccp4srs_1_1_tree.html#a70a9e13b054276780039e0d6f0edcdd9">00061</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_tree.html#a70a9e13b054276780039e0d6f0edcdd9">backward</a> ( <span class="keywordtype">int</span> secNo ) { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_tree.html#a612df27ef2431bf2ac087f7190e0f9d1" title="previous atom name">atom_backward</a>[secNo]; }
+<a name="l00062"></a><a class="code" href="classccp4srs_1_1_tree.html#ad52fadb719ce7ca269b9f6875a9ce8e6">00062</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_tree.html#ad52fadb719ce7ca269b9f6875a9ce8e6">forward</a>  ( <span class="keywordtype">int</span> secNo ) { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_tree.html#a3c63a71c2935da20a0feccad01d5ceaf" title="next atom name">atom_forward</a> [secNo]; }
+<a name="l00063"></a><a class="code" href="classccp4srs_1_1_tree.html#a9986231a0223ef6b62902823d119176f">00063</a>       <span class="keyword">inline</span> <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_tree.html#a9986231a0223ef6b62902823d119176f">connect</a>  ( <span class="keywordtype">int</span> secNo ) { <span class="keywordflow">return</span> <a class="code" href="classccp4srs_1_1_tree.html#a97ee818b7a1b1724cfb712453be05743" title="type of connection">connect_type</a> [secNo]; }
+<a name="l00064"></a>00064 
+<a name="l00065"></a>00065       <span class="keywordtype">int</span>   <a class="code" href="classccp4srs_1_1_tree.html#af50e009eb63e2bdf8da129afa193d637">readFromCIF</a>   ( mmdb::mmcif::PLoop mmCIFLoop,
+<a name="l00066"></a>00066                             <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a> &amp; atoms );
+<a name="l00067"></a>00067       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_tree.html#ade370b24c17b2d47a4cb8f89c096e5c1">writeToCIF</a>    ( mmdb::mmcif::PData mmCIFData,
+<a name="l00068"></a>00068                             mmdb::cpstr monID,
+<a name="l00069"></a>00069                             <a class="code" href="classccp4srs_1_1_container.html">Container&lt;Atom&gt;</a> &amp; atoms );
+<a name="l00070"></a>00070 
+<a name="l00071"></a>00071       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_tree.html#a357b27f65ab5b653fc17a387e9653c4f">write_mem</a>   ( PMemIO memIO, <span class="keywordtype">int</span> version );
+<a name="l00072"></a>00072       <span class="keywordtype">bool</span>  <a class="code" href="classccp4srs_1_1_tree.html#a7e39da9840cb8815e8854cd11552c3a9">read_mem</a>    ( PMemIO memIO, <span class="keywordtype">int</span> version,
+<a name="l00073"></a>00073                           <span class="keywordtype">bool</span> * Ok = NULL );
+<a name="l00074"></a>00074 
+<a name="l00075"></a>00075       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_tree.html#acfc010d5d168bb288379e6b6721fb9fa">copy</a> ( PTree tree, mmdb::ivector anmatch=NULL );
+<a name="l00076"></a>00076 
+<a name="l00077"></a>00077     <span class="keyword">protected</span>:
+<a name="l00078"></a><a class="code" href="classccp4srs_1_1_tree.html#a4056f0bb5ef8add5a55133eb8166c639">00078</a>       <span class="keywordtype">int</span>            <a class="code" href="classccp4srs_1_1_tree.html#a4056f0bb5ef8add5a55133eb8166c639" title="number of sections">n_sections</a>;     
+<a name="l00079"></a><a class="code" href="classccp4srs_1_1_tree.html#a27d256081e9d371ff22a6644d9ee8a91">00079</a>       mmdb::ivector  <a class="code" href="classccp4srs_1_1_tree.html#a27d256081e9d371ff22a6644d9ee8a91" title="tree atom name">atom_tree</a>;      
+<a name="l00080"></a><a class="code" href="classccp4srs_1_1_tree.html#a612df27ef2431bf2ac087f7190e0f9d1">00080</a>       mmdb::ivector  <a class="code" href="classccp4srs_1_1_tree.html#a612df27ef2431bf2ac087f7190e0f9d1" title="previous atom name">atom_backward</a>;  
+<a name="l00081"></a><a class="code" href="classccp4srs_1_1_tree.html#a3c63a71c2935da20a0feccad01d5ceaf">00081</a>       mmdb::ivector  <a class="code" href="classccp4srs_1_1_tree.html#a3c63a71c2935da20a0feccad01d5ceaf" title="next atom name">atom_forward</a>;   
+<a name="l00082"></a><a class="code" href="classccp4srs_1_1_tree.html#a97ee818b7a1b1724cfb712453be05743">00082</a>       mmdb::ivector  <a class="code" href="classccp4srs_1_1_tree.html#a97ee818b7a1b1724cfb712453be05743" title="type of connection">connect_type</a>;   
+<a name="l00083"></a>00083 
+<a name="l00084"></a>00084   };
+<a name="l00085"></a>00085 
+<a name="l00086"></a>00086 }  <span class="comment">// namespace ccp4srs</span>
+<a name="l00087"></a>00087 
+<a name="l00088"></a>00088 <span class="preprocessor">#endif // CCP4SRS_TREE_H</span>
+</pre></div></div>
+</div>
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+
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+<a href="http://www.doxygen.org/index.html">
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+</html>
diff -ruN ccp4srs-old/doc-html/html/ccp4srs__types_8cpp.html ccp4srs/doc-html/html/ccp4srs__types_8cpp.html
--- ccp4srs-old/doc-html/html/ccp4srs__types_8cpp.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__types_8cpp.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,88 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/ccp4srs_types.cpp File Reference</title>
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+<link href="search/search.css" rel="stylesheet" type="text/css"/>
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+          <img id="MSearchSelect" src="search/mag_sel.png"
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+      <li><a href="files.html"><span>File&#160;List</span></a></li>
+      <li><a href="globals.html"><span>File&#160;Members</span></a></li>
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+<div class="header">
+  <div class="summary">
+<a href="#namespaces">Namespaces</a> &#124;
+<a href="#var-members">Variables</a>  </div>
+  <div class="headertitle">
+<h1>src/ccp4srs_types.cpp File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &quot;<a class="el" href="ccp4srs__types_8h_source.html">ccp4srs_types.h</a>&quot;</code><br/>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+<tr><td colspan="2"><h2><a name="var-members"></a>
+Variables</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">const int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a4938160ce6172269adc59b8077014f7c">ccp4srs::CCP4SRS_file_version</a> = 2</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a3f27798432992515be969c17425412d3">ccp4srs::srsIndexFile</a> = &quot;index.srs&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a4132afa4ce21fdcd2ff268bf6e980cfc">ccp4srs::srsGraphFile</a> = &quot;graph.srs&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#af51e5a096118e643d5fcf5490d44c6db">ccp4srs::srsStructFile</a> = &quot;struct.srs&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">const int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#aa44a92ce883cd1c525381111cd1a4ab3">ccp4srs::AtomID_NA</a> = -10000</td></tr>
+</table>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
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+
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+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/ccp4srs__types_8h.html ccp4srs/doc-html/html/ccp4srs__types_8h.html
--- ccp4srs-old/doc-html/html/ccp4srs__types_8h.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__types_8h.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,124 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/ccp4srs_types.h File Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
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+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
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+var searchBox = new SearchBox("searchBox", "search",false,'Search');
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+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
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+          <img id="MSearchSelect" src="search/mag_sel.png"
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+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
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+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="files.html"><span>File&#160;List</span></a></li>
+      <li><a href="globals.html"><span>File&#160;Members</span></a></li>
+    </ul>
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+  <div class="summary">
+<a href="#nested-classes">Classes</a> &#124;
+<a href="#namespaces">Namespaces</a> &#124;
+<a href="#enum-members">Enumerations</a> &#124;
+<a href="#func-members">Functions</a>  </div>
+  <div class="headertitle">
+<h1>src/ccp4srs_types.h File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &quot;mmdb/mmdb_manager.h&quot;</code><br/>
+
+<p><a href="ccp4srs__types_8h_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="nested-classes"></a>
+Classes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structccp4srs_1_1_atom_pair.html">ccp4srs::AtomPair</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html">ccp4srs::DASelHnds</a></td></tr>
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+<tr><td colspan="2"><h2><a name="enum-members"></a>
+Enumerations</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40d">ccp4srs::CCP4SRS_VERSION</a> { <a class="el" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40da70b6b61e66afecc14062283f4ab22165">ccp4srs::MAJOR_VERSION</a> =  1, 
+<a class="el" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40da629c96b840f87c056420011f99867b11">ccp4srs::MINOR_VERSION</a> =  0, 
+<a class="el" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40dafef3f6fb9926961d5bb1c2c5f5464228">ccp4srs::MICRO_VERSION</a> =  0
+ }</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">ccp4srs::CCP4SRS_RC</a> { <br/>
+&#160;&#160;<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa9f7a70887f053cb4ce97d321d477ac81">ccp4srs::CCP4SRS_noDonors</a> =  4, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa2d2f9ebfa39ac8c445aaa789d3f7d73c">ccp4srs::CCP4SRS_noAcceptors</a> =  3, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aae4c2a57f461a7c55fcdbf5f5256b633c">ccp4srs::CCP4SRS_noHBonds</a> =  2, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa376037f37a8f3b5a5822abe08b8a2775">ccp4srs::CCP4SRS_Incomplete</a> =  1, 
+<br/>
+&#160;&#160;<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa09553d9a0822e1b3ab31018c2a12cbbb">ccp4srs::CCP4SRS_Ok</a> =  0, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa0f4cab4ac6672344d9c17addef3a5c2c">ccp4srs::CCP4SRS_WrongBondType</a> =  -1, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa4513ed69439ddf6233fd9311675d3ec3">ccp4srs::CCP4SRS_IndexCorrupt</a> =  -2, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aaf8be04ede882dccdaab276915605e785">ccp4srs::CCP4SRS_FileNotFound</a> =  -3, 
+<br/>
+&#160;&#160;<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa0f0128ede6fa588e9e90ab7d96e3395d">ccp4srs::CCP4SRS_EntryNotFound</a> =  -4, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa3f7eda4d59140c81cd5ca9224b569146">ccp4srs::CCP4SRS_ReadErrors</a> =  -5, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aacec935441561de176dbd7b29c608a960">ccp4srs::CCP4SRS_EmptyResidue</a> =  -6, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa6ce76e69c4e7c9b8ae5f28fcb6279c13">ccp4srs::CCP4SRS_NoAtomsFound</a> =  -7, 
+<br/>
+&#160;&#160;<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aaf41577d27e0b8306dc1dfaebbffe3a85">ccp4srs::CCP4SRS_NoBonds</a> =  -8, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa36de44e9555882901e32ff002491b4c1">ccp4srs::CCP4SRS_EmptyResSet</a> =  -9, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa770346796e3fd0232458a3dd9709d735">ccp4srs::CCP4SRS_Fail</a> =  -10, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aafabbc088bd534a406ce2a155b7c7be34">ccp4srs::CCP4SRS_SVD_Fail</a> =  -11, 
+<br/>
+&#160;&#160;<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa86978a692503eda1577d1250f402e4d4">ccp4srs::CCP4SRS_noCoordHierarchy</a> =  -12, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa785ce210fda24a93bd0df60e0a612698">ccp4srs::CCP4SRS_BrokenBonds</a> =  -13
+<br/>
+ }</td></tr>
+<tr><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a38fd31a76e47d65dbd8f9343fdc2f001">ccp4srs::DefineStructure</a> (AtomPair)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#af0f84ef74e24251a016c6d27c196fe2e">ccp4srs::DefineStructure</a> (DASelHnds)</td></tr>
+</table>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
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+
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+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/ccp4srs__types_8h_source.html ccp4srs/doc-html/html/ccp4srs__types_8h_source.html
--- ccp4srs-old/doc-html/html/ccp4srs__types_8h_source.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/ccp4srs__types_8h_source.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,182 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<div class="header">
+  <div class="headertitle">
+<h1>src/ccp4srs_types.h</h1>  </div>
+</div>
+<div class="contents">
+<a href="ccp4srs__types_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">//  $Id: ccp4srs_types.h $</span>
+<a name="l00002"></a>00002 <span class="comment">//  =================================================================</span>
+<a name="l00003"></a>00003 <span class="comment">//</span>
+<a name="l00004"></a>00004 <span class="comment">//   CCP4 SRS Library: Storage, Retrieval and Search support for</span>
+<a name="l00005"></a>00005 <span class="comment">//   CCP4 ligand data.</span>
+<a name="l00006"></a>00006 <span class="comment">//</span>
+<a name="l00007"></a>00007 <span class="comment">//   Copyright (C) Eugene Krissinel 2010-2013.</span>
+<a name="l00008"></a>00008 <span class="comment">//</span>
+<a name="l00009"></a>00009 <span class="comment">//   This library is free software: you can redistribute it and/or</span>
+<a name="l00010"></a>00010 <span class="comment">//   modify it under the terms of the GNU Lesser General Public</span>
+<a name="l00011"></a>00011 <span class="comment">//   License version 3, modified in accordance with the provisions</span>
+<a name="l00012"></a>00012 <span class="comment">//   of the license to address the requirements of UK law.</span>
+<a name="l00013"></a>00013 <span class="comment">//</span>
+<a name="l00014"></a>00014 <span class="comment">//   You should have received a copy of the modified GNU Lesser</span>
+<a name="l00015"></a>00015 <span class="comment">//   General Public License along with this library. If not, copies</span>
+<a name="l00016"></a>00016 <span class="comment">//   may be downloaded from http://www.ccp4.ac.uk/ccp4license.php</span>
+<a name="l00017"></a>00017 <span class="comment">//</span>
+<a name="l00018"></a>00018 <span class="comment">//   This program is distributed in the hope that it will be useful,</span>
+<a name="l00019"></a>00019 <span class="comment">//   but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
+<a name="l00020"></a>00020 <span class="comment">//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
+<a name="l00021"></a>00021 <span class="comment">//   GNU Lesser General Public License for more details.</span>
+<a name="l00022"></a>00022 <span class="comment">//</span>
+<a name="l00023"></a>00023 <span class="comment">//  =================================================================</span>
+<a name="l00024"></a>00024 <span class="comment">//</span>
+<a name="l00025"></a>00025 <span class="comment">//    18.09.13   &lt;--  Date of Last Modification.</span>
+<a name="l00026"></a>00026 <span class="comment">//                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
+<a name="l00027"></a>00027 <span class="comment">//  -----------------------------------------------------------------</span>
+<a name="l00028"></a>00028 <span class="comment">//</span>
+<a name="l00029"></a>00029 <span class="comment">//  **** Module  :  ccp4srs_types  &lt;interface&gt;</span>
+<a name="l00030"></a>00030 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00031"></a>00031 <span class="comment">//  **** Classes :  ccp4srs::AtomPair  - atom pair</span>
+<a name="l00032"></a>00032 <span class="comment">//       ~~~~~~~~~  ccp4srs::DASelHnds - donor-acceptor selection</span>
+<a name="l00033"></a>00033 <span class="comment">//                                       handlers</span>
+<a name="l00034"></a>00034 <span class="comment">//</span>
+<a name="l00035"></a>00035 <span class="comment">//  (C) E. Krissinel 2010-2013</span>
+<a name="l00036"></a>00036 <span class="comment">//</span>
+<a name="l00037"></a>00037 <span class="comment">//  =================================================================</span>
+<a name="l00038"></a>00038 <span class="comment">//</span>
+<a name="l00039"></a>00039 
+<a name="l00040"></a>00040 <span class="preprocessor">#ifndef CCP4SRS_TYPES_H</span>
+<a name="l00041"></a>00041 <span class="preprocessor"></span><span class="preprocessor">#define CCP4SRS_TYPES_H</span>
+<a name="l00042"></a>00042 <span class="preprocessor"></span>
+<a name="l00043"></a>00043 <span class="preprocessor">#include &quot;mmdb/mmdb_manager.h&quot;</span>
+<a name="l00044"></a>00044 
+<a name="l00045"></a>00045 <span class="keyword">namespace </span>ccp4srs  {
+<a name="l00046"></a>00046 
+<a name="l00047"></a><a class="code" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40d">00047</a>   <span class="keyword">enum</span> <a class="code" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40d">CCP4SRS_VERSION</a>  {
+<a name="l00048"></a><a class="code" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40da70b6b61e66afecc14062283f4ab22165">00048</a>     <a class="code" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40da70b6b61e66afecc14062283f4ab22165" title="major version">MAJOR_VERSION</a> = 1,  
+<a name="l00049"></a><a class="code" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40da629c96b840f87c056420011f99867b11">00049</a>     <a class="code" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40da629c96b840f87c056420011f99867b11" title="minor version">MINOR_VERSION</a> = 0,  
+<a name="l00050"></a><a class="code" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40dafef3f6fb9926961d5bb1c2c5f5464228">00050</a>     <a class="code" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40dafef3f6fb9926961d5bb1c2c5f5464228" title="micro version">MICRO_VERSION</a> = 0   
+<a name="l00051"></a>00051   };
+<a name="l00052"></a>00052 
+<a name="l00053"></a>00053   <span class="keyword">extern</span> <span class="keyword">const</span> <span class="keywordtype">int</span> <a class="code" href="namespaceccp4srs.html#a4938160ce6172269adc59b8077014f7c">CCP4SRS_file_version</a>;
+<a name="l00054"></a>00054 
+<a name="l00055"></a><a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">00055</a>   <span class="keyword">enum</span> <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">CCP4SRS_RC</a>  {
+<a name="l00056"></a><a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa9f7a70887f053cb4ce97d321d477ac81">00056</a>     <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa9f7a70887f053cb4ce97d321d477ac81">CCP4SRS_noDonors</a>         =   4,
+<a name="l00057"></a><a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa2d2f9ebfa39ac8c445aaa789d3f7d73c">00057</a>     <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa2d2f9ebfa39ac8c445aaa789d3f7d73c">CCP4SRS_noAcceptors</a>      =   3,
+<a name="l00058"></a><a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aae4c2a57f461a7c55fcdbf5f5256b633c">00058</a>     <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aae4c2a57f461a7c55fcdbf5f5256b633c">CCP4SRS_noHBonds</a>         =   2,
+<a name="l00059"></a><a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa376037f37a8f3b5a5822abe08b8a2775">00059</a>     <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa376037f37a8f3b5a5822abe08b8a2775">CCP4SRS_Incomplete</a>       =   1,
+<a name="l00060"></a><a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa09553d9a0822e1b3ab31018c2a12cbbb">00060</a>     <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa09553d9a0822e1b3ab31018c2a12cbbb">CCP4SRS_Ok</a>               =   0,
+<a name="l00061"></a><a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa0f4cab4ac6672344d9c17addef3a5c2c">00061</a>     <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa0f4cab4ac6672344d9c17addef3a5c2c">CCP4SRS_WrongBondType</a>    =  -1,
+<a name="l00062"></a><a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa4513ed69439ddf6233fd9311675d3ec3">00062</a>     <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa4513ed69439ddf6233fd9311675d3ec3">CCP4SRS_IndexCorrupt</a>     =  -2,
+<a name="l00063"></a><a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aaf8be04ede882dccdaab276915605e785">00063</a>     <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aaf8be04ede882dccdaab276915605e785">CCP4SRS_FileNotFound</a>     =  -3,
+<a name="l00064"></a><a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa0f0128ede6fa588e9e90ab7d96e3395d">00064</a>     <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa0f0128ede6fa588e9e90ab7d96e3395d">CCP4SRS_EntryNotFound</a>    =  -4,
+<a name="l00065"></a><a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa3f7eda4d59140c81cd5ca9224b569146">00065</a>     <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa3f7eda4d59140c81cd5ca9224b569146">CCP4SRS_ReadErrors</a>       =  -5,
+<a name="l00066"></a><a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aacec935441561de176dbd7b29c608a960">00066</a>     <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aacec935441561de176dbd7b29c608a960">CCP4SRS_EmptyResidue</a>     =  -6,
+<a name="l00067"></a><a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa6ce76e69c4e7c9b8ae5f28fcb6279c13">00067</a>     <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa6ce76e69c4e7c9b8ae5f28fcb6279c13">CCP4SRS_NoAtomsFound</a>     =  -7,
+<a name="l00068"></a><a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aaf41577d27e0b8306dc1dfaebbffe3a85">00068</a>     <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aaf41577d27e0b8306dc1dfaebbffe3a85">CCP4SRS_NoBonds</a>          =  -8,
+<a name="l00069"></a><a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa36de44e9555882901e32ff002491b4c1">00069</a>     <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa36de44e9555882901e32ff002491b4c1">CCP4SRS_EmptyResSet</a>      =  -9,
+<a name="l00070"></a><a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa770346796e3fd0232458a3dd9709d735">00070</a>     <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa770346796e3fd0232458a3dd9709d735">CCP4SRS_Fail</a>             = -10,
+<a name="l00071"></a><a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aafabbc088bd534a406ce2a155b7c7be34">00071</a>     <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aafabbc088bd534a406ce2a155b7c7be34">CCP4SRS_SVD_Fail</a>         = -11,
+<a name="l00072"></a><a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa86978a692503eda1577d1250f402e4d4">00072</a>     <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa86978a692503eda1577d1250f402e4d4">CCP4SRS_noCoordHierarchy</a> = -12,
+<a name="l00073"></a><a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa785ce210fda24a93bd0df60e0a612698">00073</a>     <a class="code" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa785ce210fda24a93bd0df60e0a612698">CCP4SRS_BrokenBonds</a>      = -13
+<a name="l00074"></a>00074   };
+<a name="l00075"></a>00075 
+<a name="l00076"></a>00076   <span class="keyword">extern</span> mmdb::cpstr <a class="code" href="namespaceccp4srs.html#a3f27798432992515be969c17425412d3">srsIndexFile</a>;
+<a name="l00077"></a>00077   <span class="keyword">extern</span> mmdb::cpstr <a class="code" href="namespaceccp4srs.html#a4132afa4ce21fdcd2ff268bf6e980cfc">srsGraphFile</a>;
+<a name="l00078"></a>00078   <span class="keyword">extern</span> mmdb::cpstr <a class="code" href="namespaceccp4srs.html#af51e5a096118e643d5fcf5490d44c6db">srsStructFile</a>;
+<a name="l00079"></a>00079 
+<a name="l00080"></a>00080 
+<a name="l00081"></a>00081   <span class="comment">//  special atom ids</span>
+<a name="l00082"></a>00082   <span class="keyword">extern</span> <span class="keyword">const</span> <span class="keywordtype">int</span> <a class="code" href="namespaceccp4srs.html#aa44a92ce883cd1c525381111cd1a4ab3">AtomID_NA</a>;
+<a name="l00083"></a>00083 
+<a name="l00084"></a>00084   <span class="comment">// ==================================================================</span>
+<a name="l00085"></a>00085 
+<a name="l00086"></a>00086   <a class="code" href="namespaceccp4srs.html#a38fd31a76e47d65dbd8f9343fdc2f001">DefineStructure</a>(AtomPair);
+<a name="l00087"></a>00087 
+<a name="l00088"></a><a class="code" href="structccp4srs_1_1_atom_pair.html">00088</a>   <span class="keyword">struct </span><a class="code" href="structccp4srs_1_1_atom_pair.html">AtomPair</a>  {
+<a name="l00089"></a><a class="code" href="structccp4srs_1_1_atom_pair.html#a1f8f7df44905ac32088ccfcf1b80dda2">00089</a>     mmdb::PAtom <a class="code" href="structccp4srs_1_1_atom_pair.html#a0277f099acfa557ac20bf6fd3320bcaa">a1</a>,<a class="code" href="structccp4srs_1_1_atom_pair.html#a1f8f7df44905ac32088ccfcf1b80dda2">a2</a>;
+<a name="l00090"></a>00090   };
+<a name="l00091"></a>00091 
+<a name="l00092"></a>00092   <span class="comment">// ==================================================================</span>
+<a name="l00093"></a>00093 
+<a name="l00094"></a>00094   <span class="comment">//   SDASelHandles is optionally used in MakeBonds(..), when</span>
+<a name="l00095"></a>00095   <span class="comment">// the latter works for hydrogen bond calculations.</span>
+<a name="l00096"></a>00096   <a class="code" href="namespaceccp4srs.html#a38fd31a76e47d65dbd8f9343fdc2f001">DefineStructure</a>(<a class="code" href="structccp4srs_1_1_d_a_sel_hnds.html">DASelHnds</a>);
+<a name="l00097"></a>00097 
+<a name="l00098"></a><a class="code" href="structccp4srs_1_1_d_a_sel_hnds.html">00098</a>   <span class="keyword">struct </span><a class="code" href="structccp4srs_1_1_d_a_sel_hnds.html">DASelHnds</a>  {
+<a name="l00099"></a><a class="code" href="structccp4srs_1_1_d_a_sel_hnds.html#a0291cf6e8fc47959f00d5dfa536d4d3c">00099</a>     <span class="keywordtype">int</span>  <a class="code" href="structccp4srs_1_1_d_a_sel_hnds.html#a0291cf6e8fc47959f00d5dfa536d4d3c">selHndDonor</a>;
+<a name="l00100"></a><a class="code" href="structccp4srs_1_1_d_a_sel_hnds.html#a6df62532c19c06870cb386b3e1d4cc3c">00100</a>     <span class="keywordtype">int</span>  <a class="code" href="structccp4srs_1_1_d_a_sel_hnds.html#a6df62532c19c06870cb386b3e1d4cc3c">selHndAcceptor</a>;
+<a name="l00101"></a><a class="code" href="structccp4srs_1_1_d_a_sel_hnds.html#a0dd02cde05c05d8d5f1c99c55aa6e251">00101</a>     <span class="keywordtype">int</span>  <a class="code" href="structccp4srs_1_1_d_a_sel_hnds.html#a0dd02cde05c05d8d5f1c99c55aa6e251">selHndHydrogen</a>;
+<a name="l00102"></a><a class="code" href="structccp4srs_1_1_d_a_sel_hnds.html#ab9e53854d32fb72fb9003efc870354df">00102</a>     mmdb::SELECTION_KEY <a class="code" href="structccp4srs_1_1_d_a_sel_hnds.html#ab9e53854d32fb72fb9003efc870354df">selKey</a>;
+<a name="l00103"></a>00103     <span class="keywordtype">void</span> <a class="code" href="structccp4srs_1_1_d_a_sel_hnds.html#a3e8624665274bf47da9408f3b21f35d8">getNewHandles</a>    ( mmdb::PManager MMDB );
+<a name="l00104"></a>00104     <span class="keywordtype">void</span> <a class="code" href="structccp4srs_1_1_d_a_sel_hnds.html#aaca5f89914d27b9869b6f082931c53d5">makeSelIndexes</a>   ( mmdb::PManager MMDB );
+<a name="l00105"></a>00105     <span class="keywordtype">void</span> <a class="code" href="structccp4srs_1_1_d_a_sel_hnds.html#a582873aa43d2c8708e99db1485013bef">deleteSelections</a> ( mmdb::PManager MMDB );
+<a name="l00106"></a>00106   };
+<a name="l00107"></a>00107 
+<a name="l00108"></a>00108 }  <span class="comment">// namespace ccp4srs</span>
+<a name="l00109"></a>00109 
+<a name="l00110"></a>00110 <span class="preprocessor">#endif // CCP4SRS_TYPES_H</span>
+</pre></div></div>
+</div>
+<!--- window showing the filter options -->
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+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
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diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_angle-members.html ccp4srs/doc-html/html/classccp4srs_1_1_angle-members.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_angle-members.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_angle-members.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,93 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
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+<script type="text/javaScript" src="search/search.js"></script>
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+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>ccp4srs::Angle Member List</h1>  </div>
+</div>
+<div class="contents">
+This is the complete list of members for <a class="el" href="classccp4srs_1_1_angle.html">ccp4srs::Angle</a>, including all inherited members.<table>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_angle.html#abf55314566cb2fa1d3764d0485284113">angle</a></td><td><a class="el" href="classccp4srs_1_1_angle.html">ccp4srs::Angle</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_angle.html#a5ec6da380214e7100ff46e3e79898e15">Angle</a>()</td><td><a class="el" href="classccp4srs_1_1_angle.html">ccp4srs::Angle</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_angle.html#a39e05de948ddbf9c944bf0b14123caf8">angle_esd</a></td><td><a class="el" href="classccp4srs_1_1_angle.html">ccp4srs::Angle</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_angle.html#a64770743097878619e8dccf787f93802">atom1</a>()</td><td><a class="el" href="classccp4srs_1_1_angle.html">ccp4srs::Angle</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_angle.html#a1be24203719da0b250775f7c0b5710ed">atom2</a>()</td><td><a class="el" href="classccp4srs_1_1_angle.html">ccp4srs::Angle</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_angle.html#a6d62c8acfe549d3d439a061f2bbcada9">atom3</a>()</td><td><a class="el" href="classccp4srs_1_1_angle.html">ccp4srs::Angle</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_angle.html#ab59c639612d7dcae2b34213a647cdb45">atom_1</a></td><td><a class="el" href="classccp4srs_1_1_angle.html">ccp4srs::Angle</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_angle.html#a8a4fd7f9e6196f259b6ec0989b5cb64c">atom_2</a></td><td><a class="el" href="classccp4srs_1_1_angle.html">ccp4srs::Angle</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_angle.html#a545fb1039055e640aa938964b64c7d0a">atom_3</a></td><td><a class="el" href="classccp4srs_1_1_angle.html">ccp4srs::Angle</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_angle.html#a085c530866442b6b3dfb8c969de2bfe8">copy</a>(PAngle ang, mmdb::ivector anmatch=NULL)</td><td><a class="el" href="classccp4srs_1_1_angle.html">ccp4srs::Angle</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_angle.html#a31b7030dec4dd77c0eefa3444c75901f">esd</a>()</td><td><a class="el" href="classccp4srs_1_1_angle.html">ccp4srs::Angle</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_angle.html#a257cefe6949d4371175d4c1573a1d40e">makeCIFTags</a>(mmdb::mmcif::PLoop mmCIFLoop)</td><td><a class="el" href="classccp4srs_1_1_angle.html">ccp4srs::Angle</a></td><td><code> [static]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_angle.html#a2f34c77527204676236a28c863f5adee">read_mem</a>(PMemIO memIO, int version, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_angle.html">ccp4srs::Angle</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_angle.html#a9a366216e8c07f33829fd26db9df4f00">readFromCIF</a>(mmdb::mmcif::PLoop mmCIFLoop, int angleNo, Container&lt; Atom &gt; &amp;atoms)</td><td><a class="el" href="classccp4srs_1_1_angle.html">ccp4srs::Angle</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_angle.html#a6ec0de44c0f607bcb5634a907fe9018a">value</a>()</td><td><a class="el" href="classccp4srs_1_1_angle.html">ccp4srs::Angle</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_angle.html#a5fcc085237045429dd4a946595c1488f">write_mem</a>(PMemIO memIO, int version)</td><td><a class="el" href="classccp4srs_1_1_angle.html">ccp4srs::Angle</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_angle.html#a8a293c96f55ee3b13cc9b9db86d265cd">writeToCIF</a>(mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID, Container&lt; Atom &gt; &amp;atoms)</td><td><a class="el" href="classccp4srs_1_1_angle.html">ccp4srs::Angle</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_angle.html#a8b6036ed3908589a9cee50f60f5e3806">~Angle</a>()</td><td><a class="el" href="classccp4srs_1_1_angle.html">ccp4srs::Angle</a></td><td><code> [virtual]</code></td></tr>
+</table></div>
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+<a href="http://www.doxygen.org/index.html">
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diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_angle.html ccp4srs/doc-html/html/classccp4srs_1_1_angle.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_angle.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_angle.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,468 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="navpath">
+    <ul>
+      <li><a class="el" href="namespaceccp4srs.html">ccp4srs</a>      </li>
+      <li><a class="el" href="classccp4srs_1_1_angle.html">Angle</a>      </li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pub-static-methods">Static Public Member Functions</a> &#124;
+<a href="#pro-attribs">Protected Attributes</a>  </div>
+  <div class="headertitle">
+<h1>ccp4srs::Angle Class Reference</h1>  </div>
+</div>
+<div class="contents">
+<!-- doxytag: class="ccp4srs::Angle" -->
+<p><code>#include &lt;<a class="el" href="ccp4srs__angle_8h_source.html">ccp4srs_angle.h</a>&gt;</code></p>
+
+<p><a href="classccp4srs_1_1_angle-members.html">List of all members.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_angle.html#a5ec6da380214e7100ff46e3e79898e15">Angle</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_angle.html#a8b6036ed3908589a9cee50f60f5e3806">~Angle</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_angle.html#a64770743097878619e8dccf787f93802">atom1</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_angle.html#a1be24203719da0b250775f7c0b5710ed">atom2</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_angle.html#a6d62c8acfe549d3d439a061f2bbcada9">atom3</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_angle.html#a6ec0de44c0f607bcb5634a907fe9018a">value</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_angle.html#a31b7030dec4dd77c0eefa3444c75901f">esd</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_angle.html#a9a366216e8c07f33829fd26db9df4f00">readFromCIF</a> (mmdb::mmcif::PLoop mmCIFLoop, int angleNo, <a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;atoms)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_angle.html#a8a293c96f55ee3b13cc9b9db86d265cd">writeToCIF</a> (mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID, <a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;atoms)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_angle.html#a5fcc085237045429dd4a946595c1488f">write_mem</a> (PMemIO memIO, int version)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_angle.html#a2f34c77527204676236a28c863f5adee">read_mem</a> (PMemIO memIO, int version, bool *Ok=NULL)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_angle.html#a085c530866442b6b3dfb8c969de2bfe8">copy</a> (PAngle ang, mmdb::ivector anmatch=NULL)</td></tr>
+<tr><td colspan="2"><h2><a name="pub-static-methods"></a>
+Static Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">static void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_angle.html#a257cefe6949d4371175d4c1573a1d40e">makeCIFTags</a> (mmdb::mmcif::PLoop mmCIFLoop)</td></tr>
+<tr><td colspan="2"><h2><a name="pro-attribs"></a>
+Protected Attributes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_angle.html#ab59c639612d7dcae2b34213a647cdb45">atom_1</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_angle.html#a8a4fd7f9e6196f259b6ec0989b5cb64c">atom_2</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_angle.html#a545fb1039055e640aa938964b64c7d0a">atom_3</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_angle.html#abf55314566cb2fa1d3764d0485284113">angle</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_angle.html#a39e05de948ddbf9c944bf0b14123caf8">angle_esd</a></td></tr>
+</table>
+<hr/><h2>Constructor &amp; Destructor Documentation</h2>
+<a class="anchor" id="a5ec6da380214e7100ff46e3e79898e15"></a><!-- doxytag: member="ccp4srs::Angle::Angle" ref="a5ec6da380214e7100ff46e3e79898e15" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::Angle::Angle </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a8b6036ed3908589a9cee50f60f5e3806"></a><!-- doxytag: member="ccp4srs::Angle::~Angle" ref="a8b6036ed3908589a9cee50f60f5e3806" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::Angle::~Angle </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [virtual]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Function Documentation</h2>
+<a class="anchor" id="a64770743097878619e8dccf787f93802"></a><!-- doxytag: member="ccp4srs::Angle::atom1" ref="a64770743097878619e8dccf787f93802" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Angle::atom1 </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a1be24203719da0b250775f7c0b5710ed"></a><!-- doxytag: member="ccp4srs::Angle::atom2" ref="a1be24203719da0b250775f7c0b5710ed" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Angle::atom2 </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a6d62c8acfe549d3d439a061f2bbcada9"></a><!-- doxytag: member="ccp4srs::Angle::atom3" ref="a6d62c8acfe549d3d439a061f2bbcada9" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Angle::atom3 </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a085c530866442b6b3dfb8c969de2bfe8"></a><!-- doxytag: member="ccp4srs::Angle::copy" ref="a085c530866442b6b3dfb8c969de2bfe8" args="(PAngle ang, mmdb::ivector anmatch=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Angle::copy </td>
+          <td>(</td>
+          <td class="paramtype">PAngle&#160;</td>
+          <td class="paramname"> <em>ang</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::ivector&#160;</td>
+          <td class="paramname"> <em>anmatch</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a31b7030dec4dd77c0eefa3444c75901f"></a><!-- doxytag: member="ccp4srs::Angle::esd" ref="a31b7030dec4dd77c0eefa3444c75901f" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype ccp4srs::Angle::esd </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a257cefe6949d4371175d4c1573a1d40e"></a><!-- doxytag: member="ccp4srs::Angle::makeCIFTags" ref="a257cefe6949d4371175d4c1573a1d40e" args="(mmdb::mmcif::PLoop mmCIFLoop)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Angle::makeCIFTags </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>mmCIFLoop</em>&#160;)</td>
+          <td><code> [static]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a2f34c77527204676236a28c863f5adee"></a><!-- doxytag: member="ccp4srs::Angle::read_mem" ref="a2f34c77527204676236a28c863f5adee" args="(PMemIO memIO, int version, bool *Ok=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::Angle::read_mem </td>
+          <td>(</td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a9a366216e8c07f33829fd26db9df4f00"></a><!-- doxytag: member="ccp4srs::Angle::readFromCIF" ref="a9a366216e8c07f33829fd26db9df4f00" args="(mmdb::mmcif::PLoop mmCIFLoop, int angleNo, Container&lt; Atom &gt; &amp;atoms)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Angle::readFromCIF </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>mmCIFLoop</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>angleNo</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;&#160;</td>
+          <td class="paramname"> <em>atoms</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a6ec0de44c0f607bcb5634a907fe9018a"></a><!-- doxytag: member="ccp4srs::Angle::value" ref="a6ec0de44c0f607bcb5634a907fe9018a" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype ccp4srs::Angle::value </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a5fcc085237045429dd4a946595c1488f"></a><!-- doxytag: member="ccp4srs::Angle::write_mem" ref="a5fcc085237045429dd4a946595c1488f" args="(PMemIO memIO, int version)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Angle::write_mem </td>
+          <td>(</td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a8a293c96f55ee3b13cc9b9db86d265cd"></a><!-- doxytag: member="ccp4srs::Angle::writeToCIF" ref="a8a293c96f55ee3b13cc9b9db86d265cd" args="(mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID, Container&lt; Atom &gt; &amp;atoms)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Angle::writeToCIF </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>mmCIFLoop</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>monID</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;&#160;</td>
+          <td class="paramname"> <em>atoms</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Data Documentation</h2>
+<a class="anchor" id="abf55314566cb2fa1d3764d0485284113"></a><!-- doxytag: member="ccp4srs::Angle::angle" ref="abf55314566cb2fa1d3764d0485284113" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_angle.html#abf55314566cb2fa1d3764d0485284113">ccp4srs::Angle::angle</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a39e05de948ddbf9c944bf0b14123caf8"></a><!-- doxytag: member="ccp4srs::Angle::angle_esd" ref="a39e05de948ddbf9c944bf0b14123caf8" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_angle.html#a39e05de948ddbf9c944bf0b14123caf8">ccp4srs::Angle::angle_esd</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ab59c639612d7dcae2b34213a647cdb45"></a><!-- doxytag: member="ccp4srs::Angle::atom_1" ref="ab59c639612d7dcae2b34213a647cdb45" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_angle.html#ab59c639612d7dcae2b34213a647cdb45">ccp4srs::Angle::atom_1</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a8a4fd7f9e6196f259b6ec0989b5cb64c"></a><!-- doxytag: member="ccp4srs::Angle::atom_2" ref="a8a4fd7f9e6196f259b6ec0989b5cb64c" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_angle.html#a8a4fd7f9e6196f259b6ec0989b5cb64c">ccp4srs::Angle::atom_2</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a545fb1039055e640aa938964b64c7d0a"></a><!-- doxytag: member="ccp4srs::Angle::atom_3" ref="a545fb1039055e640aa938964b64c7d0a" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_angle.html#a545fb1039055e640aa938964b64c7d0a">ccp4srs::Angle::atom_3</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following files:<ul>
+<li>src/<a class="el" href="ccp4srs__angle_8h_source.html">ccp4srs_angle.h</a></li>
+<li>src/<a class="el" href="ccp4srs__angle_8cpp.html">ccp4srs_angle.cpp</a></li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
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+
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+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
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+</html>
diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_atom-members.html ccp4srs/doc-html/html/classccp4srs_1_1_atom-members.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_atom-members.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_atom-members.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,153 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
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+<body onload='searchBox.OnSelectItem(0);'>
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+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
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+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
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+          <input type="text" id="MSearchField" value="Search" accesskey="S"
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+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>ccp4srs::Atom Member List</h1>  </div>
+</div>
+<div class="contents">
+This is the complete list of members for <a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a>, including all inherited members.<table>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a66084d9a746b51608e8f0f8e28138e9d">Atom</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a0e7a7e76f9fba1a8277dae436f900821">atomCharge</a></td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a75168bfe9aa3e0e24ba5f81854323039">atomName</a></td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#acb4d50d536b22d4dd3f971072354f784">atomSP</a></td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#aeaa06e2eac23c671be3f49c0caaa7d12">atomValency</a></td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#ac470c0fd96b775b2b1d979c353449ee4">atomWeight</a></td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#ac0274e4727f43cedf27380121215cbfa">ccp4_chirality</a>() const </td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a199caf3c186d47d5ca6e13e235471a84">charge</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a621e19772fdb901353b6f60288afdb70">chemElement</a></td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a88df4aee528a9e551c126e9e8adab2f3">chirality</a>() const </td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a5aa8172f59efa4ac90359b2be7424d92">copy</a>(PAtom atom)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a78344a993072c3e8918a54c3259d55d8">element</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a8d78d445f18a9f9e83d82f66e715b274">element_pdb</a>(mmdb::pstr elem)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#af9d89db887cdbfc5523a79ece1c1e117">energy_type</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#ac429b2d0c02fe21432c4b651ad181fdb">energyType</a></td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#ab45d65bdba2966ce382687548921cd56">hb_type</a>() const </td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a276b8b3e31130e6f0116af498e3a7766">id</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#ab6a22850541822e026c9d6a241079fd6">Init</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a4cbbb8a7a4d9f69eca5caadfffa6c956">ion_radius</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#aeb773fbdd5b04c0311969ad498622185">ionRadius</a></td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a7da89fae287dcf0c0838108fd442ec53">isLeaving</a>() const </td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#ac7f1f1f474b56199e70bb0dcd364bb4b">leaving</a>() const </td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a40ec4d3c3ea0384ab4d2c56b3ee5389b">makeAtom</a>(mmdb::RPAtom a)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a2528b66c2480aa6e3db8d6cfba0c4586">makeAtom</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#ac1bcbe4ebfbf35c7d0369d41afa07714">makeCIFTags</a>(mmdb::mmcif::PLoop mmCIFLoop)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [static]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#af28439c95edf554364f29e988b47acd1">merge</a>(PAtom atom)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a641d281e9661ff8ca51bc768b2db5628">mlib_x</a></td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a92043cd1d43d17069c0c8f96020218b9">mlib_y</a></td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a0b6c2ba6990da454ea672a64e285653f">mlib_z</a></td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#ad8288e82eeab398bf90da3f35ebe15c5">name</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a357cfea9384684a64bb3220d02b3afa7">name_pdb</a>(mmdb::pstr aname)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#acda740ae967221e50f1d383ce70d58d9">old_name</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#abd73ea1b813b1321048f850b88914982">old_name_pdb</a>(mmdb::pstr aname)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a45682b942f2f9262bc8fa1b5316a702b">oldAtomName</a></td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a49ff7aadab557a536541009606a2db12">pdb_x</a></td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a901c15656be6fa36e191df297d25521d">pdb_y</a></td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#ae33b2033023270f96202151aed27a710">pdb_z</a></td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#aec57c2566b6a42361a8215d7b15a7e29">pdbx_x</a></td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a1d138de5fa3e222554a95b796c246d40">pdbx_y</a></td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a424a6001bc93ea1c8256f9f1fb48a585">pdbx_z</a></td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#aa363093b5746f782b8c4e60a73ec6438">property</a></td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a1dc09ecc6dee155b93e5c3431d4c548e">rcsb_chirality</a>() const </td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#af0bbf72624e0f7de9900ec931b673410">rcsb_name</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#ace51a15043535b0fef9b2816dba48cdb">rcsb_name_pdb</a>(mmdb::pstr aname)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a198154f097c4f42a4ae1dd73d5394734">rcsbAtomName</a></td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a150503215d6820dda3726b107e8e1bc7">read_mem</a>(PMemIO memIO, int version, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a94f5f81532b98126f3383f29c077473c">readFromCIF</a>(mmdb::mmcif::PStruct mmCIFStruct)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a0e4f39d4293b8e1907b0295e215c4230">readFromCIF_ccp4</a>(mmdb::mmcif::PLoop mmCIFLoop, int atomNo)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a12b7ff09ff7aa0cc7581a55e89ac9e0e">readFromCIF_rcsb</a>(mmdb::mmcif::PLoop mmCIFLoop, int atomNo)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a4839e285360f50dbe4dbfff765ece82c">set_chirality</a>(char c)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#abab85177d8d15e5dfc51e12ed9af4d69">set_energy_type</a>(mmdb::cpstr etype)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a983a276a7821c272f3952f4edfb826c6">set_hb_type</a>(char h)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a132fd6895be46a1afa96bb0529c0a6ba">set_ion_radius</a>(mmdb::realtype r)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a67142fe2e03f768fea4dc3334826ef2e">set_old_name</a>(mmdb::cpstr name)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#af46102bc6356f36610eda68ced6e9202">set_rcsb_chirality</a>(char c)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#aa9fe3297f6d6de92f1520a6631361861">set_sp</a>(int s)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#af50fcb98ad0f4a42768079e985adec5b">set_valency</a>(int v)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#aa2c293fa289d7a24bc8858578dd3357e">set_vdw_radius</a>(mmdb::realtype r)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a8912626b88300dcb9e736cf1b4369f82">set_vdwh_radius</a>(mmdb::realtype r)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a9ae7f9281596f659071394247d484ffb">sp</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a86606a9614641a62a9b477c0b90c3a87">valency</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a2c283b644afb507ec45667611a685827">vdw_radius</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a2a2e411586e9a0be619a5ab5c634169d">vdwh_radius</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#afd0adf07dd4f24e87acb6977335ff2ba">vdwhRadius</a></td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a74216b4c442b716656e5a55e908cea11">vdwRadius</a></td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a4c6e0a23b45563f10657d839d4479961">weight</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#adaebb2b3897e6758befc7c76d77c0420">write_mem</a>(PMemIO memIO, int version)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#ac83667146ec86aeab8fdcce133c2fea0">writeToCIF</a>(mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID)</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a9af114ebe576f3a0af965579100da463">x</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a7f9331955d7f98b1d2e869f8741a2188">x_mlib</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#ac0fc0e47750a53f2be7ab60efc604d3b">x_pdbx</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a10fc0f0f21af2cd5311c7d957b59f52b">y</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#acc50ad679a297a2626a6662cd0b61d3e">y_mlib</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a65cdadf3090a0fa712b6c47040adb578">y_pdbx</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a9d07e03f19613858142105d9f287466e">z</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a73c4871fccf3ce91502449de659f835a">z_mlib</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#aed837e19a61e89ce1e1eda0c35f10b2e">z_pdbx</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_atom.html#a27de39105bac03d49c949780edda55fd">~Atom</a>()</td><td><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></td><td><code> [virtual]</code></td></tr>
+</table></div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
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+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_atom.html ccp4srs/doc-html/html/classccp4srs_1_1_atom.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_atom.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_atom.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,1493 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: ccp4srs::Atom Class Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
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+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
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+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
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+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="navpath">
+    <ul>
+      <li><a class="el" href="namespaceccp4srs.html">ccp4srs</a>      </li>
+      <li><a class="el" href="classccp4srs_1_1_atom.html">Atom</a>      </li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pub-static-methods">Static Public Member Functions</a> &#124;
+<a href="#pro-methods">Protected Member Functions</a> &#124;
+<a href="#pro-attribs">Protected Attributes</a>  </div>
+  <div class="headertitle">
+<h1>ccp4srs::Atom Class Reference</h1>  </div>
+</div>
+<div class="contents">
+<!-- doxytag: class="ccp4srs::Atom" -->
+<p><code>#include &lt;<a class="el" href="ccp4srs__atom_8h_source.html">ccp4srs_atom.h</a>&gt;</code></p>
+
+<p><a href="classccp4srs_1_1_atom-members.html">List of all members.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a66084d9a746b51608e8f0f8e28138e9d">Atom</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a27de39105bac03d49c949780edda55fd">~Atom</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a276b8b3e31130e6f0116af498e3a7766">id</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#ad8288e82eeab398bf90da3f35ebe15c5">name</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#af0bbf72624e0f7de9900ec931b673410">rcsb_name</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#acda740ae967221e50f1d383ce70d58d9">old_name</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a78344a993072c3e8918a54c3259d55d8">element</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#af9d89db887cdbfc5523a79ece1c1e117">energy_type</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a9af114ebe576f3a0af965579100da463">x</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a10fc0f0f21af2cd5311c7d957b59f52b">y</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a9d07e03f19613858142105d9f287466e">z</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#ac0fc0e47750a53f2be7ab60efc604d3b">x_pdbx</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a65cdadf3090a0fa712b6c47040adb578">y_pdbx</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#aed837e19a61e89ce1e1eda0c35f10b2e">z_pdbx</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a7f9331955d7f98b1d2e869f8741a2188">x_mlib</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#acc50ad679a297a2626a6662cd0b61d3e">y_mlib</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a73c4871fccf3ce91502449de659f835a">z_mlib</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a199caf3c186d47d5ca6e13e235471a84">charge</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a4c6e0a23b45563f10657d839d4479961">weight</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a2c283b644afb507ec45667611a685827">vdw_radius</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a2a2e411586e9a0be619a5ab5c634169d">vdwh_radius</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a4cbbb8a7a4d9f69eca5caadfffa6c956">ion_radius</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a86606a9614641a62a9b477c0b90c3a87">valency</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a9ae7f9281596f659071394247d484ffb">sp</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">char&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a1dc09ecc6dee155b93e5c3431d4c548e">rcsb_chirality</a> () const </td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">char&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#ac0274e4727f43cedf27380121215cbfa">ccp4_chirality</a> () const </td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">char&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a88df4aee528a9e551c126e9e8adab2f3">chirality</a> () const </td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">char&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#ac7f1f1f474b56199e70bb0dcd364bb4b">leaving</a> () const </td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a7da89fae287dcf0c0838108fd442ec53">isLeaving</a> () const </td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">char&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#ab45d65bdba2966ce382687548921cd56">hb_type</a> () const </td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a357cfea9384684a64bb3220d02b3afa7">name_pdb</a> (mmdb::pstr aname)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#ace51a15043535b0fef9b2816dba48cdb">rcsb_name_pdb</a> (mmdb::pstr aname)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#abd73ea1b813b1321048f850b88914982">old_name_pdb</a> (mmdb::pstr aname)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a8d78d445f18a9f9e83d82f66e715b274">element_pdb</a> (mmdb::pstr elem)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#abab85177d8d15e5dfc51e12ed9af4d69">set_energy_type</a> (mmdb::cpstr etype)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a67142fe2e03f768fea4dc3334826ef2e">set_old_name</a> (mmdb::cpstr name)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#af46102bc6356f36610eda68ced6e9202">set_rcsb_chirality</a> (char c)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a4839e285360f50dbe4dbfff765ece82c">set_chirality</a> (char c)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a983a276a7821c272f3952f4edfb826c6">set_hb_type</a> (char h)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#aa2c293fa289d7a24bc8858578dd3357e">set_vdw_radius</a> (mmdb::realtype r)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a8912626b88300dcb9e736cf1b4369f82">set_vdwh_radius</a> (mmdb::realtype r)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a132fd6895be46a1afa96bb0529c0a6ba">set_ion_radius</a> (mmdb::realtype r)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#af50fcb98ad0f4a42768079e985adec5b">set_valency</a> (int v)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#aa9fe3297f6d6de92f1520a6631361861">set_sp</a> (int s)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a40ec4d3c3ea0384ab4d2c56b3ee5389b">makeAtom</a> (mmdb::RPAtom a)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::PAtom&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a2528b66c2480aa6e3db8d6cfba0c4586">makeAtom</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a0e4f39d4293b8e1907b0295e215c4230">readFromCIF_ccp4</a> (mmdb::mmcif::PLoop mmCIFLoop, int atomNo)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a12b7ff09ff7aa0cc7581a55e89ac9e0e">readFromCIF_rcsb</a> (mmdb::mmcif::PLoop mmCIFLoop, int atomNo)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a94f5f81532b98126f3383f29c077473c">readFromCIF</a> (mmdb::mmcif::PStruct mmCIFStruct)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#ac83667146ec86aeab8fdcce133c2fea0">writeToCIF</a> (mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a5aa8172f59efa4ac90359b2be7424d92">copy</a> (PAtom atom)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#af28439c95edf554364f29e988b47acd1">merge</a> (PAtom atom)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#adaebb2b3897e6758befc7c76d77c0420">write_mem</a> (PMemIO memIO, int version)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a150503215d6820dda3726b107e8e1bc7">read_mem</a> (PMemIO memIO, int version, bool *Ok=NULL)</td></tr>
+<tr><td colspan="2"><h2><a name="pub-static-methods"></a>
+Static Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">static void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#ac1bcbe4ebfbf35c7d0369d41afa07714">makeCIFTags</a> (mmdb::mmcif::PLoop mmCIFLoop)</td></tr>
+<tr><td colspan="2"><h2><a name="pro-methods"></a>
+Protected Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#ab6a22850541822e026c9d6a241079fd6">Init</a> ()</td></tr>
+<tr><td colspan="2"><h2><a name="pro-attribs"></a>
+Protected Attributes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::AtomName&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a75168bfe9aa3e0e24ba5f81854323039">atomName</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">atom name  <a href="#a75168bfe9aa3e0e24ba5f81854323039"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::AtomName&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a198154f097c4f42a4ae1dd73d5394734">rcsbAtomName</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">alternative atom name  <a href="#a198154f097c4f42a4ae1dd73d5394734"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::AtomName&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a45682b942f2f9262bc8fa1b5316a702b">oldAtomName</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">old atom name  <a href="#a45682b942f2f9262bc8fa1b5316a702b"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::Element&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a621e19772fdb901353b6f60288afdb70">chemElement</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">chemical element name  <a href="#a621e19772fdb901353b6f60288afdb70"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::EnergyType&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#ac429b2d0c02fe21432c4b651ad181fdb">energyType</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">energy type  <a href="#ac429b2d0c02fe21432c4b651ad181fdb"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a641d281e9661ff8ca51bc768b2db5628">mlib_x</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a92043cd1d43d17069c0c8f96020218b9">mlib_y</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a0b6c2ba6990da454ea672a64e285653f">mlib_z</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">m-lib cartesian coordinates  <a href="#a0b6c2ba6990da454ea672a64e285653f"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a49ff7aadab557a536541009606a2db12">pdb_x</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a901c15656be6fa36e191df297d25521d">pdb_y</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#ae33b2033023270f96202151aed27a710">pdb_z</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">pdb cartesian coordinates  <a href="#ae33b2033023270f96202151aed27a710"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#aec57c2566b6a42361a8215d7b15a7e29">pdbx_x</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a1d138de5fa3e222554a95b796c246d40">pdbx_y</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a424a6001bc93ea1c8256f9f1fb48a585">pdbx_z</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">pdbx cartesian coordinates  <a href="#a424a6001bc93ea1c8256f9f1fb48a585"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a0e7a7e76f9fba1a8277dae436f900821">atomCharge</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">partial charge  <a href="#a0e7a7e76f9fba1a8277dae436f900821"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#ac470c0fd96b775b2b1d979c353449ee4">atomWeight</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">atomic weight (in a.u.)  <a href="#ac470c0fd96b775b2b1d979c353449ee4"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#a74216b4c442b716656e5a55e908cea11">vdwRadius</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Van-Der-Waals radius.  <a href="#a74216b4c442b716656e5a55e908cea11"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#afd0adf07dd4f24e87acb6977335ff2ba">vdwhRadius</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Van-Der-Waals radius with hydrogen.  <a href="#afd0adf07dd4f24e87acb6977335ff2ba"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#aeb773fbdd5b04c0311969ad498622185">ionRadius</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">ion radius  <a href="#aeb773fbdd5b04c0311969ad498622185"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#aeaa06e2eac23c671be3f49c0caaa7d12">atomValency</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">valency  <a href="#aeaa06e2eac23c671be3f49c0caaa7d12"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#acb4d50d536b22d4dd3f971072354f784">atomSP</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">sp-hybridization  <a href="#acb4d50d536b22d4dd3f971072354f784"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">char&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html#aa363093b5746f782b8c4e60a73ec6438">property</a> [4]</td></tr>
+</table>
+<hr/><h2>Constructor &amp; Destructor Documentation</h2>
+<a class="anchor" id="a66084d9a746b51608e8f0f8e28138e9d"></a><!-- doxytag: member="ccp4srs::Atom::Atom" ref="a66084d9a746b51608e8f0f8e28138e9d" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::Atom::Atom </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a27de39105bac03d49c949780edda55fd"></a><!-- doxytag: member="ccp4srs::Atom::~Atom" ref="a27de39105bac03d49c949780edda55fd" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::Atom::~Atom </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [virtual]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Function Documentation</h2>
+<a class="anchor" id="ac0274e4727f43cedf27380121215cbfa"></a><!-- doxytag: member="ccp4srs::Atom::ccp4_chirality" ref="ac0274e4727f43cedf27380121215cbfa" args="() const " -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">char ccp4srs::Atom::ccp4_chirality </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td> const<code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a199caf3c186d47d5ca6e13e235471a84"></a><!-- doxytag: member="ccp4srs::Atom::charge" ref="a199caf3c186d47d5ca6e13e235471a84" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype ccp4srs::Atom::charge </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a88df4aee528a9e551c126e9e8adab2f3"></a><!-- doxytag: member="ccp4srs::Atom::chirality" ref="a88df4aee528a9e551c126e9e8adab2f3" args="() const " -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">char ccp4srs::Atom::chirality </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td> const</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a5aa8172f59efa4ac90359b2be7424d92"></a><!-- doxytag: member="ccp4srs::Atom::copy" ref="a5aa8172f59efa4ac90359b2be7424d92" args="(PAtom atom)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Atom::copy </td>
+          <td>(</td>
+          <td class="paramtype">PAtom&#160;</td>
+          <td class="paramname"> <em>atom</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a78344a993072c3e8918a54c3259d55d8"></a><!-- doxytag: member="ccp4srs::Atom::element" ref="a78344a993072c3e8918a54c3259d55d8" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::cpstr ccp4srs::Atom::element </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a8d78d445f18a9f9e83d82f66e715b274"></a><!-- doxytag: member="ccp4srs::Atom::element_pdb" ref="a8d78d445f18a9f9e83d82f66e715b274" args="(mmdb::pstr elem)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::cpstr ccp4srs::Atom::element_pdb </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::pstr&#160;</td>
+          <td class="paramname"> <em>elem</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="af9d89db887cdbfc5523a79ece1c1e117"></a><!-- doxytag: member="ccp4srs::Atom::energy_type" ref="af9d89db887cdbfc5523a79ece1c1e117" args="()" -->
+<div class="memitem">
+<div class="memproto">
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+        <tr>
+          <td class="memname">mmdb::cpstr ccp4srs::Atom::energy_type </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
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+<div class="memitem">
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+        <tr>
+          <td class="memname">char ccp4srs::Atom::hb_type </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td> const<code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
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+<div class="memproto">
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+        <tr>
+          <td class="memname">mmdb::cpstr ccp4srs::Atom::id </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
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+<a class="anchor" id="ab6a22850541822e026c9d6a241079fd6"></a><!-- doxytag: member="ccp4srs::Atom::Init" ref="ab6a22850541822e026c9d6a241079fd6" args="()" -->
+<div class="memitem">
+<div class="memproto">
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+        <tr>
+          <td class="memname">void ccp4srs::Atom::Init </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
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+<p>[0]: RCSB chirality : 'R', 'S' or 'N' [1]: MLib chirality : 'R', 'S' or 'N' [2]: leaving atom: 'Y' or 'N' [3]: hydrogen bond type: 'D' donor 'A' acceptor 'B' both 'H' hydrogen candidate 'N' neither </p>
+
+</div>
+</div>
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+<div class="memproto">
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+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
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+<div class="memproto">
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+        <tr>
+          <td class="memname">bool ccp4srs::Atom::isLeaving </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td> const<code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ac7f1f1f474b56199e70bb0dcd364bb4b"></a><!-- doxytag: member="ccp4srs::Atom::leaving" ref="ac7f1f1f474b56199e70bb0dcd364bb4b" args="() const " -->
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+<div class="memproto">
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+        <tr>
+          <td class="memname">char ccp4srs::Atom::leaving </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td> const<code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a40ec4d3c3ea0384ab4d2c56b3ee5389b"></a><!-- doxytag: member="ccp4srs::Atom::makeAtom" ref="a40ec4d3c3ea0384ab4d2c56b3ee5389b" args="(mmdb::RPAtom a)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Atom::makeAtom </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::RPAtom&#160;</td>
+          <td class="paramname"> <em>a</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
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+        <tr>
+          <td class="memname">mmdb::PAtom ccp4srs::Atom::makeAtom </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
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+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Atom::makeCIFTags </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>mmCIFLoop</em>&#160;)</td>
+          <td><code> [static]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="af28439c95edf554364f29e988b47acd1"></a><!-- doxytag: member="ccp4srs::Atom::merge" ref="af28439c95edf554364f29e988b47acd1" args="(PAtom atom)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Atom::merge </td>
+          <td>(</td>
+          <td class="paramtype">PAtom&#160;</td>
+          <td class="paramname"> <em>atom</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
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+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::cpstr ccp4srs::Atom::name </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
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+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::cpstr ccp4srs::Atom::name_pdb </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::pstr&#160;</td>
+          <td class="paramname"> <em>aname</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
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+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::cpstr ccp4srs::Atom::old_name </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
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+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::cpstr ccp4srs::Atom::old_name_pdb </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::pstr&#160;</td>
+          <td class="paramname"> <em>aname</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
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+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">char ccp4srs::Atom::rcsb_chirality </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td> const<code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="af0bbf72624e0f7de9900ec931b673410"></a><!-- doxytag: member="ccp4srs::Atom::rcsb_name" ref="af0bbf72624e0f7de9900ec931b673410" args="()" -->
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+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::cpstr ccp4srs::Atom::rcsb_name </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
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+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::cpstr ccp4srs::Atom::rcsb_name_pdb </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::pstr&#160;</td>
+          <td class="paramname"> <em>aname</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
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+</div>
+</div>
+<a class="anchor" id="a150503215d6820dda3726b107e8e1bc7"></a><!-- doxytag: member="ccp4srs::Atom::read_mem" ref="a150503215d6820dda3726b107e8e1bc7" args="(PMemIO memIO, int version, bool *Ok=NULL)" -->
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+        <tr>
+          <td class="memname">bool ccp4srs::Atom::read_mem </td>
+          <td>(</td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
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+</div>
+</div>
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+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Atom::readFromCIF </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PStruct&#160;</td>
+          <td class="paramname"> <em>mmCIFStruct</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
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+</div>
+</div>
+<a class="anchor" id="a0e4f39d4293b8e1907b0295e215c4230"></a><!-- doxytag: member="ccp4srs::Atom::readFromCIF_ccp4" ref="a0e4f39d4293b8e1907b0295e215c4230" args="(mmdb::mmcif::PLoop mmCIFLoop, int atomNo)" -->
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+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Atom::readFromCIF_ccp4 </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>mmCIFLoop</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>atomNo</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
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+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Atom::readFromCIF_rcsb </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>mmCIFLoop</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>atomNo</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
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+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Atom::set_chirality </td>
+          <td>(</td>
+          <td class="paramtype">char&#160;</td>
+          <td class="paramname"> <em>c</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
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+</div>
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+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Atom::set_energy_type </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>etype</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
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+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Atom::set_hb_type </td>
+          <td>(</td>
+          <td class="paramtype">char&#160;</td>
+          <td class="paramname"> <em>h</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
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+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Atom::set_ion_radius </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::realtype&#160;</td>
+          <td class="paramname"> <em>r</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
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+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Atom::set_old_name </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>name</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
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+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Atom::set_rcsb_chirality </td>
+          <td>(</td>
+          <td class="paramtype">char&#160;</td>
+          <td class="paramname"> <em>c</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
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+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Atom::set_sp </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>s</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="af50fcb98ad0f4a42768079e985adec5b"></a><!-- doxytag: member="ccp4srs::Atom::set_valency" ref="af50fcb98ad0f4a42768079e985adec5b" args="(int v)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Atom::set_valency </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>v</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
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+        <tr>
+          <td class="memname">void ccp4srs::Atom::set_vdw_radius </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::realtype&#160;</td>
+          <td class="paramname"> <em>r</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
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+<div class="memitem">
+<div class="memproto">
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+        <tr>
+          <td class="memname">void ccp4srs::Atom::set_vdwh_radius </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::realtype&#160;</td>
+          <td class="paramname"> <em>r</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
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+<a class="anchor" id="a9ae7f9281596f659071394247d484ffb"></a><!-- doxytag: member="ccp4srs::Atom::sp" ref="a9ae7f9281596f659071394247d484ffb" args="()" -->
+<div class="memitem">
+<div class="memproto">
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+        <tr>
+          <td class="memname">int ccp4srs::Atom::sp </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a86606a9614641a62a9b477c0b90c3a87"></a><!-- doxytag: member="ccp4srs::Atom::valency" ref="a86606a9614641a62a9b477c0b90c3a87" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Atom::valency </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a2c283b644afb507ec45667611a685827"></a><!-- doxytag: member="ccp4srs::Atom::vdw_radius" ref="a2c283b644afb507ec45667611a685827" args="()" -->
+<div class="memitem">
+<div class="memproto">
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+        <tr>
+          <td class="memname">mmdb::realtype ccp4srs::Atom::vdw_radius </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
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+<div class="memproto">
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+        <tr>
+          <td class="memname">mmdb::realtype ccp4srs::Atom::vdwh_radius </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a4c6e0a23b45563f10657d839d4479961"></a><!-- doxytag: member="ccp4srs::Atom::weight" ref="a4c6e0a23b45563f10657d839d4479961" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype ccp4srs::Atom::weight </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="adaebb2b3897e6758befc7c76d77c0420"></a><!-- doxytag: member="ccp4srs::Atom::write_mem" ref="adaebb2b3897e6758befc7c76d77c0420" args="(PMemIO memIO, int version)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Atom::write_mem </td>
+          <td>(</td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ac83667146ec86aeab8fdcce133c2fea0"></a><!-- doxytag: member="ccp4srs::Atom::writeToCIF" ref="ac83667146ec86aeab8fdcce133c2fea0" args="(mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Atom::writeToCIF </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>mmCIFLoop</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>monID</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a9af114ebe576f3a0af965579100da463"></a><!-- doxytag: member="ccp4srs::Atom::x" ref="a9af114ebe576f3a0af965579100da463" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype ccp4srs::Atom::x </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a7f9331955d7f98b1d2e869f8741a2188"></a><!-- doxytag: member="ccp4srs::Atom::x_mlib" ref="a7f9331955d7f98b1d2e869f8741a2188" args="()" -->
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+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype ccp4srs::Atom::x_mlib </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ac0fc0e47750a53f2be7ab60efc604d3b"></a><!-- doxytag: member="ccp4srs::Atom::x_pdbx" ref="ac0fc0e47750a53f2be7ab60efc604d3b" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype ccp4srs::Atom::x_pdbx </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a10fc0f0f21af2cd5311c7d957b59f52b"></a><!-- doxytag: member="ccp4srs::Atom::y" ref="a10fc0f0f21af2cd5311c7d957b59f52b" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype ccp4srs::Atom::y </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="acc50ad679a297a2626a6662cd0b61d3e"></a><!-- doxytag: member="ccp4srs::Atom::y_mlib" ref="acc50ad679a297a2626a6662cd0b61d3e" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype ccp4srs::Atom::y_mlib </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a65cdadf3090a0fa712b6c47040adb578"></a><!-- doxytag: member="ccp4srs::Atom::y_pdbx" ref="a65cdadf3090a0fa712b6c47040adb578" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype ccp4srs::Atom::y_pdbx </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a9d07e03f19613858142105d9f287466e"></a><!-- doxytag: member="ccp4srs::Atom::z" ref="a9d07e03f19613858142105d9f287466e" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype ccp4srs::Atom::z </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a73c4871fccf3ce91502449de659f835a"></a><!-- doxytag: member="ccp4srs::Atom::z_mlib" ref="a73c4871fccf3ce91502449de659f835a" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype ccp4srs::Atom::z_mlib </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aed837e19a61e89ce1e1eda0c35f10b2e"></a><!-- doxytag: member="ccp4srs::Atom::z_pdbx" ref="aed837e19a61e89ce1e1eda0c35f10b2e" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype ccp4srs::Atom::z_pdbx </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Data Documentation</h2>
+<a class="anchor" id="a0e7a7e76f9fba1a8277dae436f900821"></a><!-- doxytag: member="ccp4srs::Atom::atomCharge" ref="a0e7a7e76f9fba1a8277dae436f900821" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_atom.html#a0e7a7e76f9fba1a8277dae436f900821">ccp4srs::Atom::atomCharge</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>partial charge </p>
+
+</div>
+</div>
+<a class="anchor" id="a75168bfe9aa3e0e24ba5f81854323039"></a><!-- doxytag: member="ccp4srs::Atom::atomName" ref="a75168bfe9aa3e0e24ba5f81854323039" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::AtomName <a class="el" href="classccp4srs_1_1_atom.html#a75168bfe9aa3e0e24ba5f81854323039">ccp4srs::Atom::atomName</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>atom name </p>
+
+</div>
+</div>
+<a class="anchor" id="acb4d50d536b22d4dd3f971072354f784"></a><!-- doxytag: member="ccp4srs::Atom::atomSP" ref="acb4d50d536b22d4dd3f971072354f784" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_atom.html#acb4d50d536b22d4dd3f971072354f784">ccp4srs::Atom::atomSP</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>sp-hybridization </p>
+
+</div>
+</div>
+<a class="anchor" id="aeaa06e2eac23c671be3f49c0caaa7d12"></a><!-- doxytag: member="ccp4srs::Atom::atomValency" ref="aeaa06e2eac23c671be3f49c0caaa7d12" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_atom.html#aeaa06e2eac23c671be3f49c0caaa7d12">ccp4srs::Atom::atomValency</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>valency </p>
+
+</div>
+</div>
+<a class="anchor" id="ac470c0fd96b775b2b1d979c353449ee4"></a><!-- doxytag: member="ccp4srs::Atom::atomWeight" ref="ac470c0fd96b775b2b1d979c353449ee4" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_atom.html#ac470c0fd96b775b2b1d979c353449ee4">ccp4srs::Atom::atomWeight</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>atomic weight (in a.u.) </p>
+
+</div>
+</div>
+<a class="anchor" id="a621e19772fdb901353b6f60288afdb70"></a><!-- doxytag: member="ccp4srs::Atom::chemElement" ref="a621e19772fdb901353b6f60288afdb70" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::Element <a class="el" href="classccp4srs_1_1_atom.html#a621e19772fdb901353b6f60288afdb70">ccp4srs::Atom::chemElement</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>chemical element name </p>
+
+</div>
+</div>
+<a class="anchor" id="ac429b2d0c02fe21432c4b651ad181fdb"></a><!-- doxytag: member="ccp4srs::Atom::energyType" ref="ac429b2d0c02fe21432c4b651ad181fdb" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::EnergyType <a class="el" href="classccp4srs_1_1_atom.html#ac429b2d0c02fe21432c4b651ad181fdb">ccp4srs::Atom::energyType</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>energy type </p>
+
+</div>
+</div>
+<a class="anchor" id="aeb773fbdd5b04c0311969ad498622185"></a><!-- doxytag: member="ccp4srs::Atom::ionRadius" ref="aeb773fbdd5b04c0311969ad498622185" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_atom.html#aeb773fbdd5b04c0311969ad498622185">ccp4srs::Atom::ionRadius</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>ion radius </p>
+
+</div>
+</div>
+<a class="anchor" id="a641d281e9661ff8ca51bc768b2db5628"></a><!-- doxytag: member="ccp4srs::Atom::mlib_x" ref="a641d281e9661ff8ca51bc768b2db5628" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_atom.html#a641d281e9661ff8ca51bc768b2db5628">ccp4srs::Atom::mlib_x</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a92043cd1d43d17069c0c8f96020218b9"></a><!-- doxytag: member="ccp4srs::Atom::mlib_y" ref="a92043cd1d43d17069c0c8f96020218b9" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_atom.html#a92043cd1d43d17069c0c8f96020218b9">ccp4srs::Atom::mlib_y</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a0b6c2ba6990da454ea672a64e285653f"></a><!-- doxytag: member="ccp4srs::Atom::mlib_z" ref="a0b6c2ba6990da454ea672a64e285653f" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_atom.html#a0b6c2ba6990da454ea672a64e285653f">ccp4srs::Atom::mlib_z</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>m-lib cartesian coordinates </p>
+
+</div>
+</div>
+<a class="anchor" id="a45682b942f2f9262bc8fa1b5316a702b"></a><!-- doxytag: member="ccp4srs::Atom::oldAtomName" ref="a45682b942f2f9262bc8fa1b5316a702b" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::AtomName <a class="el" href="classccp4srs_1_1_atom.html#a45682b942f2f9262bc8fa1b5316a702b">ccp4srs::Atom::oldAtomName</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>old atom name </p>
+
+</div>
+</div>
+<a class="anchor" id="a49ff7aadab557a536541009606a2db12"></a><!-- doxytag: member="ccp4srs::Atom::pdb_x" ref="a49ff7aadab557a536541009606a2db12" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_atom.html#a49ff7aadab557a536541009606a2db12">ccp4srs::Atom::pdb_x</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a901c15656be6fa36e191df297d25521d"></a><!-- doxytag: member="ccp4srs::Atom::pdb_y" ref="a901c15656be6fa36e191df297d25521d" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_atom.html#a901c15656be6fa36e191df297d25521d">ccp4srs::Atom::pdb_y</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ae33b2033023270f96202151aed27a710"></a><!-- doxytag: member="ccp4srs::Atom::pdb_z" ref="ae33b2033023270f96202151aed27a710" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_atom.html#ae33b2033023270f96202151aed27a710">ccp4srs::Atom::pdb_z</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>pdb cartesian coordinates </p>
+
+</div>
+</div>
+<a class="anchor" id="aec57c2566b6a42361a8215d7b15a7e29"></a><!-- doxytag: member="ccp4srs::Atom::pdbx_x" ref="aec57c2566b6a42361a8215d7b15a7e29" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_atom.html#aec57c2566b6a42361a8215d7b15a7e29">ccp4srs::Atom::pdbx_x</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a1d138de5fa3e222554a95b796c246d40"></a><!-- doxytag: member="ccp4srs::Atom::pdbx_y" ref="a1d138de5fa3e222554a95b796c246d40" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_atom.html#a1d138de5fa3e222554a95b796c246d40">ccp4srs::Atom::pdbx_y</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a424a6001bc93ea1c8256f9f1fb48a585"></a><!-- doxytag: member="ccp4srs::Atom::pdbx_z" ref="a424a6001bc93ea1c8256f9f1fb48a585" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_atom.html#a424a6001bc93ea1c8256f9f1fb48a585">ccp4srs::Atom::pdbx_z</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>pdbx cartesian coordinates </p>
+
+</div>
+</div>
+<a class="anchor" id="aa363093b5746f782b8c4e60a73ec6438"></a><!-- doxytag: member="ccp4srs::Atom::property" ref="aa363093b5746f782b8c4e60a73ec6438" args="[4]" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">char <a class="el" href="classccp4srs_1_1_atom.html#aa363093b5746f782b8c4e60a73ec6438">ccp4srs::Atom::property</a>[4]<code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+<p>property vector: </p>
+
+</div>
+</div>
+<a class="anchor" id="a198154f097c4f42a4ae1dd73d5394734"></a><!-- doxytag: member="ccp4srs::Atom::rcsbAtomName" ref="a198154f097c4f42a4ae1dd73d5394734" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::AtomName <a class="el" href="classccp4srs_1_1_atom.html#a198154f097c4f42a4ae1dd73d5394734">ccp4srs::Atom::rcsbAtomName</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>alternative atom name </p>
+
+</div>
+</div>
+<a class="anchor" id="afd0adf07dd4f24e87acb6977335ff2ba"></a><!-- doxytag: member="ccp4srs::Atom::vdwhRadius" ref="afd0adf07dd4f24e87acb6977335ff2ba" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_atom.html#afd0adf07dd4f24e87acb6977335ff2ba">ccp4srs::Atom::vdwhRadius</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>Van-Der-Waals radius with hydrogen. </p>
+
+</div>
+</div>
+<a class="anchor" id="a74216b4c442b716656e5a55e908cea11"></a><!-- doxytag: member="ccp4srs::Atom::vdwRadius" ref="a74216b4c442b716656e5a55e908cea11" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_atom.html#a74216b4c442b716656e5a55e908cea11">ccp4srs::Atom::vdwRadius</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>Van-Der-Waals radius. </p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following files:<ul>
+<li>src/<a class="el" href="ccp4srs__atom_8h_source.html">ccp4srs_atom.h</a></li>
+<li>src/<a class="el" href="ccp4srs__atom_8cpp.html">ccp4srs_atom.cpp</a></li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
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+        name="MSearchResults" id="MSearchResults">
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+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_base-members.html ccp4srs/doc-html/html/classccp4srs_1_1_base-members.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_base-members.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_base-members.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,110 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
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+          </span>
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+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>ccp4srs::Base Member List</h1>  </div>
+</div>
+<div class="contents">
+This is the complete list of members for <a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a>, including all inherited members.<table>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a0c37b44fe77e9f171d5f40281a6e82ae">Base</a>()</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#ab67f138edc7ae19791be69dde485c719">freeMemory</a>()</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#af9a1789b20b43e97a8eb6a56b4ef32c4">getAtNames</a>(int entryNo, mmdb::PAtomName AtName, int &amp;nAtoms, int &amp;nH)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#afbe234eef9c84fde630b72fbcfe27946">getAtNames</a>(mmdb::io::PFile structFile, int entryNo, mmdb::PAtomName AtName, int &amp;nAtoms, int &amp;nH)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a7e47408dacc9bd80de046504e235cc06">getAtoms</a>(mmdb::cpstr entryID, int &amp;nNonHAtoms, mmdb::PAtomName NonHAtName, int &amp;nHAtoms, mmdb::PAtomName HAtName, mmdb::ivector Hconnect, mmdb::ivector Elem, mmdb::ivector Chiral)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a8bb61486d7dd2df0566b8e3a1c7f1c89">getBonds</a>(mmdb::cpstr entryID, mmdb::ivector nBonds, mmdb::imatrix bondPair, int &amp;nAtoms, int maxNAtoms, int maxNBonds)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a57b706684f3e84c741099ff904e01152">getEntryNo</a>(mmdb::cpstr entryID)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a17b78139832b00d7025236171ab31b7e">getGraph</a>(mmdb::io::PFile graphFile, mmdb::math::RPGraph G)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a8421066e4a9117cd380ff4362c355986">getGraph</a>(mmdb::io::PFile graphFile, int entryNo, mmdb::math::RPGraph G, int Hflag)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#af00d1ee772d045c048aa292457755b50">getGraph</a>(mmdb::io::PFile graphFile, mmdb::math::RPGraph G, int Hflag)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a418f3d4d079e0c4b93ebc6fff1fd0639">getGraph</a>(int entryNo, mmdb::math::RPGraph G, int Hflag)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a1f9dd08ea6c39fc0bb0a3885e6b3efac">getGraph</a>(mmdb::cpstr entryID, mmdb::math::RPGraph G, int Hflag)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a656b776b70ead2f8346b352b3bd1311e">getGraphFile</a>()</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a88c88924e247250d08cc4795b345c66a">getHetInfo</a>(mmdb::cpstr entryID, mmdb::pstr Formula, mmdb::pstr Hname, mmdb::pstr Hsynonym, mmdb::pstr Hcharge, mmdb::PAtomName &amp;ClinkAtom, mmdb::PElement &amp;ClinkEle, mmdb::PAtomName &amp;SlinkAtom, mmdb::PElement &amp;SlinkEle, int &amp;nLeavingAtoms)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#affa058db2078bc7835e9c78ca3bdde81">getIndex</a>(mmdb::cpstr entryID)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a399ff3d49a14dd3bb8250058f6452f4f">getIndex</a>(int n)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a339033984c68dd221cd6db184b734694">getMonomer</a>(mmdb::cpstr entryID)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a6f3f6564a30198bfe82215bceb6806e2">getMonomer</a>(int entryNo, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#ad25bf7474ec0574a39081ec5eeaefc5b">getMonomer</a>(mmdb::cpstr entryID, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a646d2c4349be4a740f2121dfd2091150">getNofAtoms</a>(mmdb::cpstr entryID)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a025a5622f0bfb83808cdad7cbf7af974">getNofAtoms</a>(int entryNo)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#af0653379d9db757dcc64c44c0e9ce070">getNofAtoms</a>(int entryNo, int &amp;nNonHAtoms, int &amp;nHAtoms)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#ac5481a8eeeb26ead06d7df61f605dac9">getPath</a>(mmdb::pstr &amp;S, mmdb::cpstr FName)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a03eac100b52d1f2d2d13981799f928bb">getStructFile</a>()</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#ada41928311fa3ba94bcb48a1ebf4b4df">index</a></td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a9fb463b8df4034fefb6e136ab56d135b">init_base</a>()</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#ae95af9ff2fb5c9d0edb437be3bcbe016">loadIndex</a>(mmdb::cpstr srsPath)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a663ef26d53b80f6c8b1f9c9cdeb70d2c">loadStructure</a>(mmdb::cpstr entryID)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#adf128b2adae954f6b25463c70ede5a58">memIO</a></td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#aeb551e05e822e5eb3673aba1fa85bda6">n_entries</a>()</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a863fd5090d78f3bada7f351dd2f33859">nEntries</a></td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#af3caa0403ce8a1c4489948fa4fc62b0c">srsDir</a></td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#ad18087156761086530c1f01f3078f869">srsVersion</a></td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a6d15803597f5a515c19848a5e8dbe164">unloadStructure</a>(mmdb::cpstr entryID)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a2c46b036cb9701ac6a2d22fcec3fbdcf">~Base</a>()</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+</table></div>
+<!--- window showing the filter options -->
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+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
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diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_base.html ccp4srs/doc-html/html/classccp4srs_1_1_base.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_base.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_base.html	2014-09-09 21:34:12.000000000 -0700
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+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
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+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="navpath">
+    <ul>
+      <li><a class="el" href="namespaceccp4srs.html">ccp4srs</a>      </li>
+      <li><a class="el" href="classccp4srs_1_1_base.html">Base</a>      </li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pro-methods">Protected Member Functions</a> &#124;
+<a href="#pro-attribs">Protected Attributes</a>  </div>
+  <div class="headertitle">
+<h1>ccp4srs::Base Class Reference</h1>  </div>
+</div>
+<div class="contents">
+<!-- doxytag: class="ccp4srs::Base" -->
+<p><code>#include &lt;<a class="el" href="ccp4srs__base_8h_source.html">ccp4srs_base.h</a>&gt;</code></p>
+<!-- startSectionHeader --><div class="dynheader">
+Inheritance diagram for ccp4srs::Base:<!-- endSectionHeader --></div>
+<!-- startSectionSummary --><!-- endSectionSummary --><!-- startSectionContent --><div class="dyncontent">
+<div class="center"><img src="classccp4srs_1_1_base__inherit__graph.png" border="0" usemap="#ccp4srs_1_1_base_inherit__map" alt="Inheritance graph"/></div>
+<map name="ccp4srs_1_1_base_inherit__map" id="ccp4srs_1_1_base_inherit__map">
+<area shape="rect" href="classccp4srs_1_1_chem.html" title="ccp4srs::Chem" alt="" coords="16,84,141,111"/><area shape="rect" href="classccp4srs_1_1_manager.html" title="ccp4srs::Manager" alt="" coords="5,161,152,188"/></map>
+<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center><!-- endSectionContent --></div>
+
+<p><a href="classccp4srs_1_1_base-members.html">List of all members.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#a0c37b44fe77e9f171d5f40281a6e82ae">Base</a> ()</td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Constructor.  <a href="#a0c37b44fe77e9f171d5f40281a6e82ae"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#a2c46b036cb9701ac6a2d22fcec3fbdcf">~Base</a> ()</td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Destructor.  <a href="#a2c46b036cb9701ac6a2d22fcec3fbdcf"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#ae95af9ff2fb5c9d0edb437be3bcbe016">loadIndex</a> (mmdb::cpstr srsPath)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#a663ef26d53b80f6c8b1f9c9cdeb70d2c">loadStructure</a> (mmdb::cpstr entryID)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">PIndex&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#affa058db2078bc7835e9c78ca3bdde81">getIndex</a> (mmdb::cpstr entryID)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">PIndex&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#a399ff3d49a14dd3bb8250058f6452f4f">getIndex</a> (int n)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#a6d15803597f5a515c19848a5e8dbe164">unloadStructure</a> (mmdb::cpstr entryID)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::pstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#ac5481a8eeeb26ead06d7df61f605dac9">getPath</a> (mmdb::pstr &amp;S, mmdb::cpstr FName)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::io::PFile&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#a03eac100b52d1f2d2d13981799f928bb">getStructFile</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::io::PFile&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#a656b776b70ead2f8346b352b3bd1311e">getGraphFile</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#aeb551e05e822e5eb3673aba1fa85bda6">n_entries</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#a57b706684f3e84c741099ff904e01152">getEntryNo</a> (mmdb::cpstr entryID)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">PMonomer&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#a339033984c68dd221cd6db184b734694">getMonomer</a> (mmdb::cpstr entryID)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">PMonomer&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#a6f3f6564a30198bfe82215bceb6806e2">getMonomer</a> (int entryNo, mmdb::io::PFile structFile)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">PMonomer&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#ad25bf7474ec0574a39081ec5eeaefc5b">getMonomer</a> (mmdb::cpstr entryID, mmdb::io::PFile structFile)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#a646d2c4349be4a740f2121dfd2091150">getNofAtoms</a> (mmdb::cpstr entryID)</td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns the number of atoms in the references monomer.  <a href="#a646d2c4349be4a740f2121dfd2091150"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#a025a5622f0bfb83808cdad7cbf7af974">getNofAtoms</a> (int entryNo)</td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns the number of atoms in the references monomer.  <a href="#a025a5622f0bfb83808cdad7cbf7af974"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#af0653379d9db757dcc64c44c0e9ce070">getNofAtoms</a> (int entryNo, int &amp;nNonHAtoms, int &amp;nHAtoms)</td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns number of non-hydrogen and hydrogen atoms for referenced structure.  <a href="#af0653379d9db757dcc64c44c0e9ce070"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#af9a1789b20b43e97a8eb6a56b4ef32c4">getAtNames</a> (int entryNo, mmdb::PAtomName AtName, int &amp;nAtoms, int &amp;nH)</td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns atom names, total number of atoms and number of hydrogens (nH) for referenced monomer.  <a href="#af9a1789b20b43e97a8eb6a56b4ef32c4"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#afbe234eef9c84fde630b72fbcfe27946">getAtNames</a> (mmdb::io::PFile structFile, int entryNo, mmdb::PAtomName AtName, int &amp;nAtoms, int &amp;nH)</td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns atom names, total number of atoms and number of hydrogens (nH) for referenced monomer.  <a href="#afbe234eef9c84fde630b72fbcfe27946"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#a7e47408dacc9bd80de046504e235cc06">getAtoms</a> (mmdb::cpstr entryID, int &amp;nNonHAtoms, mmdb::PAtomName NonHAtName, int &amp;nHAtoms, mmdb::PAtomName HAtName, mmdb::ivector Hconnect, mmdb::ivector Elem, mmdb::ivector Chiral)</td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Retrieves various atom properties for referenced structure.  <a href="#a7e47408dacc9bd80de046504e235cc06"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#a8bb61486d7dd2df0566b8e3a1c7f1c89">getBonds</a> (mmdb::cpstr entryID, mmdb::ivector nBonds, mmdb::imatrix bondPair, int &amp;nAtoms, int maxNAtoms, int maxNBonds)</td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Retrieves bonds for referenced structure.  <a href="#a8bb61486d7dd2df0566b8e3a1c7f1c89"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#a88c88924e247250d08cc4795b345c66a">getHetInfo</a> (mmdb::cpstr entryID, mmdb::pstr Formula, mmdb::pstr Hname, mmdb::pstr Hsynonym, mmdb::pstr Hcharge, mmdb::PAtomName &amp;ClinkAtom, mmdb::PElement &amp;ClinkEle, mmdb::PAtomName &amp;SlinkAtom, mmdb::PElement &amp;SlinkEle, int &amp;nLeavingAtoms)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#a17b78139832b00d7025236171ab31b7e">getGraph</a> (mmdb::io::PFile graphFile, mmdb::math::RPGraph G)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#a8421066e4a9117cd380ff4362c355986">getGraph</a> (mmdb::io::PFile graphFile, int entryNo, mmdb::math::RPGraph G, int Hflag)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#af00d1ee772d045c048aa292457755b50">getGraph</a> (mmdb::io::PFile graphFile, mmdb::math::RPGraph G, int Hflag)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#a418f3d4d079e0c4b93ebc6fff1fd0639">getGraph</a> (int entryNo, mmdb::math::RPGraph G, int Hflag)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#a1f9dd08ea6c39fc0bb0a3885e6b3efac">getGraph</a> (mmdb::cpstr entryID, mmdb::math::RPGraph G, int Hflag)</td></tr>
+<tr><td colspan="2"><h2><a name="pro-methods"></a>
+Protected Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#a9fb463b8df4034fefb6e136ab56d135b">init_base</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#ab67f138edc7ae19791be69dde485c719">freeMemory</a> ()</td></tr>
+<tr><td colspan="2"><h2><a name="pro-attribs"></a>
+Protected Attributes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classccp4srs_1_1_mem_i_o.html">MemIO</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#adf128b2adae954f6b25463c70ede5a58">memIO</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">PPIndex&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#ada41928311fa3ba94bcb48a1ebf4b4df">index</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::pstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#af3caa0403ce8a1c4489948fa4fc62b0c">srsDir</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#ad18087156761086530c1f01f3078f869">srsVersion</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_base.html#a863fd5090d78f3bada7f351dd2f33859">nEntries</a></td></tr>
+</table>
+<hr/><h2>Constructor &amp; Destructor Documentation</h2>
+<a class="anchor" id="a0c37b44fe77e9f171d5f40281a6e82ae"></a><!-- doxytag: member="ccp4srs::Base::Base" ref="a0c37b44fe77e9f171d5f40281a6e82ae" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::Base::Base </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>Constructor. </p>
+
+</div>
+</div>
+<a class="anchor" id="a2c46b036cb9701ac6a2d22fcec3fbdcf"></a><!-- doxytag: member="ccp4srs::Base::~Base" ref="a2c46b036cb9701ac6a2d22fcec3fbdcf" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::Base::~Base </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>Destructor. </p>
+
+</div>
+</div>
+<hr/><h2>Member Function Documentation</h2>
+<a class="anchor" id="ab67f138edc7ae19791be69dde485c719"></a><!-- doxytag: member="ccp4srs::Base::freeMemory" ref="ab67f138edc7ae19791be69dde485c719" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Base::freeMemory </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="afbe234eef9c84fde630b72fbcfe27946"></a><!-- doxytag: member="ccp4srs::Base::getAtNames" ref="afbe234eef9c84fde630b72fbcfe27946" args="(mmdb::io::PFile structFile, int entryNo, mmdb::PAtomName AtName, int &amp;nAtoms, int &amp;nH)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Base::getAtNames </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::io::PFile&#160;</td>
+          <td class="paramname"> <em>structFile</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>entryNo</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::PAtomName&#160;</td>
+          <td class="paramname"> <em>AtName</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>nAtoms</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>nH</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>Returns atom names, total number of atoms and number of hydrogens (nH) for referenced monomer. </p>
+<dl><dt><b>Parameters:</b></dt><dd>
+  <table class="params">
+    <tr><td class="paramdir">[in]</td><td class="paramname">structFile</td><td>pre-open SRS structure file </td></tr>
+    <tr><td class="paramdir">[in]</td><td class="paramname">entryNo</td><td>entry number (0...<a class="el" href="classccp4srs_1_1_base.html#aeb551e05e822e5eb3673aba1fa85bda6">n_entries()</a>-1) </td></tr>
+    <tr><td class="paramdir">[out]</td><td class="paramname">AtName</td><td>array of atom names, prealocated with sufficient length </td></tr>
+    <tr><td class="paramdir">[out]</td><td class="paramname">nAtoms</td><td>total number of atoms </td></tr>
+    <tr><td class="paramdir">[out]</td><td class="paramname">nH</td><td>number of hydrogens </td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>CCP4SRS_Ok, CCP4SRS_FileNotFound, CCP4SRS_EntryNotFound and CCP4SRS_ReadErrors. </dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="af9a1789b20b43e97a8eb6a56b4ef32c4"></a><!-- doxytag: member="ccp4srs::Base::getAtNames" ref="af9a1789b20b43e97a8eb6a56b4ef32c4" args="(int entryNo, mmdb::PAtomName AtName, int &amp;nAtoms, int &amp;nH)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Base::getAtNames </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>entryNo</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::PAtomName&#160;</td>
+          <td class="paramname"> <em>AtName</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>nAtoms</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>nH</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>Returns atom names, total number of atoms and number of hydrogens (nH) for referenced monomer. </p>
+<dl><dt><b>Parameters:</b></dt><dd>
+  <table class="params">
+    <tr><td class="paramdir">[in]</td><td class="paramname">entryNo</td><td>entry number (0...<a class="el" href="classccp4srs_1_1_base.html#aeb551e05e822e5eb3673aba1fa85bda6">n_entries()</a>-1) </td></tr>
+    <tr><td class="paramdir">[out]</td><td class="paramname">AtName</td><td>array of atom names, prealocated with sufficient length </td></tr>
+    <tr><td class="paramdir">[out]</td><td class="paramname">nAtoms</td><td>total number of atoms </td></tr>
+    <tr><td class="paramdir">[out]</td><td class="paramname">nH</td><td>number of hydrogens </td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>CCP4SRS_Ok, CCP4SRS_FileNotFound, CCP4SRS_EntryNotFound and CCP4SRS_ReadErrors. </dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="a7e47408dacc9bd80de046504e235cc06"></a><!-- doxytag: member="ccp4srs::Base::getAtoms" ref="a7e47408dacc9bd80de046504e235cc06" args="(mmdb::cpstr entryID, int &amp;nNonHAtoms, mmdb::PAtomName NonHAtName, int &amp;nHAtoms, mmdb::PAtomName HAtName, mmdb::ivector Hconnect, mmdb::ivector Elem, mmdb::ivector Chiral)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Base::getAtoms </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>entryID</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>nNonHAtoms</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::PAtomName&#160;</td>
+          <td class="paramname"> <em>NonHAtName</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>nHAtoms</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::PAtomName&#160;</td>
+          <td class="paramname"> <em>HAtName</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::ivector&#160;</td>
+          <td class="paramname"> <em>Hconnect</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::ivector&#160;</td>
+          <td class="paramname"> <em>Elem</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::ivector&#160;</td>
+          <td class="paramname"> <em>Chiral</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>Retrieves various atom properties for referenced structure. </p>
+<dl><dt><b>Parameters:</b></dt><dd>
+  <table class="params">
+    <tr><td class="paramdir">[in]</td><td class="paramname">entryID</td><td>monomer's cif id </td></tr>
+    <tr><td class="paramdir">[out]</td><td class="paramname">nNonHAtoms</td><td>number of non-hydrogen atoms </td></tr>
+    <tr><td class="paramdir">[out]</td><td class="paramname">nNonHAtomName</td><td>non-hydrogen atom names </td></tr>
+    <tr><td class="paramdir">[out]</td><td class="paramname">nHAtoms</td><td>number of hydrogen atoms </td></tr>
+    <tr><td class="paramdir">[out]</td><td class="paramname">nNonHAtomName</td><td>hydrogen atom names </td></tr>
+    <tr><td class="paramdir">[out]</td><td class="paramname">Hconnect</td><td>connectivity to non-hydrogen atoms: hydrogen HAtName[i] is connected to non-hydrogen NonHAtom[Hconnect[i]], if Hconnect[i]&gt;=0. </td></tr>
+    <tr><td class="paramdir">[out]</td><td class="paramname">Elem</td><td>element IDs </td></tr>
+    <tr><td class="paramdir">[out]</td><td class="paramname">Chiral</td><td>chirality IDs </td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>CCP4SRS_Ok, CCP4SRS_FileNotFound, CCP4SRS_EntryNotFound, CCP4SRS_ReadErrors and CCP4SRS_BrokenBonds. </dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="a8bb61486d7dd2df0566b8e3a1c7f1c89"></a><!-- doxytag: member="ccp4srs::Base::getBonds" ref="a8bb61486d7dd2df0566b8e3a1c7f1c89" args="(mmdb::cpstr entryID, mmdb::ivector nBonds, mmdb::imatrix bondPair, int &amp;nAtoms, int maxNAtoms, int maxNBonds)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Base::getBonds </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>entryID</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::ivector&#160;</td>
+          <td class="paramname"> <em>nBonds</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::imatrix&#160;</td>
+          <td class="paramname"> <em>bondPair</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>nAtoms</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>maxNAtoms</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>maxNBonds</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>Retrieves bonds for referenced structure. </p>
+<dl><dt><b>Parameters:</b></dt><dd>
+  <table class="params">
+    <tr><td class="paramdir">[in]</td><td class="paramname">entryID</td><td>monomer's cif id </td></tr>
+    <tr><td class="paramdir">[out]</td><td class="paramname">nBonds</td><td>number of bonds for ith atom </td></tr>
+    <tr><td class="paramdir">[out]</td><td class="paramname">bondPair</td><td>bonded atoms: bondPair[i][j] (0&lt;=i&lt;nAtoms, 0&lt;=j&lt;=nBonds[i]) gives the number of atom connected to ith atom; only pairs i&lt;j are returned </td></tr>
+    <tr><td class="paramdir">[in]</td><td class="paramname">maxNAtoms</td><td>length of nBonds[] and bondPairs[] </td></tr>
+    <tr><td class="paramdir">[in]</td><td class="paramname">maxNBonds</td><td>length of bondPairs[][] </td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>CCP4SRS_Ok, CCP4SRS_FileNotFound, CCP4SRS_EntryNotFound and CCP4SRS_ReadErrors. </dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="a57b706684f3e84c741099ff904e01152"></a><!-- doxytag: member="ccp4srs::Base::getEntryNo" ref="a57b706684f3e84c741099ff904e01152" args="(mmdb::cpstr entryID)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Base::getEntryNo </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>entryID</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a17b78139832b00d7025236171ab31b7e"></a><!-- doxytag: member="ccp4srs::Base::getGraph" ref="a17b78139832b00d7025236171ab31b7e" args="(mmdb::io::PFile graphFile, mmdb::math::RPGraph G)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Base::getGraph </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::io::PFile&#160;</td>
+          <td class="paramname"> <em>graphFile</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::math::RPGraph&#160;</td>
+          <td class="paramname"> <em>G</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a8421066e4a9117cd380ff4362c355986"></a><!-- doxytag: member="ccp4srs::Base::getGraph" ref="a8421066e4a9117cd380ff4362c355986" args="(mmdb::io::PFile graphFile, int entryNo, mmdb::math::RPGraph G, int Hflag)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Base::getGraph </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::io::PFile&#160;</td>
+          <td class="paramname"> <em>graphFile</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>entryNo</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::math::RPGraph&#160;</td>
+          <td class="paramname"> <em>G</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>Hflag</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a418f3d4d079e0c4b93ebc6fff1fd0639"></a><!-- doxytag: member="ccp4srs::Base::getGraph" ref="a418f3d4d079e0c4b93ebc6fff1fd0639" args="(int entryNo, mmdb::math::RPGraph G, int Hflag)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Base::getGraph </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>entryNo</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::math::RPGraph&#160;</td>
+          <td class="paramname"> <em>G</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>Hflag</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a1f9dd08ea6c39fc0bb0a3885e6b3efac"></a><!-- doxytag: member="ccp4srs::Base::getGraph" ref="a1f9dd08ea6c39fc0bb0a3885e6b3efac" args="(mmdb::cpstr entryID, mmdb::math::RPGraph G, int Hflag)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Base::getGraph </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>entryID</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::math::RPGraph&#160;</td>
+          <td class="paramname"> <em>G</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>Hflag</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="af00d1ee772d045c048aa292457755b50"></a><!-- doxytag: member="ccp4srs::Base::getGraph" ref="af00d1ee772d045c048aa292457755b50" args="(mmdb::io::PFile graphFile, mmdb::math::RPGraph G, int Hflag)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Base::getGraph </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::io::PFile&#160;</td>
+          <td class="paramname"> <em>graphFile</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::math::RPGraph&#160;</td>
+          <td class="paramname"> <em>G</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>Hflag</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a656b776b70ead2f8346b352b3bd1311e"></a><!-- doxytag: member="ccp4srs::Base::getGraphFile" ref="a656b776b70ead2f8346b352b3bd1311e" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::io::PFile ccp4srs::Base::getGraphFile </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a88c88924e247250d08cc4795b345c66a"></a><!-- doxytag: member="ccp4srs::Base::getHetInfo" ref="a88c88924e247250d08cc4795b345c66a" args="(mmdb::cpstr entryID, mmdb::pstr Formula, mmdb::pstr Hname, mmdb::pstr Hsynonym, mmdb::pstr Hcharge, mmdb::PAtomName &amp;ClinkAtom, mmdb::PElement &amp;ClinkEle, mmdb::PAtomName &amp;SlinkAtom, mmdb::PElement &amp;SlinkEle, int &amp;nLeavingAtoms)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Base::getHetInfo </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>entryID</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::pstr&#160;</td>
+          <td class="paramname"> <em>Formula</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::pstr&#160;</td>
+          <td class="paramname"> <em>Hname</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::pstr&#160;</td>
+          <td class="paramname"> <em>Hsynonym</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::pstr&#160;</td>
+          <td class="paramname"> <em>Hcharge</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::PAtomName &amp;&#160;</td>
+          <td class="paramname"> <em>ClinkAtom</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::PElement &amp;&#160;</td>
+          <td class="paramname"> <em>ClinkEle</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::PAtomName &amp;&#160;</td>
+          <td class="paramname"> <em>SlinkAtom</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::PElement &amp;&#160;</td>
+          <td class="paramname"> <em>SlinkEle</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>nLeavingAtoms</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a399ff3d49a14dd3bb8250058f6452f4f"></a><!-- doxytag: member="ccp4srs::Base::getIndex" ref="a399ff3d49a14dd3bb8250058f6452f4f" args="(int n)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">PIndex ccp4srs::Base::getIndex </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>n</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="affa058db2078bc7835e9c78ca3bdde81"></a><!-- doxytag: member="ccp4srs::Base::getIndex" ref="affa058db2078bc7835e9c78ca3bdde81" args="(mmdb::cpstr entryID)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">PIndex ccp4srs::Base::getIndex </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>entryID</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ad25bf7474ec0574a39081ec5eeaefc5b"></a><!-- doxytag: member="ccp4srs::Base::getMonomer" ref="ad25bf7474ec0574a39081ec5eeaefc5b" args="(mmdb::cpstr entryID, mmdb::io::PFile structFile)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">PMonomer ccp4srs::Base::getMonomer </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>entryID</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::io::PFile&#160;</td>
+          <td class="paramname"> <em>structFile</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a339033984c68dd221cd6db184b734694"></a><!-- doxytag: member="ccp4srs::Base::getMonomer" ref="a339033984c68dd221cd6db184b734694" args="(mmdb::cpstr entryID)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">PMonomer ccp4srs::Base::getMonomer </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>entryID</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a6f3f6564a30198bfe82215bceb6806e2"></a><!-- doxytag: member="ccp4srs::Base::getMonomer" ref="a6f3f6564a30198bfe82215bceb6806e2" args="(int entryNo, mmdb::io::PFile structFile)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">PMonomer ccp4srs::Base::getMonomer </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>entryNo</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::io::PFile&#160;</td>
+          <td class="paramname"> <em>structFile</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a025a5622f0bfb83808cdad7cbf7af974"></a><!-- doxytag: member="ccp4srs::Base::getNofAtoms" ref="a025a5622f0bfb83808cdad7cbf7af974" args="(int entryNo)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Base::getNofAtoms </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>entryNo</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>Returns the number of atoms in the references monomer. </p>
+<dl><dt><b>Parameters:</b></dt><dd>
+  <table class="params">
+    <tr><td class="paramdir">[in]</td><td class="paramname">entryNo</td><td>entry number (0...<a class="el" href="classccp4srs_1_1_base.html#aeb551e05e822e5eb3673aba1fa85bda6">n_entries()</a>-1) </td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>Non-negative return delivers the number of atoms, otherwise CCP4SRS_EntryNotFound indicates that the requested structure was not found in the database </dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="af0653379d9db757dcc64c44c0e9ce070"></a><!-- doxytag: member="ccp4srs::Base::getNofAtoms" ref="af0653379d9db757dcc64c44c0e9ce070" args="(int entryNo, int &amp;nNonHAtoms, int &amp;nHAtoms)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Base::getNofAtoms </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>entryNo</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>nNonHAtoms</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>nHAtoms</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>Returns number of non-hydrogen and hydrogen atoms for referenced structure. </p>
+<dl><dt><b>Parameters:</b></dt><dd>
+  <table class="params">
+    <tr><td class="paramdir">[in]</td><td class="paramname">entryNo</td><td>entry number (0...<a class="el" href="classccp4srs_1_1_base.html#aeb551e05e822e5eb3673aba1fa85bda6">n_entries()</a>-1) </td></tr>
+    <tr><td class="paramdir">[out]</td><td class="paramname">nNonHAtoms</td><td>number of non-hydrogen atoms </td></tr>
+    <tr><td class="paramdir">[out]</td><td class="paramname">nHAtoms</td><td>number of hydrogen atoms </td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>CCP4SRS_Ok or CCP4SRS_EntryNotFound. </dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="a646d2c4349be4a740f2121dfd2091150"></a><!-- doxytag: member="ccp4srs::Base::getNofAtoms" ref="a646d2c4349be4a740f2121dfd2091150" args="(mmdb::cpstr entryID)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Base::getNofAtoms </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>entryID</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>Returns the number of atoms in the references monomer. </p>
+<dl><dt><b>Parameters:</b></dt><dd>
+  <table class="params">
+    <tr><td class="paramname">inp]</td><td>entryID 3-letter cif code </td></tr>
+  </table>
+  </dd>
+</dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>Non-negative return delivers the number of atoms, otherwise CCP4SRS_EntryNotFound indicates that the requested structure was not found in the database </dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="ac5481a8eeeb26ead06d7df61f605dac9"></a><!-- doxytag: member="ccp4srs::Base::getPath" ref="ac5481a8eeeb26ead06d7df61f605dac9" args="(mmdb::pstr &amp;S, mmdb::cpstr FName)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::pstr ccp4srs::Base::getPath </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::pstr &amp;&#160;</td>
+          <td class="paramname"> <em>S</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>FName</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a03eac100b52d1f2d2d13981799f928bb"></a><!-- doxytag: member="ccp4srs::Base::getStructFile" ref="a03eac100b52d1f2d2d13981799f928bb" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::io::PFile ccp4srs::Base::getStructFile </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a9fb463b8df4034fefb6e136ab56d135b"></a><!-- doxytag: member="ccp4srs::Base::init_base" ref="a9fb463b8df4034fefb6e136ab56d135b" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Base::init_base </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ae95af9ff2fb5c9d0edb437be3bcbe016"></a><!-- doxytag: member="ccp4srs::Base::loadIndex" ref="ae95af9ff2fb5c9d0edb437be3bcbe016" args="(mmdb::cpstr srsPath)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Base::loadIndex </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>srsPath</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a663ef26d53b80f6c8b1f9c9cdeb70d2c"></a><!-- doxytag: member="ccp4srs::Base::loadStructure" ref="a663ef26d53b80f6c8b1f9c9cdeb70d2c" args="(mmdb::cpstr entryID)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Base::loadStructure </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>entryID</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aeb551e05e822e5eb3673aba1fa85bda6"></a><!-- doxytag: member="ccp4srs::Base::n_entries" ref="aeb551e05e822e5eb3673aba1fa85bda6" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Base::n_entries </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a6d15803597f5a515c19848a5e8dbe164"></a><!-- doxytag: member="ccp4srs::Base::unloadStructure" ref="a6d15803597f5a515c19848a5e8dbe164" args="(mmdb::cpstr entryID)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Base::unloadStructure </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>entryID</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Data Documentation</h2>
+<a class="anchor" id="ada41928311fa3ba94bcb48a1ebf4b4df"></a><!-- doxytag: member="ccp4srs::Base::index" ref="ada41928311fa3ba94bcb48a1ebf4b4df" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">PPIndex <a class="el" href="classccp4srs_1_1_base.html#ada41928311fa3ba94bcb48a1ebf4b4df">ccp4srs::Base::index</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="adf128b2adae954f6b25463c70ede5a58"></a><!-- doxytag: member="ccp4srs::Base::memIO" ref="adf128b2adae954f6b25463c70ede5a58" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="classccp4srs_1_1_mem_i_o.html">MemIO</a> <a class="el" href="classccp4srs_1_1_base.html#adf128b2adae954f6b25463c70ede5a58">ccp4srs::Base::memIO</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a863fd5090d78f3bada7f351dd2f33859"></a><!-- doxytag: member="ccp4srs::Base::nEntries" ref="a863fd5090d78f3bada7f351dd2f33859" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_base.html#a863fd5090d78f3bada7f351dd2f33859">ccp4srs::Base::nEntries</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="af3caa0403ce8a1c4489948fa4fc62b0c"></a><!-- doxytag: member="ccp4srs::Base::srsDir" ref="af3caa0403ce8a1c4489948fa4fc62b0c" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::pstr <a class="el" href="classccp4srs_1_1_base.html#af3caa0403ce8a1c4489948fa4fc62b0c">ccp4srs::Base::srsDir</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ad18087156761086530c1f01f3078f869"></a><!-- doxytag: member="ccp4srs::Base::srsVersion" ref="ad18087156761086530c1f01f3078f869" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_base.html#ad18087156761086530c1f01f3078f869">ccp4srs::Base::srsVersion</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following files:<ul>
+<li>src/<a class="el" href="ccp4srs__base_8h_source.html">ccp4srs_base.h</a></li>
+<li>src/<a class="el" href="ccp4srs__base_8cpp.html">ccp4srs_base.cpp</a></li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
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diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_bond-members.html ccp4srs/doc-html/html/classccp4srs_1_1_bond-members.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_bond-members.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_bond-members.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,105 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
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+<script type="text/javaScript" src="search/search.js"></script>
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+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>ccp4srs::Bond Member List</h1>  </div>
+</div>
+<div class="contents">
+This is the complete list of members for <a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a>, including all inherited members.<table>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba1511fd16010981add30c1e054980f193">Aromatic</a> enum value</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#a6ec052956ddec875a707d7e375ce0748">atom1</a>()</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#a364bc6a611e192c07d0bf5236a3503b9">atom2</a>()</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#ad359689c475101246c6c3061d31c2541">atom_1</a></td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#a277aee984c745dcdfd338f19e7df1e48">atom_2</a></td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#acd3c055b0b0827de95e44ca9a9ac972a">Bond</a>()</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#a43513fb523b43f7f5f407a0bae151a95">bond_length</a></td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#af438937a89d3cb3c7f2342ca6f38301c">bond_length_esd</a></td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#ac6365bacbc07dd7cf914b6c7ad6cd5d7">bond_order</a></td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#acefa794143d2ab128897441895cdf562">compare</a>(Container&lt; Atom &gt; &amp;atoms, PBond bond, Container&lt; Atom &gt; &amp;bond_atoms)</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#a4bb135bfcd9ee6078a2770fe9f15319c">copy</a>(Container&lt; Atom &gt; &amp;atoms, PBond bond, Container&lt; Atom &gt; &amp;bond_atoms)</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#a0c6c410020c5fad46d2987d9fc8de65e">copy</a>(PBond bond, mmdb::ivector anmatch=NULL)</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795babaf2bbca3b364f84e83bbc9927b45e39">Covalent</a> enum value</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba3e459a041fa6b33d363df5a335413e13">Deloc</a> enum value</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba0311fe9d41fd3830910b1e4f93d9a83a">Double</a> enum value</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#a3ebb971fa0af7886f076da460b4875e9">length</a>()</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#a28f3638c15b007dddaab637362635009">length_esd</a>()</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#a781542dae98140ea687a5d83a3e02e8e">makeCIFTags</a>(mmdb::mmcif::PLoop mmCIFLoop)</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td><code> [static]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba1be67f1d82568ea8bb92f456440e7f01">Metal</a> enum value</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba3a534360bb854109f0ad2d34f1858997">noOrder</a> enum value</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#ae18a9e08399e96910028f01a376d41f0">order</a>()</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#a47ad8a18d4c0363dc1f04f3cfbc670ec">read_mem</a>(PMemIO memIO, int version, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#a24976c4962050d858ca00fa6f72684e2">readFromCIF</a>(mmdb::mmcif::PStruct mmCIFStruct, Container&lt; Atom &gt; &amp;atoms)</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#ac6a267f1cb4e7553d746537cf36e5ea3">readFromCIF_ccp4</a>(mmdb::mmcif::PLoop mmCIFLoop, int bondNo, Container&lt; Atom &gt; &amp;atoms)</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#a54c6291defa953cc5f5750b0f116719c">readFromCIF_rcsb</a>(mmdb::mmcif::PLoop mmCIFLoop, int bondNo, Container&lt; Atom &gt; &amp;atoms)</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba338d16bbed971e9a0c912ff78efed793">Single</a> enum value</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795baf6c5cfdf98463c48cd5772a18e49ad6f">Triple</a> enum value</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#aa44d448aa0181e6d51048beda35052f4">write_mem</a>(PMemIO memIO, int version)</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#a89214f5f730f603bdd8dacea6317428f">writeToCIF</a>(mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID, Container&lt; Atom &gt; &amp;atoms)</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_bond.html#a695a8236689b60df2ad108c7cc55eb1a">~Bond</a>()</td><td><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></td><td><code> [virtual]</code></td></tr>
+</table></div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
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diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_bond.html ccp4srs/doc-html/html/classccp4srs_1_1_bond.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_bond.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_bond.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,656 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: ccp4srs::Bond Class Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
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+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
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+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
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+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="navpath">
+    <ul>
+      <li><a class="el" href="namespaceccp4srs.html">ccp4srs</a>      </li>
+      <li><a class="el" href="classccp4srs_1_1_bond.html">Bond</a>      </li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="summary">
+<a href="#pub-types">Public Types</a> &#124;
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pub-static-methods">Static Public Member Functions</a> &#124;
+<a href="#pro-attribs">Protected Attributes</a>  </div>
+  <div class="headertitle">
+<h1>ccp4srs::Bond Class Reference</h1>  </div>
+</div>
+<div class="contents">
+<!-- doxytag: class="ccp4srs::Bond" -->
+<p><code>#include &lt;<a class="el" href="ccp4srs__bond_8h_source.html">ccp4srs_bond.h</a>&gt;</code></p>
+
+<p><a href="classccp4srs_1_1_bond-members.html">List of all members.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="pub-types"></a>
+Public Types</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom">{ <br/>
+&#160;&#160;<a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba3a534360bb854109f0ad2d34f1858997">noOrder</a>, 
+<a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba338d16bbed971e9a0c912ff78efed793">Single</a>, 
+<a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba1511fd16010981add30c1e054980f193">Aromatic</a>, 
+<a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba0311fe9d41fd3830910b1e4f93d9a83a">Double</a>, 
+<br/>
+&#160;&#160;<a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795baf6c5cfdf98463c48cd5772a18e49ad6f">Triple</a>, 
+<a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba3e459a041fa6b33d363df5a335413e13">Deloc</a>, 
+<a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795babaf2bbca3b364f84e83bbc9927b45e39">Covalent</a>, 
+<a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba1be67f1d82568ea8bb92f456440e7f01">Metal</a>
+<br/>
+ }</td></tr>
+<tr><td colspan="2"><h2><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html#acd3c055b0b0827de95e44ca9a9ac972a">Bond</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html#a695a8236689b60df2ad108c7cc55eb1a">~Bond</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html#a6ec052956ddec875a707d7e375ce0748">atom1</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html#a364bc6a611e192c07d0bf5236a3503b9">atom2</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html#ae18a9e08399e96910028f01a376d41f0">order</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html#a3ebb971fa0af7886f076da460b4875e9">length</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html#a28f3638c15b007dddaab637362635009">length_esd</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html#ac6a267f1cb4e7553d746537cf36e5ea3">readFromCIF_ccp4</a> (mmdb::mmcif::PLoop mmCIFLoop, int bondNo, <a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;atoms)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html#a54c6291defa953cc5f5750b0f116719c">readFromCIF_rcsb</a> (mmdb::mmcif::PLoop mmCIFLoop, int bondNo, <a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;atoms)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html#a24976c4962050d858ca00fa6f72684e2">readFromCIF</a> (mmdb::mmcif::PStruct mmCIFStruct, <a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;atoms)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html#a89214f5f730f603bdd8dacea6317428f">writeToCIF</a> (mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID, <a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;atoms)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html#acefa794143d2ab128897441895cdf562">compare</a> (<a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;atoms, PBond bond, <a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;bond_atoms)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html#a4bb135bfcd9ee6078a2770fe9f15319c">copy</a> (<a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;atoms, PBond bond, <a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;bond_atoms)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html#aa44d448aa0181e6d51048beda35052f4">write_mem</a> (PMemIO memIO, int version)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html#a47ad8a18d4c0363dc1f04f3cfbc670ec">read_mem</a> (PMemIO memIO, int version, bool *Ok=NULL)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html#a0c6c410020c5fad46d2987d9fc8de65e">copy</a> (PBond bond, mmdb::ivector anmatch=NULL)</td></tr>
+<tr><td colspan="2"><h2><a name="pub-static-methods"></a>
+Static Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">static void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html#a781542dae98140ea687a5d83a3e02e8e">makeCIFTags</a> (mmdb::mmcif::PLoop mmCIFLoop)</td></tr>
+<tr><td colspan="2"><h2><a name="pro-attribs"></a>
+Protected Attributes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html#ad359689c475101246c6c3061d31c2541">atom_1</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html#a277aee984c745dcdfd338f19e7df1e48">atom_2</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">ordinal numbers of bonded atoms [0,1,.  <a href="#a277aee984c745dcdfd338f19e7df1e48"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html#ac6365bacbc07dd7cf914b6c7ad6cd5d7">bond_order</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">bond order  <a href="#ac6365bacbc07dd7cf914b6c7ad6cd5d7"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html#a43513fb523b43f7f5f407a0bae151a95">bond_length</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_bond.html#af438937a89d3cb3c7f2342ca6f38301c">bond_length_esd</a></td></tr>
+</table>
+<hr/><h2>Member Enumeration Documentation</h2>
+<a class="anchor" id="a85174d1fd8631c6fe1cf12d60ee8795b"></a><!-- doxytag: member="ccp4srs::Bond::@0" ref="a85174d1fd8631c6fe1cf12d60ee8795b" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">anonymous enum</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+<dl><dt><b>Enumerator: </b></dt><dd><table border="0" cellspacing="2" cellpadding="0">
+<tr><td valign="top"><em><a class="anchor" id="a85174d1fd8631c6fe1cf12d60ee8795ba3a534360bb854109f0ad2d34f1858997"></a><!-- doxytag: member="noOrder" ref="a85174d1fd8631c6fe1cf12d60ee8795ba3a534360bb854109f0ad2d34f1858997" args="" -->noOrder</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a85174d1fd8631c6fe1cf12d60ee8795ba338d16bbed971e9a0c912ff78efed793"></a><!-- doxytag: member="Single" ref="a85174d1fd8631c6fe1cf12d60ee8795ba338d16bbed971e9a0c912ff78efed793" args="" -->Single</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a85174d1fd8631c6fe1cf12d60ee8795ba1511fd16010981add30c1e054980f193"></a><!-- doxytag: member="Aromatic" ref="a85174d1fd8631c6fe1cf12d60ee8795ba1511fd16010981add30c1e054980f193" args="" -->Aromatic</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a85174d1fd8631c6fe1cf12d60ee8795ba0311fe9d41fd3830910b1e4f93d9a83a"></a><!-- doxytag: member="Double" ref="a85174d1fd8631c6fe1cf12d60ee8795ba0311fe9d41fd3830910b1e4f93d9a83a" args="" -->Double</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a85174d1fd8631c6fe1cf12d60ee8795baf6c5cfdf98463c48cd5772a18e49ad6f"></a><!-- doxytag: member="Triple" ref="a85174d1fd8631c6fe1cf12d60ee8795baf6c5cfdf98463c48cd5772a18e49ad6f" args="" -->Triple</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a85174d1fd8631c6fe1cf12d60ee8795ba3e459a041fa6b33d363df5a335413e13"></a><!-- doxytag: member="Deloc" ref="a85174d1fd8631c6fe1cf12d60ee8795ba3e459a041fa6b33d363df5a335413e13" args="" -->Deloc</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a85174d1fd8631c6fe1cf12d60ee8795babaf2bbca3b364f84e83bbc9927b45e39"></a><!-- doxytag: member="Covalent" ref="a85174d1fd8631c6fe1cf12d60ee8795babaf2bbca3b364f84e83bbc9927b45e39" args="" -->Covalent</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a85174d1fd8631c6fe1cf12d60ee8795ba1be67f1d82568ea8bb92f456440e7f01"></a><!-- doxytag: member="Metal" ref="a85174d1fd8631c6fe1cf12d60ee8795ba1be67f1d82568ea8bb92f456440e7f01" args="" -->Metal</em>&nbsp;</td><td>
+</td></tr>
+</table>
+</dd>
+</dl>
+
+</div>
+</div>
+<hr/><h2>Constructor &amp; Destructor Documentation</h2>
+<a class="anchor" id="acd3c055b0b0827de95e44ca9a9ac972a"></a><!-- doxytag: member="ccp4srs::Bond::Bond" ref="acd3c055b0b0827de95e44ca9a9ac972a" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::Bond::Bond </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a695a8236689b60df2ad108c7cc55eb1a"></a><!-- doxytag: member="ccp4srs::Bond::~Bond" ref="a695a8236689b60df2ad108c7cc55eb1a" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::Bond::~Bond </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [virtual]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Function Documentation</h2>
+<a class="anchor" id="a6ec052956ddec875a707d7e375ce0748"></a><!-- doxytag: member="ccp4srs::Bond::atom1" ref="a6ec052956ddec875a707d7e375ce0748" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Bond::atom1 </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a364bc6a611e192c07d0bf5236a3503b9"></a><!-- doxytag: member="ccp4srs::Bond::atom2" ref="a364bc6a611e192c07d0bf5236a3503b9" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Bond::atom2 </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="acefa794143d2ab128897441895cdf562"></a><!-- doxytag: member="ccp4srs::Bond::compare" ref="acefa794143d2ab128897441895cdf562" args="(Container&lt; Atom &gt; &amp;atoms, PBond bond, Container&lt; Atom &gt; &amp;bond_atoms)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::Bond::compare </td>
+          <td>(</td>
+          <td class="paramtype"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;&#160;</td>
+          <td class="paramname"> <em>atoms</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">PBond&#160;</td>
+          <td class="paramname"> <em>bond</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;&#160;</td>
+          <td class="paramname"> <em>bond_atoms</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a4bb135bfcd9ee6078a2770fe9f15319c"></a><!-- doxytag: member="ccp4srs::Bond::copy" ref="a4bb135bfcd9ee6078a2770fe9f15319c" args="(Container&lt; Atom &gt; &amp;atoms, PBond bond, Container&lt; Atom &gt; &amp;bond_atoms)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::Bond::copy </td>
+          <td>(</td>
+          <td class="paramtype"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;&#160;</td>
+          <td class="paramname"> <em>atoms</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">PBond&#160;</td>
+          <td class="paramname"> <em>bond</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;&#160;</td>
+          <td class="paramname"> <em>bond_atoms</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a0c6c410020c5fad46d2987d9fc8de65e"></a><!-- doxytag: member="ccp4srs::Bond::copy" ref="a0c6c410020c5fad46d2987d9fc8de65e" args="(PBond bond, mmdb::ivector anmatch=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Bond::copy </td>
+          <td>(</td>
+          <td class="paramtype">PBond&#160;</td>
+          <td class="paramname"> <em>bond</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::ivector&#160;</td>
+          <td class="paramname"> <em>anmatch</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a3ebb971fa0af7886f076da460b4875e9"></a><!-- doxytag: member="ccp4srs::Bond::length" ref="a3ebb971fa0af7886f076da460b4875e9" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype ccp4srs::Bond::length </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a28f3638c15b007dddaab637362635009"></a><!-- doxytag: member="ccp4srs::Bond::length_esd" ref="a28f3638c15b007dddaab637362635009" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype ccp4srs::Bond::length_esd </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a781542dae98140ea687a5d83a3e02e8e"></a><!-- doxytag: member="ccp4srs::Bond::makeCIFTags" ref="a781542dae98140ea687a5d83a3e02e8e" args="(mmdb::mmcif::PLoop mmCIFLoop)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Bond::makeCIFTags </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>mmCIFLoop</em>&#160;)</td>
+          <td><code> [static]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ae18a9e08399e96910028f01a376d41f0"></a><!-- doxytag: member="ccp4srs::Bond::order" ref="ae18a9e08399e96910028f01a376d41f0" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Bond::order </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a47ad8a18d4c0363dc1f04f3cfbc670ec"></a><!-- doxytag: member="ccp4srs::Bond::read_mem" ref="a47ad8a18d4c0363dc1f04f3cfbc670ec" args="(PMemIO memIO, int version, bool *Ok=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::Bond::read_mem </td>
+          <td>(</td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a24976c4962050d858ca00fa6f72684e2"></a><!-- doxytag: member="ccp4srs::Bond::readFromCIF" ref="a24976c4962050d858ca00fa6f72684e2" args="(mmdb::mmcif::PStruct mmCIFStruct, Container&lt; Atom &gt; &amp;atoms)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Bond::readFromCIF </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PStruct&#160;</td>
+          <td class="paramname"> <em>mmCIFStruct</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;&#160;</td>
+          <td class="paramname"> <em>atoms</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ac6a267f1cb4e7553d746537cf36e5ea3"></a><!-- doxytag: member="ccp4srs::Bond::readFromCIF_ccp4" ref="ac6a267f1cb4e7553d746537cf36e5ea3" args="(mmdb::mmcif::PLoop mmCIFLoop, int bondNo, Container&lt; Atom &gt; &amp;atoms)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Bond::readFromCIF_ccp4 </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>mmCIFLoop</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>bondNo</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;&#160;</td>
+          <td class="paramname"> <em>atoms</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a54c6291defa953cc5f5750b0f116719c"></a><!-- doxytag: member="ccp4srs::Bond::readFromCIF_rcsb" ref="a54c6291defa953cc5f5750b0f116719c" args="(mmdb::mmcif::PLoop mmCIFLoop, int bondNo, Container&lt; Atom &gt; &amp;atoms)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Bond::readFromCIF_rcsb </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>mmCIFLoop</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>bondNo</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;&#160;</td>
+          <td class="paramname"> <em>atoms</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aa44d448aa0181e6d51048beda35052f4"></a><!-- doxytag: member="ccp4srs::Bond::write_mem" ref="aa44d448aa0181e6d51048beda35052f4" args="(PMemIO memIO, int version)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Bond::write_mem </td>
+          <td>(</td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a89214f5f730f603bdd8dacea6317428f"></a><!-- doxytag: member="ccp4srs::Bond::writeToCIF" ref="a89214f5f730f603bdd8dacea6317428f" args="(mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID, Container&lt; Atom &gt; &amp;atoms)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Bond::writeToCIF </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>mmCIFLoop</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>monID</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;&#160;</td>
+          <td class="paramname"> <em>atoms</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Data Documentation</h2>
+<a class="anchor" id="ad359689c475101246c6c3061d31c2541"></a><!-- doxytag: member="ccp4srs::Bond::atom_1" ref="ad359689c475101246c6c3061d31c2541" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_bond.html#ad359689c475101246c6c3061d31c2541">ccp4srs::Bond::atom_1</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a277aee984c745dcdfd338f19e7df1e48"></a><!-- doxytag: member="ccp4srs::Bond::atom_2" ref="a277aee984c745dcdfd338f19e7df1e48" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_bond.html#a277aee984c745dcdfd338f19e7df1e48">ccp4srs::Bond::atom_2</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>ordinal numbers of bonded atoms [0,1,. </p>
+<p>] </p>
+
+</div>
+</div>
+<a class="anchor" id="a43513fb523b43f7f5f407a0bae151a95"></a><!-- doxytag: member="ccp4srs::Bond::bond_length" ref="a43513fb523b43f7f5f407a0bae151a95" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_bond.html#a43513fb523b43f7f5f407a0bae151a95">ccp4srs::Bond::bond_length</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+<p>bond length in A; set to 0.0 if not provided </p>
+
+</div>
+</div>
+<a class="anchor" id="af438937a89d3cb3c7f2342ca6f38301c"></a><!-- doxytag: member="ccp4srs::Bond::bond_length_esd" ref="af438937a89d3cb3c7f2342ca6f38301c" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_bond.html#af438937a89d3cb3c7f2342ca6f38301c">ccp4srs::Bond::bond_length_esd</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+<p>bond length esd in A; set to 0.0 if not provided </p>
+
+</div>
+</div>
+<a class="anchor" id="ac6365bacbc07dd7cf914b6c7ad6cd5d7"></a><!-- doxytag: member="ccp4srs::Bond::bond_order" ref="ac6365bacbc07dd7cf914b6c7ad6cd5d7" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_bond.html#ac6365bacbc07dd7cf914b6c7ad6cd5d7">ccp4srs::Bond::bond_order</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>bond order </p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following files:<ul>
+<li>src/<a class="el" href="ccp4srs__bond_8h_source.html">ccp4srs_bond.h</a></li>
+<li>src/<a class="el" href="ccp4srs__bond_8cpp.html">ccp4srs_bond.cpp</a></li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
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+        name="MSearchResults" id="MSearchResults">
+</iframe>
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+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_chem-members.html ccp4srs/doc-html/html/classccp4srs_1_1_chem-members.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_chem-members.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_chem-members.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,132 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
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+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>ccp4srs::Chem Member List</h1>  </div>
+</div>
+<div class="contents">
+This is the complete list of members for <a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a>, including all inherited members.<table>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#acada705ca803ac2b68bb2c787a83fcb1">addHydrogens</a>(mmdb::PResidue R, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#ac1ae2d0c6f7f79b3f5b02a6a3b082b81">addHydrogens</a>(mmdb::PChain chain, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a75fb480c106432f52d7301eae93d2942">addHydrogens</a>(mmdb::PModel model, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a45ea7718ea3dea244ba51f6f318d3623">addHydrogens</a>(mmdb::PManager MMDB, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a0c37b44fe77e9f171d5f40281a6e82ae">Base</a>()</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#ab5d4ff0f43b6785dc2c3cec72d4b8eec">CalcHBonds</a>(mmdb::PPResidue Res1, int nres1, mmdb::PPResidue Res2, int nres2, RPAtomPair HBond, int &amp;nHBonds, RPAtomPair SBridge, int &amp;nSBridges, mmdb::io::PFile structFile=NULL, mmdb::pstr altLoc=NULL, bool ignoreNegSigOcc=false)</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a6ca2d1c22ede07e88978645ab6a5887e">Chem</a>()</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#ab67f138edc7ae19791be69dde485c719">freeMemory</a>()</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#af9a1789b20b43e97a8eb6a56b4ef32c4">getAtNames</a>(int entryNo, mmdb::PAtomName AtName, int &amp;nAtoms, int &amp;nH)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#afbe234eef9c84fde630b72fbcfe27946">getAtNames</a>(mmdb::io::PFile structFile, int entryNo, mmdb::PAtomName AtName, int &amp;nAtoms, int &amp;nH)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a7e47408dacc9bd80de046504e235cc06">getAtoms</a>(mmdb::cpstr entryID, int &amp;nNonHAtoms, mmdb::PAtomName NonHAtName, int &amp;nHAtoms, mmdb::PAtomName HAtName, mmdb::ivector Hconnect, mmdb::ivector Elem, mmdb::ivector Chiral)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a8bb61486d7dd2df0566b8e3a1c7f1c89">getBonds</a>(mmdb::cpstr entryID, mmdb::ivector nBonds, mmdb::imatrix bondPair, int &amp;nAtoms, int maxNAtoms, int maxNBonds)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a301341ad4a91bf6cc4e7641efeb56309">getEnergyTypes</a>(mmdb::PResidue R, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#acb540af5e9036d7765dfdaa762fb6b2f">getEnergyTypes</a>(mmdb::PPResidue R, int nRes, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a6993968f40984c210ffad03588321d70">getEnergyTypes</a>(mmdb::PChain chain, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a6a9f477d2484e2e2d71328934432e1f8">getEnergyTypes</a>(mmdb::PModel model, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a227201ea4eedc8464c764dd015b7b190">getEnergyTypes</a>(mmdb::PManager MMDB, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a57b706684f3e84c741099ff904e01152">getEntryNo</a>(mmdb::cpstr entryID)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a17b78139832b00d7025236171ab31b7e">getGraph</a>(mmdb::io::PFile graphFile, mmdb::math::RPGraph G)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a8421066e4a9117cd380ff4362c355986">getGraph</a>(mmdb::io::PFile graphFile, int entryNo, mmdb::math::RPGraph G, int Hflag)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#af00d1ee772d045c048aa292457755b50">getGraph</a>(mmdb::io::PFile graphFile, mmdb::math::RPGraph G, int Hflag)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a418f3d4d079e0c4b93ebc6fff1fd0639">getGraph</a>(int entryNo, mmdb::math::RPGraph G, int Hflag)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a1f9dd08ea6c39fc0bb0a3885e6b3efac">getGraph</a>(mmdb::cpstr entryID, mmdb::math::RPGraph G, int Hflag)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a656b776b70ead2f8346b352b3bd1311e">getGraphFile</a>()</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a88c88924e247250d08cc4795b345c66a">getHetInfo</a>(mmdb::cpstr entryID, mmdb::pstr Formula, mmdb::pstr Hname, mmdb::pstr Hsynonym, mmdb::pstr Hcharge, mmdb::PAtomName &amp;ClinkAtom, mmdb::PElement &amp;ClinkEle, mmdb::PAtomName &amp;SlinkAtom, mmdb::PElement &amp;SlinkEle, int &amp;nLeavingAtoms)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#affa058db2078bc7835e9c78ca3bdde81">getIndex</a>(mmdb::cpstr entryID)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a399ff3d49a14dd3bb8250058f6452f4f">getIndex</a>(int n)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a339033984c68dd221cd6db184b734694">getMonomer</a>(mmdb::cpstr entryID)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a6f3f6564a30198bfe82215bceb6806e2">getMonomer</a>(int entryNo, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#ad25bf7474ec0574a39081ec5eeaefc5b">getMonomer</a>(mmdb::cpstr entryID, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a646d2c4349be4a740f2121dfd2091150">getNofAtoms</a>(mmdb::cpstr entryID)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a025a5622f0bfb83808cdad7cbf7af974">getNofAtoms</a>(int entryNo)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#af0653379d9db757dcc64c44c0e9ce070">getNofAtoms</a>(int entryNo, int &amp;nNonHAtoms, int &amp;nHAtoms)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#ac5481a8eeeb26ead06d7df61f605dac9">getPath</a>(mmdb::pstr &amp;S, mmdb::cpstr FName)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a03eac100b52d1f2d2d13981799f928bb">getStructFile</a>()</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#ada41928311fa3ba94bcb48a1ebf4b4df">index</a></td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a9fb463b8df4034fefb6e136ab56d135b">init_base</a>()</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a7ed4ac373981270bc1af2b8cc99b461d">init_chem</a>()</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#ae95af9ff2fb5c9d0edb437be3bcbe016">loadIndex</a>(mmdb::cpstr srsPath)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a663ef26d53b80f6c8b1f9c9cdeb70d2c">loadStructure</a>(mmdb::cpstr entryID)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#ad60a617bc151e054eb306e8c6bf592f4">makeBonds</a>(mmdb::PResidue R, mmdb::pstr altLoc, mmdb::io::PFile structFile, PDASelHnds selHandles, bool ignoreNegSigOcc)</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#aa32277562470e13dfe292f01bc269c17">maxDAAcos</a></td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a6655092e23b55ff3d6465a60101c135d">maxDAdist</a></td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#aa5d2547bfa92f55c755aa57fce717a65">maxDDAcos</a></td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a7408580f10d8868ae368f3faa1253577">maxDHAcos</a></td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a71cea07257deb2795443e04e07ee4bed">maxHAAcos</a></td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#ada14781ad5390841304d35f262705c57">maxHAdist2</a></td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#aeeb0e6bc6cc2e1a3f5ce78d59d8b496d">maxSBdist</a></td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#adf128b2adae954f6b25463c70ede5a58">memIO</a></td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a2e63b74dcf71dbf8583a64342de3848c">minDAdist</a></td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#aeb551e05e822e5eb3673aba1fa85bda6">n_entries</a>()</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a863fd5090d78f3bada7f351dd2f33859">nEntries</a></td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#af3caa0403ce8a1c4489948fa4fc62b0c">srsDir</a></td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#ad18087156761086530c1f01f3078f869">srsVersion</a></td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a6d15803597f5a515c19848a5e8dbe164">unloadStructure</a>(mmdb::cpstr entryID)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a2c46b036cb9701ac6a2d22fcec3fbdcf">~Base</a>()</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a939cae4367e5e32664e60c725fabafbe">~Chem</a>()</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+</table></div>
+<!--- window showing the filter options -->
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+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
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diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_chem.html ccp4srs/doc-html/html/classccp4srs_1_1_chem.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_chem.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_chem.html	2014-09-09 21:34:12.000000000 -0700
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: ccp4srs::Chem Class Reference</title>
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+<script type="text/javaScript" src="search/search.js"></script>
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+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
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+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="navpath">
+    <ul>
+      <li><a class="el" href="namespaceccp4srs.html">ccp4srs</a>      </li>
+      <li><a class="el" href="classccp4srs_1_1_chem.html">Chem</a>      </li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pro-methods">Protected Member Functions</a> &#124;
+<a href="#pro-attribs">Protected Attributes</a>  </div>
+  <div class="headertitle">
+<h1>ccp4srs::Chem Class Reference</h1>  </div>
+</div>
+<div class="contents">
+<!-- doxytag: class="ccp4srs::Chem" --><!-- doxytag: inherits="ccp4srs::Base" -->
+<p><code>#include &lt;<a class="el" href="ccp4srs__chem_8h_source.html">ccp4srs_chem.h</a>&gt;</code></p>
+<!-- startSectionHeader --><div class="dynheader">
+Inheritance diagram for ccp4srs::Chem:<!-- endSectionHeader --></div>
+<!-- startSectionSummary --><!-- endSectionSummary --><!-- startSectionContent --><div class="dyncontent">
+<div class="center"><img src="classccp4srs_1_1_chem__inherit__graph.png" border="0" usemap="#ccp4srs_1_1_chem_inherit__map" alt="Inheritance graph"/></div>
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+<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center><!-- endSectionContent --></div>
+
+<p><a href="classccp4srs_1_1_chem-members.html">List of all members.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chem.html#a6ca2d1c22ede07e88978645ab6a5887e">Chem</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chem.html#a939cae4367e5e32664e60c725fabafbe">~Chem</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">CCP4SRS_RC</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chem.html#a301341ad4a91bf6cc4e7641efeb56309">getEnergyTypes</a> (mmdb::PResidue R, mmdb::io::PFile structFile)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">CCP4SRS_RC</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chem.html#acb540af5e9036d7765dfdaa762fb6b2f">getEnergyTypes</a> (mmdb::PPResidue R, int nRes, mmdb::io::PFile structFile)</td></tr>
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+          <td class="memname">ccp4srs::Chem::Chem </td>
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+          <td class="paramname"> <em>structFile</em>&#160;</td>
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+          <td class="paramtype">mmdb::io::PFile&#160;</td>
+          <td class="paramname"> <em>structFile</em>&#160;</td>
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+          <td class="paramname"> <em>structFile</em>&#160;</td>
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+          <td class="paramtype">RPAtomPair&#160;</td>
+          <td class="paramname"> <em>SBridge</em>, </td>
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+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a7ed4ac373981270bc1af2b8cc99b461d"></a><!-- doxytag: member="ccp4srs::Chem::init_chem" ref="a7ed4ac373981270bc1af2b8cc99b461d" args="()" -->
+<div class="memitem">
+<div class="memproto">
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+        <tr>
+          <td class="memname">void ccp4srs::Chem::init_chem </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ad60a617bc151e054eb306e8c6bf592f4"></a><!-- doxytag: member="ccp4srs::Chem::makeBonds" ref="ad60a617bc151e054eb306e8c6bf592f4" args="(mmdb::PResidue R, mmdb::pstr altLoc, mmdb::io::PFile structFile, PDASelHnds selHandles, bool ignoreNegSigOcc)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">CCP4SRS_RC</a> ccp4srs::Chem::makeBonds </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::PResidue&#160;</td>
+          <td class="paramname"> <em>R</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::pstr&#160;</td>
+          <td class="paramname"> <em>altLoc</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::io::PFile&#160;</td>
+          <td class="paramname"> <em>structFile</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">PDASelHnds&#160;</td>
+          <td class="paramname"> <em>selHandles</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool&#160;</td>
+          <td class="paramname"> <em>ignoreNegSigOcc</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Data Documentation</h2>
+<a class="anchor" id="aa32277562470e13dfe292f01bc269c17"></a><!-- doxytag: member="ccp4srs::Chem::maxDAAcos" ref="aa32277562470e13dfe292f01bc269c17" args="" -->
+<div class="memitem">
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+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_chem.html#aa32277562470e13dfe292f01bc269c17">ccp4srs::Chem::maxDAAcos</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
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+</div>
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+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_chem.html#a6655092e23b55ff3d6465a60101c135d">ccp4srs::Chem::maxDAdist</a><code> [protected]</code></td>
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+      </table>
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+<div class="memdoc">
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+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_chem.html#aa5d2547bfa92f55c755aa57fce717a65">ccp4srs::Chem::maxDDAcos</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
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+<a class="anchor" id="a7408580f10d8868ae368f3faa1253577"></a><!-- doxytag: member="ccp4srs::Chem::maxDHAcos" ref="a7408580f10d8868ae368f3faa1253577" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
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+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a71cea07257deb2795443e04e07ee4bed"></a><!-- doxytag: member="ccp4srs::Chem::maxHAAcos" ref="a71cea07257deb2795443e04e07ee4bed" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_chem.html#a71cea07257deb2795443e04e07ee4bed">ccp4srs::Chem::maxHAAcos</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ada14781ad5390841304d35f262705c57"></a><!-- doxytag: member="ccp4srs::Chem::maxHAdist2" ref="ada14781ad5390841304d35f262705c57" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_chem.html#ada14781ad5390841304d35f262705c57">ccp4srs::Chem::maxHAdist2</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aeeb0e6bc6cc2e1a3f5ce78d59d8b496d"></a><!-- doxytag: member="ccp4srs::Chem::maxSBdist" ref="aeeb0e6bc6cc2e1a3f5ce78d59d8b496d" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_chem.html#aeeb0e6bc6cc2e1a3f5ce78d59d8b496d">ccp4srs::Chem::maxSBdist</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a2e63b74dcf71dbf8583a64342de3848c"></a><!-- doxytag: member="ccp4srs::Chem::minDAdist" ref="a2e63b74dcf71dbf8583a64342de3848c" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_chem.html#a2e63b74dcf71dbf8583a64342de3848c">ccp4srs::Chem::minDAdist</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following files:<ul>
+<li>src/<a class="el" href="ccp4srs__chem_8h_source.html">ccp4srs_chem.h</a></li>
+<li>src/<a class="el" href="ccp4srs__chem_8cpp.html">ccp4srs_chem.cpp</a></li>
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+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
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+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
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+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
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+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
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+               onmouseout="return searchBox.OnSearchSelectHide()"
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+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>ccp4srs::ChiCenter Member List</h1>  </div>
+</div>
+<div class="contents">
+This is the complete list of members for <a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a>, including all inherited members.<table>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chi_center.html#ae27490ac46e2f3904ee230fe0c5b80af">atom1</a>()</td><td><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chi_center.html#a5e1600b63a2e92494176dc328c6fc8a6">atom2</a>()</td><td><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chi_center.html#ac668dea1c66f203a26e46a1c87b37760">atom3</a>()</td><td><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chi_center.html#a246c77c96df7921a1d1c989de4a50f8f">atom_1</a></td><td><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chi_center.html#aa80d6d7fbec0a8497b62af13b16e2a12">atom_2</a></td><td><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chi_center.html#a2b249cab1cc7c2ea80ea9259914fcd34">atom_3</a></td><td><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chi_center.html#a5fe75db982419a5d7f3c3ff8b2e41f46">atom_center</a></td><td><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chi_center.html#a0264f7a5c26c795bda84de7b233e70ab">center</a>()</td><td><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chi_center.html#a536462552b25777be443867ec6a28b48">ChiCenter</a>()</td><td><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chi_center.html#ac2387dc7a46c0c4451bcd08e23b25ae5">chicenter_id</a></td><td><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chi_center.html#ab3dc0fe1813d51055e829586a27ddd15">copy</a>(PChiCenter chicenter, mmdb::ivector anmatch=NULL)</td><td><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chi_center.html#a1aa5ee605cdc3756abcb075279eeb8af">get_chirality</a>()</td><td><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chi_center.html#a9bd5958f4cb3519a6a745d1db16b135b">id</a>()</td><td><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chi_center.html#a93d09528c86718358137aaf48c1a8ce1">makeCIFTags</a>(mmdb::mmcif::PLoop mmCIFLoop)</td><td><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td><td><code> [static]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chi_center.html#a64588b20c5010e22ad5d571343a7e6d0">read_mem</a>(PMemIO memIO, int version, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chi_center.html#a8c038c3d35ef4effbe5e02db4cdf9f88">readFromCIF</a>(mmdb::mmcif::PLoop mmCIFLoop, int chiNo, Container&lt; Atom &gt; &amp;atoms)</td><td><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chi_center.html#a17574c6830e27efde72575acdf154d80">sign</a>()</td><td><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chi_center.html#a6fc568ab5bcd12bc56b58d6b9f2933a1">volume_sign</a></td><td><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chi_center.html#ac36306727683e319c2282b936bd11d37">write_mem</a>(PMemIO memIO, int version)</td><td><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chi_center.html#a04b85d396a4ebc8d5163d3184206329d">writeToCIF</a>(mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID, Container&lt; Atom &gt; &amp;atoms)</td><td><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chi_center.html#a051ae00e2cdb590a2dd7f4899c264cb9">~ChiCenter</a>()</td><td><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></td><td><code> [virtual]</code></td></tr>
+</table></div>
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+
+<!-- iframe showing the search results (closed by default) -->
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+        name="MSearchResults" id="MSearchResults">
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+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
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diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_chi_center.html ccp4srs/doc-html/html/classccp4srs_1_1_chi_center.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_chi_center.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_chi_center.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,531 @@
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+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: ccp4srs::ChiCenter Class Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
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+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
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+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="navpath">
+    <ul>
+      <li><a class="el" href="namespaceccp4srs.html">ccp4srs</a>      </li>
+      <li><a class="el" href="classccp4srs_1_1_chi_center.html">ChiCenter</a>      </li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pub-static-methods">Static Public Member Functions</a> &#124;
+<a href="#pro-attribs">Protected Attributes</a>  </div>
+  <div class="headertitle">
+<h1>ccp4srs::ChiCenter Class Reference</h1>  </div>
+</div>
+<div class="contents">
+<!-- doxytag: class="ccp4srs::ChiCenter" -->
+<p><code>#include &lt;<a class="el" href="ccp4srs__chicenter_8h_source.html">ccp4srs_chicenter.h</a>&gt;</code></p>
+
+<p><a href="classccp4srs_1_1_chi_center-members.html">List of all members.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chi_center.html#a536462552b25777be443867ec6a28b48">ChiCenter</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chi_center.html#a051ae00e2cdb590a2dd7f4899c264cb9">~ChiCenter</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chi_center.html#a9bd5958f4cb3519a6a745d1db16b135b">id</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chi_center.html#a0264f7a5c26c795bda84de7b233e70ab">center</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chi_center.html#ae27490ac46e2f3904ee230fe0c5b80af">atom1</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chi_center.html#a5e1600b63a2e92494176dc328c6fc8a6">atom2</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chi_center.html#ac668dea1c66f203a26e46a1c87b37760">atom3</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chi_center.html#a17574c6830e27efde72575acdf154d80">sign</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">char&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chi_center.html#a1aa5ee605cdc3756abcb075279eeb8af">get_chirality</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chi_center.html#a8c038c3d35ef4effbe5e02db4cdf9f88">readFromCIF</a> (mmdb::mmcif::PLoop mmCIFLoop, int chiNo, <a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;atoms)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chi_center.html#a04b85d396a4ebc8d5163d3184206329d">writeToCIF</a> (mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID, <a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;atoms)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chi_center.html#ac36306727683e319c2282b936bd11d37">write_mem</a> (PMemIO memIO, int version)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chi_center.html#a64588b20c5010e22ad5d571343a7e6d0">read_mem</a> (PMemIO memIO, int version, bool *Ok=NULL)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chi_center.html#ab3dc0fe1813d51055e829586a27ddd15">copy</a> (PChiCenter chicenter, mmdb::ivector anmatch=NULL)</td></tr>
+<tr><td colspan="2"><h2><a name="pub-static-methods"></a>
+Static Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">static void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chi_center.html#a93d09528c86718358137aaf48c1a8ce1">makeCIFTags</a> (mmdb::mmcif::PLoop mmCIFLoop)</td></tr>
+<tr><td colspan="2"><h2><a name="pro-attribs"></a>
+Protected Attributes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespaceccp4srs.html#ae91f970060d687d02ccfb78cbd6222bb">ChiCenterID</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chi_center.html#ac2387dc7a46c0c4451bcd08e23b25ae5">chicenter_id</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">chiral center id  <a href="#ac2387dc7a46c0c4451bcd08e23b25ae5"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chi_center.html#a5fe75db982419a5d7f3c3ff8b2e41f46">atom_center</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">chiral center atom [0,1,...]  <a href="#a5fe75db982419a5d7f3c3ff8b2e41f46"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chi_center.html#a246c77c96df7921a1d1c989de4a50f8f">atom_1</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chi_center.html#aa80d6d7fbec0a8497b62af13b16e2a12">atom_2</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">ordinal numbers of atoms that  <a href="#aa80d6d7fbec0a8497b62af13b16e2a12"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chi_center.html#a2b249cab1cc7c2ea80ea9259914fcd34">atom_3</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">form the center [0,1,...]  <a href="#a2b249cab1cc7c2ea80ea9259914fcd34"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_chi_center.html#a6fc568ab5bcd12bc56b58d6b9f2933a1">volume_sign</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">chirality  <a href="#a6fc568ab5bcd12bc56b58d6b9f2933a1"></a><br/></td></tr>
+</table>
+<hr/><h2>Constructor &amp; Destructor Documentation</h2>
+<a class="anchor" id="a536462552b25777be443867ec6a28b48"></a><!-- doxytag: member="ccp4srs::ChiCenter::ChiCenter" ref="a536462552b25777be443867ec6a28b48" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::ChiCenter::ChiCenter </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a051ae00e2cdb590a2dd7f4899c264cb9"></a><!-- doxytag: member="ccp4srs::ChiCenter::~ChiCenter" ref="a051ae00e2cdb590a2dd7f4899c264cb9" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::ChiCenter::~ChiCenter </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [virtual]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Function Documentation</h2>
+<a class="anchor" id="ae27490ac46e2f3904ee230fe0c5b80af"></a><!-- doxytag: member="ccp4srs::ChiCenter::atom1" ref="ae27490ac46e2f3904ee230fe0c5b80af" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::ChiCenter::atom1 </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a5e1600b63a2e92494176dc328c6fc8a6"></a><!-- doxytag: member="ccp4srs::ChiCenter::atom2" ref="a5e1600b63a2e92494176dc328c6fc8a6" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::ChiCenter::atom2 </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ac668dea1c66f203a26e46a1c87b37760"></a><!-- doxytag: member="ccp4srs::ChiCenter::atom3" ref="ac668dea1c66f203a26e46a1c87b37760" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::ChiCenter::atom3 </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a0264f7a5c26c795bda84de7b233e70ab"></a><!-- doxytag: member="ccp4srs::ChiCenter::center" ref="a0264f7a5c26c795bda84de7b233e70ab" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::ChiCenter::center </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ab3dc0fe1813d51055e829586a27ddd15"></a><!-- doxytag: member="ccp4srs::ChiCenter::copy" ref="ab3dc0fe1813d51055e829586a27ddd15" args="(PChiCenter chicenter, mmdb::ivector anmatch=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::ChiCenter::copy </td>
+          <td>(</td>
+          <td class="paramtype">PChiCenter&#160;</td>
+          <td class="paramname"> <em>chicenter</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::ivector&#160;</td>
+          <td class="paramname"> <em>anmatch</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a1aa5ee605cdc3756abcb075279eeb8af"></a><!-- doxytag: member="ccp4srs::ChiCenter::get_chirality" ref="a1aa5ee605cdc3756abcb075279eeb8af" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">char ccp4srs::ChiCenter::get_chirality </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a9bd5958f4cb3519a6a745d1db16b135b"></a><!-- doxytag: member="ccp4srs::ChiCenter::id" ref="a9bd5958f4cb3519a6a745d1db16b135b" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::cpstr ccp4srs::ChiCenter::id </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a93d09528c86718358137aaf48c1a8ce1"></a><!-- doxytag: member="ccp4srs::ChiCenter::makeCIFTags" ref="a93d09528c86718358137aaf48c1a8ce1" args="(mmdb::mmcif::PLoop mmCIFLoop)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::ChiCenter::makeCIFTags </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>mmCIFLoop</em>&#160;)</td>
+          <td><code> [static]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a64588b20c5010e22ad5d571343a7e6d0"></a><!-- doxytag: member="ccp4srs::ChiCenter::read_mem" ref="a64588b20c5010e22ad5d571343a7e6d0" args="(PMemIO memIO, int version, bool *Ok=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::ChiCenter::read_mem </td>
+          <td>(</td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a8c038c3d35ef4effbe5e02db4cdf9f88"></a><!-- doxytag: member="ccp4srs::ChiCenter::readFromCIF" ref="a8c038c3d35ef4effbe5e02db4cdf9f88" args="(mmdb::mmcif::PLoop mmCIFLoop, int chiNo, Container&lt; Atom &gt; &amp;atoms)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::ChiCenter::readFromCIF </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>mmCIFLoop</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>chiNo</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;&#160;</td>
+          <td class="paramname"> <em>atoms</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a17574c6830e27efde72575acdf154d80"></a><!-- doxytag: member="ccp4srs::ChiCenter::sign" ref="a17574c6830e27efde72575acdf154d80" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::ChiCenter::sign </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ac36306727683e319c2282b936bd11d37"></a><!-- doxytag: member="ccp4srs::ChiCenter::write_mem" ref="ac36306727683e319c2282b936bd11d37" args="(PMemIO memIO, int version)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::ChiCenter::write_mem </td>
+          <td>(</td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a04b85d396a4ebc8d5163d3184206329d"></a><!-- doxytag: member="ccp4srs::ChiCenter::writeToCIF" ref="a04b85d396a4ebc8d5163d3184206329d" args="(mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID, Container&lt; Atom &gt; &amp;atoms)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::ChiCenter::writeToCIF </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>mmCIFLoop</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>monID</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;&#160;</td>
+          <td class="paramname"> <em>atoms</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Data Documentation</h2>
+<a class="anchor" id="a246c77c96df7921a1d1c989de4a50f8f"></a><!-- doxytag: member="ccp4srs::ChiCenter::atom_1" ref="a246c77c96df7921a1d1c989de4a50f8f" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_chi_center.html#a246c77c96df7921a1d1c989de4a50f8f">ccp4srs::ChiCenter::atom_1</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aa80d6d7fbec0a8497b62af13b16e2a12"></a><!-- doxytag: member="ccp4srs::ChiCenter::atom_2" ref="aa80d6d7fbec0a8497b62af13b16e2a12" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_chi_center.html#aa80d6d7fbec0a8497b62af13b16e2a12">ccp4srs::ChiCenter::atom_2</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>ordinal numbers of atoms that </p>
+
+</div>
+</div>
+<a class="anchor" id="a2b249cab1cc7c2ea80ea9259914fcd34"></a><!-- doxytag: member="ccp4srs::ChiCenter::atom_3" ref="a2b249cab1cc7c2ea80ea9259914fcd34" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_chi_center.html#a2b249cab1cc7c2ea80ea9259914fcd34">ccp4srs::ChiCenter::atom_3</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>form the center [0,1,...] </p>
+
+</div>
+</div>
+<a class="anchor" id="a5fe75db982419a5d7f3c3ff8b2e41f46"></a><!-- doxytag: member="ccp4srs::ChiCenter::atom_center" ref="a5fe75db982419a5d7f3c3ff8b2e41f46" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_chi_center.html#a5fe75db982419a5d7f3c3ff8b2e41f46">ccp4srs::ChiCenter::atom_center</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>chiral center atom [0,1,...] </p>
+
+</div>
+</div>
+<a class="anchor" id="ac2387dc7a46c0c4451bcd08e23b25ae5"></a><!-- doxytag: member="ccp4srs::ChiCenter::chicenter_id" ref="ac2387dc7a46c0c4451bcd08e23b25ae5" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="namespaceccp4srs.html#ae91f970060d687d02ccfb78cbd6222bb">ChiCenterID</a> <a class="el" href="classccp4srs_1_1_chi_center.html#ac2387dc7a46c0c4451bcd08e23b25ae5">ccp4srs::ChiCenter::chicenter_id</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>chiral center id </p>
+
+</div>
+</div>
+<a class="anchor" id="a6fc568ab5bcd12bc56b58d6b9f2933a1"></a><!-- doxytag: member="ccp4srs::ChiCenter::volume_sign" ref="a6fc568ab5bcd12bc56b58d6b9f2933a1" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_chi_center.html#a6fc568ab5bcd12bc56b58d6b9f2933a1">ccp4srs::ChiCenter::volume_sign</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>chirality </p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following files:<ul>
+<li>src/<a class="el" href="ccp4srs__chicenter_8h_source.html">ccp4srs_chicenter.h</a></li>
+<li>src/<a class="el" href="ccp4srs__chicenter_8cpp.html">ccp4srs_chicenter.cpp</a></li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
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+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_container-members.html ccp4srs/doc-html/html/classccp4srs_1_1_container-members.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_container-members.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_container-members.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,86 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
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+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>ccp4srs::Container&lt; T &gt; Member List</h1>  </div>
+</div>
+<div class="contents">
+This is the complete list of members for <a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container&lt; T &gt;</a>, including all inherited members.<table>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_container.html#a6caf1893b780f2cf196c85ee141baf18">add</a>(T *obj)</td><td><a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container&lt; T &gt;</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_container.html#ae9929d576289dd2313aaf4b2d9c377e9">at</a>(int pos)</td><td><a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container&lt; T &gt;</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_container.html#acdff89dd6d441d731b517565021e3881">Container</a>()</td><td><a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container&lt; T &gt;</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_container.html#aeed888e25348f83a53021beaa21a0b1e">empty</a>()</td><td><a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container&lt; T &gt;</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_container.html#a6afe8d51f68e07697d7362464e433cac">index</a>(mmdb::cpstr id)</td><td><a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container&lt; T &gt;</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748">n_objects</a></td><td><a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container&lt; T &gt;</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_container.html#abbc5e6eeb9ea4d37b8d2025892ebd9ff">numberOf</a>()</td><td><a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container&lt; T &gt;</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_container.html#a25a4ad3660f2ef6760c949be2c1372a8">object</a></td><td><a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container&lt; T &gt;</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_container.html#a9f42bc8ec160490ba2dd8d7a8eeae15e">read_mem</a>(PMemIO memIO, int version, bool *Ok)</td><td><a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container&lt; T &gt;</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_container.html#ae3d1a80023e670f0828814b887af5dc8">write_mem</a>(PMemIO memIO, int version)</td><td><a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container&lt; T &gt;</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_container.html#a831fc7371918ff96de32b96c35fe31a2">~Container</a>()</td><td><a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container&lt; T &gt;</a></td><td><code> [inline, virtual]</code></td></tr>
+</table></div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
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+
+<!-- iframe showing the search results (closed by default) -->
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+        name="MSearchResults" id="MSearchResults">
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+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_container.html ccp4srs/doc-html/html/classccp4srs_1_1_container.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_container.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_container.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,336 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: ccp4srs::Container&lt; T &gt; Class Template Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
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+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
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+--></script>
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+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
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+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
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+          <img id="MSearchSelect" src="search/mag_sel.png"
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+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
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+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
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+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
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+      <li><a class="el" href="namespaceccp4srs.html">ccp4srs</a>      </li>
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+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pro-attribs">Protected Attributes</a>  </div>
+  <div class="headertitle">
+<h1>ccp4srs::Container&lt; T &gt; Class Template Reference</h1>  </div>
+</div>
+<div class="contents">
+<!-- doxytag: class="ccp4srs::Container" -->
+<p><code>#include &lt;<a class="el" href="ccp4srs__container_8h_source.html">ccp4srs_container.h</a>&gt;</code></p>
+
+<p><a href="classccp4srs_1_1_container-members.html">List of all members.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_container.html#acdff89dd6d441d731b517565021e3881">Container</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_container.html#a831fc7371918ff96de32b96c35fe31a2">~Container</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_container.html#aeed888e25348f83a53021beaa21a0b1e">empty</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_container.html#abbc5e6eeb9ea4d37b8d2025892ebd9ff">numberOf</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">T *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_container.html#ae9929d576289dd2313aaf4b2d9c377e9">at</a> (int pos)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_container.html#a6afe8d51f68e07697d7362464e433cac">index</a> (mmdb::cpstr id)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_container.html#a6caf1893b780f2cf196c85ee141baf18">add</a> (T *obj)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_container.html#ae3d1a80023e670f0828814b887af5dc8">write_mem</a> (PMemIO memIO, int version)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_container.html#a9f42bc8ec160490ba2dd8d7a8eeae15e">read_mem</a> (PMemIO memIO, int version, bool *Ok)</td></tr>
+<tr><td colspan="2"><h2><a name="pro-attribs"></a>
+Protected Attributes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748">n_objects</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">T **&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_container.html#a25a4ad3660f2ef6760c949be2c1372a8">object</a></td></tr>
+</table>
+<h3>template&lt;class T&gt;<br/>
+ class ccp4srs::Container&lt; T &gt;</h3>
+
+<hr/><h2>Constructor &amp; Destructor Documentation</h2>
+<a class="anchor" id="acdff89dd6d441d731b517565021e3881"></a><!-- doxytag: member="ccp4srs::Container::Container" ref="acdff89dd6d441d731b517565021e3881" args="()" -->
+<div class="memitem">
+<div class="memproto">
+<div class="memtemplate">
+template&lt;class T&gt; </div>
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container</a>&lt; T &gt;::<a class="el" href="classccp4srs_1_1_container.html">Container</a> </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a831fc7371918ff96de32b96c35fe31a2"></a><!-- doxytag: member="ccp4srs::Container::~Container" ref="a831fc7371918ff96de32b96c35fe31a2" args="()" -->
+<div class="memitem">
+<div class="memproto">
+<div class="memtemplate">
+template&lt;class T&gt; </div>
+      <table class="memname">
+        <tr>
+          <td class="memname">virtual <a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container</a>&lt; T &gt;::~<a class="el" href="classccp4srs_1_1_container.html">Container</a> </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline, virtual]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Function Documentation</h2>
+<a class="anchor" id="a6caf1893b780f2cf196c85ee141baf18"></a><!-- doxytag: member="ccp4srs::Container::add" ref="a6caf1893b780f2cf196c85ee141baf18" args="(T *obj)" -->
+<div class="memitem">
+<div class="memproto">
+<div class="memtemplate">
+template&lt;class T&gt; </div>
+      <table class="memname">
+        <tr>
+          <td class="memname">void <a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container</a>&lt; T &gt;::add </td>
+          <td>(</td>
+          <td class="paramtype">T *&#160;</td>
+          <td class="paramname"> <em>obj</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ae9929d576289dd2313aaf4b2d9c377e9"></a><!-- doxytag: member="ccp4srs::Container::at" ref="ae9929d576289dd2313aaf4b2d9c377e9" args="(int pos)" -->
+<div class="memitem">
+<div class="memproto">
+<div class="memtemplate">
+template&lt;class T&gt; </div>
+      <table class="memname">
+        <tr>
+          <td class="memname">T* <a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container</a>&lt; T &gt;::at </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>pos</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aeed888e25348f83a53021beaa21a0b1e"></a><!-- doxytag: member="ccp4srs::Container::empty" ref="aeed888e25348f83a53021beaa21a0b1e" args="()" -->
+<div class="memitem">
+<div class="memproto">
+<div class="memtemplate">
+template&lt;class T&gt; </div>
+      <table class="memname">
+        <tr>
+          <td class="memname">void <a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container</a>&lt; T &gt;::empty </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a6afe8d51f68e07697d7362464e433cac"></a><!-- doxytag: member="ccp4srs::Container::index" ref="a6afe8d51f68e07697d7362464e433cac" args="(mmdb::cpstr id)" -->
+<div class="memitem">
+<div class="memproto">
+<div class="memtemplate">
+template&lt;class T&gt; </div>
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container</a>&lt; T &gt;::index </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>id</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="abbc5e6eeb9ea4d37b8d2025892ebd9ff"></a><!-- doxytag: member="ccp4srs::Container::numberOf" ref="abbc5e6eeb9ea4d37b8d2025892ebd9ff" args="()" -->
+<div class="memitem">
+<div class="memproto">
+<div class="memtemplate">
+template&lt;class T&gt; </div>
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container</a>&lt; T &gt;::numberOf </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a9f42bc8ec160490ba2dd8d7a8eeae15e"></a><!-- doxytag: member="ccp4srs::Container::read_mem" ref="a9f42bc8ec160490ba2dd8d7a8eeae15e" args="(PMemIO memIO, int version, bool *Ok)" -->
+<div class="memitem">
+<div class="memproto">
+<div class="memtemplate">
+template&lt;class T&gt; </div>
+      <table class="memname">
+        <tr>
+          <td class="memname">bool <a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container</a>&lt; T &gt;::read_mem </td>
+          <td>(</td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ae3d1a80023e670f0828814b887af5dc8"></a><!-- doxytag: member="ccp4srs::Container::write_mem" ref="ae3d1a80023e670f0828814b887af5dc8" args="(PMemIO memIO, int version)" -->
+<div class="memitem">
+<div class="memproto">
+<div class="memtemplate">
+template&lt;class T&gt; </div>
+      <table class="memname">
+        <tr>
+          <td class="memname">void <a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container</a>&lt; T &gt;::write_mem </td>
+          <td>(</td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Data Documentation</h2>
+<a class="anchor" id="abf366ff76d063e04beddf484e4993748"></a><!-- doxytag: member="ccp4srs::Container::n_objects" ref="abf366ff76d063e04beddf484e4993748" args="" -->
+<div class="memitem">
+<div class="memproto">
+<div class="memtemplate">
+template&lt;class T&gt; </div>
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container</a>&lt; T &gt;::<a class="el" href="classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748">n_objects</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a25a4ad3660f2ef6760c949be2c1372a8"></a><!-- doxytag: member="ccp4srs::Container::object" ref="a25a4ad3660f2ef6760c949be2c1372a8" args="" -->
+<div class="memitem">
+<div class="memproto">
+<div class="memtemplate">
+template&lt;class T&gt; </div>
+      <table class="memname">
+        <tr>
+          <td class="memname">T** <a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container</a>&lt; T &gt;::<a class="el" href="classccp4srs_1_1_container.html#a25a4ad3660f2ef6760c949be2c1372a8">object</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>src/<a class="el" href="ccp4srs__container_8h_source.html">ccp4srs_container.h</a></li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
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+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_entry-members.html ccp4srs/doc-html/html/classccp4srs_1_1_entry-members.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_entry-members.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_entry-members.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,85 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>ccp4srs::Entry Member List</h1>  </div>
+</div>
+<div class="contents">
+This is the complete list of members for <a class="el" href="classccp4srs_1_1_entry.html">ccp4srs::Entry</a>, including all inherited members.<table>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_entry.html#aa72cb70c4f1c115a2134e2da80b9bc34">Entry</a>()</td><td><a class="el" href="classccp4srs_1_1_entry.html">ccp4srs::Entry</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88cae7d526eebfeb15c8370f473885073095">Link</a> enum value</td><td><a class="el" href="classccp4srs_1_1_entry.html">ccp4srs::Entry</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88ca447bc9153594c5d2b79e47041f4982b6">Monomer</a> enum value</td><td><a class="el" href="classccp4srs_1_1_entry.html">ccp4srs::Entry</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88ca616c951330c4d0b080622857146e2457">None</a> enum value</td><td><a class="el" href="classccp4srs_1_1_entry.html">ccp4srs::Entry</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_entry.html#a262e2814d9a1bc35fbbfd75e46397343">read</a>(mmdb::io::RFile f, int version, PMemIO memIO=NULL)</td><td><a class="el" href="classccp4srs_1_1_entry.html">ccp4srs::Entry</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_entry.html#a2d3193b4e34c21b286526931e2e5b62d">read_mem</a>(PMemIO memIO, int version, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_entry.html">ccp4srs::Entry</a></td><td><code> [protected, virtual]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_entry.html#a401d0e96699c34bef6b408e054f14540">type</a>()</td><td><a class="el" href="classccp4srs_1_1_entry.html">ccp4srs::Entry</a></td><td><code> [inline, virtual]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_entry.html#a46d1eaa50c45f6e40ff054b30b93790d">write</a>(mmdb::io::RFile f, int version, PMemIO memIO=NULL)</td><td><a class="el" href="classccp4srs_1_1_entry.html">ccp4srs::Entry</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_entry.html#a817f6f566baf41280c5cee0fc3507871">write_mem</a>(PMemIO memIO, int version)</td><td><a class="el" href="classccp4srs_1_1_entry.html">ccp4srs::Entry</a></td><td><code> [protected, virtual]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_entry.html#a191661efae468b8e2a62b69a247bcd3a">~Entry</a>()</td><td><a class="el" href="classccp4srs_1_1_entry.html">ccp4srs::Entry</a></td><td><code> [virtual]</code></td></tr>
+</table></div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
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+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_entry.html ccp4srs/doc-html/html/classccp4srs_1_1_entry.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_entry.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_entry.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,324 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: ccp4srs::Entry Class Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
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+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="navpath">
+    <ul>
+      <li><a class="el" href="namespaceccp4srs.html">ccp4srs</a>      </li>
+      <li><a class="el" href="classccp4srs_1_1_entry.html">Entry</a>      </li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="summary">
+<a href="#pub-types">Public Types</a> &#124;
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pro-methods">Protected Member Functions</a>  </div>
+  <div class="headertitle">
+<h1>ccp4srs::Entry Class Reference</h1>  </div>
+</div>
+<div class="contents">
+<!-- doxytag: class="ccp4srs::Entry" -->
+<p><code>#include &lt;<a class="el" href="ccp4srs__entry_8h_source.html">ccp4srs_entry.h</a>&gt;</code></p>
+<!-- startSectionHeader --><div class="dynheader">
+Inheritance diagram for ccp4srs::Entry:<!-- endSectionHeader --></div>
+<!-- startSectionSummary --><!-- endSectionSummary --><!-- startSectionContent --><div class="dyncontent">
+<div class="center"><img src="classccp4srs_1_1_entry__inherit__graph.png" border="0" usemap="#ccp4srs_1_1_entry_inherit__map" alt="Inheritance graph"/></div>
+<map name="ccp4srs_1_1_entry_inherit__map" id="ccp4srs_1_1_entry_inherit__map">
+<area shape="rect" href="classccp4srs_1_1_monomer.html" title="ccp4srs::Monomer" alt="" coords="5,84,157,111"/></map>
+<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center><!-- endSectionContent --></div>
+
+<p><a href="classccp4srs_1_1_entry-members.html">List of all members.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="pub-types"></a>
+Public Types</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom">{ <a class="el" href="classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88ca616c951330c4d0b080622857146e2457">None</a>, 
+<a class="el" href="classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88ca447bc9153594c5d2b79e47041f4982b6">Monomer</a>, 
+<a class="el" href="classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88cae7d526eebfeb15c8370f473885073095">Link</a>
+ }</td></tr>
+<tr><td colspan="2"><h2><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_entry.html#aa72cb70c4f1c115a2134e2da80b9bc34">Entry</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_entry.html#a191661efae468b8e2a62b69a247bcd3a">~Entry</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">virtual int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_entry.html#a401d0e96699c34bef6b408e054f14540">type</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_entry.html#a46d1eaa50c45f6e40ff054b30b93790d">write</a> (mmdb::io::RFile f, int version, PMemIO memIO=NULL)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_entry.html#a262e2814d9a1bc35fbbfd75e46397343">read</a> (mmdb::io::RFile f, int version, PMemIO memIO=NULL)</td></tr>
+<tr><td colspan="2"><h2><a name="pro-methods"></a>
+Protected Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_entry.html#a817f6f566baf41280c5cee0fc3507871">write_mem</a> (PMemIO memIO, int version)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">virtual bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_entry.html#a2d3193b4e34c21b286526931e2e5b62d">read_mem</a> (PMemIO memIO, int version, bool *Ok=NULL)</td></tr>
+</table>
+<hr/><h2>Member Enumeration Documentation</h2>
+<a class="anchor" id="a6167625e2b80805e2ba7e3f78a1cd88c"></a><!-- doxytag: member="ccp4srs::Entry::@2" ref="a6167625e2b80805e2ba7e3f78a1cd88c" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">anonymous enum</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+<dl><dt><b>Enumerator: </b></dt><dd><table border="0" cellspacing="2" cellpadding="0">
+<tr><td valign="top"><em><a class="anchor" id="a6167625e2b80805e2ba7e3f78a1cd88ca616c951330c4d0b080622857146e2457"></a><!-- doxytag: member="None" ref="a6167625e2b80805e2ba7e3f78a1cd88ca616c951330c4d0b080622857146e2457" args="" -->None</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a6167625e2b80805e2ba7e3f78a1cd88ca447bc9153594c5d2b79e47041f4982b6"></a><!-- doxytag: member="Monomer" ref="a6167625e2b80805e2ba7e3f78a1cd88ca447bc9153594c5d2b79e47041f4982b6" args="" -->Monomer</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a6167625e2b80805e2ba7e3f78a1cd88cae7d526eebfeb15c8370f473885073095"></a><!-- doxytag: member="Link" ref="a6167625e2b80805e2ba7e3f78a1cd88cae7d526eebfeb15c8370f473885073095" args="" -->Link</em>&nbsp;</td><td>
+</td></tr>
+</table>
+</dd>
+</dl>
+
+</div>
+</div>
+<hr/><h2>Constructor &amp; Destructor Documentation</h2>
+<a class="anchor" id="aa72cb70c4f1c115a2134e2da80b9bc34"></a><!-- doxytag: member="ccp4srs::Entry::Entry" ref="aa72cb70c4f1c115a2134e2da80b9bc34" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::Entry::Entry </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a191661efae468b8e2a62b69a247bcd3a"></a><!-- doxytag: member="ccp4srs::Entry::~Entry" ref="a191661efae468b8e2a62b69a247bcd3a" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::Entry::~Entry </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [virtual]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Function Documentation</h2>
+<a class="anchor" id="a262e2814d9a1bc35fbbfd75e46397343"></a><!-- doxytag: member="ccp4srs::Entry::read" ref="a262e2814d9a1bc35fbbfd75e46397343" args="(mmdb::io::RFile f, int version, PMemIO memIO=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Entry::read </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::io::RFile&#160;</td>
+          <td class="paramname"> <em>f</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a2d3193b4e34c21b286526931e2e5b62d"></a><!-- doxytag: member="ccp4srs::Entry::read_mem" ref="a2d3193b4e34c21b286526931e2e5b62d" args="(PMemIO memIO, int version, bool *Ok=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::Entry::read_mem </td>
+          <td>(</td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td><code> [protected, virtual]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>Reimplemented in <a class="el" href="classccp4srs_1_1_monomer.html#ac12b93e766cfbcfd4288512df739a56e">ccp4srs::Monomer</a>.</p>
+
+</div>
+</div>
+<a class="anchor" id="a401d0e96699c34bef6b408e054f14540"></a><!-- doxytag: member="ccp4srs::Entry::type" ref="a401d0e96699c34bef6b408e054f14540" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">virtual int ccp4srs::Entry::type </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline, virtual]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>Reimplemented in <a class="el" href="classccp4srs_1_1_monomer.html#a01201fb01a7ed370e593563b129c74af">ccp4srs::Monomer</a>.</p>
+
+</div>
+</div>
+<a class="anchor" id="a46d1eaa50c45f6e40ff054b30b93790d"></a><!-- doxytag: member="ccp4srs::Entry::write" ref="a46d1eaa50c45f6e40ff054b30b93790d" args="(mmdb::io::RFile f, int version, PMemIO memIO=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Entry::write </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::io::RFile&#160;</td>
+          <td class="paramname"> <em>f</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a817f6f566baf41280c5cee0fc3507871"></a><!-- doxytag: member="ccp4srs::Entry::write_mem" ref="a817f6f566baf41280c5cee0fc3507871" args="(PMemIO memIO, int version)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Entry::write_mem </td>
+          <td>(</td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td><code> [protected, virtual]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>Reimplemented in <a class="el" href="classccp4srs_1_1_monomer.html#ac0eb44f5d4ec3da57994cd741c8d6b0b">ccp4srs::Monomer</a>.</p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following files:<ul>
+<li>src/<a class="el" href="ccp4srs__entry_8h_source.html">ccp4srs_entry.h</a></li>
+<li>src/<a class="el" href="ccp4srs__entry_8cpp.html">ccp4srs_entry.cpp</a></li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_entry__inherit__graph.map ccp4srs/doc-html/html/classccp4srs_1_1_entry__inherit__graph.map
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_entry__inherit__graph.map	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_entry__inherit__graph.map	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,3 @@
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+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>ccp4srs::Index Member List</h1>  </div>
+</div>
+<div class="contents">
+This is the complete list of members for <a class="el" href="classccp4srs_1_1_index.html">ccp4srs::Index</a>, including all inherited members.<table>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_index.html#af2a41a666517311e8877a3ec9e288916">Comp1</a></td><td><a class="el" href="classccp4srs_1_1_index.html">ccp4srs::Index</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_index.html#af4ce5b42fe2cf6364f9916d0a42f08b2">Comp2</a></td><td><a class="el" href="classccp4srs_1_1_index.html">ccp4srs::Index</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_index.html#a0bd1aedcf3b32bdd48d0de5cd2cc563e">entryID</a></td><td><a class="el" href="classccp4srs_1_1_index.html">ccp4srs::Index</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_index.html#a3be74bae1c6afc52ea36690b45ec5b96">fGraphPos</a></td><td><a class="el" href="classccp4srs_1_1_index.html">ccp4srs::Index</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_index.html#a21a1eddc77e99baf8df0b7450dee548b">fStructPos</a></td><td><a class="el" href="classccp4srs_1_1_index.html">ccp4srs::Index</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_index.html#aaff51df26ae81aff0425bda97d6f7030">Index</a>()</td><td><a class="el" href="classccp4srs_1_1_index.html">ccp4srs::Index</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_index.html#aedec88e9928356d4f7c913d449ca0d3e">IndexInit</a>()</td><td><a class="el" href="classccp4srs_1_1_index.html">ccp4srs::Index</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_index.html#afda5436941f171c791be43b9d28f43a5">MakeCompositions</a>(PMonomer monomer)</td><td><a class="el" href="classccp4srs_1_1_index.html">ccp4srs::Index</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_index.html#abba65d2d400f004fa3815a06101ac478">nAtoms</a></td><td><a class="el" href="classccp4srs_1_1_index.html">ccp4srs::Index</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_index.html#a5906658999e6e4e095589e0cdffabf11">nBonds</a></td><td><a class="el" href="classccp4srs_1_1_index.html">ccp4srs::Index</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_index.html#aa97eb5251314eeb77e5acd2af72ce1aa">nNonHAtoms</a></td><td><a class="el" href="classccp4srs_1_1_index.html">ccp4srs::Index</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_index.html#a17c3250780def030676fef212a19731c">read</a>(mmdb::io::RFile f, int version, PMemIO memIO=NULL)</td><td><a class="el" href="classccp4srs_1_1_index.html">ccp4srs::Index</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_index.html#a06b50353c15a21a56688b3e00aad2e2d">read_mem</a>(PMemIO memIO, int version, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_index.html">ccp4srs::Index</a></td><td><code> [protected, virtual]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_index.html#a2d6f487a5a3e945f92b90fc6f034f08b">write</a>(mmdb::io::RFile f, int version, PMemIO memIO=NULL)</td><td><a class="el" href="classccp4srs_1_1_index.html">ccp4srs::Index</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_index.html#a5591c13f7296928d053492322b8bd02b">write_mem</a>(PMemIO memIO, int version)</td><td><a class="el" href="classccp4srs_1_1_index.html">ccp4srs::Index</a></td><td><code> [protected, virtual]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_index.html#a5a0d5db83db471eae5aa87dcfa6a151c">~Index</a>()</td><td><a class="el" href="classccp4srs_1_1_index.html">ccp4srs::Index</a></td><td><code> [virtual]</code></td></tr>
+</table></div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
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+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
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+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_index.html ccp4srs/doc-html/html/classccp4srs_1_1_index.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_index.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_index.html	2014-09-09 21:34:12.000000000 -0700
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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: ccp4srs::Index Class Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="navpath">
+    <ul>
+      <li><a class="el" href="namespaceccp4srs.html">ccp4srs</a>      </li>
+      <li><a class="el" href="classccp4srs_1_1_index.html">Index</a>      </li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pub-attribs">Public Attributes</a> &#124;
+<a href="#pro-methods">Protected Member Functions</a>  </div>
+  <div class="headertitle">
+<h1>ccp4srs::Index Class Reference</h1>  </div>
+</div>
+<div class="contents">
+<!-- doxytag: class="ccp4srs::Index" -->
+<p><code>#include &lt;<a class="el" href="ccp4srs__index_8h_source.html">ccp4srs_index.h</a>&gt;</code></p>
+
+<p><a href="classccp4srs_1_1_index-members.html">List of all members.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_index.html#aaff51df26ae81aff0425bda97d6f7030">Index</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_index.html#a5a0d5db83db471eae5aa87dcfa6a151c">~Index</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_index.html#afda5436941f171c791be43b9d28f43a5">MakeCompositions</a> (PMonomer monomer)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_index.html#a2d6f487a5a3e945f92b90fc6f034f08b">write</a> (mmdb::io::RFile f, int version, PMemIO memIO=NULL)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_index.html#a17c3250780def030676fef212a19731c">read</a> (mmdb::io::RFile f, int version, PMemIO memIO=NULL)</td></tr>
+<tr><td colspan="2"><h2><a name="pub-attribs"></a>
+Public Attributes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::ResName&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_index.html#a0bd1aedcf3b32bdd48d0de5cd2cc563e">entryID</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">monomer or link ID  <a href="#a0bd1aedcf3b32bdd48d0de5cd2cc563e"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_index.html#abba65d2d400f004fa3815a06101ac478">nAtoms</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">number of atoms in the entry  <a href="#abba65d2d400f004fa3815a06101ac478"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_index.html#aa97eb5251314eeb77e5acd2af72ce1aa">nNonHAtoms</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">number of non-hydrogen atoms in the entry  <a href="#aa97eb5251314eeb77e5acd2af72ce1aa"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_index.html#a5906658999e6e4e095589e0cdffabf11">nBonds</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">number of bonds in the entry  <a href="#a5906658999e6e4e095589e0cdffabf11"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">long&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_index.html#a3be74bae1c6afc52ea36690b45ec5b96">fGraphPos</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">file offset for CGraph  <a href="#a3be74bae1c6afc52ea36690b45ec5b96"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">long&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_index.html#a21a1eddc77e99baf8df0b7450dee548b">fStructPos</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">file offset for CCP4SRSMonomer  <a href="#a21a1eddc77e99baf8df0b7450dee548b"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::pstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_index.html#af2a41a666517311e8877a3ec9e288916">Comp1</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">composition string  <a href="#af2a41a666517311e8877a3ec9e288916"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::pstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_index.html#af4ce5b42fe2cf6364f9916d0a42f08b2">Comp2</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">composition string with leaving atom  <a href="#af4ce5b42fe2cf6364f9916d0a42f08b2"></a><br/></td></tr>
+<tr><td colspan="2"><h2><a name="pro-methods"></a>
+Protected Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_index.html#aedec88e9928356d4f7c913d449ca0d3e">IndexInit</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_index.html#a5591c13f7296928d053492322b8bd02b">write_mem</a> (PMemIO memIO, int version)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">virtual bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_index.html#a06b50353c15a21a56688b3e00aad2e2d">read_mem</a> (PMemIO memIO, int version, bool *Ok=NULL)</td></tr>
+</table>
+<hr/><h2>Constructor &amp; Destructor Documentation</h2>
+<a class="anchor" id="aaff51df26ae81aff0425bda97d6f7030"></a><!-- doxytag: member="ccp4srs::Index::Index" ref="aaff51df26ae81aff0425bda97d6f7030" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::Index::Index </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a5a0d5db83db471eae5aa87dcfa6a151c"></a><!-- doxytag: member="ccp4srs::Index::~Index" ref="a5a0d5db83db471eae5aa87dcfa6a151c" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::Index::~Index </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [virtual]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Function Documentation</h2>
+<a class="anchor" id="aedec88e9928356d4f7c913d449ca0d3e"></a><!-- doxytag: member="ccp4srs::Index::IndexInit" ref="aedec88e9928356d4f7c913d449ca0d3e" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Index::IndexInit </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="afda5436941f171c791be43b9d28f43a5"></a><!-- doxytag: member="ccp4srs::Index::MakeCompositions" ref="afda5436941f171c791be43b9d28f43a5" args="(PMonomer monomer)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Index::MakeCompositions </td>
+          <td>(</td>
+          <td class="paramtype">PMonomer&#160;</td>
+          <td class="paramname"> <em>monomer</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a17c3250780def030676fef212a19731c"></a><!-- doxytag: member="ccp4srs::Index::read" ref="a17c3250780def030676fef212a19731c" args="(mmdb::io::RFile f, int version, PMemIO memIO=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Index::read </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::io::RFile&#160;</td>
+          <td class="paramname"> <em>f</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a06b50353c15a21a56688b3e00aad2e2d"></a><!-- doxytag: member="ccp4srs::Index::read_mem" ref="a06b50353c15a21a56688b3e00aad2e2d" args="(PMemIO memIO, int version, bool *Ok=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::Index::read_mem </td>
+          <td>(</td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td><code> [protected, virtual]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a2d6f487a5a3e945f92b90fc6f034f08b"></a><!-- doxytag: member="ccp4srs::Index::write" ref="a2d6f487a5a3e945f92b90fc6f034f08b" args="(mmdb::io::RFile f, int version, PMemIO memIO=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Index::write </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::io::RFile&#160;</td>
+          <td class="paramname"> <em>f</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a5591c13f7296928d053492322b8bd02b"></a><!-- doxytag: member="ccp4srs::Index::write_mem" ref="a5591c13f7296928d053492322b8bd02b" args="(PMemIO memIO, int version)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Index::write_mem </td>
+          <td>(</td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td><code> [protected, virtual]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Data Documentation</h2>
+<a class="anchor" id="af2a41a666517311e8877a3ec9e288916"></a><!-- doxytag: member="ccp4srs::Index::Comp1" ref="af2a41a666517311e8877a3ec9e288916" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::pstr <a class="el" href="classccp4srs_1_1_index.html#af2a41a666517311e8877a3ec9e288916">ccp4srs::Index::Comp1</a></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>composition string </p>
+
+</div>
+</div>
+<a class="anchor" id="af4ce5b42fe2cf6364f9916d0a42f08b2"></a><!-- doxytag: member="ccp4srs::Index::Comp2" ref="af4ce5b42fe2cf6364f9916d0a42f08b2" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::pstr <a class="el" href="classccp4srs_1_1_index.html#af4ce5b42fe2cf6364f9916d0a42f08b2">ccp4srs::Index::Comp2</a></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>composition string with leaving atom </p>
+
+</div>
+</div>
+<a class="anchor" id="a0bd1aedcf3b32bdd48d0de5cd2cc563e"></a><!-- doxytag: member="ccp4srs::Index::entryID" ref="a0bd1aedcf3b32bdd48d0de5cd2cc563e" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::ResName <a class="el" href="classccp4srs_1_1_index.html#a0bd1aedcf3b32bdd48d0de5cd2cc563e">ccp4srs::Index::entryID</a></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>monomer or link ID </p>
+
+</div>
+</div>
+<a class="anchor" id="a3be74bae1c6afc52ea36690b45ec5b96"></a><!-- doxytag: member="ccp4srs::Index::fGraphPos" ref="a3be74bae1c6afc52ea36690b45ec5b96" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">long <a class="el" href="classccp4srs_1_1_index.html#a3be74bae1c6afc52ea36690b45ec5b96">ccp4srs::Index::fGraphPos</a></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>file offset for CGraph </p>
+
+</div>
+</div>
+<a class="anchor" id="a21a1eddc77e99baf8df0b7450dee548b"></a><!-- doxytag: member="ccp4srs::Index::fStructPos" ref="a21a1eddc77e99baf8df0b7450dee548b" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">long <a class="el" href="classccp4srs_1_1_index.html#a21a1eddc77e99baf8df0b7450dee548b">ccp4srs::Index::fStructPos</a></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>file offset for CCP4SRSMonomer </p>
+
+</div>
+</div>
+<a class="anchor" id="abba65d2d400f004fa3815a06101ac478"></a><!-- doxytag: member="ccp4srs::Index::nAtoms" ref="abba65d2d400f004fa3815a06101ac478" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_index.html#abba65d2d400f004fa3815a06101ac478">ccp4srs::Index::nAtoms</a></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>number of atoms in the entry </p>
+
+</div>
+</div>
+<a class="anchor" id="a5906658999e6e4e095589e0cdffabf11"></a><!-- doxytag: member="ccp4srs::Index::nBonds" ref="a5906658999e6e4e095589e0cdffabf11" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_index.html#a5906658999e6e4e095589e0cdffabf11">ccp4srs::Index::nBonds</a></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>number of bonds in the entry </p>
+
+</div>
+</div>
+<a class="anchor" id="aa97eb5251314eeb77e5acd2af72ce1aa"></a><!-- doxytag: member="ccp4srs::Index::nNonHAtoms" ref="aa97eb5251314eeb77e5acd2af72ce1aa" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_index.html#aa97eb5251314eeb77e5acd2af72ce1aa">ccp4srs::Index::nNonHAtoms</a></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>number of non-hydrogen atoms in the entry </p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following files:<ul>
+<li>src/<a class="el" href="ccp4srs__index_8h_source.html">ccp4srs_index.h</a></li>
+<li>src/<a class="el" href="ccp4srs__index_8cpp.html">ccp4srs_index.cpp</a></li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
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+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_manager-members.html ccp4srs/doc-html/html/classccp4srs_1_1_manager-members.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_manager-members.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_manager-members.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,134 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>ccp4srs::Manager Member List</h1>  </div>
+</div>
+<div class="contents">
+This is the complete list of members for <a class="el" href="classccp4srs_1_1_manager.html">ccp4srs::Manager</a>, including all inherited members.<table>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#acada705ca803ac2b68bb2c787a83fcb1">addHydrogens</a>(mmdb::PResidue R, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#ac1ae2d0c6f7f79b3f5b02a6a3b082b81">addHydrogens</a>(mmdb::PChain chain, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a75fb480c106432f52d7301eae93d2942">addHydrogens</a>(mmdb::PModel model, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a45ea7718ea3dea244ba51f6f318d3623">addHydrogens</a>(mmdb::PManager MMDB, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a0c37b44fe77e9f171d5f40281a6e82ae">Base</a>()</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#ab5d4ff0f43b6785dc2c3cec72d4b8eec">CalcHBonds</a>(mmdb::PPResidue Res1, int nres1, mmdb::PPResidue Res2, int nres2, RPAtomPair HBond, int &amp;nHBonds, RPAtomPair SBridge, int &amp;nSBridges, mmdb::io::PFile structFile=NULL, mmdb::pstr altLoc=NULL, bool ignoreNegSigOcc=false)</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a6ca2d1c22ede07e88978645ab6a5887e">Chem</a>()</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#ab67f138edc7ae19791be69dde485c719">freeMemory</a>()</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#af9a1789b20b43e97a8eb6a56b4ef32c4">getAtNames</a>(int entryNo, mmdb::PAtomName AtName, int &amp;nAtoms, int &amp;nH)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#afbe234eef9c84fde630b72fbcfe27946">getAtNames</a>(mmdb::io::PFile structFile, int entryNo, mmdb::PAtomName AtName, int &amp;nAtoms, int &amp;nH)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a7e47408dacc9bd80de046504e235cc06">getAtoms</a>(mmdb::cpstr entryID, int &amp;nNonHAtoms, mmdb::PAtomName NonHAtName, int &amp;nHAtoms, mmdb::PAtomName HAtName, mmdb::ivector Hconnect, mmdb::ivector Elem, mmdb::ivector Chiral)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a8bb61486d7dd2df0566b8e3a1c7f1c89">getBonds</a>(mmdb::cpstr entryID, mmdb::ivector nBonds, mmdb::imatrix bondPair, int &amp;nAtoms, int maxNAtoms, int maxNBonds)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a301341ad4a91bf6cc4e7641efeb56309">getEnergyTypes</a>(mmdb::PResidue R, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#acb540af5e9036d7765dfdaa762fb6b2f">getEnergyTypes</a>(mmdb::PPResidue R, int nRes, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a6993968f40984c210ffad03588321d70">getEnergyTypes</a>(mmdb::PChain chain, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a6a9f477d2484e2e2d71328934432e1f8">getEnergyTypes</a>(mmdb::PModel model, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a227201ea4eedc8464c764dd015b7b190">getEnergyTypes</a>(mmdb::PManager MMDB, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a57b706684f3e84c741099ff904e01152">getEntryNo</a>(mmdb::cpstr entryID)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a17b78139832b00d7025236171ab31b7e">getGraph</a>(mmdb::io::PFile graphFile, mmdb::math::RPGraph G)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a8421066e4a9117cd380ff4362c355986">getGraph</a>(mmdb::io::PFile graphFile, int entryNo, mmdb::math::RPGraph G, int Hflag)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#af00d1ee772d045c048aa292457755b50">getGraph</a>(mmdb::io::PFile graphFile, mmdb::math::RPGraph G, int Hflag)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a418f3d4d079e0c4b93ebc6fff1fd0639">getGraph</a>(int entryNo, mmdb::math::RPGraph G, int Hflag)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a1f9dd08ea6c39fc0bb0a3885e6b3efac">getGraph</a>(mmdb::cpstr entryID, mmdb::math::RPGraph G, int Hflag)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a656b776b70ead2f8346b352b3bd1311e">getGraphFile</a>()</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a88c88924e247250d08cc4795b345c66a">getHetInfo</a>(mmdb::cpstr entryID, mmdb::pstr Formula, mmdb::pstr Hname, mmdb::pstr Hsynonym, mmdb::pstr Hcharge, mmdb::PAtomName &amp;ClinkAtom, mmdb::PElement &amp;ClinkEle, mmdb::PAtomName &amp;SlinkAtom, mmdb::PElement &amp;SlinkEle, int &amp;nLeavingAtoms)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#affa058db2078bc7835e9c78ca3bdde81">getIndex</a>(mmdb::cpstr entryID)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a399ff3d49a14dd3bb8250058f6452f4f">getIndex</a>(int n)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a339033984c68dd221cd6db184b734694">getMonomer</a>(mmdb::cpstr entryID)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a6f3f6564a30198bfe82215bceb6806e2">getMonomer</a>(int entryNo, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#ad25bf7474ec0574a39081ec5eeaefc5b">getMonomer</a>(mmdb::cpstr entryID, mmdb::io::PFile structFile)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a646d2c4349be4a740f2121dfd2091150">getNofAtoms</a>(mmdb::cpstr entryID)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a025a5622f0bfb83808cdad7cbf7af974">getNofAtoms</a>(int entryNo)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#af0653379d9db757dcc64c44c0e9ce070">getNofAtoms</a>(int entryNo, int &amp;nNonHAtoms, int &amp;nHAtoms)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#ac5481a8eeeb26ead06d7df61f605dac9">getPath</a>(mmdb::pstr &amp;S, mmdb::cpstr FName)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a03eac100b52d1f2d2d13981799f928bb">getStructFile</a>()</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#ada41928311fa3ba94bcb48a1ebf4b4df">index</a></td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a9fb463b8df4034fefb6e136ab56d135b">init_base</a>()</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a7ed4ac373981270bc1af2b8cc99b461d">init_chem</a>()</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#ae95af9ff2fb5c9d0edb437be3bcbe016">loadIndex</a>(mmdb::cpstr srsPath)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a663ef26d53b80f6c8b1f9c9cdeb70d2c">loadStructure</a>(mmdb::cpstr entryID)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#ad60a617bc151e054eb306e8c6bf592f4">makeBonds</a>(mmdb::PResidue R, mmdb::pstr altLoc, mmdb::io::PFile structFile, PDASelHnds selHandles, bool ignoreNegSigOcc)</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_manager.html#a7b1bcc6f68308560b402c5b3f8533158">Manager</a>()</td><td><a class="el" href="classccp4srs_1_1_manager.html">ccp4srs::Manager</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#aa32277562470e13dfe292f01bc269c17">maxDAAcos</a></td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a6655092e23b55ff3d6465a60101c135d">maxDAdist</a></td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#aa5d2547bfa92f55c755aa57fce717a65">maxDDAcos</a></td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a7408580f10d8868ae368f3faa1253577">maxDHAcos</a></td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a71cea07257deb2795443e04e07ee4bed">maxHAAcos</a></td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#ada14781ad5390841304d35f262705c57">maxHAdist2</a></td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#aeeb0e6bc6cc2e1a3f5ce78d59d8b496d">maxSBdist</a></td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#adf128b2adae954f6b25463c70ede5a58">memIO</a></td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a2e63b74dcf71dbf8583a64342de3848c">minDAdist</a></td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#aeb551e05e822e5eb3673aba1fa85bda6">n_entries</a>()</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a863fd5090d78f3bada7f351dd2f33859">nEntries</a></td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#af3caa0403ce8a1c4489948fa4fc62b0c">srsDir</a></td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#ad18087156761086530c1f01f3078f869">srsVersion</a></td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a6d15803597f5a515c19848a5e8dbe164">unloadStructure</a>(mmdb::cpstr entryID)</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_base.html#a2c46b036cb9701ac6a2d22fcec3fbdcf">~Base</a>()</td><td><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_chem.html#a939cae4367e5e32664e60c725fabafbe">~Chem</a>()</td><td><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_manager.html#ac6d91d47cb19b9f6ea6c7b64a7f69bb5">~Manager</a>()</td><td><a class="el" href="classccp4srs_1_1_manager.html">ccp4srs::Manager</a></td><td></td></tr>
+</table></div>
+<!--- window showing the filter options -->
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+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
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diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_manager.html ccp4srs/doc-html/html/classccp4srs_1_1_manager.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_manager.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_manager.html	2014-09-09 21:34:12.000000000 -0700
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+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
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+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
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+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="navpath">
+    <ul>
+      <li><a class="el" href="namespaceccp4srs.html">ccp4srs</a>      </li>
+      <li><a class="el" href="classccp4srs_1_1_manager.html">Manager</a>      </li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="summary">
+<a href="#pub-methods">Public Member Functions</a>  </div>
+  <div class="headertitle">
+<h1>ccp4srs::Manager Class Reference</h1>  </div>
+</div>
+<div class="contents">
+<!-- doxytag: class="ccp4srs::Manager" --><!-- doxytag: inherits="ccp4srs::Chem" -->
+<p><code>#include &lt;<a class="el" href="ccp4srs__manager_8h_source.html">ccp4srs_manager.h</a>&gt;</code></p>
+<!-- startSectionHeader --><div class="dynheader">
+Inheritance diagram for ccp4srs::Manager:<!-- endSectionHeader --></div>
+<!-- startSectionSummary --><!-- endSectionSummary --><!-- startSectionContent --><div class="dyncontent">
+<div class="center"><img src="classccp4srs_1_1_manager__inherit__graph.png" border="0" usemap="#ccp4srs_1_1_manager_inherit__map" alt="Inheritance graph"/></div>
+<map name="ccp4srs_1_1_manager_inherit__map" id="ccp4srs_1_1_manager_inherit__map">
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+<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center><!-- endSectionContent --></div>
+
+<p><a href="classccp4srs_1_1_manager-members.html">List of all members.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_manager.html#a7b1bcc6f68308560b402c5b3f8533158">Manager</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_manager.html#ac6d91d47cb19b9f6ea6c7b64a7f69bb5">~Manager</a> ()</td></tr>
+</table>
+<hr/><h2>Constructor &amp; Destructor Documentation</h2>
+<a class="anchor" id="a7b1bcc6f68308560b402c5b3f8533158"></a><!-- doxytag: member="ccp4srs::Manager::Manager" ref="a7b1bcc6f68308560b402c5b3f8533158" args="()" -->
+<div class="memitem">
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+        <tr>
+          <td class="memname">ccp4srs::Manager::Manager </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ac6d91d47cb19b9f6ea6c7b64a7f69bb5"></a><!-- doxytag: member="ccp4srs::Manager::~Manager" ref="ac6d91d47cb19b9f6ea6c7b64a7f69bb5" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::Manager::~Manager </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following files:<ul>
+<li>src/<a class="el" href="ccp4srs__manager_8h_source.html">ccp4srs_manager.h</a></li>
+<li>src/<a class="el" href="ccp4srs__manager_8cpp.html">ccp4srs_manager.cpp</a></li>
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+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
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+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
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+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>ccp4srs::MemIO Member List</h1>  </div>
+</div>
+<div class="contents">
+This is the complete list of members for <a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a>, including all inherited members.<table>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaac65c121a2ac9e371d3e059cb480cf60d">CantOpenFile</a> enum value</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa6cf46f9d24d202ae6ac26ddb6aeb625d">CompressionError</a> enum value</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa117fc645808ac4d9c4e53452bc608d51">EmptyFile</a> enum value</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a4cda073662a49aa45b0c744ec88de39a">free</a>()</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a0bbc28ba1593463385ae8f28b65225fa">get_bool</a>(bool &amp;B, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#aa1d1ea86d64ee50cab284d4a18f55ab8">get_buffer</a>(const int length)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#adad4a428c7530e61362f46d37b87d524">get_buffer</a>(mmdb::pstr *buf, int *length)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a296d38484504311f2773ff313298dda9">get_byte</a>(mmdb::byte &amp;B, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#adf95c15823dd0fb1067002d2ee3d8095">get_float</a>(mmdb::realtype &amp;R, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a7bc9b6d871402f5b5601d05ad4012326">get_ibyte</a>(int &amp;I, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a2d311d3bf0798e1c2bcb1cbe7f5d622f">get_integer</a>(int &amp;I, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a55e1b2e8f826ab2d6c0aef09f3beac9f">get_ishort</a>(int &amp;I, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a6cab031cef522531846e3ced7984f276">get_line</a>(mmdb::pstr L, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a950878f651e3bb037cf7ddc4a9c00201">get_long</a>(long &amp;I, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#afcc2e5eede7a829347985f646f24dcb3">get_real</a>(mmdb::realtype &amp;R, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#af2d1b382de42e06ce1dc5ae4ad6bb20f">get_short</a>(short &amp;I, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a039402bc82d9d0de0bd3664769355573">get_shortreal</a>(mmdb::shortreal &amp;R, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a22abd9cc96e80e4d3e71f0d1acbf1c4d">get_string</a>(mmdb::pstr &amp;L, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#ab932bc5aa0e98c9e681a3f3a9cc532c8">get_word</a>(mmdb::word &amp;W, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a5e4ae24f25179a720de85f185f8074ff">length</a>()</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#af2490447442255fa19b2a1c05c011f96">MemIO</a>()</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaadf48b9ed60d08687c2fbd5271b328c70">MemReadError</a> enum value</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63">Ok</a> enum value</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#ac3420c8a37ce57f324cf66eb4ccb9b13">put_bool</a>(bool B)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a3c30e4f73927173a9ce5731fab39d170">put_byte</a>(mmdb::byte B)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#ad82c1eca930cc9d5535f2da1ab3cde1a">put_float</a>(mmdb::realtype R)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a55ccb2d1a276365eadb422c75e982de3">put_ibyte</a>(int I)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a6c563469a6978a9c1c62a33457c90661">put_integer</a>(int I)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a1a5cd9341de994fa17ae8efae3d61732">put_ishort</a>(int I)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a98548fca1e008178fef523b271db5423">put_line</a>(mmdb::cpstr L)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#af300f12e3fe4b3d878f80caf19b66341">put_long</a>(long I)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a1d8e03e12f2420c9650f4a8956a1c0a7">put_real</a>(mmdb::realtype R)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a7117ff86d20006f7a693ea3a36035674">put_short</a>(short I)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a4eb6ba2e97922bf9509d828ee075aa8e">put_shortreal</a>(mmdb::shortreal R)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#aa35e6bbff841d942f793e50ee813fc97">put_string</a>(mmdb::cpstr L)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#abf6e925edc35b60fe7816223ceb7a15f">put_word</a>(mmdb::word W)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#ad8c19ab9e2bd98b40caf95cc6d7e071e">read</a>(mmdb::cpstr fileName, mmdb::io::GZ_MODE gzMode=mmdb::io::GZM_NONE)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#aebd3a0d6614c77b533433bc75de6d069">read</a>(mmdb::io::RFile f)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a7df5365c01565a15ac3bca748e46146b">read_buffer</a>(void *dest, const int length, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaab76082bd26e6e49c9c7794410cec3ca2">ReadError</a> enum value</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a855507e19582e7ab9b7236fb9d453da3">reset</a>()</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#ac84f72f62362171b812f386ef786a677">set_buffer_length</a>(const int len)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#abfd614fba0e035434e9c7f1c4a58ad89">setCompressionLevel</a>(int compressionLevel)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaaec9637fa3da0cf0cc0385a15d95af350">SizeError</a> enum value</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa63962a5b2f5046aa5e8a6b0b46271824">UncompressionError</a> enum value</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#ae2fd4e637343f3f9ac5ccfc3af085293">write</a>(mmdb::cpstr fileName, mmdb::io::GZ_MODE gzMode=mmdb::io::GZM_NONE)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a501f0773dd4ebb8f8f9b369cf59f07e0">write</a>(mmdb::io::RFile f)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a98b3d03fd613c62e0d16bfda509aa630">write_buffer</a>(const void *src, const int length)</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa29a865c4c24a0a158c5fc0514a29e517">WriteError</a> enum value</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_mem_i_o.html#abb2d68b86867b62480e6f036a2f8bcbb">~MemIO</a>()</td><td><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td><td><code> [virtual]</code></td></tr>
+</table></div>
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diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_mem_i_o.html ccp4srs/doc-html/html/classccp4srs_1_1_mem_i_o.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_mem_i_o.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_mem_i_o.html	2014-09-09 21:34:12.000000000 -0700
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+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
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+    <ul>
+      <li><a class="el" href="namespaceccp4srs.html">ccp4srs</a>      </li>
+      <li><a class="el" href="classccp4srs_1_1_mem_i_o.html">MemIO</a>      </li>
+    </ul>
+  </div>
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+<div class="header">
+  <div class="summary">
+<a href="#pub-types">Public Types</a> &#124;
+<a href="#pub-methods">Public Member Functions</a>  </div>
+  <div class="headertitle">
+<h1>ccp4srs::MemIO Class Reference</h1>  </div>
+</div>
+<div class="contents">
+<!-- doxytag: class="ccp4srs::MemIO" -->
+<p><code>#include &lt;<a class="el" href="memio___8h_source.html">memio_.h</a>&gt;</code></p>
+
+<p><a href="classccp4srs_1_1_mem_i_o-members.html">List of all members.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="pub-types"></a>
+Public Types</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom">{ <br/>
+&#160;&#160;<a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63">Ok</a>, 
+<a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaac65c121a2ac9e371d3e059cb480cf60d">CantOpenFile</a>, 
+<a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa117fc645808ac4d9c4e53452bc608d51">EmptyFile</a>, 
+<a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaab76082bd26e6e49c9c7794410cec3ca2">ReadError</a>, 
+<br/>
+&#160;&#160;<a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa29a865c4c24a0a158c5fc0514a29e517">WriteError</a>, 
+<a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaadf48b9ed60d08687c2fbd5271b328c70">MemReadError</a>, 
+<a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa6cf46f9d24d202ae6ac26ddb6aeb625d">CompressionError</a>, 
+<a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa63962a5b2f5046aa5e8a6b0b46271824">UncompressionError</a>, 
+<br/>
+&#160;&#160;<a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaaec9637fa3da0cf0cc0385a15d95af350">SizeError</a>
+<br/>
+ }</td></tr>
+<tr><td colspan="2"><h2><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#af2490447442255fa19b2a1c05c011f96">MemIO</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#abb2d68b86867b62480e6f036a2f8bcbb">~MemIO</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#abfd614fba0e035434e9c7f1c4a58ad89">setCompressionLevel</a> (int compressionLevel)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#ad8c19ab9e2bd98b40caf95cc6d7e071e">read</a> (mmdb::cpstr fileName, mmdb::io::GZ_MODE gzMode=mmdb::io::GZM_NONE)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#aebd3a0d6614c77b533433bc75de6d069">read</a> (mmdb::io::RFile f)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#ae2fd4e637343f3f9ac5ccfc3af085293">write</a> (mmdb::cpstr fileName, mmdb::io::GZ_MODE gzMode=mmdb::io::GZM_NONE)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a501f0773dd4ebb8f8f9b369cf59f07e0">write</a> (mmdb::io::RFile f)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a5e4ae24f25179a720de85f185f8074ff">length</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a855507e19582e7ab9b7236fb9d453da3">reset</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a4cda073662a49aa45b0c744ec88de39a">free</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#aa1d1ea86d64ee50cab284d4a18f55ab8">get_buffer</a> (const int length)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#ac84f72f62362171b812f386ef786a677">set_buffer_length</a> (const int len)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#adad4a428c7530e61362f46d37b87d524">get_buffer</a> (mmdb::pstr *buf, int *length)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a98b3d03fd613c62e0d16bfda509aa630">write_buffer</a> (const void *src, const int length)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a7df5365c01565a15ac3bca748e46146b">read_buffer</a> (void *dest, const int length, bool *Ok=NULL)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a6c563469a6978a9c1c62a33457c90661">put_integer</a> (int I)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a1a5cd9341de994fa17ae8efae3d61732">put_ishort</a> (int I)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a55ccb2d1a276365eadb422c75e982de3">put_ibyte</a> (int I)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a3c30e4f73927173a9ce5731fab39d170">put_byte</a> (mmdb::byte B)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a7117ff86d20006f7a693ea3a36035674">put_short</a> (short I)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#af300f12e3fe4b3d878f80caf19b66341">put_long</a> (long I)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#abf6e925edc35b60fe7816223ceb7a15f">put_word</a> (mmdb::word W)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a1d8e03e12f2420c9650f4a8956a1c0a7">put_real</a> (mmdb::realtype R)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#ad82c1eca930cc9d5535f2da1ab3cde1a">put_float</a> (mmdb::realtype R)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a4eb6ba2e97922bf9509d828ee075aa8e">put_shortreal</a> (mmdb::shortreal R)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a98548fca1e008178fef523b271db5423">put_line</a> (mmdb::cpstr L)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#aa35e6bbff841d942f793e50ee813fc97">put_string</a> (mmdb::cpstr L)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#ac3420c8a37ce57f324cf66eb4ccb9b13">put_bool</a> (bool B)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a2d311d3bf0798e1c2bcb1cbe7f5d622f">get_integer</a> (int &amp;I, bool *Ok=NULL)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a55e1b2e8f826ab2d6c0aef09f3beac9f">get_ishort</a> (int &amp;I, bool *Ok=NULL)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a7bc9b6d871402f5b5601d05ad4012326">get_ibyte</a> (int &amp;I, bool *Ok=NULL)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a296d38484504311f2773ff313298dda9">get_byte</a> (mmdb::byte &amp;B, bool *Ok=NULL)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#af2d1b382de42e06ce1dc5ae4ad6bb20f">get_short</a> (short &amp;I, bool *Ok=NULL)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a950878f651e3bb037cf7ddc4a9c00201">get_long</a> (long &amp;I, bool *Ok=NULL)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#ab932bc5aa0e98c9e681a3f3a9cc532c8">get_word</a> (mmdb::word &amp;W, bool *Ok=NULL)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#afcc2e5eede7a829347985f646f24dcb3">get_real</a> (mmdb::realtype &amp;R, bool *Ok=NULL)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#adf95c15823dd0fb1067002d2ee3d8095">get_float</a> (mmdb::realtype &amp;R, bool *Ok=NULL)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a039402bc82d9d0de0bd3664769355573">get_shortreal</a> (mmdb::shortreal &amp;R, bool *Ok=NULL)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a6cab031cef522531846e3ced7984f276">get_line</a> (mmdb::pstr L, bool *Ok=NULL)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a22abd9cc96e80e4d3e71f0d1acbf1c4d">get_string</a> (mmdb::pstr &amp;L, bool *Ok=NULL)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html#a0bbc28ba1593463385ae8f28b65225fa">get_bool</a> (bool &amp;B, bool *Ok=NULL)</td></tr>
+</table>
+<hr/><h2>Member Enumeration Documentation</h2>
+<a class="anchor" id="a58ea0e99940fe1f006ed20ecc2f35cba"></a><!-- doxytag: member="ccp4srs::MemIO::@5" ref="a58ea0e99940fe1f006ed20ecc2f35cba" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">anonymous enum</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+<dl><dt><b>Enumerator: </b></dt><dd><table border="0" cellspacing="2" cellpadding="0">
+<tr><td valign="top"><em><a class="anchor" id="a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63"></a><!-- doxytag: member="Ok" ref="a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63" args="" -->Ok</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a58ea0e99940fe1f006ed20ecc2f35cbaac65c121a2ac9e371d3e059cb480cf60d"></a><!-- doxytag: member="CantOpenFile" ref="a58ea0e99940fe1f006ed20ecc2f35cbaac65c121a2ac9e371d3e059cb480cf60d" args="" -->CantOpenFile</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a58ea0e99940fe1f006ed20ecc2f35cbaa117fc645808ac4d9c4e53452bc608d51"></a><!-- doxytag: member="EmptyFile" ref="a58ea0e99940fe1f006ed20ecc2f35cbaa117fc645808ac4d9c4e53452bc608d51" args="" -->EmptyFile</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a58ea0e99940fe1f006ed20ecc2f35cbaab76082bd26e6e49c9c7794410cec3ca2"></a><!-- doxytag: member="ReadError" ref="a58ea0e99940fe1f006ed20ecc2f35cbaab76082bd26e6e49c9c7794410cec3ca2" args="" -->ReadError</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a58ea0e99940fe1f006ed20ecc2f35cbaa29a865c4c24a0a158c5fc0514a29e517"></a><!-- doxytag: member="WriteError" ref="a58ea0e99940fe1f006ed20ecc2f35cbaa29a865c4c24a0a158c5fc0514a29e517" args="" -->WriteError</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a58ea0e99940fe1f006ed20ecc2f35cbaadf48b9ed60d08687c2fbd5271b328c70"></a><!-- doxytag: member="MemReadError" ref="a58ea0e99940fe1f006ed20ecc2f35cbaadf48b9ed60d08687c2fbd5271b328c70" args="" -->MemReadError</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a58ea0e99940fe1f006ed20ecc2f35cbaa6cf46f9d24d202ae6ac26ddb6aeb625d"></a><!-- doxytag: member="CompressionError" ref="a58ea0e99940fe1f006ed20ecc2f35cbaa6cf46f9d24d202ae6ac26ddb6aeb625d" args="" -->CompressionError</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a58ea0e99940fe1f006ed20ecc2f35cbaa63962a5b2f5046aa5e8a6b0b46271824"></a><!-- doxytag: member="UncompressionError" ref="a58ea0e99940fe1f006ed20ecc2f35cbaa63962a5b2f5046aa5e8a6b0b46271824" args="" -->UncompressionError</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a58ea0e99940fe1f006ed20ecc2f35cbaaec9637fa3da0cf0cc0385a15d95af350"></a><!-- doxytag: member="SizeError" ref="a58ea0e99940fe1f006ed20ecc2f35cbaaec9637fa3da0cf0cc0385a15d95af350" args="" -->SizeError</em>&nbsp;</td><td>
+</td></tr>
+</table>
+</dd>
+</dl>
+
+</div>
+</div>
+<hr/><h2>Constructor &amp; Destructor Documentation</h2>
+<a class="anchor" id="af2490447442255fa19b2a1c05c011f96"></a><!-- doxytag: member="ccp4srs::MemIO::MemIO" ref="af2490447442255fa19b2a1c05c011f96" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::MemIO::MemIO </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="abb2d68b86867b62480e6f036a2f8bcbb"></a><!-- doxytag: member="ccp4srs::MemIO::~MemIO" ref="abb2d68b86867b62480e6f036a2f8bcbb" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::MemIO::~MemIO </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [virtual]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Function Documentation</h2>
+<a class="anchor" id="a4cda073662a49aa45b0c744ec88de39a"></a><!-- doxytag: member="ccp4srs::MemIO::free" ref="a4cda073662a49aa45b0c744ec88de39a" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::MemIO::free </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a0bbc28ba1593463385ae8f28b65225fa"></a><!-- doxytag: member="ccp4srs::MemIO::get_bool" ref="a0bbc28ba1593463385ae8f28b65225fa" args="(bool &amp;B, bool *Ok=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::MemIO::get_bool </td>
+          <td>(</td>
+          <td class="paramtype">bool &amp;&#160;</td>
+          <td class="paramname"> <em>B</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aa1d1ea86d64ee50cab284d4a18f55ab8"></a><!-- doxytag: member="ccp4srs::MemIO::get_buffer" ref="aa1d1ea86d64ee50cab284d4a18f55ab8" args="(const int length)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void * ccp4srs::MemIO::get_buffer </td>
+          <td>(</td>
+          <td class="paramtype">const int&#160;</td>
+          <td class="paramname"> <em>length</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="adad4a428c7530e61362f46d37b87d524"></a><!-- doxytag: member="ccp4srs::MemIO::get_buffer" ref="adad4a428c7530e61362f46d37b87d524" args="(mmdb::pstr *buf, int *length)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::MemIO::get_buffer </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::pstr *&#160;</td>
+          <td class="paramname"> <em>buf</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int *&#160;</td>
+          <td class="paramname"> <em>length</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a296d38484504311f2773ff313298dda9"></a><!-- doxytag: member="ccp4srs::MemIO::get_byte" ref="a296d38484504311f2773ff313298dda9" args="(mmdb::byte &amp;B, bool *Ok=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::MemIO::get_byte </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::byte &amp;&#160;</td>
+          <td class="paramname"> <em>B</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="adf95c15823dd0fb1067002d2ee3d8095"></a><!-- doxytag: member="ccp4srs::MemIO::get_float" ref="adf95c15823dd0fb1067002d2ee3d8095" args="(mmdb::realtype &amp;R, bool *Ok=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::MemIO::get_float </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::realtype &amp;&#160;</td>
+          <td class="paramname"> <em>R</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a7bc9b6d871402f5b5601d05ad4012326"></a><!-- doxytag: member="ccp4srs::MemIO::get_ibyte" ref="a7bc9b6d871402f5b5601d05ad4012326" args="(int &amp;I, bool *Ok=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::MemIO::get_ibyte </td>
+          <td>(</td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>I</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a2d311d3bf0798e1c2bcb1cbe7f5d622f"></a><!-- doxytag: member="ccp4srs::MemIO::get_integer" ref="a2d311d3bf0798e1c2bcb1cbe7f5d622f" args="(int &amp;I, bool *Ok=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::MemIO::get_integer </td>
+          <td>(</td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>I</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a55e1b2e8f826ab2d6c0aef09f3beac9f"></a><!-- doxytag: member="ccp4srs::MemIO::get_ishort" ref="a55e1b2e8f826ab2d6c0aef09f3beac9f" args="(int &amp;I, bool *Ok=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::MemIO::get_ishort </td>
+          <td>(</td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>I</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a6cab031cef522531846e3ced7984f276"></a><!-- doxytag: member="ccp4srs::MemIO::get_line" ref="a6cab031cef522531846e3ced7984f276" args="(mmdb::pstr L, bool *Ok=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::MemIO::get_line </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::pstr&#160;</td>
+          <td class="paramname"> <em>L</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a950878f651e3bb037cf7ddc4a9c00201"></a><!-- doxytag: member="ccp4srs::MemIO::get_long" ref="a950878f651e3bb037cf7ddc4a9c00201" args="(long &amp;I, bool *Ok=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::MemIO::get_long </td>
+          <td>(</td>
+          <td class="paramtype">long &amp;&#160;</td>
+          <td class="paramname"> <em>I</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="afcc2e5eede7a829347985f646f24dcb3"></a><!-- doxytag: member="ccp4srs::MemIO::get_real" ref="afcc2e5eede7a829347985f646f24dcb3" args="(mmdb::realtype &amp;R, bool *Ok=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::MemIO::get_real </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::realtype &amp;&#160;</td>
+          <td class="paramname"> <em>R</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="af2d1b382de42e06ce1dc5ae4ad6bb20f"></a><!-- doxytag: member="ccp4srs::MemIO::get_short" ref="af2d1b382de42e06ce1dc5ae4ad6bb20f" args="(short &amp;I, bool *Ok=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::MemIO::get_short </td>
+          <td>(</td>
+          <td class="paramtype">short &amp;&#160;</td>
+          <td class="paramname"> <em>I</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a039402bc82d9d0de0bd3664769355573"></a><!-- doxytag: member="ccp4srs::MemIO::get_shortreal" ref="a039402bc82d9d0de0bd3664769355573" args="(mmdb::shortreal &amp;R, bool *Ok=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::MemIO::get_shortreal </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::shortreal &amp;&#160;</td>
+          <td class="paramname"> <em>R</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
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+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a22abd9cc96e80e4d3e71f0d1acbf1c4d"></a><!-- doxytag: member="ccp4srs::MemIO::get_string" ref="a22abd9cc96e80e4d3e71f0d1acbf1c4d" args="(mmdb::pstr &amp;L, bool *Ok=NULL)" -->
+<div class="memitem">
+<div class="memproto">
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+        <tr>
+          <td class="memname">bool ccp4srs::MemIO::get_string </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::pstr &amp;&#160;</td>
+          <td class="paramname"> <em>L</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
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+</div>
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+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::MemIO::get_word </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::word &amp;&#160;</td>
+          <td class="paramname"> <em>W</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a5e4ae24f25179a720de85f185f8074ff"></a><!-- doxytag: member="ccp4srs::MemIO::length" ref="a5e4ae24f25179a720de85f185f8074ff" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::MemIO::length </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ac3420c8a37ce57f324cf66eb4ccb9b13"></a><!-- doxytag: member="ccp4srs::MemIO::put_bool" ref="ac3420c8a37ce57f324cf66eb4ccb9b13" args="(bool B)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::MemIO::put_bool </td>
+          <td>(</td>
+          <td class="paramtype">bool&#160;</td>
+          <td class="paramname"> <em>B</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a3c30e4f73927173a9ce5731fab39d170"></a><!-- doxytag: member="ccp4srs::MemIO::put_byte" ref="a3c30e4f73927173a9ce5731fab39d170" args="(mmdb::byte B)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::MemIO::put_byte </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::byte&#160;</td>
+          <td class="paramname"> <em>B</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ad82c1eca930cc9d5535f2da1ab3cde1a"></a><!-- doxytag: member="ccp4srs::MemIO::put_float" ref="ad82c1eca930cc9d5535f2da1ab3cde1a" args="(mmdb::realtype R)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::MemIO::put_float </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::realtype&#160;</td>
+          <td class="paramname"> <em>R</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a55ccb2d1a276365eadb422c75e982de3"></a><!-- doxytag: member="ccp4srs::MemIO::put_ibyte" ref="a55ccb2d1a276365eadb422c75e982de3" args="(int I)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::MemIO::put_ibyte </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>I</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a6c563469a6978a9c1c62a33457c90661"></a><!-- doxytag: member="ccp4srs::MemIO::put_integer" ref="a6c563469a6978a9c1c62a33457c90661" args="(int I)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::MemIO::put_integer </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>I</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a1a5cd9341de994fa17ae8efae3d61732"></a><!-- doxytag: member="ccp4srs::MemIO::put_ishort" ref="a1a5cd9341de994fa17ae8efae3d61732" args="(int I)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::MemIO::put_ishort </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>I</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a98548fca1e008178fef523b271db5423"></a><!-- doxytag: member="ccp4srs::MemIO::put_line" ref="a98548fca1e008178fef523b271db5423" args="(mmdb::cpstr L)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::MemIO::put_line </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>L</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="af300f12e3fe4b3d878f80caf19b66341"></a><!-- doxytag: member="ccp4srs::MemIO::put_long" ref="af300f12e3fe4b3d878f80caf19b66341" args="(long I)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::MemIO::put_long </td>
+          <td>(</td>
+          <td class="paramtype">long&#160;</td>
+          <td class="paramname"> <em>I</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a1d8e03e12f2420c9650f4a8956a1c0a7"></a><!-- doxytag: member="ccp4srs::MemIO::put_real" ref="a1d8e03e12f2420c9650f4a8956a1c0a7" args="(mmdb::realtype R)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::MemIO::put_real </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::realtype&#160;</td>
+          <td class="paramname"> <em>R</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a7117ff86d20006f7a693ea3a36035674"></a><!-- doxytag: member="ccp4srs::MemIO::put_short" ref="a7117ff86d20006f7a693ea3a36035674" args="(short I)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::MemIO::put_short </td>
+          <td>(</td>
+          <td class="paramtype">short&#160;</td>
+          <td class="paramname"> <em>I</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a4eb6ba2e97922bf9509d828ee075aa8e"></a><!-- doxytag: member="ccp4srs::MemIO::put_shortreal" ref="a4eb6ba2e97922bf9509d828ee075aa8e" args="(mmdb::shortreal R)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::MemIO::put_shortreal </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::shortreal&#160;</td>
+          <td class="paramname"> <em>R</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aa35e6bbff841d942f793e50ee813fc97"></a><!-- doxytag: member="ccp4srs::MemIO::put_string" ref="aa35e6bbff841d942f793e50ee813fc97" args="(mmdb::cpstr L)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::MemIO::put_string </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>L</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="abf6e925edc35b60fe7816223ceb7a15f"></a><!-- doxytag: member="ccp4srs::MemIO::put_word" ref="abf6e925edc35b60fe7816223ceb7a15f" args="(mmdb::word W)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::MemIO::put_word </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::word&#160;</td>
+          <td class="paramname"> <em>W</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aebd3a0d6614c77b533433bc75de6d069"></a><!-- doxytag: member="ccp4srs::MemIO::read" ref="aebd3a0d6614c77b533433bc75de6d069" args="(mmdb::io::RFile f)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::MemIO::read </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::io::RFile&#160;</td>
+          <td class="paramname"> <em>f</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ad8c19ab9e2bd98b40caf95cc6d7e071e"></a><!-- doxytag: member="ccp4srs::MemIO::read" ref="ad8c19ab9e2bd98b40caf95cc6d7e071e" args="(mmdb::cpstr fileName, mmdb::io::GZ_MODE gzMode=mmdb::io::GZM_NONE)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::MemIO::read </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>fileName</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::io::GZ_MODE&#160;</td>
+          <td class="paramname"> <em>gzMode</em> = <code>mmdb::io::GZM_NONE</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a7df5365c01565a15ac3bca748e46146b"></a><!-- doxytag: member="ccp4srs::MemIO::read_buffer" ref="a7df5365c01565a15ac3bca748e46146b" args="(void *dest, const int length, bool *Ok=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::MemIO::read_buffer </td>
+          <td>(</td>
+          <td class="paramtype">void *&#160;</td>
+          <td class="paramname"> <em>dest</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const int&#160;</td>
+          <td class="paramname"> <em>length</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a855507e19582e7ab9b7236fb9d453da3"></a><!-- doxytag: member="ccp4srs::MemIO::reset" ref="a855507e19582e7ab9b7236fb9d453da3" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::MemIO::reset </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ac84f72f62362171b812f386ef786a677"></a><!-- doxytag: member="ccp4srs::MemIO::set_buffer_length" ref="ac84f72f62362171b812f386ef786a677" args="(const int len)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::MemIO::set_buffer_length </td>
+          <td>(</td>
+          <td class="paramtype">const int&#160;</td>
+          <td class="paramname"> <em>len</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="abfd614fba0e035434e9c7f1c4a58ad89"></a><!-- doxytag: member="ccp4srs::MemIO::setCompressionLevel" ref="abfd614fba0e035434e9c7f1c4a58ad89" args="(int compressionLevel)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::MemIO::setCompressionLevel </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>compressionLevel</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ae2fd4e637343f3f9ac5ccfc3af085293"></a><!-- doxytag: member="ccp4srs::MemIO::write" ref="ae2fd4e637343f3f9ac5ccfc3af085293" args="(mmdb::cpstr fileName, mmdb::io::GZ_MODE gzMode=mmdb::io::GZM_NONE)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::MemIO::write </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>fileName</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::io::GZ_MODE&#160;</td>
+          <td class="paramname"> <em>gzMode</em> = <code>mmdb::io::GZM_NONE</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a501f0773dd4ebb8f8f9b369cf59f07e0"></a><!-- doxytag: member="ccp4srs::MemIO::write" ref="a501f0773dd4ebb8f8f9b369cf59f07e0" args="(mmdb::io::RFile f)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::MemIO::write </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::io::RFile&#160;</td>
+          <td class="paramname"> <em>f</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a98b3d03fd613c62e0d16bfda509aa630"></a><!-- doxytag: member="ccp4srs::MemIO::write_buffer" ref="a98b3d03fd613c62e0d16bfda509aa630" args="(const void *src, const int length)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::MemIO::write_buffer </td>
+          <td>(</td>
+          <td class="paramtype">const void *&#160;</td>
+          <td class="paramname"> <em>src</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const int&#160;</td>
+          <td class="paramname"> <em>length</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following files:<ul>
+<li>src/<a class="el" href="memio___8h_source.html">memio_.h</a></li>
+<li>src/<a class="el" href="memio___8cpp.html">memio_.cpp</a></li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
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diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_monomer-members.html ccp4srs/doc-html/html/classccp4srs_1_1_monomer-members.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_monomer-members.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_monomer-members.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,150 @@
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+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
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+  </div>
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+<div class="header">
+  <div class="headertitle">
+<h1>ccp4srs::Monomer Member List</h1>  </div>
+</div>
+<div class="contents">
+This is the complete list of members for <a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a>, including all inherited members.<table>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#ae1c9221ebd49b62830621cd40524d215">add</a>(PAtom atom)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a88d4f2d1f97364930fed4bf349b23cb1">add</a>(PBond bond)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a3eab75471f83c2c92834a1e30400642e">add</a>(PAngle angle)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a394b2b32b99cd3c6e0b3654593436a2f">add</a>(PPlane plane)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#acdfa8628139cfb914f2aecdb1e2f37d2">add</a>(PTree stree)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a555cba2de4ecd6d3d7c192a52a9d44a3">add</a>(PTorsion torsion)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a1820529a0bee358372e53ea0fb0c0a56">add</a>(PChiCenter chicenter)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a67a965eb782472588f1a5f4e693c509e">addHydrogens</a>(mmdb::PResidue R)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a61b179edff80a9d168997038093cc92f">angle</a>(int n)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a9177ec12ea5aeaa59228831d4127e592">angles</a></td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#ac3492a092c5436d182acae9b6712da7f">atom</a>(int n)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a9ac9e9e610a1a0450130d5e5c4242d34">atom_no</a>(mmdb::cpstr aname)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#abd7decc2129038a1416f324fee53afa1">atoms</a></td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a6b01e3fa4cb59dc507460ea0715823fa">bond</a>(int n)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a19495bb3c7e8d1c27f12f06729979d9e">bonds</a></td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a6bbfc74c882e403c57984d7310d4fb98">chem_formula</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#ab5a8d9361def2e547d1e65bf180f3252">chem_name</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a37432cca1867e01cd9af6d4569c2326a">chem_type</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a3c1ea4e271769745f01c8dc4146c683e">chicenter</a>(int n)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a96a126d39760ce281f8bf04186e29c13">chicenters</a></td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_entry.html#aa72cb70c4f1c115a2134e2da80b9bc34">Entry</a>()</td><td><a class="el" href="classccp4srs_1_1_entry.html">ccp4srs::Entry</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a8d4b4084ca5c0e0fa42075f59eaf3e08">get_angles</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a1ca9838123fea51260be3c44abd6771f">get_atoms</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#af36aeb36b83f49d3b4fc28d4737b5efd">get_bonds</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a7b6acc92258007c15351989930e8672f">get_bound</a>(int atomNo, mmdb::cpstr elem, int serNo)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#ae60200771fdf1a869023dacebfb98278">get_bound</a>(int atomNo, int n)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a8ae0097e0e9950fc3f443f373a0a9359">get_bound</a>(mmdb::cpstr aname, int n)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a591d5f8275f5b5756442d96221039ef3">get_chicenters</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#aa454ac38a87c19006580a42bc38958fc">get_planes</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a7b31b6675690c2edc0baa0e070d349ad">get_torsions</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a351a18b323af41b74d1b415fcd1df640">get_tree</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#abb514ab63af7e9dbb68f59bc13551618">getAtomNameMatch</a>(mmdb::PPAtom A, int nat, mmdb::pstr altLoc, mmdb::ivector anmatch)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a17d26aa3a5b3b637cf6148499013c345">getAtomNameMatch</a>(Container&lt; Atom &gt; *A, mmdb::ivector anmatch)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a9d1a2b0facb208344413158d74446755">getGraph</a>(int *retCode)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a6c3ad68f13fb779921605d0e696add1c">getLeavingAtoms</a>(int &amp;nLeavingAtoms, mmdb::ivector &amp;leavingAtom, mmdb::ivector &amp;bondedAtom)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a1eca7f4a9537bddf81de26df20984183">ID</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a6a50cfb8d8e87162309106c66f5fc155">Init</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88cae7d526eebfeb15c8370f473885073095">Link</a> enum value</td><td><a class="el" href="classccp4srs_1_1_entry.html">ccp4srs::Entry</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a5e3fb1e64eab3e764cc83ff1e6c61fa3">makeCIF</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a6453406b0256cf9fbf74177a7db8770b">merge</a>(PMonomer monomer)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#aeb6bee62372a765e8aca0c1496689b3a">monFormula</a></td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a34240535a6e703495662936dba863026">monID</a></td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a53b8d5232f3b2085d531eca33fb7c55a">monName</a></td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#abd3a6efc83918f121e3e83165681ccd5">Monomer</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88ca447bc9153594c5d2b79e47041f4982b6">ccp4srs::Entry::Monomer</a> enum value</td><td><a class="el" href="classccp4srs_1_1_entry.html">ccp4srs::Entry</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#af0a573429afbbea61647c9851f0deba7">monType</a></td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a832521f11b1adb4a0deb9fd92b4bc725">n_angles</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a3e3e771e2d60581384b1169648b4d751">n_atoms</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a6a6e470c174fd570667bf43f95757c0d">n_bonds</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a047ec20b44f73aa0027fdd071aa265d6">n_chicenters</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a123cf02246e052730361055de3f0d477">n_planes</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a0bf10d776d5d992424b99d88d884f101">n_torsions</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88ca616c951330c4d0b080622857146e2457">None</a> enum value</td><td><a class="el" href="classccp4srs_1_1_entry.html">ccp4srs::Entry</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a271e6aaeed7ace67e36f2c5fea626d70">oldID</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a896cc0c3979b65913de25be2c2f75ec9">oldMonID</a></td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#afdebf230f6aa9bf2692a82b919d59918">plane</a>(int n)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a2f927ab2a3e517f9fe6cba6e89954cfe">planes</a></td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_entry.html#a262e2814d9a1bc35fbbfd75e46397343">read</a>(mmdb::io::RFile f, int version, PMemIO memIO=NULL)</td><td><a class="el" href="classccp4srs_1_1_entry.html">ccp4srs::Entry</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#ac12b93e766cfbcfd4288512df739a56e">read_mem</a>(PMemIO memIO, int version, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [protected, virtual]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#aa9b0a99023e890070aec088182f8a65b">readFromCIF</a>(mmdb::mmcif::PData mmCIFData, mmdb::pstr error_desc=NULL)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a9e457d3f7633b79b598b66f382fa5c5c">readFromCIF_ccp4</a>(mmdb::mmcif::PData mmCIFData, mmdb::pstr error_desc)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#aaaec1b93dd1dcfe0e20484fd4bbc2a72">readFromCIF_rcsb</a>(mmdb::mmcif::PData mmCIFData, mmdb::pstr error_desc)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a4e12236b18de645dabd1afe57b46ebc0">readMonIDFromCIF</a>(mmdb::mmcif::PLoop loop)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#acbe4714fc7593d649b5e8901668d5c5c">readMonIDFromCIF</a>(mmdb::mmcif::PStruct mmCIFStruct)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a42598d1f669c5e539cb024bb023e0551">reset</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a3d9cd816f0e032e64e0d47ed7673ec63">setOldID</a>(mmdb::cpstr oldID)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#aef8794097a333f1e4e20dd3d876f1432">struct_tree</a></td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a1fdc6bd34cea4b7ea59d5399a8367f70">torsion</a>(int n)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a70123373bff5c842e122856fb75634ab">torsions</a></td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a79a4445aa7279951aa8426dc79114ebf">tree</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a01201fb01a7ed370e593563b129c74af">type</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [inline, virtual]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_entry.html#a46d1eaa50c45f6e40ff054b30b93790d">write</a>(mmdb::io::RFile f, int version, PMemIO memIO=NULL)</td><td><a class="el" href="classccp4srs_1_1_entry.html">ccp4srs::Entry</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#ac0eb44f5d4ec3da57994cd741c8d6b0b">write_mem</a>(PMemIO memIO, int version)</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td><code> [protected, virtual]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_entry.html#a191661efae468b8e2a62b69a247bcd3a">~Entry</a>()</td><td><a class="el" href="classccp4srs_1_1_entry.html">ccp4srs::Entry</a></td><td><code> [virtual]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_monomer.html#a33207c3c799fe120851007002464e2e2">~Monomer</a>()</td><td><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></td><td></td></tr>
+</table></div>
+<!--- window showing the filter options -->
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+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
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diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_monomer.html ccp4srs/doc-html/html/classccp4srs_1_1_monomer.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_monomer.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_monomer.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,1422 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<title>ccp4srs: ccp4srs::Monomer Class Reference</title>
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+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="navpath">
+    <ul>
+      <li><a class="el" href="namespaceccp4srs.html">ccp4srs</a>      </li>
+      <li><a class="el" href="classccp4srs_1_1_monomer.html">Monomer</a>      </li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pro-methods">Protected Member Functions</a> &#124;
+<a href="#pro-attribs">Protected Attributes</a>  </div>
+  <div class="headertitle">
+<h1>ccp4srs::Monomer Class Reference</h1>  </div>
+</div>
+<div class="contents">
+<!-- doxytag: class="ccp4srs::Monomer" --><!-- doxytag: inherits="ccp4srs::Entry" -->
+<p><code>#include &lt;<a class="el" href="ccp4srs__monomer_8h_source.html">ccp4srs_monomer.h</a>&gt;</code></p>
+<!-- startSectionHeader --><div class="dynheader">
+Inheritance diagram for ccp4srs::Monomer:<!-- endSectionHeader --></div>
+<!-- startSectionSummary --><!-- endSectionSummary --><!-- startSectionContent --><div class="dyncontent">
+<div class="center"><img src="classccp4srs_1_1_monomer__inherit__graph.png" border="0" usemap="#ccp4srs_1_1_monomer_inherit__map" alt="Inheritance graph"/></div>
+<map name="ccp4srs_1_1_monomer_inherit__map" id="ccp4srs_1_1_monomer_inherit__map">
+<area shape="rect" href="classccp4srs_1_1_entry.html" title="ccp4srs::Entry" alt="" coords="23,7,140,33"/></map>
+<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center><!-- endSectionContent --></div>
+
+<p><a href="classccp4srs_1_1_monomer-members.html">List of all members.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#abd3a6efc83918f121e3e83165681ccd5">Monomer</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a33207c3c799fe120851007002464e2e2">~Monomer</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">virtual int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a01201fb01a7ed370e593563b129c74af">type</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a42598d1f669c5e539cb024bb023e0551">reset</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a1eca7f4a9537bddf81de26df20984183">ID</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a271e6aaeed7ace67e36f2c5fea626d70">oldID</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a3d9cd816f0e032e64e0d47ed7673ec63">setOldID</a> (mmdb::cpstr oldID)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#ab5a8d9361def2e547d1e65bf180f3252">chem_name</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a37432cca1867e01cd9af6d4569c2326a">chem_type</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a6bbfc74c882e403c57984d7310d4fb98">chem_formula</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a3e3e771e2d60581384b1169648b4d751">n_atoms</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a6a6e470c174fd570667bf43f95757c0d">n_bonds</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a832521f11b1adb4a0deb9fd92b4bc725">n_angles</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a0bf10d776d5d992424b99d88d884f101">n_torsions</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a047ec20b44f73aa0027fdd071aa265d6">n_chicenters</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a123cf02246e052730361055de3f0d477">n_planes</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">PAtom&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#ac3492a092c5436d182acae9b6712da7f">atom</a> (int n)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">PBond&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a6b01e3fa4cb59dc507460ea0715823fa">bond</a> (int n)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">PAngle&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a61b179edff80a9d168997038093cc92f">angle</a> (int n)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">PPlane&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#afdebf230f6aa9bf2692a82b919d59918">plane</a> (int n)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">PTree&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a79a4445aa7279951aa8426dc79114ebf">tree</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">PTorsion&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a1fdc6bd34cea4b7ea59d5399a8367f70">torsion</a> (int n)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">PChiCenter&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a3c1ea4e271769745f01c8dc4146c683e">chicenter</a> (int n)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#ae1c9221ebd49b62830621cd40524d215">add</a> (PAtom atom)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a88d4f2d1f97364930fed4bf349b23cb1">add</a> (PBond bond)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a3eab75471f83c2c92834a1e30400642e">add</a> (PAngle angle)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a394b2b32b99cd3c6e0b3654593436a2f">add</a> (PPlane plane)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#acdfa8628139cfb914f2aecdb1e2f37d2">add</a> (PTree stree)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a555cba2de4ecd6d3d7c192a52a9d44a3">add</a> (PTorsion torsion)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a1820529a0bee358372e53ea0fb0c0a56">add</a> (PChiCenter chicenter)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a1ca9838123fea51260be3c44abd6771f">get_atoms</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_bond.html">Bond</a> &gt; *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#af36aeb36b83f49d3b4fc28d4737b5efd">get_bonds</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_angle.html">Angle</a> &gt; *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a8d4b4084ca5c0e0fa42075f59eaf3e08">get_angles</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_torsion.html">Torsion</a> &gt; *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a7b31b6675690c2edc0baa0e070d349ad">get_torsions</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_chi_center.html">ChiCenter</a> &gt; *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a591d5f8275f5b5756442d96221039ef3">get_chicenters</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_plane.html">Plane</a> &gt; *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#aa454ac38a87c19006580a42bc38958fc">get_planes</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classccp4srs_1_1_tree.html">Tree</a> *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a351a18b323af41b74d1b415fcd1df640">get_tree</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a9ac9e9e610a1a0450130d5e5c4242d34">atom_no</a> (mmdb::cpstr aname)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a7b6acc92258007c15351989930e8672f">get_bound</a> (int atomNo, mmdb::cpstr elem, int serNo)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#ae60200771fdf1a869023dacebfb98278">get_bound</a> (int atomNo, int n)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a8ae0097e0e9950fc3f443f373a0a9359">get_bound</a> (mmdb::cpstr aname, int n)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">CCP4SRS_RC</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a67a965eb782472588f1a5f4e693c509e">addHydrogens</a> (mmdb::PResidue R)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#abb514ab63af7e9dbb68f59bc13551618">getAtomNameMatch</a> (mmdb::PPAtom A, int nat, mmdb::pstr altLoc, mmdb::ivector anmatch)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a17d26aa3a5b3b637cf6148499013c345">getAtomNameMatch</a> (<a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; *A, mmdb::ivector anmatch)</td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Matches atoms in given container with atoms in the monomer by atom names.  <a href="#a17d26aa3a5b3b637cf6148499013c345"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::math::PGraph&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a9d1a2b0facb208344413158d74446755">getGraph</a> (int *retCode)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a6c3ad68f13fb779921605d0e696add1c">getLeavingAtoms</a> (int &amp;nLeavingAtoms, mmdb::ivector &amp;leavingAtom, mmdb::ivector &amp;bondedAtom)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#aa9b0a99023e890070aec088182f8a65b">readFromCIF</a> (mmdb::mmcif::PData mmCIFData, mmdb::pstr error_desc=NULL)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::mmcif::PData&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a5e3fb1e64eab3e764cc83ff1e6c61fa3">makeCIF</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a6453406b0256cf9fbf74177a7db8770b">merge</a> (PMonomer monomer)</td></tr>
+<tr><td colspan="2"><h2><a name="pro-methods"></a>
+Protected Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a6a50cfb8d8e87162309106c66f5fc155">Init</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a4e12236b18de645dabd1afe57b46ebc0">readMonIDFromCIF</a> (mmdb::mmcif::PLoop loop)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#acbe4714fc7593d649b5e8901668d5c5c">readMonIDFromCIF</a> (mmdb::mmcif::PStruct mmCIFStruct)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a9e457d3f7633b79b598b66f382fa5c5c">readFromCIF_ccp4</a> (mmdb::mmcif::PData mmCIFData, mmdb::pstr error_desc)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#aaaec1b93dd1dcfe0e20484fd4bbc2a72">readFromCIF_rcsb</a> (mmdb::mmcif::PData mmCIFData, mmdb::pstr error_desc)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#ac0eb44f5d4ec3da57994cd741c8d6b0b">write_mem</a> (PMemIO memIO, int version)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">virtual bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#ac12b93e766cfbcfd4288512df739a56e">read_mem</a> (PMemIO memIO, int version, bool *Ok=NULL)</td></tr>
+<tr><td colspan="2"><h2><a name="pro-attribs"></a>
+Protected Attributes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::ResName&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a34240535a6e703495662936dba863026">monID</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::ResName&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a896cc0c3979b65913de25be2c2f75ec9">oldMonID</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::pstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a53b8d5232f3b2085d531eca33fb7c55a">monName</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::pstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#af0a573429afbbea61647c9851f0deba7">monType</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::pstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#aeb6bee62372a765e8aca0c1496689b3a">monFormula</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#abd7decc2129038a1416f324fee53afa1">atoms</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_bond.html">Bond</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a19495bb3c7e8d1c27f12f06729979d9e">bonds</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_angle.html">Angle</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a9177ec12ea5aeaa59228831d4127e592">angles</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_torsion.html">Torsion</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a70123373bff5c842e122856fb75634ab">torsions</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_chi_center.html">ChiCenter</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a96a126d39760ce281f8bf04186e29c13">chicenters</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_plane.html">Plane</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#a2f927ab2a3e517f9fe6cba6e89954cfe">planes</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classccp4srs_1_1_tree.html">Tree</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_monomer.html#aef8794097a333f1e4e20dd3d876f1432">struct_tree</a></td></tr>
+</table>
+<hr/><h2>Constructor &amp; Destructor Documentation</h2>
+<a class="anchor" id="abd3a6efc83918f121e3e83165681ccd5"></a><!-- doxytag: member="ccp4srs::Monomer::Monomer" ref="abd3a6efc83918f121e3e83165681ccd5" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::Monomer::Monomer </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a33207c3c799fe120851007002464e2e2"></a><!-- doxytag: member="ccp4srs::Monomer::~Monomer" ref="a33207c3c799fe120851007002464e2e2" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::Monomer::~Monomer </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Function Documentation</h2>
+<a class="anchor" id="ae1c9221ebd49b62830621cd40524d215"></a><!-- doxytag: member="ccp4srs::Monomer::add" ref="ae1c9221ebd49b62830621cd40524d215" args="(PAtom atom)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Monomer::add </td>
+          <td>(</td>
+          <td class="paramtype">PAtom&#160;</td>
+          <td class="paramname"> <em>atom</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a88d4f2d1f97364930fed4bf349b23cb1"></a><!-- doxytag: member="ccp4srs::Monomer::add" ref="a88d4f2d1f97364930fed4bf349b23cb1" args="(PBond bond)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Monomer::add </td>
+          <td>(</td>
+          <td class="paramtype">PBond&#160;</td>
+          <td class="paramname"> <em>bond</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a3eab75471f83c2c92834a1e30400642e"></a><!-- doxytag: member="ccp4srs::Monomer::add" ref="a3eab75471f83c2c92834a1e30400642e" args="(PAngle angle)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Monomer::add </td>
+          <td>(</td>
+          <td class="paramtype">PAngle&#160;</td>
+          <td class="paramname"> <em>angle</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a394b2b32b99cd3c6e0b3654593436a2f"></a><!-- doxytag: member="ccp4srs::Monomer::add" ref="a394b2b32b99cd3c6e0b3654593436a2f" args="(PPlane plane)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Monomer::add </td>
+          <td>(</td>
+          <td class="paramtype">PPlane&#160;</td>
+          <td class="paramname"> <em>plane</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="acdfa8628139cfb914f2aecdb1e2f37d2"></a><!-- doxytag: member="ccp4srs::Monomer::add" ref="acdfa8628139cfb914f2aecdb1e2f37d2" args="(PTree stree)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Monomer::add </td>
+          <td>(</td>
+          <td class="paramtype">PTree&#160;</td>
+          <td class="paramname"> <em>stree</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a555cba2de4ecd6d3d7c192a52a9d44a3"></a><!-- doxytag: member="ccp4srs::Monomer::add" ref="a555cba2de4ecd6d3d7c192a52a9d44a3" args="(PTorsion torsion)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Monomer::add </td>
+          <td>(</td>
+          <td class="paramtype">PTorsion&#160;</td>
+          <td class="paramname"> <em>torsion</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a1820529a0bee358372e53ea0fb0c0a56"></a><!-- doxytag: member="ccp4srs::Monomer::add" ref="a1820529a0bee358372e53ea0fb0c0a56" args="(PChiCenter chicenter)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Monomer::add </td>
+          <td>(</td>
+          <td class="paramtype">PChiCenter&#160;</td>
+          <td class="paramname"> <em>chicenter</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a67a965eb782472588f1a5f4e693c509e"></a><!-- doxytag: member="ccp4srs::Monomer::addHydrogens" ref="a67a965eb782472588f1a5f4e693c509e" args="(mmdb::PResidue R)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">CCP4SRS_RC</a> ccp4srs::Monomer::addHydrogens </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::PResidue&#160;</td>
+          <td class="paramname"> <em>R</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a61b179edff80a9d168997038093cc92f"></a><!-- doxytag: member="ccp4srs::Monomer::angle" ref="a61b179edff80a9d168997038093cc92f" args="(int n)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">PAngle ccp4srs::Monomer::angle </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>n</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ac3492a092c5436d182acae9b6712da7f"></a><!-- doxytag: member="ccp4srs::Monomer::atom" ref="ac3492a092c5436d182acae9b6712da7f" args="(int n)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">PAtom ccp4srs::Monomer::atom </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>n</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a9ac9e9e610a1a0450130d5e5c4242d34"></a><!-- doxytag: member="ccp4srs::Monomer::atom_no" ref="a9ac9e9e610a1a0450130d5e5c4242d34" args="(mmdb::cpstr aname)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Monomer::atom_no </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>aname</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a6b01e3fa4cb59dc507460ea0715823fa"></a><!-- doxytag: member="ccp4srs::Monomer::bond" ref="a6b01e3fa4cb59dc507460ea0715823fa" args="(int n)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">PBond ccp4srs::Monomer::bond </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>n</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a6bbfc74c882e403c57984d7310d4fb98"></a><!-- doxytag: member="ccp4srs::Monomer::chem_formula" ref="a6bbfc74c882e403c57984d7310d4fb98" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::cpstr ccp4srs::Monomer::chem_formula </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ab5a8d9361def2e547d1e65bf180f3252"></a><!-- doxytag: member="ccp4srs::Monomer::chem_name" ref="ab5a8d9361def2e547d1e65bf180f3252" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::cpstr ccp4srs::Monomer::chem_name </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a37432cca1867e01cd9af6d4569c2326a"></a><!-- doxytag: member="ccp4srs::Monomer::chem_type" ref="a37432cca1867e01cd9af6d4569c2326a" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::cpstr ccp4srs::Monomer::chem_type </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a3c1ea4e271769745f01c8dc4146c683e"></a><!-- doxytag: member="ccp4srs::Monomer::chicenter" ref="a3c1ea4e271769745f01c8dc4146c683e" args="(int n)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">PChiCenter ccp4srs::Monomer::chicenter </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>n</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a8d4b4084ca5c0e0fa42075f59eaf3e08"></a><!-- doxytag: member="ccp4srs::Monomer::get_angles" ref="a8d4b4084ca5c0e0fa42075f59eaf3e08" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt;<a class="el" href="classccp4srs_1_1_angle.html">Angle</a>&gt;* ccp4srs::Monomer::get_angles </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a1ca9838123fea51260be3c44abd6771f"></a><!-- doxytag: member="ccp4srs::Monomer::get_atoms" ref="a1ca9838123fea51260be3c44abd6771f" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt;<a class="el" href="classccp4srs_1_1_atom.html">Atom</a>&gt;* ccp4srs::Monomer::get_atoms </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="af36aeb36b83f49d3b4fc28d4737b5efd"></a><!-- doxytag: member="ccp4srs::Monomer::get_bonds" ref="af36aeb36b83f49d3b4fc28d4737b5efd" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt;<a class="el" href="classccp4srs_1_1_bond.html">Bond</a>&gt;* ccp4srs::Monomer::get_bonds </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a7b6acc92258007c15351989930e8672f"></a><!-- doxytag: member="ccp4srs::Monomer::get_bound" ref="a7b6acc92258007c15351989930e8672f" args="(int atomNo, mmdb::cpstr elem, int serNo)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Monomer::get_bound </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>atomNo</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>elem</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>serNo</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ae60200771fdf1a869023dacebfb98278"></a><!-- doxytag: member="ccp4srs::Monomer::get_bound" ref="ae60200771fdf1a869023dacebfb98278" args="(int atomNo, int n)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Monomer::get_bound </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>atomNo</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>n</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a8ae0097e0e9950fc3f443f373a0a9359"></a><!-- doxytag: member="ccp4srs::Monomer::get_bound" ref="a8ae0097e0e9950fc3f443f373a0a9359" args="(mmdb::cpstr aname, int n)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Monomer::get_bound </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>aname</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>n</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a591d5f8275f5b5756442d96221039ef3"></a><!-- doxytag: member="ccp4srs::Monomer::get_chicenters" ref="a591d5f8275f5b5756442d96221039ef3" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt;<a class="el" href="classccp4srs_1_1_chi_center.html">ChiCenter</a>&gt;* ccp4srs::Monomer::get_chicenters </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aa454ac38a87c19006580a42bc38958fc"></a><!-- doxytag: member="ccp4srs::Monomer::get_planes" ref="aa454ac38a87c19006580a42bc38958fc" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt;<a class="el" href="classccp4srs_1_1_plane.html">Plane</a>&gt;* ccp4srs::Monomer::get_planes </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a7b31b6675690c2edc0baa0e070d349ad"></a><!-- doxytag: member="ccp4srs::Monomer::get_torsions" ref="a7b31b6675690c2edc0baa0e070d349ad" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt;<a class="el" href="classccp4srs_1_1_torsion.html">Torsion</a>&gt;* ccp4srs::Monomer::get_torsions </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a351a18b323af41b74d1b415fcd1df640"></a><!-- doxytag: member="ccp4srs::Monomer::get_tree" ref="a351a18b323af41b74d1b415fcd1df640" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="classccp4srs_1_1_tree.html">Tree</a>* ccp4srs::Monomer::get_tree </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="abb514ab63af7e9dbb68f59bc13551618"></a><!-- doxytag: member="ccp4srs::Monomer::getAtomNameMatch" ref="abb514ab63af7e9dbb68f59bc13551618" args="(mmdb::PPAtom A, int nat, mmdb::pstr altLoc, mmdb::ivector anmatch)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Monomer::getAtomNameMatch </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::PPAtom&#160;</td>
+          <td class="paramname"> <em>A</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>nat</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::pstr&#160;</td>
+          <td class="paramname"> <em>altLoc</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::ivector&#160;</td>
+          <td class="paramname"> <em>anmatch</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a17d26aa3a5b3b637cf6148499013c345"></a><!-- doxytag: member="ccp4srs::Monomer::getAtomNameMatch" ref="a17d26aa3a5b3b637cf6148499013c345" args="(Container&lt; Atom &gt; *A, mmdb::ivector anmatch)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Monomer::getAtomNameMatch </td>
+          <td>(</td>
+          <td class="paramtype"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; *&#160;</td>
+          <td class="paramname"> <em>A</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::ivector&#160;</td>
+          <td class="paramname"> <em>anmatch</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>Matches atoms in given container with atoms in the monomer by atom names. </p>
+<dl><dt><b>Parameters:</b></dt><dd>
+  <table class="params">
+    <tr><td class="paramdir">[in]</td><td class="paramname">A</td><td>pointer to atom container </td></tr>
+    <tr><td class="paramdir">[out]</td><td class="paramname">anmatch</td><td>allocated integer vector [0..A-&gt;numberOf()-1], where the match will be returned: </p>
+<ul>
+<li><b>anmatch</b>[i]&gt;=0 : atom A-&gt;at(i) matches anmathch[i]-th atom in the monomer </li>
+<li><b>anmatch</b>[i]&lt;0 : atom A-&gt;at(i) does not have a name match in the monomer </li>
+</ul>
+</td></tr>
+  </table>
+  </dd>
+</dl>
+
+</div>
+</div>
+<a class="anchor" id="a9d1a2b0facb208344413158d74446755"></a><!-- doxytag: member="ccp4srs::Monomer::getGraph" ref="a9d1a2b0facb208344413158d74446755" args="(int *retCode)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::math::PGraph ccp4srs::Monomer::getGraph </td>
+          <td>(</td>
+          <td class="paramtype">int *&#160;</td>
+          <td class="paramname"> <em>retCode</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a6c3ad68f13fb779921605d0e696add1c"></a><!-- doxytag: member="ccp4srs::Monomer::getLeavingAtoms" ref="a6c3ad68f13fb779921605d0e696add1c" args="(int &amp;nLeavingAtoms, mmdb::ivector &amp;leavingAtom, mmdb::ivector &amp;bondedAtom)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Monomer::getLeavingAtoms </td>
+          <td>(</td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>nLeavingAtoms</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::ivector &amp;&#160;</td>
+          <td class="paramname"> <em>leavingAtom</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::ivector &amp;&#160;</td>
+          <td class="paramname"> <em>bondedAtom</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a1eca7f4a9537bddf81de26df20984183"></a><!-- doxytag: member="ccp4srs::Monomer::ID" ref="a1eca7f4a9537bddf81de26df20984183" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::cpstr ccp4srs::Monomer::ID </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a6a50cfb8d8e87162309106c66f5fc155"></a><!-- doxytag: member="ccp4srs::Monomer::Init" ref="a6a50cfb8d8e87162309106c66f5fc155" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Monomer::Init </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a5e3fb1e64eab3e764cc83ff1e6c61fa3"></a><!-- doxytag: member="ccp4srs::Monomer::makeCIF" ref="a5e3fb1e64eab3e764cc83ff1e6c61fa3" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::mmcif::PData ccp4srs::Monomer::makeCIF </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a6453406b0256cf9fbf74177a7db8770b"></a><!-- doxytag: member="ccp4srs::Monomer::merge" ref="a6453406b0256cf9fbf74177a7db8770b" args="(PMonomer monomer)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Monomer::merge </td>
+          <td>(</td>
+          <td class="paramtype">PMonomer&#160;</td>
+          <td class="paramname"> <em>monomer</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a832521f11b1adb4a0deb9fd92b4bc725"></a><!-- doxytag: member="ccp4srs::Monomer::n_angles" ref="a832521f11b1adb4a0deb9fd92b4bc725" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Monomer::n_angles </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a3e3e771e2d60581384b1169648b4d751"></a><!-- doxytag: member="ccp4srs::Monomer::n_atoms" ref="a3e3e771e2d60581384b1169648b4d751" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Monomer::n_atoms </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a6a6e470c174fd570667bf43f95757c0d"></a><!-- doxytag: member="ccp4srs::Monomer::n_bonds" ref="a6a6e470c174fd570667bf43f95757c0d" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Monomer::n_bonds </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a047ec20b44f73aa0027fdd071aa265d6"></a><!-- doxytag: member="ccp4srs::Monomer::n_chicenters" ref="a047ec20b44f73aa0027fdd071aa265d6" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Monomer::n_chicenters </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a123cf02246e052730361055de3f0d477"></a><!-- doxytag: member="ccp4srs::Monomer::n_planes" ref="a123cf02246e052730361055de3f0d477" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Monomer::n_planes </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a0bf10d776d5d992424b99d88d884f101"></a><!-- doxytag: member="ccp4srs::Monomer::n_torsions" ref="a0bf10d776d5d992424b99d88d884f101" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Monomer::n_torsions </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a271e6aaeed7ace67e36f2c5fea626d70"></a><!-- doxytag: member="ccp4srs::Monomer::oldID" ref="a271e6aaeed7ace67e36f2c5fea626d70" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::cpstr ccp4srs::Monomer::oldID </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="afdebf230f6aa9bf2692a82b919d59918"></a><!-- doxytag: member="ccp4srs::Monomer::plane" ref="afdebf230f6aa9bf2692a82b919d59918" args="(int n)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">PPlane ccp4srs::Monomer::plane </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>n</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ac12b93e766cfbcfd4288512df739a56e"></a><!-- doxytag: member="ccp4srs::Monomer::read_mem" ref="ac12b93e766cfbcfd4288512df739a56e" args="(PMemIO memIO, int version, bool *Ok=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::Monomer::read_mem </td>
+          <td>(</td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td><code> [protected, virtual]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>Reimplemented from <a class="el" href="classccp4srs_1_1_entry.html#a2d3193b4e34c21b286526931e2e5b62d">ccp4srs::Entry</a>.</p>
+
+</div>
+</div>
+<a class="anchor" id="aa9b0a99023e890070aec088182f8a65b"></a><!-- doxytag: member="ccp4srs::Monomer::readFromCIF" ref="aa9b0a99023e890070aec088182f8a65b" args="(mmdb::mmcif::PData mmCIFData, mmdb::pstr error_desc=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Monomer::readFromCIF </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PData&#160;</td>
+          <td class="paramname"> <em>mmCIFData</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::pstr&#160;</td>
+          <td class="paramname"> <em>error_desc</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a9e457d3f7633b79b598b66f382fa5c5c"></a><!-- doxytag: member="ccp4srs::Monomer::readFromCIF_ccp4" ref="a9e457d3f7633b79b598b66f382fa5c5c" args="(mmdb::mmcif::PData mmCIFData, mmdb::pstr error_desc)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Monomer::readFromCIF_ccp4 </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PData&#160;</td>
+          <td class="paramname"> <em>mmCIFData</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::pstr&#160;</td>
+          <td class="paramname"> <em>error_desc</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aaaec1b93dd1dcfe0e20484fd4bbc2a72"></a><!-- doxytag: member="ccp4srs::Monomer::readFromCIF_rcsb" ref="aaaec1b93dd1dcfe0e20484fd4bbc2a72" args="(mmdb::mmcif::PData mmCIFData, mmdb::pstr error_desc)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Monomer::readFromCIF_rcsb </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PData&#160;</td>
+          <td class="paramname"> <em>mmCIFData</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::pstr&#160;</td>
+          <td class="paramname"> <em>error_desc</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="acbe4714fc7593d649b5e8901668d5c5c"></a><!-- doxytag: member="ccp4srs::Monomer::readMonIDFromCIF" ref="acbe4714fc7593d649b5e8901668d5c5c" args="(mmdb::mmcif::PStruct mmCIFStruct)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Monomer::readMonIDFromCIF </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PStruct&#160;</td>
+          <td class="paramname"> <em>mmCIFStruct</em>&#160;)</td>
+          <td><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a4e12236b18de645dabd1afe57b46ebc0"></a><!-- doxytag: member="ccp4srs::Monomer::readMonIDFromCIF" ref="a4e12236b18de645dabd1afe57b46ebc0" args="(mmdb::mmcif::PLoop loop)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Monomer::readMonIDFromCIF </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>loop</em>&#160;)</td>
+          <td><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a42598d1f669c5e539cb024bb023e0551"></a><!-- doxytag: member="ccp4srs::Monomer::reset" ref="a42598d1f669c5e539cb024bb023e0551" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Monomer::reset </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a3d9cd816f0e032e64e0d47ed7673ec63"></a><!-- doxytag: member="ccp4srs::Monomer::setOldID" ref="a3d9cd816f0e032e64e0d47ed7673ec63" args="(mmdb::cpstr oldID)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Monomer::setOldID </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>oldID</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a1fdc6bd34cea4b7ea59d5399a8367f70"></a><!-- doxytag: member="ccp4srs::Monomer::torsion" ref="a1fdc6bd34cea4b7ea59d5399a8367f70" args="(int n)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">PTorsion ccp4srs::Monomer::torsion </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>n</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a79a4445aa7279951aa8426dc79114ebf"></a><!-- doxytag: member="ccp4srs::Monomer::tree" ref="a79a4445aa7279951aa8426dc79114ebf" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">PTree ccp4srs::Monomer::tree </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a01201fb01a7ed370e593563b129c74af"></a><!-- doxytag: member="ccp4srs::Monomer::type" ref="a01201fb01a7ed370e593563b129c74af" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">virtual int ccp4srs::Monomer::type </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline, virtual]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>Reimplemented from <a class="el" href="classccp4srs_1_1_entry.html#a401d0e96699c34bef6b408e054f14540">ccp4srs::Entry</a>.</p>
+
+</div>
+</div>
+<a class="anchor" id="ac0eb44f5d4ec3da57994cd741c8d6b0b"></a><!-- doxytag: member="ccp4srs::Monomer::write_mem" ref="ac0eb44f5d4ec3da57994cd741c8d6b0b" args="(PMemIO memIO, int version)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Monomer::write_mem </td>
+          <td>(</td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td><code> [protected, virtual]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>Reimplemented from <a class="el" href="classccp4srs_1_1_entry.html#a817f6f566baf41280c5cee0fc3507871">ccp4srs::Entry</a>.</p>
+
+</div>
+</div>
+<hr/><h2>Member Data Documentation</h2>
+<a class="anchor" id="a9177ec12ea5aeaa59228831d4127e592"></a><!-- doxytag: member="ccp4srs::Monomer::angles" ref="a9177ec12ea5aeaa59228831d4127e592" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt;<a class="el" href="classccp4srs_1_1_angle.html">Angle</a>&gt; <a class="el" href="classccp4srs_1_1_monomer.html#a9177ec12ea5aeaa59228831d4127e592">ccp4srs::Monomer::angles</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="abd7decc2129038a1416f324fee53afa1"></a><!-- doxytag: member="ccp4srs::Monomer::atoms" ref="abd7decc2129038a1416f324fee53afa1" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt;<a class="el" href="classccp4srs_1_1_atom.html">Atom</a>&gt; <a class="el" href="classccp4srs_1_1_monomer.html#abd7decc2129038a1416f324fee53afa1">ccp4srs::Monomer::atoms</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a19495bb3c7e8d1c27f12f06729979d9e"></a><!-- doxytag: member="ccp4srs::Monomer::bonds" ref="a19495bb3c7e8d1c27f12f06729979d9e" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt;<a class="el" href="classccp4srs_1_1_bond.html">Bond</a>&gt; <a class="el" href="classccp4srs_1_1_monomer.html#a19495bb3c7e8d1c27f12f06729979d9e">ccp4srs::Monomer::bonds</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a96a126d39760ce281f8bf04186e29c13"></a><!-- doxytag: member="ccp4srs::Monomer::chicenters" ref="a96a126d39760ce281f8bf04186e29c13" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt;<a class="el" href="classccp4srs_1_1_chi_center.html">ChiCenter</a>&gt; <a class="el" href="classccp4srs_1_1_monomer.html#a96a126d39760ce281f8bf04186e29c13">ccp4srs::Monomer::chicenters</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aeb6bee62372a765e8aca0c1496689b3a"></a><!-- doxytag: member="ccp4srs::Monomer::monFormula" ref="aeb6bee62372a765e8aca0c1496689b3a" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::pstr <a class="el" href="classccp4srs_1_1_monomer.html#aeb6bee62372a765e8aca0c1496689b3a">ccp4srs::Monomer::monFormula</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a34240535a6e703495662936dba863026"></a><!-- doxytag: member="ccp4srs::Monomer::monID" ref="a34240535a6e703495662936dba863026" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::ResName <a class="el" href="classccp4srs_1_1_monomer.html#a34240535a6e703495662936dba863026">ccp4srs::Monomer::monID</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a53b8d5232f3b2085d531eca33fb7c55a"></a><!-- doxytag: member="ccp4srs::Monomer::monName" ref="a53b8d5232f3b2085d531eca33fb7c55a" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::pstr <a class="el" href="classccp4srs_1_1_monomer.html#a53b8d5232f3b2085d531eca33fb7c55a">ccp4srs::Monomer::monName</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="af0a573429afbbea61647c9851f0deba7"></a><!-- doxytag: member="ccp4srs::Monomer::monType" ref="af0a573429afbbea61647c9851f0deba7" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::pstr <a class="el" href="classccp4srs_1_1_monomer.html#af0a573429afbbea61647c9851f0deba7">ccp4srs::Monomer::monType</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a896cc0c3979b65913de25be2c2f75ec9"></a><!-- doxytag: member="ccp4srs::Monomer::oldMonID" ref="a896cc0c3979b65913de25be2c2f75ec9" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::ResName <a class="el" href="classccp4srs_1_1_monomer.html#a896cc0c3979b65913de25be2c2f75ec9">ccp4srs::Monomer::oldMonID</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a2f927ab2a3e517f9fe6cba6e89954cfe"></a><!-- doxytag: member="ccp4srs::Monomer::planes" ref="a2f927ab2a3e517f9fe6cba6e89954cfe" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt;<a class="el" href="classccp4srs_1_1_plane.html">Plane</a>&gt; <a class="el" href="classccp4srs_1_1_monomer.html#a2f927ab2a3e517f9fe6cba6e89954cfe">ccp4srs::Monomer::planes</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aef8794097a333f1e4e20dd3d876f1432"></a><!-- doxytag: member="ccp4srs::Monomer::struct_tree" ref="aef8794097a333f1e4e20dd3d876f1432" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="classccp4srs_1_1_tree.html">Tree</a> <a class="el" href="classccp4srs_1_1_monomer.html#aef8794097a333f1e4e20dd3d876f1432">ccp4srs::Monomer::struct_tree</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a70123373bff5c842e122856fb75634ab"></a><!-- doxytag: member="ccp4srs::Monomer::torsions" ref="a70123373bff5c842e122856fb75634ab" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt;<a class="el" href="classccp4srs_1_1_torsion.html">Torsion</a>&gt; <a class="el" href="classccp4srs_1_1_monomer.html#a70123373bff5c842e122856fb75634ab">ccp4srs::Monomer::torsions</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following files:<ul>
+<li>src/<a class="el" href="ccp4srs__monomer_8h_source.html">ccp4srs_monomer.h</a></li>
+<li>src/<a class="el" href="ccp4srs__monomer_8cpp.html">ccp4srs_monomer.cpp</a></li>
+</ul>
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+
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+<a href="http://www.doxygen.org/index.html">
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--- ccp4srs-old/doc-html/html/classccp4srs_1_1_monomer__inherit__graph.map	1969-12-31 16:00:00.000000000 -0800
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--- ccp4srs-old/doc-html/html/classccp4srs_1_1_monomer__inherit__graph.md5	1969-12-31 16:00:00.000000000 -0800
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diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_plane-members.html ccp4srs/doc-html/html/classccp4srs_1_1_plane-members.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_plane-members.html	1969-12-31 16:00:00.000000000 -0800
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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
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+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
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+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
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+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
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+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>ccp4srs::Plane Member List</h1>  </div>
+</div>
+<div class="contents">
+This is the complete list of members for <a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a>, including all inherited members.<table>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_plane.html#ad1e544c70729b5a17dba23301ba6ca7e">atom</a>(int atomNo)</td><td><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_plane.html#a91e4f55f473565e42c27b6aab5311222">atoms</a>()</td><td><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_plane.html#a9db264baa4154922dfac882f4f437d34">copy</a>(PPlane plane, mmdb::ivector anmatch=NULL)</td><td><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_plane.html#a5837e387b59c8d350271fd11a644ee8d">dist_esd</a></td><td><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_plane.html#a8da6c13ce79682d5f17e23f7c3e84849">empty</a>()</td><td><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5edad0a61a72f29321313e1bc19920df40f9">EmptyLoop</a> enum value</td><td><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_plane.html#ad9f1d004296b308a0955997695277ff4">esd</a>(int atomNo)</td><td><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_plane.html#a4fd16b46609257ebe87c7b7347597b2b">esds</a>()</td><td><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_plane.html#ac47f99cd6bf3190767da8fc85d01dc18">id</a>()</td><td><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_plane.html#a1ac0cfa095deac2bd97e99ce2b30de96">makeCIFTags</a>(mmdb::mmcif::PLoop mmCIFLoop)</td><td><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td><code> [static]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_plane.html#aa76a845ff6abce3d2c8f40db13717842">n_atoms</a></td><td><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5eda95f4f7898a15589a3db43827444d2692">NoMorePlanes</a> enum value</td><td><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5edae47dd3ee9591c478c387ddbe09f7ef34">Ok</a> enum value</td><td><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_plane.html#ab45260579cf6dd22ecdaa93ad3b5c183">Plane</a>()</td><td><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_plane.html#a4c8155332953ddb6cf79acf018c98c85">plane_atoms</a></td><td><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_plane.html#afdfdff5528e19537d834061022c2b2bf">plane_id</a></td><td><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_plane.html#a148162145438f6f97414eee0aa72275a">read_mem</a>(PMemIO memIO, int version, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_plane.html#a656a93b833de401dcac75db47b5bcf57">readFromCIF</a>(mmdb::mmcif::PLoop mmCIFLoop, int planeNo, Container&lt; Atom &gt; &amp;atoms)</td><td><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_plane.html#a61ab65ef97a61c79d1190673a5a1b8e3">size</a>()</td><td><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_plane.html#a759255f2b21b770caa535f129e5f60bb">write_mem</a>(PMemIO memIO, int version)</td><td><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_plane.html#abd5b6df5e6d2bdafdd064a04974cf82a">writeToCIF</a>(mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID, Container&lt; Atom &gt; &amp;atoms)</td><td><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_plane.html#a521911d044ea2aa8ca4e769b9d8d4e58">~Plane</a>()</td><td><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></td><td><code> [virtual]</code></td></tr>
+</table></div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
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+        name="MSearchResults" id="MSearchResults">
+</iframe>
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+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_plane.html ccp4srs/doc-html/html/classccp4srs_1_1_plane.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_plane.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_plane.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,536 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: ccp4srs::Plane Class Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
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+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
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+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="navpath">
+    <ul>
+      <li><a class="el" href="namespaceccp4srs.html">ccp4srs</a>      </li>
+      <li><a class="el" href="classccp4srs_1_1_plane.html">Plane</a>      </li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="summary">
+<a href="#pub-types">Public Types</a> &#124;
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pub-static-methods">Static Public Member Functions</a> &#124;
+<a href="#pro-methods">Protected Member Functions</a> &#124;
+<a href="#pro-attribs">Protected Attributes</a>  </div>
+  <div class="headertitle">
+<h1>ccp4srs::Plane Class Reference</h1>  </div>
+</div>
+<div class="contents">
+<!-- doxytag: class="ccp4srs::Plane" -->
+<p><code>#include &lt;<a class="el" href="ccp4srs__plane_8h_source.html">ccp4srs_plane.h</a>&gt;</code></p>
+
+<p><a href="classccp4srs_1_1_plane-members.html">List of all members.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="pub-types"></a>
+Public Types</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom">{ <a class="el" href="classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5edae47dd3ee9591c478c387ddbe09f7ef34">Ok</a> = 0, 
+<a class="el" href="classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5edad0a61a72f29321313e1bc19920df40f9">EmptyLoop</a> = -11111, 
+<a class="el" href="classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5eda95f4f7898a15589a3db43827444d2692">NoMorePlanes</a> = -11112
+ }</td></tr>
+<tr><td colspan="2"><h2><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_plane.html#ab45260579cf6dd22ecdaa93ad3b5c183">Plane</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_plane.html#a521911d044ea2aa8ca4e769b9d8d4e58">~Plane</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_plane.html#ac47f99cd6bf3190767da8fc85d01dc18">id</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_plane.html#a61ab65ef97a61c79d1190673a5a1b8e3">size</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::ivector&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_plane.html#a91e4f55f473565e42c27b6aab5311222">atoms</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::rvector&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_plane.html#a4fd16b46609257ebe87c7b7347597b2b">esds</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_plane.html#ad1e544c70729b5a17dba23301ba6ca7e">atom</a> (int atomNo)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_plane.html#ad9f1d004296b308a0955997695277ff4">esd</a> (int atomNo)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_plane.html#a656a93b833de401dcac75db47b5bcf57">readFromCIF</a> (mmdb::mmcif::PLoop mmCIFLoop, int planeNo, <a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;atoms)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_plane.html#abd5b6df5e6d2bdafdd064a04974cf82a">writeToCIF</a> (mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID, <a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;atoms)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_plane.html#a759255f2b21b770caa535f129e5f60bb">write_mem</a> (PMemIO memIO, int version)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_plane.html#a148162145438f6f97414eee0aa72275a">read_mem</a> (PMemIO memIO, int version, bool *Ok=NULL)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_plane.html#a9db264baa4154922dfac882f4f437d34">copy</a> (PPlane plane, mmdb::ivector anmatch=NULL)</td></tr>
+<tr><td colspan="2"><h2><a name="pub-static-methods"></a>
+Static Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">static void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_plane.html#a1ac0cfa095deac2bd97e99ce2b30de96">makeCIFTags</a> (mmdb::mmcif::PLoop mmCIFLoop)</td></tr>
+<tr><td colspan="2"><h2><a name="pro-methods"></a>
+Protected Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_plane.html#a8da6c13ce79682d5f17e23f7c3e84849">empty</a> ()</td></tr>
+<tr><td colspan="2"><h2><a name="pro-attribs"></a>
+Protected Attributes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespaceccp4srs.html#ac768cc62149be89b81a30d88a09f0166">PlaneID</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_plane.html#afdfdff5528e19537d834061022c2b2bf">plane_id</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">plane id  <a href="#afdfdff5528e19537d834061022c2b2bf"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_plane.html#aa76a845ff6abce3d2c8f40db13717842">n_atoms</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">plane size  <a href="#aa76a845ff6abce3d2c8f40db13717842"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::ivector&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_plane.html#a4c8155332953ddb6cf79acf018c98c85">plane_atoms</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">vector of plain's atom names  <a href="#a4c8155332953ddb6cf79acf018c98c85"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::rvector&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_plane.html#a5837e387b59c8d350271fd11a644ee8d">dist_esd</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">vector of distance esds from the plane  <a href="#a5837e387b59c8d350271fd11a644ee8d"></a><br/></td></tr>
+</table>
+<hr/><h2>Member Enumeration Documentation</h2>
+<a class="anchor" id="a629b7441d8798a5fc692feefd6cbe5ed"></a><!-- doxytag: member="ccp4srs::Plane::@3" ref="a629b7441d8798a5fc692feefd6cbe5ed" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">anonymous enum</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+<dl><dt><b>Enumerator: </b></dt><dd><table border="0" cellspacing="2" cellpadding="0">
+<tr><td valign="top"><em><a class="anchor" id="a629b7441d8798a5fc692feefd6cbe5edae47dd3ee9591c478c387ddbe09f7ef34"></a><!-- doxytag: member="Ok" ref="a629b7441d8798a5fc692feefd6cbe5edae47dd3ee9591c478c387ddbe09f7ef34" args="" -->Ok</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a629b7441d8798a5fc692feefd6cbe5edad0a61a72f29321313e1bc19920df40f9"></a><!-- doxytag: member="EmptyLoop" ref="a629b7441d8798a5fc692feefd6cbe5edad0a61a72f29321313e1bc19920df40f9" args="" -->EmptyLoop</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a629b7441d8798a5fc692feefd6cbe5eda95f4f7898a15589a3db43827444d2692"></a><!-- doxytag: member="NoMorePlanes" ref="a629b7441d8798a5fc692feefd6cbe5eda95f4f7898a15589a3db43827444d2692" args="" -->NoMorePlanes</em>&nbsp;</td><td>
+</td></tr>
+</table>
+</dd>
+</dl>
+
+</div>
+</div>
+<hr/><h2>Constructor &amp; Destructor Documentation</h2>
+<a class="anchor" id="ab45260579cf6dd22ecdaa93ad3b5c183"></a><!-- doxytag: member="ccp4srs::Plane::Plane" ref="ab45260579cf6dd22ecdaa93ad3b5c183" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::Plane::Plane </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a521911d044ea2aa8ca4e769b9d8d4e58"></a><!-- doxytag: member="ccp4srs::Plane::~Plane" ref="a521911d044ea2aa8ca4e769b9d8d4e58" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::Plane::~Plane </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [virtual]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Function Documentation</h2>
+<a class="anchor" id="ad1e544c70729b5a17dba23301ba6ca7e"></a><!-- doxytag: member="ccp4srs::Plane::atom" ref="ad1e544c70729b5a17dba23301ba6ca7e" args="(int atomNo)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Plane::atom </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>atomNo</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a91e4f55f473565e42c27b6aab5311222"></a><!-- doxytag: member="ccp4srs::Plane::atoms" ref="a91e4f55f473565e42c27b6aab5311222" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::ivector ccp4srs::Plane::atoms </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a9db264baa4154922dfac882f4f437d34"></a><!-- doxytag: member="ccp4srs::Plane::copy" ref="a9db264baa4154922dfac882f4f437d34" args="(PPlane plane, mmdb::ivector anmatch=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Plane::copy </td>
+          <td>(</td>
+          <td class="paramtype">PPlane&#160;</td>
+          <td class="paramname"> <em>plane</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::ivector&#160;</td>
+          <td class="paramname"> <em>anmatch</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a8da6c13ce79682d5f17e23f7c3e84849"></a><!-- doxytag: member="ccp4srs::Plane::empty" ref="a8da6c13ce79682d5f17e23f7c3e84849" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Plane::empty </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ad9f1d004296b308a0955997695277ff4"></a><!-- doxytag: member="ccp4srs::Plane::esd" ref="ad9f1d004296b308a0955997695277ff4" args="(int atomNo)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype ccp4srs::Plane::esd </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>atomNo</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a4fd16b46609257ebe87c7b7347597b2b"></a><!-- doxytag: member="ccp4srs::Plane::esds" ref="a4fd16b46609257ebe87c7b7347597b2b" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::rvector ccp4srs::Plane::esds </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ac47f99cd6bf3190767da8fc85d01dc18"></a><!-- doxytag: member="ccp4srs::Plane::id" ref="ac47f99cd6bf3190767da8fc85d01dc18" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::cpstr ccp4srs::Plane::id </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a1ac0cfa095deac2bd97e99ce2b30de96"></a><!-- doxytag: member="ccp4srs::Plane::makeCIFTags" ref="a1ac0cfa095deac2bd97e99ce2b30de96" args="(mmdb::mmcif::PLoop mmCIFLoop)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Plane::makeCIFTags </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>mmCIFLoop</em>&#160;)</td>
+          <td><code> [static]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a148162145438f6f97414eee0aa72275a"></a><!-- doxytag: member="ccp4srs::Plane::read_mem" ref="a148162145438f6f97414eee0aa72275a" args="(PMemIO memIO, int version, bool *Ok=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::Plane::read_mem </td>
+          <td>(</td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a656a93b833de401dcac75db47b5bcf57"></a><!-- doxytag: member="ccp4srs::Plane::readFromCIF" ref="a656a93b833de401dcac75db47b5bcf57" args="(mmdb::mmcif::PLoop mmCIFLoop, int planeNo, Container&lt; Atom &gt; &amp;atoms)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Plane::readFromCIF </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>mmCIFLoop</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>planeNo</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;&#160;</td>
+          <td class="paramname"> <em>atoms</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a61ab65ef97a61c79d1190673a5a1b8e3"></a><!-- doxytag: member="ccp4srs::Plane::size" ref="a61ab65ef97a61c79d1190673a5a1b8e3" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Plane::size </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a759255f2b21b770caa535f129e5f60bb"></a><!-- doxytag: member="ccp4srs::Plane::write_mem" ref="a759255f2b21b770caa535f129e5f60bb" args="(PMemIO memIO, int version)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Plane::write_mem </td>
+          <td>(</td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="abd5b6df5e6d2bdafdd064a04974cf82a"></a><!-- doxytag: member="ccp4srs::Plane::writeToCIF" ref="abd5b6df5e6d2bdafdd064a04974cf82a" args="(mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID, Container&lt; Atom &gt; &amp;atoms)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Plane::writeToCIF </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>mmCIFLoop</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>monID</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;&#160;</td>
+          <td class="paramname"> <em>atoms</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Data Documentation</h2>
+<a class="anchor" id="a5837e387b59c8d350271fd11a644ee8d"></a><!-- doxytag: member="ccp4srs::Plane::dist_esd" ref="a5837e387b59c8d350271fd11a644ee8d" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::rvector <a class="el" href="classccp4srs_1_1_plane.html#a5837e387b59c8d350271fd11a644ee8d">ccp4srs::Plane::dist_esd</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>vector of distance esds from the plane </p>
+
+</div>
+</div>
+<a class="anchor" id="aa76a845ff6abce3d2c8f40db13717842"></a><!-- doxytag: member="ccp4srs::Plane::n_atoms" ref="aa76a845ff6abce3d2c8f40db13717842" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_plane.html#aa76a845ff6abce3d2c8f40db13717842">ccp4srs::Plane::n_atoms</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>plane size </p>
+
+</div>
+</div>
+<a class="anchor" id="a4c8155332953ddb6cf79acf018c98c85"></a><!-- doxytag: member="ccp4srs::Plane::plane_atoms" ref="a4c8155332953ddb6cf79acf018c98c85" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::ivector <a class="el" href="classccp4srs_1_1_plane.html#a4c8155332953ddb6cf79acf018c98c85">ccp4srs::Plane::plane_atoms</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>vector of plain's atom names </p>
+
+</div>
+</div>
+<a class="anchor" id="afdfdff5528e19537d834061022c2b2bf"></a><!-- doxytag: member="ccp4srs::Plane::plane_id" ref="afdfdff5528e19537d834061022c2b2bf" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="namespaceccp4srs.html#ac768cc62149be89b81a30d88a09f0166">PlaneID</a> <a class="el" href="classccp4srs_1_1_plane.html#afdfdff5528e19537d834061022c2b2bf">ccp4srs::Plane::plane_id</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>plane id </p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following files:<ul>
+<li>src/<a class="el" href="ccp4srs__plane_8h_source.html">ccp4srs_plane.h</a></li>
+<li>src/<a class="el" href="ccp4srs__plane_8cpp.html">ccp4srs_plane.cpp</a></li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
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+
+<!-- iframe showing the search results (closed by default) -->
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+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_torsion-members.html ccp4srs/doc-html/html/classccp4srs_1_1_torsion-members.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_torsion-members.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_torsion-members.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,99 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
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+<body onload='searchBox.OnSelectItem(0);'>
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+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
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+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
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+          </span>
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+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>ccp4srs::Torsion Member List</h1>  </div>
+</div>
+<div class="contents">
+This is the complete list of members for <a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a>, including all inherited members.<table>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#af30f2e612259dedd1e569db13ff583fd">atom1</a>()</td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#ae34ef1ddabf50dd732bf66336bb4a2eb">atom2</a>()</td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#a37c594eb8a06aa962efd46c8d5c0e1b9">atom3</a>()</td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#afb752f1836193a0af5befba252e16703">atom4</a>()</td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#ae6bb750e2ebd67defafc5bd38515e923">atom_1</a></td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#aae803284861c24535f6ea3cab02f00b8">atom_2</a></td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#a16456310c79412ef19e6b3dd22baf3b3">atom_3</a></td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#a73c5cc1a3f37ac0998b1316beb35c579">atom_4</a></td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#a2a6ff05c37b9ce514fe557ab3817a072">copy</a>(PTorsion trs, mmdb::ivector anmatch=NULL)</td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#a44095b8e5025c92a4b443a8715beceee">esd</a>()</td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#a63cbef738a4be2da8a46367802f83e3d">id</a>()</td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#ae33b6fc8d12fdbd48a299cf488e16f0e">makeCIFTags</a>(mmdb::mmcif::PLoop mmCIFLoop)</td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td><code> [static]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#a8fd30d637a8002a46ff4c50cadc8d34f">period</a>()</td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#af65ef2e18a3b6494070300afec0099e1">read_mem</a>(PMemIO memIO, int version, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#aaf9375ff9aeb22a2a148763276ec80d1">readFromCIF</a>(mmdb::mmcif::PLoop mmCIFLoop, int angleNo, Container&lt; Atom &gt; &amp;atoms)</td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#a1939dda0f4d9e56c3762acade101e938">Torsion</a>()</td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#a68b1d2a3529f1b153db01830a6cde818">torsion</a></td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#a34011e29f9c0faa8bc15a31274dd27c3">torsion_esd</a></td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#ab82fe72dc4fb966139befa1636f0c4bd">torsion_id</a></td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#a681cd0d538d13fa8d30dee2eb0c7df20">torsion_period</a></td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#a001451fd28649a8df65416d7e551b7a9">value</a>()</td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#a9b4f1d2c543776a8e0412eae4c7db651">write_mem</a>(PMemIO memIO, int version)</td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#ae53494ec218062be243d5e7b36f43dd0">writeToCIF</a>(mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID, Container&lt; Atom &gt; &amp;atoms)</td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_torsion.html#a45434048948cdf6fc5f01a6e3ca149a8">~Torsion</a>()</td><td><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></td><td><code> [virtual]</code></td></tr>
+</table></div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
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+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
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diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_torsion.html ccp4srs/doc-html/html/classccp4srs_1_1_torsion.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_torsion.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_torsion.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,575 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: ccp4srs::Torsion Class Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
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+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
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+          <img id="MSearchSelect" src="search/mag_sel.png"
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+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
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+    </ul>
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+      <li><a class="el" href="namespaceccp4srs.html">ccp4srs</a>      </li>
+      <li><a class="el" href="classccp4srs_1_1_torsion.html">Torsion</a>      </li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pub-static-methods">Static Public Member Functions</a> &#124;
+<a href="#pro-attribs">Protected Attributes</a>  </div>
+  <div class="headertitle">
+<h1>ccp4srs::Torsion Class Reference</h1>  </div>
+</div>
+<div class="contents">
+<!-- doxytag: class="ccp4srs::Torsion" -->
+<p><code>#include &lt;<a class="el" href="ccp4srs__torsion_8h_source.html">ccp4srs_torsion.h</a>&gt;</code></p>
+
+<p><a href="classccp4srs_1_1_torsion-members.html">List of all members.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#a1939dda0f4d9e56c3762acade101e938">Torsion</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#a45434048948cdf6fc5f01a6e3ca149a8">~Torsion</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#a63cbef738a4be2da8a46367802f83e3d">id</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#af30f2e612259dedd1e569db13ff583fd">atom1</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#ae34ef1ddabf50dd732bf66336bb4a2eb">atom2</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#a37c594eb8a06aa962efd46c8d5c0e1b9">atom3</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#afb752f1836193a0af5befba252e16703">atom4</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#a8fd30d637a8002a46ff4c50cadc8d34f">period</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#a001451fd28649a8df65416d7e551b7a9">value</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#a44095b8e5025c92a4b443a8715beceee">esd</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#aaf9375ff9aeb22a2a148763276ec80d1">readFromCIF</a> (mmdb::mmcif::PLoop mmCIFLoop, int angleNo, <a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;atoms)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#ae53494ec218062be243d5e7b36f43dd0">writeToCIF</a> (mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID, <a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;atoms)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#a9b4f1d2c543776a8e0412eae4c7db651">write_mem</a> (PMemIO memIO, int version)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#af65ef2e18a3b6494070300afec0099e1">read_mem</a> (PMemIO memIO, int version, bool *Ok=NULL)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#a2a6ff05c37b9ce514fe557ab3817a072">copy</a> (PTorsion trs, mmdb::ivector anmatch=NULL)</td></tr>
+<tr><td colspan="2"><h2><a name="pub-static-methods"></a>
+Static Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">static void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#ae33b6fc8d12fdbd48a299cf488e16f0e">makeCIFTags</a> (mmdb::mmcif::PLoop mmCIFLoop)</td></tr>
+<tr><td colspan="2"><h2><a name="pro-attribs"></a>
+Protected Attributes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespaceccp4srs.html#a192f47d1deb71790866bce922f50bba1">TorsionID</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#ab82fe72dc4fb966139befa1636f0c4bd">torsion_id</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">torsion angle id  <a href="#ab82fe72dc4fb966139befa1636f0c4bd"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#ae6bb750e2ebd67defafc5bd38515e923">atom_1</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#aae803284861c24535f6ea3cab02f00b8">atom_2</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">ordinal numbers of atoms  <a href="#aae803284861c24535f6ea3cab02f00b8"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#a16456310c79412ef19e6b3dd22baf3b3">atom_3</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#a73c5cc1a3f37ac0998b1316beb35c579">atom_4</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#a681cd0d538d13fa8d30dee2eb0c7df20">torsion_period</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">that form the angle [0,1,...]  <a href="#a681cd0d538d13fa8d30dee2eb0c7df20"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#a68b1d2a3529f1b153db01830a6cde818">torsion</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">torsion angle in degrees  <a href="#a68b1d2a3529f1b153db01830a6cde818"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::realtype&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_torsion.html#a34011e29f9c0faa8bc15a31274dd27c3">torsion_esd</a></td></tr>
+</table>
+<hr/><h2>Constructor &amp; Destructor Documentation</h2>
+<a class="anchor" id="a1939dda0f4d9e56c3762acade101e938"></a><!-- doxytag: member="ccp4srs::Torsion::Torsion" ref="a1939dda0f4d9e56c3762acade101e938" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::Torsion::Torsion </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a45434048948cdf6fc5f01a6e3ca149a8"></a><!-- doxytag: member="ccp4srs::Torsion::~Torsion" ref="a45434048948cdf6fc5f01a6e3ca149a8" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::Torsion::~Torsion </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [virtual]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Function Documentation</h2>
+<a class="anchor" id="af30f2e612259dedd1e569db13ff583fd"></a><!-- doxytag: member="ccp4srs::Torsion::atom1" ref="af30f2e612259dedd1e569db13ff583fd" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Torsion::atom1 </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ae34ef1ddabf50dd732bf66336bb4a2eb"></a><!-- doxytag: member="ccp4srs::Torsion::atom2" ref="ae34ef1ddabf50dd732bf66336bb4a2eb" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Torsion::atom2 </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a37c594eb8a06aa962efd46c8d5c0e1b9"></a><!-- doxytag: member="ccp4srs::Torsion::atom3" ref="a37c594eb8a06aa962efd46c8d5c0e1b9" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Torsion::atom3 </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="afb752f1836193a0af5befba252e16703"></a><!-- doxytag: member="ccp4srs::Torsion::atom4" ref="afb752f1836193a0af5befba252e16703" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Torsion::atom4 </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a2a6ff05c37b9ce514fe557ab3817a072"></a><!-- doxytag: member="ccp4srs::Torsion::copy" ref="a2a6ff05c37b9ce514fe557ab3817a072" args="(PTorsion trs, mmdb::ivector anmatch=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Torsion::copy </td>
+          <td>(</td>
+          <td class="paramtype">PTorsion&#160;</td>
+          <td class="paramname"> <em>trs</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::ivector&#160;</td>
+          <td class="paramname"> <em>anmatch</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a44095b8e5025c92a4b443a8715beceee"></a><!-- doxytag: member="ccp4srs::Torsion::esd" ref="a44095b8e5025c92a4b443a8715beceee" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype ccp4srs::Torsion::esd </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a63cbef738a4be2da8a46367802f83e3d"></a><!-- doxytag: member="ccp4srs::Torsion::id" ref="a63cbef738a4be2da8a46367802f83e3d" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::cpstr ccp4srs::Torsion::id </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ae33b6fc8d12fdbd48a299cf488e16f0e"></a><!-- doxytag: member="ccp4srs::Torsion::makeCIFTags" ref="ae33b6fc8d12fdbd48a299cf488e16f0e" args="(mmdb::mmcif::PLoop mmCIFLoop)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Torsion::makeCIFTags </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>mmCIFLoop</em>&#160;)</td>
+          <td><code> [static]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a8fd30d637a8002a46ff4c50cadc8d34f"></a><!-- doxytag: member="ccp4srs::Torsion::period" ref="a8fd30d637a8002a46ff4c50cadc8d34f" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Torsion::period </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="af65ef2e18a3b6494070300afec0099e1"></a><!-- doxytag: member="ccp4srs::Torsion::read_mem" ref="af65ef2e18a3b6494070300afec0099e1" args="(PMemIO memIO, int version, bool *Ok=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::Torsion::read_mem </td>
+          <td>(</td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aaf9375ff9aeb22a2a148763276ec80d1"></a><!-- doxytag: member="ccp4srs::Torsion::readFromCIF" ref="aaf9375ff9aeb22a2a148763276ec80d1" args="(mmdb::mmcif::PLoop mmCIFLoop, int angleNo, Container&lt; Atom &gt; &amp;atoms)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Torsion::readFromCIF </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>mmCIFLoop</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>angleNo</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;&#160;</td>
+          <td class="paramname"> <em>atoms</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a001451fd28649a8df65416d7e551b7a9"></a><!-- doxytag: member="ccp4srs::Torsion::value" ref="a001451fd28649a8df65416d7e551b7a9" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype ccp4srs::Torsion::value </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a9b4f1d2c543776a8e0412eae4c7db651"></a><!-- doxytag: member="ccp4srs::Torsion::write_mem" ref="a9b4f1d2c543776a8e0412eae4c7db651" args="(PMemIO memIO, int version)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Torsion::write_mem </td>
+          <td>(</td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ae53494ec218062be243d5e7b36f43dd0"></a><!-- doxytag: member="ccp4srs::Torsion::writeToCIF" ref="ae53494ec218062be243d5e7b36f43dd0" args="(mmdb::mmcif::PLoop mmCIFLoop, mmdb::cpstr monID, Container&lt; Atom &gt; &amp;atoms)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Torsion::writeToCIF </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>mmCIFLoop</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>monID</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;&#160;</td>
+          <td class="paramname"> <em>atoms</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Data Documentation</h2>
+<a class="anchor" id="ae6bb750e2ebd67defafc5bd38515e923"></a><!-- doxytag: member="ccp4srs::Torsion::atom_1" ref="ae6bb750e2ebd67defafc5bd38515e923" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_torsion.html#ae6bb750e2ebd67defafc5bd38515e923">ccp4srs::Torsion::atom_1</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aae803284861c24535f6ea3cab02f00b8"></a><!-- doxytag: member="ccp4srs::Torsion::atom_2" ref="aae803284861c24535f6ea3cab02f00b8" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_torsion.html#aae803284861c24535f6ea3cab02f00b8">ccp4srs::Torsion::atom_2</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>ordinal numbers of atoms </p>
+
+</div>
+</div>
+<a class="anchor" id="a16456310c79412ef19e6b3dd22baf3b3"></a><!-- doxytag: member="ccp4srs::Torsion::atom_3" ref="a16456310c79412ef19e6b3dd22baf3b3" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_torsion.html#a16456310c79412ef19e6b3dd22baf3b3">ccp4srs::Torsion::atom_3</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a73c5cc1a3f37ac0998b1316beb35c579"></a><!-- doxytag: member="ccp4srs::Torsion::atom_4" ref="a73c5cc1a3f37ac0998b1316beb35c579" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_torsion.html#a73c5cc1a3f37ac0998b1316beb35c579">ccp4srs::Torsion::atom_4</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a68b1d2a3529f1b153db01830a6cde818"></a><!-- doxytag: member="ccp4srs::Torsion::torsion" ref="a68b1d2a3529f1b153db01830a6cde818" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_torsion.html#a68b1d2a3529f1b153db01830a6cde818">ccp4srs::Torsion::torsion</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>torsion angle in degrees </p>
+
+</div>
+</div>
+<a class="anchor" id="a34011e29f9c0faa8bc15a31274dd27c3"></a><!-- doxytag: member="ccp4srs::Torsion::torsion_esd" ref="a34011e29f9c0faa8bc15a31274dd27c3" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::realtype <a class="el" href="classccp4srs_1_1_torsion.html#a34011e29f9c0faa8bc15a31274dd27c3">ccp4srs::Torsion::torsion_esd</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+<p>torsion angle esd in degrees; set to 0.0 if not provided </p>
+
+</div>
+</div>
+<a class="anchor" id="ab82fe72dc4fb966139befa1636f0c4bd"></a><!-- doxytag: member="ccp4srs::Torsion::torsion_id" ref="ab82fe72dc4fb966139befa1636f0c4bd" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname"><a class="el" href="namespaceccp4srs.html#a192f47d1deb71790866bce922f50bba1">TorsionID</a> <a class="el" href="classccp4srs_1_1_torsion.html#ab82fe72dc4fb966139befa1636f0c4bd">ccp4srs::Torsion::torsion_id</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>torsion angle id </p>
+
+</div>
+</div>
+<a class="anchor" id="a681cd0d538d13fa8d30dee2eb0c7df20"></a><!-- doxytag: member="ccp4srs::Torsion::torsion_period" ref="a681cd0d538d13fa8d30dee2eb0c7df20" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_torsion.html#a681cd0d538d13fa8d30dee2eb0c7df20">ccp4srs::Torsion::torsion_period</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>that form the angle [0,1,...] </p>
+<p>torsion period </p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following files:<ul>
+<li>src/<a class="el" href="ccp4srs__torsion_8h_source.html">ccp4srs_torsion.h</a></li>
+<li>src/<a class="el" href="ccp4srs__torsion_8cpp.html">ccp4srs_torsion.cpp</a></li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
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+
+<!-- iframe showing the search results (closed by default) -->
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+        name="MSearchResults" id="MSearchResults">
+</iframe>
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+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_tree-members.html ccp4srs/doc-html/html/classccp4srs_1_1_tree-members.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_tree-members.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_tree-members.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,93 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>ccp4srs::Tree Member List</h1>  </div>
+</div>
+<div class="contents">
+This is the complete list of members for <a class="el" href="classccp4srs_1_1_tree.html">ccp4srs::Tree</a>, including all inherited members.<table>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_tree.html#aa05e210175e281b0b975b22040cbf45d">atom</a>(int secNo)</td><td><a class="el" href="classccp4srs_1_1_tree.html">ccp4srs::Tree</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_tree.html#a612df27ef2431bf2ac087f7190e0f9d1">atom_backward</a></td><td><a class="el" href="classccp4srs_1_1_tree.html">ccp4srs::Tree</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_tree.html#a3c63a71c2935da20a0feccad01d5ceaf">atom_forward</a></td><td><a class="el" href="classccp4srs_1_1_tree.html">ccp4srs::Tree</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_tree.html#a27d256081e9d371ff22a6644d9ee8a91">atom_tree</a></td><td><a class="el" href="classccp4srs_1_1_tree.html">ccp4srs::Tree</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_tree.html#a70a9e13b054276780039e0d6f0edcdd9">backward</a>(int secNo)</td><td><a class="el" href="classccp4srs_1_1_tree.html">ccp4srs::Tree</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_tree.html#a9986231a0223ef6b62902823d119176f">connect</a>(int secNo)</td><td><a class="el" href="classccp4srs_1_1_tree.html">ccp4srs::Tree</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_tree.html#a97ee818b7a1b1724cfb712453be05743">connect_type</a></td><td><a class="el" href="classccp4srs_1_1_tree.html">ccp4srs::Tree</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_tree.html#acfc010d5d168bb288379e6b6721fb9fa">copy</a>(PTree tree, mmdb::ivector anmatch=NULL)</td><td><a class="el" href="classccp4srs_1_1_tree.html">ccp4srs::Tree</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_tree.html#a5f5e595cfdb5623cc59c0651ff7a25d3">empty</a>()</td><td><a class="el" href="classccp4srs_1_1_tree.html">ccp4srs::Tree</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_tree.html#ad52fadb719ce7ca269b9f6875a9ce8e6">forward</a>(int secNo)</td><td><a class="el" href="classccp4srs_1_1_tree.html">ccp4srs::Tree</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_tree.html#a4056f0bb5ef8add5a55133eb8166c639">n_sections</a></td><td><a class="el" href="classccp4srs_1_1_tree.html">ccp4srs::Tree</a></td><td><code> [protected]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_tree.html#a7e39da9840cb8815e8854cd11552c3a9">read_mem</a>(PMemIO memIO, int version, bool *Ok=NULL)</td><td><a class="el" href="classccp4srs_1_1_tree.html">ccp4srs::Tree</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_tree.html#af50e009eb63e2bdf8da129afa193d637">readFromCIF</a>(mmdb::mmcif::PLoop mmCIFLoop, Container&lt; Atom &gt; &amp;atoms)</td><td><a class="el" href="classccp4srs_1_1_tree.html">ccp4srs::Tree</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_tree.html#a308ddfce7a902729218e39356db92cc0">size</a>()</td><td><a class="el" href="classccp4srs_1_1_tree.html">ccp4srs::Tree</a></td><td><code> [inline]</code></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_tree.html#a342a1de215612310580d0cd6a06262cb">Tree</a>()</td><td><a class="el" href="classccp4srs_1_1_tree.html">ccp4srs::Tree</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_tree.html#a357b27f65ab5b653fc17a387e9653c4f">write_mem</a>(PMemIO memIO, int version)</td><td><a class="el" href="classccp4srs_1_1_tree.html">ccp4srs::Tree</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_tree.html#ade370b24c17b2d47a4cb8f89c096e5c1">writeToCIF</a>(mmdb::mmcif::PData mmCIFData, mmdb::cpstr monID, Container&lt; Atom &gt; &amp;atoms)</td><td><a class="el" href="classccp4srs_1_1_tree.html">ccp4srs::Tree</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="classccp4srs_1_1_tree.html#ab5a113a9574397dbb5e7679211ee3c24">~Tree</a>()</td><td><a class="el" href="classccp4srs_1_1_tree.html">ccp4srs::Tree</a></td><td><code> [virtual]</code></td></tr>
+</table></div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
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+
+<!-- iframe showing the search results (closed by default) -->
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+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/classccp4srs_1_1_tree.html ccp4srs/doc-html/html/classccp4srs_1_1_tree.html
--- ccp4srs-old/doc-html/html/classccp4srs_1_1_tree.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/classccp4srs_1_1_tree.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,477 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: ccp4srs::Tree Class Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
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+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="navpath">
+    <ul>
+      <li><a class="el" href="namespaceccp4srs.html">ccp4srs</a>      </li>
+      <li><a class="el" href="classccp4srs_1_1_tree.html">Tree</a>      </li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pro-attribs">Protected Attributes</a>  </div>
+  <div class="headertitle">
+<h1>ccp4srs::Tree Class Reference</h1>  </div>
+</div>
+<div class="contents">
+<!-- doxytag: class="ccp4srs::Tree" -->
+<p><code>#include &lt;<a class="el" href="ccp4srs__tree_8h_source.html">ccp4srs_tree.h</a>&gt;</code></p>
+
+<p><a href="classccp4srs_1_1_tree-members.html">List of all members.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_tree.html#a342a1de215612310580d0cd6a06262cb">Tree</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_tree.html#ab5a113a9574397dbb5e7679211ee3c24">~Tree</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_tree.html#a5f5e595cfdb5623cc59c0651ff7a25d3">empty</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_tree.html#a308ddfce7a902729218e39356db92cc0">size</a> ()</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_tree.html#aa05e210175e281b0b975b22040cbf45d">atom</a> (int secNo)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_tree.html#a70a9e13b054276780039e0d6f0edcdd9">backward</a> (int secNo)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_tree.html#ad52fadb719ce7ca269b9f6875a9ce8e6">forward</a> (int secNo)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_tree.html#a9986231a0223ef6b62902823d119176f">connect</a> (int secNo)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_tree.html#af50e009eb63e2bdf8da129afa193d637">readFromCIF</a> (mmdb::mmcif::PLoop mmCIFLoop, <a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;atoms)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_tree.html#ade370b24c17b2d47a4cb8f89c096e5c1">writeToCIF</a> (mmdb::mmcif::PData mmCIFData, mmdb::cpstr monID, <a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;atoms)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_tree.html#a357b27f65ab5b653fc17a387e9653c4f">write_mem</a> (PMemIO memIO, int version)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_tree.html#a7e39da9840cb8815e8854cd11552c3a9">read_mem</a> (PMemIO memIO, int version, bool *Ok=NULL)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_tree.html#acfc010d5d168bb288379e6b6721fb9fa">copy</a> (PTree tree, mmdb::ivector anmatch=NULL)</td></tr>
+<tr><td colspan="2"><h2><a name="pro-attribs"></a>
+Protected Attributes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_tree.html#a4056f0bb5ef8add5a55133eb8166c639">n_sections</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">number of sections  <a href="#a4056f0bb5ef8add5a55133eb8166c639"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::ivector&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_tree.html#a27d256081e9d371ff22a6644d9ee8a91">atom_tree</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">tree atom name  <a href="#a27d256081e9d371ff22a6644d9ee8a91"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::ivector&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_tree.html#a612df27ef2431bf2ac087f7190e0f9d1">atom_backward</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">previous atom name  <a href="#a612df27ef2431bf2ac087f7190e0f9d1"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::ivector&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_tree.html#a3c63a71c2935da20a0feccad01d5ceaf">atom_forward</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">next atom name  <a href="#a3c63a71c2935da20a0feccad01d5ceaf"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::ivector&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_tree.html#a97ee818b7a1b1724cfb712453be05743">connect_type</a></td></tr>
+<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">type of connection  <a href="#a97ee818b7a1b1724cfb712453be05743"></a><br/></td></tr>
+</table>
+<hr/><h2>Constructor &amp; Destructor Documentation</h2>
+<a class="anchor" id="a342a1de215612310580d0cd6a06262cb"></a><!-- doxytag: member="ccp4srs::Tree::Tree" ref="a342a1de215612310580d0cd6a06262cb" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::Tree::Tree </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ab5a113a9574397dbb5e7679211ee3c24"></a><!-- doxytag: member="ccp4srs::Tree::~Tree" ref="ab5a113a9574397dbb5e7679211ee3c24" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::Tree::~Tree </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [virtual]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Function Documentation</h2>
+<a class="anchor" id="aa05e210175e281b0b975b22040cbf45d"></a><!-- doxytag: member="ccp4srs::Tree::atom" ref="aa05e210175e281b0b975b22040cbf45d" args="(int secNo)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Tree::atom </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>secNo</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a70a9e13b054276780039e0d6f0edcdd9"></a><!-- doxytag: member="ccp4srs::Tree::backward" ref="a70a9e13b054276780039e0d6f0edcdd9" args="(int secNo)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Tree::backward </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>secNo</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a9986231a0223ef6b62902823d119176f"></a><!-- doxytag: member="ccp4srs::Tree::connect" ref="a9986231a0223ef6b62902823d119176f" args="(int secNo)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Tree::connect </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>secNo</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="acfc010d5d168bb288379e6b6721fb9fa"></a><!-- doxytag: member="ccp4srs::Tree::copy" ref="acfc010d5d168bb288379e6b6721fb9fa" args="(PTree tree, mmdb::ivector anmatch=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Tree::copy </td>
+          <td>(</td>
+          <td class="paramtype">PTree&#160;</td>
+          <td class="paramname"> <em>tree</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::ivector&#160;</td>
+          <td class="paramname"> <em>anmatch</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a5f5e595cfdb5623cc59c0651ff7a25d3"></a><!-- doxytag: member="ccp4srs::Tree::empty" ref="a5f5e595cfdb5623cc59c0651ff7a25d3" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Tree::empty </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ad52fadb719ce7ca269b9f6875a9ce8e6"></a><!-- doxytag: member="ccp4srs::Tree::forward" ref="ad52fadb719ce7ca269b9f6875a9ce8e6" args="(int secNo)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Tree::forward </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>secNo</em>&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a7e39da9840cb8815e8854cd11552c3a9"></a><!-- doxytag: member="ccp4srs::Tree::read_mem" ref="a7e39da9840cb8815e8854cd11552c3a9" args="(PMemIO memIO, int version, bool *Ok=NULL)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool ccp4srs::Tree::read_mem </td>
+          <td>(</td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool *&#160;</td>
+          <td class="paramname"> <em>Ok</em> = <code>NULL</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="af50e009eb63e2bdf8da129afa193d637"></a><!-- doxytag: member="ccp4srs::Tree::readFromCIF" ref="af50e009eb63e2bdf8da129afa193d637" args="(mmdb::mmcif::PLoop mmCIFLoop, Container&lt; Atom &gt; &amp;atoms)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Tree::readFromCIF </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>mmCIFLoop</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;&#160;</td>
+          <td class="paramname"> <em>atoms</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a308ddfce7a902729218e39356db92cc0"></a><!-- doxytag: member="ccp4srs::Tree::size" ref="a308ddfce7a902729218e39356db92cc0" args="()" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::Tree::size </td>
+          <td>(</td>
+          <td class="paramname">&#160;)</td>
+          <td><code> [inline]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a357b27f65ab5b653fc17a387e9653c4f"></a><!-- doxytag: member="ccp4srs::Tree::write_mem" ref="a357b27f65ab5b653fc17a387e9653c4f" args="(PMemIO memIO, int version)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Tree::write_mem </td>
+          <td>(</td>
+          <td class="paramtype">PMemIO&#160;</td>
+          <td class="paramname"> <em>memIO</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>version</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ade370b24c17b2d47a4cb8f89c096e5c1"></a><!-- doxytag: member="ccp4srs::Tree::writeToCIF" ref="ade370b24c17b2d47a4cb8f89c096e5c1" args="(mmdb::mmcif::PData mmCIFData, mmdb::cpstr monID, Container&lt; Atom &gt; &amp;atoms)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::Tree::writeToCIF </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PData&#160;</td>
+          <td class="paramname"> <em>mmCIFData</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>monID</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype"><a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;&#160;</td>
+          <td class="paramname"> <em>atoms</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Data Documentation</h2>
+<a class="anchor" id="a612df27ef2431bf2ac087f7190e0f9d1"></a><!-- doxytag: member="ccp4srs::Tree::atom_backward" ref="a612df27ef2431bf2ac087f7190e0f9d1" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::ivector <a class="el" href="classccp4srs_1_1_tree.html#a612df27ef2431bf2ac087f7190e0f9d1">ccp4srs::Tree::atom_backward</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>previous atom name </p>
+
+</div>
+</div>
+<a class="anchor" id="a3c63a71c2935da20a0feccad01d5ceaf"></a><!-- doxytag: member="ccp4srs::Tree::atom_forward" ref="a3c63a71c2935da20a0feccad01d5ceaf" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::ivector <a class="el" href="classccp4srs_1_1_tree.html#a3c63a71c2935da20a0feccad01d5ceaf">ccp4srs::Tree::atom_forward</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>next atom name </p>
+
+</div>
+</div>
+<a class="anchor" id="a27d256081e9d371ff22a6644d9ee8a91"></a><!-- doxytag: member="ccp4srs::Tree::atom_tree" ref="a27d256081e9d371ff22a6644d9ee8a91" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::ivector <a class="el" href="classccp4srs_1_1_tree.html#a27d256081e9d371ff22a6644d9ee8a91">ccp4srs::Tree::atom_tree</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>tree atom name </p>
+
+</div>
+</div>
+<a class="anchor" id="a97ee818b7a1b1724cfb712453be05743"></a><!-- doxytag: member="ccp4srs::Tree::connect_type" ref="a97ee818b7a1b1724cfb712453be05743" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::ivector <a class="el" href="classccp4srs_1_1_tree.html#a97ee818b7a1b1724cfb712453be05743">ccp4srs::Tree::connect_type</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>type of connection </p>
+
+</div>
+</div>
+<a class="anchor" id="a4056f0bb5ef8add5a55133eb8166c639"></a><!-- doxytag: member="ccp4srs::Tree::n_sections" ref="a4056f0bb5ef8add5a55133eb8166c639" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="classccp4srs_1_1_tree.html#a4056f0bb5ef8add5a55133eb8166c639">ccp4srs::Tree::n_sections</a><code> [protected]</code></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+<p>number of sections </p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following files:<ul>
+<li>src/<a class="el" href="ccp4srs__tree_8h_source.html">ccp4srs_tree.h</a></li>
+<li>src/<a class="el" href="ccp4srs__tree_8cpp.html">ccp4srs_tree.cpp</a></li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
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+</td><td><a name="letter_P"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">&#160;&#160;P&#160;&#160;</div></td></tr></table>
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+++ ccp4srs/doc-html/html/files.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,109 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: File Index</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li class="current"><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
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+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="files.html"><span>File&#160;List</span></a></li>
+      <li><a href="globals.html"><span>File&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>File List</h1>  </div>
+</div>
+<div class="contents">
+Here is a list of all files with brief descriptions:<table>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__angle_8cpp.html">ccp4srs_angle.cpp</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__angle_8h.html">ccp4srs_angle.h</a> <a href="ccp4srs__angle_8h_source.html">[code]</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__atom_8cpp.html">ccp4srs_atom.cpp</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__atom_8h.html">ccp4srs_atom.h</a> <a href="ccp4srs__atom_8h_source.html">[code]</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__base_8cpp.html">ccp4srs_base.cpp</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__base_8h.html">ccp4srs_base.h</a> <a href="ccp4srs__base_8h_source.html">[code]</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__bond_8cpp.html">ccp4srs_bond.cpp</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__bond_8h.html">ccp4srs_bond.h</a> <a href="ccp4srs__bond_8h_source.html">[code]</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__chem_8cpp.html">ccp4srs_chem.cpp</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__chem_8h.html">ccp4srs_chem.h</a> <a href="ccp4srs__chem_8h_source.html">[code]</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__chicenter_8cpp.html">ccp4srs_chicenter.cpp</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__chicenter_8h.html">ccp4srs_chicenter.h</a> <a href="ccp4srs__chicenter_8h_source.html">[code]</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__container_8cpp.html">ccp4srs_container.cpp</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__container_8h.html">ccp4srs_container.h</a> <a href="ccp4srs__container_8h_source.html">[code]</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__defs_8h.html">ccp4srs_defs.h</a> <a href="ccp4srs__defs_8h_source.html">[code]</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__entry_8cpp.html">ccp4srs_entry.cpp</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__entry_8h.html">ccp4srs_entry.h</a> <a href="ccp4srs__entry_8h_source.html">[code]</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__index_8cpp.html">ccp4srs_index.cpp</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__index_8h.html">ccp4srs_index.h</a> <a href="ccp4srs__index_8h_source.html">[code]</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__manager_8cpp.html">ccp4srs_manager.cpp</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__manager_8h.html">ccp4srs_manager.h</a> <a href="ccp4srs__manager_8h_source.html">[code]</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__monomer_8cpp.html">ccp4srs_monomer.cpp</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__monomer_8h.html">ccp4srs_monomer.h</a> <a href="ccp4srs__monomer_8h_source.html">[code]</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__plane_8cpp.html">ccp4srs_plane.cpp</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__plane_8h.html">ccp4srs_plane.h</a> <a href="ccp4srs__plane_8h_source.html">[code]</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__torsion_8cpp.html">ccp4srs_torsion.cpp</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__torsion_8h.html">ccp4srs_torsion.h</a> <a href="ccp4srs__torsion_8h_source.html">[code]</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__tree_8cpp.html">ccp4srs_tree.cpp</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__tree_8h.html">ccp4srs_tree.h</a> <a href="ccp4srs__tree_8h_source.html">[code]</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__types_8cpp.html">ccp4srs_types.cpp</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="ccp4srs__types_8h.html">ccp4srs_types.h</a> <a href="ccp4srs__types_8h_source.html">[code]</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="memio___8cpp.html">memio_.cpp</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="memio___8h.html">memio_.h</a> <a href="memio___8h_source.html">[code]</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="mpfile___8cpp.html">mpfile_.cpp</a></td><td class="indexvalue"></td></tr>
+  <tr><td class="indexkey">src/<a class="el" href="mpfile___8h.html">mpfile_.h</a> <a href="mpfile___8h_source.html">[code]</a></td><td class="indexvalue"></td></tr>
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+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions.html ccp4srs/doc-html/html/functions.html
--- ccp4srs-old/doc-html/html/functions.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions.html	2014-09-09 21:34:12.000000000 -0700
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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
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+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_a"></a>- a -</h3><ul>
+<li>a1
+: <a class="el" href="structccp4srs_1_1_atom_pair.html#a0277f099acfa557ac20bf6fd3320bcaa">ccp4srs::AtomPair</a>
+</li>
+<li>a2
+: <a class="el" href="structccp4srs_1_1_atom_pair.html#a1f8f7df44905ac32088ccfcf1b80dda2">ccp4srs::AtomPair</a>
+</li>
+<li>add()
+: <a class="el" href="classccp4srs_1_1_monomer.html#ae1c9221ebd49b62830621cd40524d215">ccp4srs::Monomer</a>
+, <a class="el" href="classccp4srs_1_1_container.html#a6caf1893b780f2cf196c85ee141baf18">ccp4srs::Container&lt; T &gt;</a>
+, <a class="el" href="classccp4srs_1_1_monomer.html#a3eab75471f83c2c92834a1e30400642e">ccp4srs::Monomer</a>
+</li>
+<li>addHydrogens()
+: <a class="el" href="classccp4srs_1_1_chem.html#acada705ca803ac2b68bb2c787a83fcb1">ccp4srs::Chem</a>
+, <a class="el" href="classccp4srs_1_1_monomer.html#a67a965eb782472588f1a5f4e693c509e">ccp4srs::Monomer</a>
+</li>
+<li>Angle()
+: <a class="el" href="classccp4srs_1_1_angle.html#a5ec6da380214e7100ff46e3e79898e15">ccp4srs::Angle</a>
+</li>
+<li>angle
+: <a class="el" href="classccp4srs_1_1_angle.html#abf55314566cb2fa1d3764d0485284113">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_monomer.html#a61b179edff80a9d168997038093cc92f">ccp4srs::Monomer</a>
+</li>
+<li>angle_esd
+: <a class="el" href="classccp4srs_1_1_angle.html#a39e05de948ddbf9c944bf0b14123caf8">ccp4srs::Angle</a>
+</li>
+<li>angles
+: <a class="el" href="classccp4srs_1_1_monomer.html#a9177ec12ea5aeaa59228831d4127e592">ccp4srs::Monomer</a>
+</li>
+<li>Aromatic
+: <a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba1511fd16010981add30c1e054980f193">ccp4srs::Bond</a>
+</li>
+<li>at()
+: <a class="el" href="classccp4srs_1_1_container.html#ae9929d576289dd2313aaf4b2d9c377e9">ccp4srs::Container&lt; T &gt;</a>
+</li>
+<li>atom()
+: <a class="el" href="classccp4srs_1_1_monomer.html#ac3492a092c5436d182acae9b6712da7f">ccp4srs::Monomer</a>
+, <a class="el" href="classccp4srs_1_1_plane.html#ad1e544c70729b5a17dba23301ba6ca7e">ccp4srs::Plane</a>
+, <a class="el" href="classccp4srs_1_1_tree.html#aa05e210175e281b0b975b22040cbf45d">ccp4srs::Tree</a>
+</li>
+<li>Atom()
+: <a class="el" href="classccp4srs_1_1_atom.html#a66084d9a746b51608e8f0f8e28138e9d">ccp4srs::Atom</a>
+</li>
+<li>atom1()
+: <a class="el" href="classccp4srs_1_1_angle.html#a64770743097878619e8dccf787f93802">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_bond.html#a6ec052956ddec875a707d7e375ce0748">ccp4srs::Bond</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#ae27490ac46e2f3904ee230fe0c5b80af">ccp4srs::ChiCenter</a>
+, <a class="el" href="classccp4srs_1_1_torsion.html#af30f2e612259dedd1e569db13ff583fd">ccp4srs::Torsion</a>
+</li>
+<li>atom2()
+: <a class="el" href="classccp4srs_1_1_bond.html#a364bc6a611e192c07d0bf5236a3503b9">ccp4srs::Bond</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#a5e1600b63a2e92494176dc328c6fc8a6">ccp4srs::ChiCenter</a>
+, <a class="el" href="classccp4srs_1_1_torsion.html#ae34ef1ddabf50dd732bf66336bb4a2eb">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_angle.html#a1be24203719da0b250775f7c0b5710ed">ccp4srs::Angle</a>
+</li>
+<li>atom3()
+: <a class="el" href="classccp4srs_1_1_angle.html#a6d62c8acfe549d3d439a061f2bbcada9">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#ac668dea1c66f203a26e46a1c87b37760">ccp4srs::ChiCenter</a>
+, <a class="el" href="classccp4srs_1_1_torsion.html#a37c594eb8a06aa962efd46c8d5c0e1b9">ccp4srs::Torsion</a>
+</li>
+<li>atom4()
+: <a class="el" href="classccp4srs_1_1_torsion.html#afb752f1836193a0af5befba252e16703">ccp4srs::Torsion</a>
+</li>
+<li>atom_1
+: <a class="el" href="classccp4srs_1_1_bond.html#ad359689c475101246c6c3061d31c2541">ccp4srs::Bond</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#a246c77c96df7921a1d1c989de4a50f8f">ccp4srs::ChiCenter</a>
+, <a class="el" href="classccp4srs_1_1_torsion.html#ae6bb750e2ebd67defafc5bd38515e923">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_angle.html#ab59c639612d7dcae2b34213a647cdb45">ccp4srs::Angle</a>
+</li>
+<li>atom_2
+: <a class="el" href="classccp4srs_1_1_torsion.html#aae803284861c24535f6ea3cab02f00b8">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#aa80d6d7fbec0a8497b62af13b16e2a12">ccp4srs::ChiCenter</a>
+, <a class="el" href="classccp4srs_1_1_angle.html#a8a4fd7f9e6196f259b6ec0989b5cb64c">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_bond.html#a277aee984c745dcdfd338f19e7df1e48">ccp4srs::Bond</a>
+</li>
+<li>atom_3
+: <a class="el" href="classccp4srs_1_1_torsion.html#a16456310c79412ef19e6b3dd22baf3b3">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#a2b249cab1cc7c2ea80ea9259914fcd34">ccp4srs::ChiCenter</a>
+, <a class="el" href="classccp4srs_1_1_angle.html#a545fb1039055e640aa938964b64c7d0a">ccp4srs::Angle</a>
+</li>
+<li>atom_4
+: <a class="el" href="classccp4srs_1_1_torsion.html#a73c5cc1a3f37ac0998b1316beb35c579">ccp4srs::Torsion</a>
+</li>
+<li>atom_backward
+: <a class="el" href="classccp4srs_1_1_tree.html#a612df27ef2431bf2ac087f7190e0f9d1">ccp4srs::Tree</a>
+</li>
+<li>atom_center
+: <a class="el" href="classccp4srs_1_1_chi_center.html#a5fe75db982419a5d7f3c3ff8b2e41f46">ccp4srs::ChiCenter</a>
+</li>
+<li>atom_forward
+: <a class="el" href="classccp4srs_1_1_tree.html#a3c63a71c2935da20a0feccad01d5ceaf">ccp4srs::Tree</a>
+</li>
+<li>atom_no()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a9ac9e9e610a1a0450130d5e5c4242d34">ccp4srs::Monomer</a>
+</li>
+<li>atom_tree
+: <a class="el" href="classccp4srs_1_1_tree.html#a27d256081e9d371ff22a6644d9ee8a91">ccp4srs::Tree</a>
+</li>
+<li>atomCharge
+: <a class="el" href="classccp4srs_1_1_atom.html#a0e7a7e76f9fba1a8277dae436f900821">ccp4srs::Atom</a>
+</li>
+<li>atomName
+: <a class="el" href="classccp4srs_1_1_atom.html#a75168bfe9aa3e0e24ba5f81854323039">ccp4srs::Atom</a>
+</li>
+<li>atoms
+: <a class="el" href="classccp4srs_1_1_monomer.html#abd7decc2129038a1416f324fee53afa1">ccp4srs::Monomer</a>
+, <a class="el" href="classccp4srs_1_1_plane.html#a91e4f55f473565e42c27b6aab5311222">ccp4srs::Plane</a>
+</li>
+<li>atomSP
+: <a class="el" href="classccp4srs_1_1_atom.html#acb4d50d536b22d4dd3f971072354f784">ccp4srs::Atom</a>
+</li>
+<li>atomValency
+: <a class="el" href="classccp4srs_1_1_atom.html#aeaa06e2eac23c671be3f49c0caaa7d12">ccp4srs::Atom</a>
+</li>
+<li>atomWeight
+: <a class="el" href="classccp4srs_1_1_atom.html#ac470c0fd96b775b2b1d979c353449ee4">ccp4srs::Atom</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x62.html ccp4srs/doc-html/html/functions_0x62.html
--- ccp4srs-old/doc-html/html/functions_0x62.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x62.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,134 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li class="current"><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_b"></a>- b -</h3><ul>
+<li>backward()
+: <a class="el" href="classccp4srs_1_1_tree.html#a70a9e13b054276780039e0d6f0edcdd9">ccp4srs::Tree</a>
+</li>
+<li>Base()
+: <a class="el" href="classccp4srs_1_1_base.html#a0c37b44fe77e9f171d5f40281a6e82ae">ccp4srs::Base</a>
+</li>
+<li>Bond()
+: <a class="el" href="classccp4srs_1_1_bond.html#acd3c055b0b0827de95e44ca9a9ac972a">ccp4srs::Bond</a>
+</li>
+<li>bond()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a6b01e3fa4cb59dc507460ea0715823fa">ccp4srs::Monomer</a>
+</li>
+<li>bond_length
+: <a class="el" href="classccp4srs_1_1_bond.html#a43513fb523b43f7f5f407a0bae151a95">ccp4srs::Bond</a>
+</li>
+<li>bond_length_esd
+: <a class="el" href="classccp4srs_1_1_bond.html#af438937a89d3cb3c7f2342ca6f38301c">ccp4srs::Bond</a>
+</li>
+<li>bond_order
+: <a class="el" href="classccp4srs_1_1_bond.html#ac6365bacbc07dd7cf914b6c7ad6cd5d7">ccp4srs::Bond</a>
+</li>
+<li>bonds
+: <a class="el" href="classccp4srs_1_1_monomer.html#a19495bb3c7e8d1c27f12f06729979d9e">ccp4srs::Monomer</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
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+        name="MSearchResults" id="MSearchResults">
+</iframe>
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+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x63.html ccp4srs/doc-html/html/functions_0x63.html
--- ccp4srs-old/doc-html/html/functions_0x63.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x63.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,197 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
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+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li class="current"><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_c"></a>- c -</h3><ul>
+<li>CalcHBonds()
+: <a class="el" href="classccp4srs_1_1_chem.html#ab5d4ff0f43b6785dc2c3cec72d4b8eec">ccp4srs::Chem</a>
+</li>
+<li>CantOpenFile
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaac65c121a2ac9e371d3e059cb480cf60d">ccp4srs::MemIO</a>
+</li>
+<li>ccp4_chirality()
+: <a class="el" href="classccp4srs_1_1_atom.html#ac0274e4727f43cedf27380121215cbfa">ccp4srs::Atom</a>
+</li>
+<li>center()
+: <a class="el" href="classccp4srs_1_1_chi_center.html#a0264f7a5c26c795bda84de7b233e70ab">ccp4srs::ChiCenter</a>
+</li>
+<li>charge()
+: <a class="el" href="classccp4srs_1_1_atom.html#a199caf3c186d47d5ca6e13e235471a84">ccp4srs::Atom</a>
+</li>
+<li>Chem()
+: <a class="el" href="classccp4srs_1_1_chem.html#a6ca2d1c22ede07e88978645ab6a5887e">ccp4srs::Chem</a>
+</li>
+<li>chem_formula()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a6bbfc74c882e403c57984d7310d4fb98">ccp4srs::Monomer</a>
+</li>
+<li>chem_name()
+: <a class="el" href="classccp4srs_1_1_monomer.html#ab5a8d9361def2e547d1e65bf180f3252">ccp4srs::Monomer</a>
+</li>
+<li>chem_type()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a37432cca1867e01cd9af6d4569c2326a">ccp4srs::Monomer</a>
+</li>
+<li>chemElement
+: <a class="el" href="classccp4srs_1_1_atom.html#a621e19772fdb901353b6f60288afdb70">ccp4srs::Atom</a>
+</li>
+<li>chicenter()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a3c1ea4e271769745f01c8dc4146c683e">ccp4srs::Monomer</a>
+</li>
+<li>ChiCenter()
+: <a class="el" href="classccp4srs_1_1_chi_center.html#a536462552b25777be443867ec6a28b48">ccp4srs::ChiCenter</a>
+</li>
+<li>chicenter_id
+: <a class="el" href="classccp4srs_1_1_chi_center.html#ac2387dc7a46c0c4451bcd08e23b25ae5">ccp4srs::ChiCenter</a>
+</li>
+<li>chicenters
+: <a class="el" href="classccp4srs_1_1_monomer.html#a96a126d39760ce281f8bf04186e29c13">ccp4srs::Monomer</a>
+</li>
+<li>chirality()
+: <a class="el" href="classccp4srs_1_1_atom.html#a88df4aee528a9e551c126e9e8adab2f3">ccp4srs::Atom</a>
+</li>
+<li>chunkNo
+: <a class="el" href="structccp4srs_1_1_m_p_file_pos.html#ab84443c24cd9b322d81f2e165af4bd8a">ccp4srs::MPFilePos</a>
+</li>
+<li>Comp1
+: <a class="el" href="classccp4srs_1_1_index.html#af2a41a666517311e8877a3ec9e288916">ccp4srs::Index</a>
+</li>
+<li>Comp2
+: <a class="el" href="classccp4srs_1_1_index.html#af4ce5b42fe2cf6364f9916d0a42f08b2">ccp4srs::Index</a>
+</li>
+<li>compare()
+: <a class="el" href="classccp4srs_1_1_bond.html#acefa794143d2ab128897441895cdf562">ccp4srs::Bond</a>
+</li>
+<li>CompressionError
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa6cf46f9d24d202ae6ac26ddb6aeb625d">ccp4srs::MemIO</a>
+</li>
+<li>connect()
+: <a class="el" href="classccp4srs_1_1_tree.html#a9986231a0223ef6b62902823d119176f">ccp4srs::Tree</a>
+</li>
+<li>connect_type
+: <a class="el" href="classccp4srs_1_1_tree.html#a97ee818b7a1b1724cfb712453be05743">ccp4srs::Tree</a>
+</li>
+<li>Container()
+: <a class="el" href="classccp4srs_1_1_container.html#acdff89dd6d441d731b517565021e3881">ccp4srs::Container&lt; T &gt;</a>
+</li>
+<li>copy()
+: <a class="el" href="classccp4srs_1_1_bond.html#a4bb135bfcd9ee6078a2770fe9f15319c">ccp4srs::Bond</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#ab3dc0fe1813d51055e829586a27ddd15">ccp4srs::ChiCenter</a>
+, <a class="el" href="classccp4srs_1_1_torsion.html#a2a6ff05c37b9ce514fe557ab3817a072">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_bond.html#a0c6c410020c5fad46d2987d9fc8de65e">ccp4srs::Bond</a>
+, <a class="el" href="classccp4srs_1_1_atom.html#a5aa8172f59efa4ac90359b2be7424d92">ccp4srs::Atom</a>
+, <a class="el" href="classccp4srs_1_1_tree.html#acfc010d5d168bb288379e6b6721fb9fa">ccp4srs::Tree</a>
+, <a class="el" href="classccp4srs_1_1_plane.html#a9db264baa4154922dfac882f4f437d34">ccp4srs::Plane</a>
+</li>
+<li>Copy()
+: <a class="el" href="structccp4srs_1_1_m_p_file_pos.html#a7f60e91b825a15d3def175dcdb71139d">ccp4srs::MPFilePos</a>
+</li>
+<li>copy()
+: <a class="el" href="classccp4srs_1_1_angle.html#a085c530866442b6b3dfb8c969de2bfe8">ccp4srs::Angle</a>
+</li>
+<li>Covalent
+: <a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795babaf2bbca3b364f84e83bbc9927b45e39">ccp4srs::Bond</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x64.html ccp4srs/doc-html/html/functions_0x64.html
--- ccp4srs-old/doc-html/html/functions_0x64.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x64.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,122 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li class="current"><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_d"></a>- d -</h3><ul>
+<li>deleteSelections()
+: <a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a582873aa43d2c8708e99db1485013bef">ccp4srs::DASelHnds</a>
+</li>
+<li>Deloc
+: <a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba3e459a041fa6b33d363df5a335413e13">ccp4srs::Bond</a>
+</li>
+<li>dist_esd
+: <a class="el" href="classccp4srs_1_1_plane.html#a5837e387b59c8d350271fd11a644ee8d">ccp4srs::Plane</a>
+</li>
+<li>Double
+: <a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba0311fe9d41fd3830910b1e4f93d9a83a">ccp4srs::Bond</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x65.html ccp4srs/doc-html/html/functions_0x65.html
--- ccp4srs-old/doc-html/html/functions_0x65.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x65.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,147 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li class="current"><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_e"></a>- e -</h3><ul>
+<li>element()
+: <a class="el" href="classccp4srs_1_1_atom.html#a78344a993072c3e8918a54c3259d55d8">ccp4srs::Atom</a>
+</li>
+<li>element_pdb()
+: <a class="el" href="classccp4srs_1_1_atom.html#a8d78d445f18a9f9e83d82f66e715b274">ccp4srs::Atom</a>
+</li>
+<li>empty()
+: <a class="el" href="classccp4srs_1_1_plane.html#a8da6c13ce79682d5f17e23f7c3e84849">ccp4srs::Plane</a>
+, <a class="el" href="classccp4srs_1_1_tree.html#a5f5e595cfdb5623cc59c0651ff7a25d3">ccp4srs::Tree</a>
+, <a class="el" href="classccp4srs_1_1_container.html#aeed888e25348f83a53021beaa21a0b1e">ccp4srs::Container&lt; T &gt;</a>
+</li>
+<li>EmptyFile
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa117fc645808ac4d9c4e53452bc608d51">ccp4srs::MemIO</a>
+</li>
+<li>EmptyLoop
+: <a class="el" href="classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5edad0a61a72f29321313e1bc19920df40f9">ccp4srs::Plane</a>
+</li>
+<li>energy_type()
+: <a class="el" href="classccp4srs_1_1_atom.html#af9d89db887cdbfc5523a79ece1c1e117">ccp4srs::Atom</a>
+</li>
+<li>energyType
+: <a class="el" href="classccp4srs_1_1_atom.html#ac429b2d0c02fe21432c4b651ad181fdb">ccp4srs::Atom</a>
+</li>
+<li>Entry()
+: <a class="el" href="classccp4srs_1_1_entry.html#aa72cb70c4f1c115a2134e2da80b9bc34">ccp4srs::Entry</a>
+</li>
+<li>entryID
+: <a class="el" href="classccp4srs_1_1_index.html#a0bd1aedcf3b32bdd48d0de5cd2cc563e">ccp4srs::Index</a>
+</li>
+<li>esd()
+: <a class="el" href="classccp4srs_1_1_torsion.html#a44095b8e5025c92a4b443a8715beceee">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_plane.html#ad9f1d004296b308a0955997695277ff4">ccp4srs::Plane</a>
+, <a class="el" href="classccp4srs_1_1_angle.html#a31b7030dec4dd77c0eefa3444c75901f">ccp4srs::Angle</a>
+</li>
+<li>esds()
+: <a class="el" href="classccp4srs_1_1_plane.html#a4fd16b46609257ebe87c7b7347597b2b">ccp4srs::Plane</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x66.html ccp4srs/doc-html/html/functions_0x66.html
--- ccp4srs-old/doc-html/html/functions_0x66.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x66.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,125 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li class="current"><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_f"></a>- f -</h3><ul>
+<li>fGraphPos
+: <a class="el" href="classccp4srs_1_1_index.html#a3be74bae1c6afc52ea36690b45ec5b96">ccp4srs::Index</a>
+</li>
+<li>forward()
+: <a class="el" href="classccp4srs_1_1_tree.html#ad52fadb719ce7ca269b9f6875a9ce8e6">ccp4srs::Tree</a>
+</li>
+<li>free()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a4cda073662a49aa45b0c744ec88de39a">ccp4srs::MemIO</a>
+</li>
+<li>freeMemory()
+: <a class="el" href="classccp4srs_1_1_base.html#ab67f138edc7ae19791be69dde485c719">ccp4srs::Base</a>
+</li>
+<li>fStructPos
+: <a class="el" href="classccp4srs_1_1_index.html#a21a1eddc77e99baf8df0b7450dee548b">ccp4srs::Index</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x67.html ccp4srs/doc-html/html/functions_0x67.html
--- ccp4srs-old/doc-html/html/functions_0x67.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x67.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,229 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li class="current"><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_g"></a>- g -</h3><ul>
+<li>get_angles()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a8d4b4084ca5c0e0fa42075f59eaf3e08">ccp4srs::Monomer</a>
+</li>
+<li>get_atoms()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a1ca9838123fea51260be3c44abd6771f">ccp4srs::Monomer</a>
+</li>
+<li>get_bonds()
+: <a class="el" href="classccp4srs_1_1_monomer.html#af36aeb36b83f49d3b4fc28d4737b5efd">ccp4srs::Monomer</a>
+</li>
+<li>get_bool()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a0bbc28ba1593463385ae8f28b65225fa">ccp4srs::MemIO</a>
+</li>
+<li>get_bound()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a7b6acc92258007c15351989930e8672f">ccp4srs::Monomer</a>
+</li>
+<li>get_buffer()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#aa1d1ea86d64ee50cab284d4a18f55ab8">ccp4srs::MemIO</a>
+</li>
+<li>get_byte()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a296d38484504311f2773ff313298dda9">ccp4srs::MemIO</a>
+</li>
+<li>get_chicenters()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a591d5f8275f5b5756442d96221039ef3">ccp4srs::Monomer</a>
+</li>
+<li>get_chirality()
+: <a class="el" href="classccp4srs_1_1_chi_center.html#a1aa5ee605cdc3756abcb075279eeb8af">ccp4srs::ChiCenter</a>
+</li>
+<li>get_float()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#adf95c15823dd0fb1067002d2ee3d8095">ccp4srs::MemIO</a>
+</li>
+<li>get_ibyte()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a7bc9b6d871402f5b5601d05ad4012326">ccp4srs::MemIO</a>
+</li>
+<li>get_integer()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a2d311d3bf0798e1c2bcb1cbe7f5d622f">ccp4srs::MemIO</a>
+</li>
+<li>get_ishort()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a55e1b2e8f826ab2d6c0aef09f3beac9f">ccp4srs::MemIO</a>
+</li>
+<li>get_line()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a6cab031cef522531846e3ced7984f276">ccp4srs::MemIO</a>
+</li>
+<li>get_long()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a950878f651e3bb037cf7ddc4a9c00201">ccp4srs::MemIO</a>
+</li>
+<li>get_planes()
+: <a class="el" href="classccp4srs_1_1_monomer.html#aa454ac38a87c19006580a42bc38958fc">ccp4srs::Monomer</a>
+</li>
+<li>get_real()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#afcc2e5eede7a829347985f646f24dcb3">ccp4srs::MemIO</a>
+</li>
+<li>get_short()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#af2d1b382de42e06ce1dc5ae4ad6bb20f">ccp4srs::MemIO</a>
+</li>
+<li>get_shortreal()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a039402bc82d9d0de0bd3664769355573">ccp4srs::MemIO</a>
+</li>
+<li>get_string()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a22abd9cc96e80e4d3e71f0d1acbf1c4d">ccp4srs::MemIO</a>
+</li>
+<li>get_torsions()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a7b31b6675690c2edc0baa0e070d349ad">ccp4srs::Monomer</a>
+</li>
+<li>get_tree()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a351a18b323af41b74d1b415fcd1df640">ccp4srs::Monomer</a>
+</li>
+<li>get_word()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#ab932bc5aa0e98c9e681a3f3a9cc532c8">ccp4srs::MemIO</a>
+</li>
+<li>getAtNames()
+: <a class="el" href="classccp4srs_1_1_base.html#af9a1789b20b43e97a8eb6a56b4ef32c4">ccp4srs::Base</a>
+</li>
+<li>getAtomNameMatch()
+: <a class="el" href="classccp4srs_1_1_monomer.html#abb514ab63af7e9dbb68f59bc13551618">ccp4srs::Monomer</a>
+</li>
+<li>getAtoms()
+: <a class="el" href="classccp4srs_1_1_base.html#a7e47408dacc9bd80de046504e235cc06">ccp4srs::Base</a>
+</li>
+<li>getBonds()
+: <a class="el" href="classccp4srs_1_1_base.html#a8bb61486d7dd2df0566b8e3a1c7f1c89">ccp4srs::Base</a>
+</li>
+<li>getEnergyTypes()
+: <a class="el" href="classccp4srs_1_1_chem.html#a301341ad4a91bf6cc4e7641efeb56309">ccp4srs::Chem</a>
+</li>
+<li>getEntryNo()
+: <a class="el" href="classccp4srs_1_1_base.html#a57b706684f3e84c741099ff904e01152">ccp4srs::Base</a>
+</li>
+<li>getGraph()
+: <a class="el" href="classccp4srs_1_1_base.html#a418f3d4d079e0c4b93ebc6fff1fd0639">ccp4srs::Base</a>
+, <a class="el" href="classccp4srs_1_1_monomer.html#a9d1a2b0facb208344413158d74446755">ccp4srs::Monomer</a>
+, <a class="el" href="classccp4srs_1_1_base.html#af00d1ee772d045c048aa292457755b50">ccp4srs::Base</a>
+</li>
+<li>getGraphFile()
+: <a class="el" href="classccp4srs_1_1_base.html#a656b776b70ead2f8346b352b3bd1311e">ccp4srs::Base</a>
+</li>
+<li>getHetInfo()
+: <a class="el" href="classccp4srs_1_1_base.html#a88c88924e247250d08cc4795b345c66a">ccp4srs::Base</a>
+</li>
+<li>getIndex()
+: <a class="el" href="classccp4srs_1_1_base.html#a399ff3d49a14dd3bb8250058f6452f4f">ccp4srs::Base</a>
+</li>
+<li>getLeavingAtoms()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a6c3ad68f13fb779921605d0e696add1c">ccp4srs::Monomer</a>
+</li>
+<li>getMonomer()
+: <a class="el" href="classccp4srs_1_1_base.html#a6f3f6564a30198bfe82215bceb6806e2">ccp4srs::Base</a>
+</li>
+<li>getNewHandles()
+: <a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a3e8624665274bf47da9408f3b21f35d8">ccp4srs::DASelHnds</a>
+</li>
+<li>getNofAtoms()
+: <a class="el" href="classccp4srs_1_1_base.html#a646d2c4349be4a740f2121dfd2091150">ccp4srs::Base</a>
+</li>
+<li>getPath()
+: <a class="el" href="classccp4srs_1_1_base.html#ac5481a8eeeb26ead06d7df61f605dac9">ccp4srs::Base</a>
+</li>
+<li>getStructFile()
+: <a class="el" href="classccp4srs_1_1_base.html#a03eac100b52d1f2d2d13981799f928bb">ccp4srs::Base</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x68.html ccp4srs/doc-html/html/functions_0x68.html
--- ccp4srs-old/doc-html/html/functions_0x68.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x68.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,113 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li class="current"><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_h"></a>- h -</h3><ul>
+<li>hb_type()
+: <a class="el" href="classccp4srs_1_1_atom.html#ab45d65bdba2966ce382687548921cd56">ccp4srs::Atom</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x69.html ccp4srs/doc-html/html/functions_0x69.html
--- ccp4srs-old/doc-html/html/functions_0x69.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x69.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,150 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
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+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li class="current"><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_i"></a>- i -</h3><ul>
+<li>id()
+: <a class="el" href="classccp4srs_1_1_atom.html#a276b8b3e31130e6f0116af498e3a7766">ccp4srs::Atom</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#a9bd5958f4cb3519a6a745d1db16b135b">ccp4srs::ChiCenter</a>
+, <a class="el" href="classccp4srs_1_1_torsion.html#a63cbef738a4be2da8a46367802f83e3d">ccp4srs::Torsion</a>
+</li>
+<li>ID()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a1eca7f4a9537bddf81de26df20984183">ccp4srs::Monomer</a>
+</li>
+<li>id()
+: <a class="el" href="classccp4srs_1_1_plane.html#ac47f99cd6bf3190767da8fc85d01dc18">ccp4srs::Plane</a>
+</li>
+<li>Index()
+: <a class="el" href="classccp4srs_1_1_index.html#aaff51df26ae81aff0425bda97d6f7030">ccp4srs::Index</a>
+</li>
+<li>index
+: <a class="el" href="classccp4srs_1_1_base.html#ada41928311fa3ba94bcb48a1ebf4b4df">ccp4srs::Base</a>
+, <a class="el" href="classccp4srs_1_1_container.html#a6afe8d51f68e07697d7362464e433cac">ccp4srs::Container&lt; T &gt;</a>
+</li>
+<li>IndexInit()
+: <a class="el" href="classccp4srs_1_1_index.html#aedec88e9928356d4f7c913d449ca0d3e">ccp4srs::Index</a>
+</li>
+<li>Init()
+: <a class="el" href="classccp4srs_1_1_atom.html#ab6a22850541822e026c9d6a241079fd6">ccp4srs::Atom</a>
+, <a class="el" href="classccp4srs_1_1_monomer.html#a6a50cfb8d8e87162309106c66f5fc155">ccp4srs::Monomer</a>
+</li>
+<li>init_base()
+: <a class="el" href="classccp4srs_1_1_base.html#a9fb463b8df4034fefb6e136ab56d135b">ccp4srs::Base</a>
+</li>
+<li>init_chem()
+: <a class="el" href="classccp4srs_1_1_chem.html#a7ed4ac373981270bc1af2b8cc99b461d">ccp4srs::Chem</a>
+</li>
+<li>ion_radius()
+: <a class="el" href="classccp4srs_1_1_atom.html#a4cbbb8a7a4d9f69eca5caadfffa6c956">ccp4srs::Atom</a>
+</li>
+<li>ionRadius
+: <a class="el" href="classccp4srs_1_1_atom.html#aeb773fbdd5b04c0311969ad498622185">ccp4srs::Atom</a>
+</li>
+<li>isLeaving()
+: <a class="el" href="classccp4srs_1_1_atom.html#a7da89fae287dcf0c0838108fd442ec53">ccp4srs::Atom</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x6c.html ccp4srs/doc-html/html/functions_0x6c.html
--- ccp4srs-old/doc-html/html/functions_0x6c.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x6c.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,129 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li class="current"><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_l"></a>- l -</h3><ul>
+<li>leaving()
+: <a class="el" href="classccp4srs_1_1_atom.html#ac7f1f1f474b56199e70bb0dcd364bb4b">ccp4srs::Atom</a>
+</li>
+<li>length()
+: <a class="el" href="classccp4srs_1_1_bond.html#a3ebb971fa0af7886f076da460b4875e9">ccp4srs::Bond</a>
+, <a class="el" href="classccp4srs_1_1_mem_i_o.html#a5e4ae24f25179a720de85f185f8074ff">ccp4srs::MemIO</a>
+</li>
+<li>length_esd()
+: <a class="el" href="classccp4srs_1_1_bond.html#a28f3638c15b007dddaab637362635009">ccp4srs::Bond</a>
+</li>
+<li>Link
+: <a class="el" href="classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88cae7d526eebfeb15c8370f473885073095">ccp4srs::Entry</a>
+</li>
+<li>loadIndex()
+: <a class="el" href="classccp4srs_1_1_base.html#ae95af9ff2fb5c9d0edb437be3bcbe016">ccp4srs::Base</a>
+</li>
+<li>loadStructure()
+: <a class="el" href="classccp4srs_1_1_base.html#a663ef26d53b80f6c8b1f9c9cdeb70d2c">ccp4srs::Base</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x6d.html ccp4srs/doc-html/html/functions_0x6d.html
--- ccp4srs-old/doc-html/html/functions_0x6d.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x6d.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,201 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li class="current"><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_m"></a>- m -</h3><ul>
+<li>makeAtom()
+: <a class="el" href="classccp4srs_1_1_atom.html#a40ec4d3c3ea0384ab4d2c56b3ee5389b">ccp4srs::Atom</a>
+</li>
+<li>makeBonds()
+: <a class="el" href="classccp4srs_1_1_chem.html#ad60a617bc151e054eb306e8c6bf592f4">ccp4srs::Chem</a>
+</li>
+<li>makeCIF()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a5e3fb1e64eab3e764cc83ff1e6c61fa3">ccp4srs::Monomer</a>
+</li>
+<li>makeCIFTags()
+: <a class="el" href="classccp4srs_1_1_chi_center.html#a93d09528c86718358137aaf48c1a8ce1">ccp4srs::ChiCenter</a>
+, <a class="el" href="classccp4srs_1_1_plane.html#a1ac0cfa095deac2bd97e99ce2b30de96">ccp4srs::Plane</a>
+, <a class="el" href="classccp4srs_1_1_angle.html#a257cefe6949d4371175d4c1573a1d40e">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_torsion.html#ae33b6fc8d12fdbd48a299cf488e16f0e">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_atom.html#ac1bcbe4ebfbf35c7d0369d41afa07714">ccp4srs::Atom</a>
+, <a class="el" href="classccp4srs_1_1_bond.html#a781542dae98140ea687a5d83a3e02e8e">ccp4srs::Bond</a>
+</li>
+<li>MakeCompositions()
+: <a class="el" href="classccp4srs_1_1_index.html#afda5436941f171c791be43b9d28f43a5">ccp4srs::Index</a>
+</li>
+<li>makeSelIndexes()
+: <a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#aaca5f89914d27b9869b6f082931c53d5">ccp4srs::DASelHnds</a>
+</li>
+<li>Manager()
+: <a class="el" href="classccp4srs_1_1_manager.html#a7b1bcc6f68308560b402c5b3f8533158">ccp4srs::Manager</a>
+</li>
+<li>maxDAAcos
+: <a class="el" href="classccp4srs_1_1_chem.html#aa32277562470e13dfe292f01bc269c17">ccp4srs::Chem</a>
+</li>
+<li>maxDAdist
+: <a class="el" href="classccp4srs_1_1_chem.html#a6655092e23b55ff3d6465a60101c135d">ccp4srs::Chem</a>
+</li>
+<li>maxDDAcos
+: <a class="el" href="classccp4srs_1_1_chem.html#aa5d2547bfa92f55c755aa57fce717a65">ccp4srs::Chem</a>
+</li>
+<li>maxDHAcos
+: <a class="el" href="classccp4srs_1_1_chem.html#a7408580f10d8868ae368f3faa1253577">ccp4srs::Chem</a>
+</li>
+<li>maxHAAcos
+: <a class="el" href="classccp4srs_1_1_chem.html#a71cea07257deb2795443e04e07ee4bed">ccp4srs::Chem</a>
+</li>
+<li>maxHAdist2
+: <a class="el" href="classccp4srs_1_1_chem.html#ada14781ad5390841304d35f262705c57">ccp4srs::Chem</a>
+</li>
+<li>maxSBdist
+: <a class="el" href="classccp4srs_1_1_chem.html#aeeb0e6bc6cc2e1a3f5ce78d59d8b496d">ccp4srs::Chem</a>
+</li>
+<li>memIO
+: <a class="el" href="classccp4srs_1_1_base.html#adf128b2adae954f6b25463c70ede5a58">ccp4srs::Base</a>
+</li>
+<li>MemIO()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#af2490447442255fa19b2a1c05c011f96">ccp4srs::MemIO</a>
+</li>
+<li>MemReadError
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaadf48b9ed60d08687c2fbd5271b328c70">ccp4srs::MemIO</a>
+</li>
+<li>merge()
+: <a class="el" href="classccp4srs_1_1_atom.html#af28439c95edf554364f29e988b47acd1">ccp4srs::Atom</a>
+, <a class="el" href="classccp4srs_1_1_monomer.html#a6453406b0256cf9fbf74177a7db8770b">ccp4srs::Monomer</a>
+</li>
+<li>Metal
+: <a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba1be67f1d82568ea8bb92f456440e7f01">ccp4srs::Bond</a>
+</li>
+<li>minDAdist
+: <a class="el" href="classccp4srs_1_1_chem.html#a2e63b74dcf71dbf8583a64342de3848c">ccp4srs::Chem</a>
+</li>
+<li>mlib_x
+: <a class="el" href="classccp4srs_1_1_atom.html#a641d281e9661ff8ca51bc768b2db5628">ccp4srs::Atom</a>
+</li>
+<li>mlib_y
+: <a class="el" href="classccp4srs_1_1_atom.html#a92043cd1d43d17069c0c8f96020218b9">ccp4srs::Atom</a>
+</li>
+<li>mlib_z
+: <a class="el" href="classccp4srs_1_1_atom.html#a0b6c2ba6990da454ea672a64e285653f">ccp4srs::Atom</a>
+</li>
+<li>monFormula
+: <a class="el" href="classccp4srs_1_1_monomer.html#aeb6bee62372a765e8aca0c1496689b3a">ccp4srs::Monomer</a>
+</li>
+<li>monID
+: <a class="el" href="classccp4srs_1_1_monomer.html#a34240535a6e703495662936dba863026">ccp4srs::Monomer</a>
+</li>
+<li>monName
+: <a class="el" href="classccp4srs_1_1_monomer.html#a53b8d5232f3b2085d531eca33fb7c55a">ccp4srs::Monomer</a>
+</li>
+<li>Monomer()
+: <a class="el" href="classccp4srs_1_1_monomer.html#abd3a6efc83918f121e3e83165681ccd5">ccp4srs::Monomer</a>
+, <a class="el" href="classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88ca447bc9153594c5d2b79e47041f4982b6">ccp4srs::Entry</a>
+</li>
+<li>monType
+: <a class="el" href="classccp4srs_1_1_monomer.html#af0a573429afbbea61647c9851f0deba7">ccp4srs::Monomer</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x6e.html ccp4srs/doc-html/html/functions_0x6e.html
--- ccp4srs-old/doc-html/html/functions_0x6e.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x6e.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,168 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li class="current"><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_n"></a>- n -</h3><ul>
+<li>n_angles()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a832521f11b1adb4a0deb9fd92b4bc725">ccp4srs::Monomer</a>
+</li>
+<li>n_atoms
+: <a class="el" href="classccp4srs_1_1_plane.html#aa76a845ff6abce3d2c8f40db13717842">ccp4srs::Plane</a>
+, <a class="el" href="classccp4srs_1_1_monomer.html#a3e3e771e2d60581384b1169648b4d751">ccp4srs::Monomer</a>
+</li>
+<li>n_bonds()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a6a6e470c174fd570667bf43f95757c0d">ccp4srs::Monomer</a>
+</li>
+<li>n_chicenters()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a047ec20b44f73aa0027fdd071aa265d6">ccp4srs::Monomer</a>
+</li>
+<li>n_entries()
+: <a class="el" href="classccp4srs_1_1_base.html#aeb551e05e822e5eb3673aba1fa85bda6">ccp4srs::Base</a>
+</li>
+<li>n_objects
+: <a class="el" href="classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748">ccp4srs::Container&lt; T &gt;</a>
+</li>
+<li>n_planes()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a123cf02246e052730361055de3f0d477">ccp4srs::Monomer</a>
+</li>
+<li>n_sections
+: <a class="el" href="classccp4srs_1_1_tree.html#a4056f0bb5ef8add5a55133eb8166c639">ccp4srs::Tree</a>
+</li>
+<li>n_torsions()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a0bf10d776d5d992424b99d88d884f101">ccp4srs::Monomer</a>
+</li>
+<li>name()
+: <a class="el" href="classccp4srs_1_1_atom.html#ad8288e82eeab398bf90da3f35ebe15c5">ccp4srs::Atom</a>
+</li>
+<li>name_pdb()
+: <a class="el" href="classccp4srs_1_1_atom.html#a357cfea9384684a64bb3220d02b3afa7">ccp4srs::Atom</a>
+</li>
+<li>nAtoms
+: <a class="el" href="classccp4srs_1_1_index.html#abba65d2d400f004fa3815a06101ac478">ccp4srs::Index</a>
+</li>
+<li>nBonds
+: <a class="el" href="classccp4srs_1_1_index.html#a5906658999e6e4e095589e0cdffabf11">ccp4srs::Index</a>
+</li>
+<li>nEntries
+: <a class="el" href="classccp4srs_1_1_base.html#a863fd5090d78f3bada7f351dd2f33859">ccp4srs::Base</a>
+</li>
+<li>nNonHAtoms
+: <a class="el" href="classccp4srs_1_1_index.html#aa97eb5251314eeb77e5acd2af72ce1aa">ccp4srs::Index</a>
+</li>
+<li>NoMorePlanes
+: <a class="el" href="classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5eda95f4f7898a15589a3db43827444d2692">ccp4srs::Plane</a>
+</li>
+<li>None
+: <a class="el" href="classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88ca616c951330c4d0b080622857146e2457">ccp4srs::Entry</a>
+</li>
+<li>noOrder
+: <a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba3a534360bb854109f0ad2d34f1858997">ccp4srs::Bond</a>
+</li>
+<li>numberOf()
+: <a class="el" href="classccp4srs_1_1_container.html#abbc5e6eeb9ea4d37b8d2025892ebd9ff">ccp4srs::Container&lt; T &gt;</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x6f.html ccp4srs/doc-html/html/functions_0x6f.html
--- ccp4srs-old/doc-html/html/functions_0x6f.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x6f.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,138 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li class="current"><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_o"></a>- o -</h3><ul>
+<li>object
+: <a class="el" href="classccp4srs_1_1_container.html#a25a4ad3660f2ef6760c949be2c1372a8">ccp4srs::Container&lt; T &gt;</a>
+</li>
+<li>offset
+: <a class="el" href="structccp4srs_1_1_m_p_file_pos.html#afb6853252f03dbbc698dea44b425d2d9">ccp4srs::MPFilePos</a>
+</li>
+<li>Ok
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63">ccp4srs::MemIO</a>
+, <a class="el" href="classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5edae47dd3ee9591c478c387ddbe09f7ef34">ccp4srs::Plane</a>
+</li>
+<li>old_name()
+: <a class="el" href="classccp4srs_1_1_atom.html#acda740ae967221e50f1d383ce70d58d9">ccp4srs::Atom</a>
+</li>
+<li>old_name_pdb()
+: <a class="el" href="classccp4srs_1_1_atom.html#abd73ea1b813b1321048f850b88914982">ccp4srs::Atom</a>
+</li>
+<li>oldAtomName
+: <a class="el" href="classccp4srs_1_1_atom.html#a45682b942f2f9262bc8fa1b5316a702b">ccp4srs::Atom</a>
+</li>
+<li>oldID()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a271e6aaeed7ace67e36f2c5fea626d70">ccp4srs::Monomer</a>
+</li>
+<li>oldMonID
+: <a class="el" href="classccp4srs_1_1_monomer.html#a896cc0c3979b65913de25be2c2f75ec9">ccp4srs::Monomer</a>
+</li>
+<li>order()
+: <a class="el" href="classccp4srs_1_1_bond.html#ae18a9e08399e96910028f01a376d41f0">ccp4srs::Bond</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x70.html ccp4srs/doc-html/html/functions_0x70.html
--- ccp4srs-old/doc-html/html/functions_0x70.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x70.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,188 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li class="current"><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_p"></a>- p -</h3><ul>
+<li>pdb_x
+: <a class="el" href="classccp4srs_1_1_atom.html#a49ff7aadab557a536541009606a2db12">ccp4srs::Atom</a>
+</li>
+<li>pdb_y
+: <a class="el" href="classccp4srs_1_1_atom.html#a901c15656be6fa36e191df297d25521d">ccp4srs::Atom</a>
+</li>
+<li>pdb_z
+: <a class="el" href="classccp4srs_1_1_atom.html#ae33b2033023270f96202151aed27a710">ccp4srs::Atom</a>
+</li>
+<li>pdbx_x
+: <a class="el" href="classccp4srs_1_1_atom.html#aec57c2566b6a42361a8215d7b15a7e29">ccp4srs::Atom</a>
+</li>
+<li>pdbx_y
+: <a class="el" href="classccp4srs_1_1_atom.html#a1d138de5fa3e222554a95b796c246d40">ccp4srs::Atom</a>
+</li>
+<li>pdbx_z
+: <a class="el" href="classccp4srs_1_1_atom.html#a424a6001bc93ea1c8256f9f1fb48a585">ccp4srs::Atom</a>
+</li>
+<li>period()
+: <a class="el" href="classccp4srs_1_1_torsion.html#a8fd30d637a8002a46ff4c50cadc8d34f">ccp4srs::Torsion</a>
+</li>
+<li>plane()
+: <a class="el" href="classccp4srs_1_1_monomer.html#afdebf230f6aa9bf2692a82b919d59918">ccp4srs::Monomer</a>
+</li>
+<li>Plane()
+: <a class="el" href="classccp4srs_1_1_plane.html#ab45260579cf6dd22ecdaa93ad3b5c183">ccp4srs::Plane</a>
+</li>
+<li>plane_atoms
+: <a class="el" href="classccp4srs_1_1_plane.html#a4c8155332953ddb6cf79acf018c98c85">ccp4srs::Plane</a>
+</li>
+<li>plane_id
+: <a class="el" href="classccp4srs_1_1_plane.html#afdfdff5528e19537d834061022c2b2bf">ccp4srs::Plane</a>
+</li>
+<li>planes
+: <a class="el" href="classccp4srs_1_1_monomer.html#a2f927ab2a3e517f9fe6cba6e89954cfe">ccp4srs::Monomer</a>
+</li>
+<li>property
+: <a class="el" href="classccp4srs_1_1_atom.html#aa363093b5746f782b8c4e60a73ec6438">ccp4srs::Atom</a>
+</li>
+<li>put_bool()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#ac3420c8a37ce57f324cf66eb4ccb9b13">ccp4srs::MemIO</a>
+</li>
+<li>put_byte()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a3c30e4f73927173a9ce5731fab39d170">ccp4srs::MemIO</a>
+</li>
+<li>put_float()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#ad82c1eca930cc9d5535f2da1ab3cde1a">ccp4srs::MemIO</a>
+</li>
+<li>put_ibyte()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a55ccb2d1a276365eadb422c75e982de3">ccp4srs::MemIO</a>
+</li>
+<li>put_integer()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a6c563469a6978a9c1c62a33457c90661">ccp4srs::MemIO</a>
+</li>
+<li>put_ishort()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a1a5cd9341de994fa17ae8efae3d61732">ccp4srs::MemIO</a>
+</li>
+<li>put_line()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a98548fca1e008178fef523b271db5423">ccp4srs::MemIO</a>
+</li>
+<li>put_long()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#af300f12e3fe4b3d878f80caf19b66341">ccp4srs::MemIO</a>
+</li>
+<li>put_real()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a1d8e03e12f2420c9650f4a8956a1c0a7">ccp4srs::MemIO</a>
+</li>
+<li>put_short()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a7117ff86d20006f7a693ea3a36035674">ccp4srs::MemIO</a>
+</li>
+<li>put_shortreal()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a4eb6ba2e97922bf9509d828ee075aa8e">ccp4srs::MemIO</a>
+</li>
+<li>put_string()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#aa35e6bbff841d942f793e50ee813fc97">ccp4srs::MemIO</a>
+</li>
+<li>put_word()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#abf6e925edc35b60fe7816223ceb7a15f">ccp4srs::MemIO</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x72.html ccp4srs/doc-html/html/functions_0x72.html
--- ccp4srs-old/doc-html/html/functions_0x72.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x72.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,175 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li class="current"><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_r"></a>- r -</h3><ul>
+<li>rcsb_chirality()
+: <a class="el" href="classccp4srs_1_1_atom.html#a1dc09ecc6dee155b93e5c3431d4c548e">ccp4srs::Atom</a>
+</li>
+<li>rcsb_name()
+: <a class="el" href="classccp4srs_1_1_atom.html#af0bbf72624e0f7de9900ec931b673410">ccp4srs::Atom</a>
+</li>
+<li>rcsb_name_pdb()
+: <a class="el" href="classccp4srs_1_1_atom.html#ace51a15043535b0fef9b2816dba48cdb">ccp4srs::Atom</a>
+</li>
+<li>rcsbAtomName
+: <a class="el" href="classccp4srs_1_1_atom.html#a198154f097c4f42a4ae1dd73d5394734">ccp4srs::Atom</a>
+</li>
+<li>read()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#aebd3a0d6614c77b533433bc75de6d069">ccp4srs::MemIO</a>
+, <a class="el" href="structccp4srs_1_1_m_p_file_pos.html#a8351d37471b7cdab264a91bb1a92db1c">ccp4srs::MPFilePos</a>
+, <a class="el" href="classccp4srs_1_1_entry.html#a262e2814d9a1bc35fbbfd75e46397343">ccp4srs::Entry</a>
+, <a class="el" href="classccp4srs_1_1_index.html#a17c3250780def030676fef212a19731c">ccp4srs::Index</a>
+, <a class="el" href="classccp4srs_1_1_mem_i_o.html#ad8c19ab9e2bd98b40caf95cc6d7e071e">ccp4srs::MemIO</a>
+</li>
+<li>read_buffer()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a7df5365c01565a15ac3bca748e46146b">ccp4srs::MemIO</a>
+</li>
+<li>read_mem()
+: <a class="el" href="classccp4srs_1_1_entry.html#a2d3193b4e34c21b286526931e2e5b62d">ccp4srs::Entry</a>
+, <a class="el" href="classccp4srs_1_1_index.html#a06b50353c15a21a56688b3e00aad2e2d">ccp4srs::Index</a>
+, <a class="el" href="classccp4srs_1_1_monomer.html#ac12b93e766cfbcfd4288512df739a56e">ccp4srs::Monomer</a>
+, <a class="el" href="classccp4srs_1_1_plane.html#a148162145438f6f97414eee0aa72275a">ccp4srs::Plane</a>
+, <a class="el" href="classccp4srs_1_1_torsion.html#af65ef2e18a3b6494070300afec0099e1">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_tree.html#a7e39da9840cb8815e8854cd11552c3a9">ccp4srs::Tree</a>
+, <a class="el" href="classccp4srs_1_1_angle.html#a2f34c77527204676236a28c863f5adee">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_atom.html#a150503215d6820dda3726b107e8e1bc7">ccp4srs::Atom</a>
+, <a class="el" href="classccp4srs_1_1_bond.html#a47ad8a18d4c0363dc1f04f3cfbc670ec">ccp4srs::Bond</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#a64588b20c5010e22ad5d571343a7e6d0">ccp4srs::ChiCenter</a>
+, <a class="el" href="classccp4srs_1_1_container.html#a9f42bc8ec160490ba2dd8d7a8eeae15e">ccp4srs::Container&lt; T &gt;</a>
+</li>
+<li>ReadError
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaab76082bd26e6e49c9c7794410cec3ca2">ccp4srs::MemIO</a>
+</li>
+<li>readFromCIF()
+: <a class="el" href="classccp4srs_1_1_torsion.html#aaf9375ff9aeb22a2a148763276ec80d1">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_tree.html#af50e009eb63e2bdf8da129afa193d637">ccp4srs::Tree</a>
+, <a class="el" href="classccp4srs_1_1_bond.html#a24976c4962050d858ca00fa6f72684e2">ccp4srs::Bond</a>
+, <a class="el" href="classccp4srs_1_1_monomer.html#aa9b0a99023e890070aec088182f8a65b">ccp4srs::Monomer</a>
+, <a class="el" href="classccp4srs_1_1_angle.html#a9a366216e8c07f33829fd26db9df4f00">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_atom.html#a94f5f81532b98126f3383f29c077473c">ccp4srs::Atom</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#a8c038c3d35ef4effbe5e02db4cdf9f88">ccp4srs::ChiCenter</a>
+, <a class="el" href="classccp4srs_1_1_plane.html#a656a93b833de401dcac75db47b5bcf57">ccp4srs::Plane</a>
+</li>
+<li>readFromCIF_ccp4()
+: <a class="el" href="classccp4srs_1_1_bond.html#ac6a267f1cb4e7553d746537cf36e5ea3">ccp4srs::Bond</a>
+, <a class="el" href="classccp4srs_1_1_atom.html#a0e4f39d4293b8e1907b0295e215c4230">ccp4srs::Atom</a>
+, <a class="el" href="classccp4srs_1_1_monomer.html#a9e457d3f7633b79b598b66f382fa5c5c">ccp4srs::Monomer</a>
+</li>
+<li>readFromCIF_rcsb()
+: <a class="el" href="classccp4srs_1_1_monomer.html#aaaec1b93dd1dcfe0e20484fd4bbc2a72">ccp4srs::Monomer</a>
+, <a class="el" href="classccp4srs_1_1_atom.html#a12b7ff09ff7aa0cc7581a55e89ac9e0e">ccp4srs::Atom</a>
+, <a class="el" href="classccp4srs_1_1_bond.html#a54c6291defa953cc5f5750b0f116719c">ccp4srs::Bond</a>
+</li>
+<li>readMonIDFromCIF()
+: <a class="el" href="classccp4srs_1_1_monomer.html#acbe4714fc7593d649b5e8901668d5c5c">ccp4srs::Monomer</a>
+</li>
+<li>reset()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a42598d1f669c5e539cb024bb023e0551">ccp4srs::Monomer</a>
+, <a class="el" href="classccp4srs_1_1_mem_i_o.html#a855507e19582e7ab9b7236fb9d453da3">ccp4srs::MemIO</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x73.html ccp4srs/doc-html/html/functions_0x73.html
--- ccp4srs-old/doc-html/html/functions_0x73.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x73.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,186 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li class="current"><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_s"></a>- s -</h3><ul>
+<li>selHndAcceptor
+: <a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a6df62532c19c06870cb386b3e1d4cc3c">ccp4srs::DASelHnds</a>
+</li>
+<li>selHndDonor
+: <a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a0291cf6e8fc47959f00d5dfa536d4d3c">ccp4srs::DASelHnds</a>
+</li>
+<li>selHndHydrogen
+: <a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a0dd02cde05c05d8d5f1c99c55aa6e251">ccp4srs::DASelHnds</a>
+</li>
+<li>selKey
+: <a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#ab9e53854d32fb72fb9003efc870354df">ccp4srs::DASelHnds</a>
+</li>
+<li>set_buffer_length()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#ac84f72f62362171b812f386ef786a677">ccp4srs::MemIO</a>
+</li>
+<li>set_chirality()
+: <a class="el" href="classccp4srs_1_1_atom.html#a4839e285360f50dbe4dbfff765ece82c">ccp4srs::Atom</a>
+</li>
+<li>set_energy_type()
+: <a class="el" href="classccp4srs_1_1_atom.html#abab85177d8d15e5dfc51e12ed9af4d69">ccp4srs::Atom</a>
+</li>
+<li>set_hb_type()
+: <a class="el" href="classccp4srs_1_1_atom.html#a983a276a7821c272f3952f4edfb826c6">ccp4srs::Atom</a>
+</li>
+<li>set_ion_radius()
+: <a class="el" href="classccp4srs_1_1_atom.html#a132fd6895be46a1afa96bb0529c0a6ba">ccp4srs::Atom</a>
+</li>
+<li>set_old_name()
+: <a class="el" href="classccp4srs_1_1_atom.html#a67142fe2e03f768fea4dc3334826ef2e">ccp4srs::Atom</a>
+</li>
+<li>set_rcsb_chirality()
+: <a class="el" href="classccp4srs_1_1_atom.html#af46102bc6356f36610eda68ced6e9202">ccp4srs::Atom</a>
+</li>
+<li>set_sp()
+: <a class="el" href="classccp4srs_1_1_atom.html#aa9fe3297f6d6de92f1520a6631361861">ccp4srs::Atom</a>
+</li>
+<li>set_valency()
+: <a class="el" href="classccp4srs_1_1_atom.html#af50fcb98ad0f4a42768079e985adec5b">ccp4srs::Atom</a>
+</li>
+<li>set_vdw_radius()
+: <a class="el" href="classccp4srs_1_1_atom.html#aa2c293fa289d7a24bc8858578dd3357e">ccp4srs::Atom</a>
+</li>
+<li>set_vdwh_radius()
+: <a class="el" href="classccp4srs_1_1_atom.html#a8912626b88300dcb9e736cf1b4369f82">ccp4srs::Atom</a>
+</li>
+<li>setCompressionLevel()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#abfd614fba0e035434e9c7f1c4a58ad89">ccp4srs::MemIO</a>
+</li>
+<li>setOldID()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a3d9cd816f0e032e64e0d47ed7673ec63">ccp4srs::Monomer</a>
+</li>
+<li>sign()
+: <a class="el" href="classccp4srs_1_1_chi_center.html#a17574c6830e27efde72575acdf154d80">ccp4srs::ChiCenter</a>
+</li>
+<li>Single
+: <a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba338d16bbed971e9a0c912ff78efed793">ccp4srs::Bond</a>
+</li>
+<li>size()
+: <a class="el" href="classccp4srs_1_1_plane.html#a61ab65ef97a61c79d1190673a5a1b8e3">ccp4srs::Plane</a>
+, <a class="el" href="classccp4srs_1_1_tree.html#a308ddfce7a902729218e39356db92cc0">ccp4srs::Tree</a>
+</li>
+<li>SizeError
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaaec9637fa3da0cf0cc0385a15d95af350">ccp4srs::MemIO</a>
+</li>
+<li>sp()
+: <a class="el" href="classccp4srs_1_1_atom.html#a9ae7f9281596f659071394247d484ffb">ccp4srs::Atom</a>
+</li>
+<li>srsDir
+: <a class="el" href="classccp4srs_1_1_base.html#af3caa0403ce8a1c4489948fa4fc62b0c">ccp4srs::Base</a>
+</li>
+<li>srsVersion
+: <a class="el" href="classccp4srs_1_1_base.html#ad18087156761086530c1f01f3078f869">ccp4srs::Base</a>
+</li>
+<li>struct_tree
+: <a class="el" href="classccp4srs_1_1_monomer.html#aef8794097a333f1e4e20dd3d876f1432">ccp4srs::Monomer</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x74.html ccp4srs/doc-html/html/functions_0x74.html
--- ccp4srs-old/doc-html/html/functions_0x74.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x74.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,142 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li class="current"><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_t"></a>- t -</h3><ul>
+<li>Torsion()
+: <a class="el" href="classccp4srs_1_1_torsion.html#a1939dda0f4d9e56c3762acade101e938">ccp4srs::Torsion</a>
+</li>
+<li>torsion
+: <a class="el" href="classccp4srs_1_1_torsion.html#a68b1d2a3529f1b153db01830a6cde818">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_monomer.html#a1fdc6bd34cea4b7ea59d5399a8367f70">ccp4srs::Monomer</a>
+</li>
+<li>torsion_esd
+: <a class="el" href="classccp4srs_1_1_torsion.html#a34011e29f9c0faa8bc15a31274dd27c3">ccp4srs::Torsion</a>
+</li>
+<li>torsion_id
+: <a class="el" href="classccp4srs_1_1_torsion.html#ab82fe72dc4fb966139befa1636f0c4bd">ccp4srs::Torsion</a>
+</li>
+<li>torsion_period
+: <a class="el" href="classccp4srs_1_1_torsion.html#a681cd0d538d13fa8d30dee2eb0c7df20">ccp4srs::Torsion</a>
+</li>
+<li>torsions
+: <a class="el" href="classccp4srs_1_1_monomer.html#a70123373bff5c842e122856fb75634ab">ccp4srs::Monomer</a>
+</li>
+<li>tree()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a79a4445aa7279951aa8426dc79114ebf">ccp4srs::Monomer</a>
+</li>
+<li>Tree()
+: <a class="el" href="classccp4srs_1_1_tree.html#a342a1de215612310580d0cd6a06262cb">ccp4srs::Tree</a>
+</li>
+<li>Triple
+: <a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795baf6c5cfdf98463c48cd5772a18e49ad6f">ccp4srs::Bond</a>
+</li>
+<li>type()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a01201fb01a7ed370e593563b129c74af">ccp4srs::Monomer</a>
+, <a class="el" href="classccp4srs_1_1_entry.html#a401d0e96699c34bef6b408e054f14540">ccp4srs::Entry</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x75.html ccp4srs/doc-html/html/functions_0x75.html
--- ccp4srs-old/doc-html/html/functions_0x75.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x75.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,116 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li class="current"><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_u"></a>- u -</h3><ul>
+<li>UncompressionError
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa63962a5b2f5046aa5e8a6b0b46271824">ccp4srs::MemIO</a>
+</li>
+<li>unloadStructure()
+: <a class="el" href="classccp4srs_1_1_base.html#a6d15803597f5a515c19848a5e8dbe164">ccp4srs::Base</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x76.html ccp4srs/doc-html/html/functions_0x76.html
--- ccp4srs-old/doc-html/html/functions_0x76.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x76.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,132 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li class="current"><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_v"></a>- v -</h3><ul>
+<li>valency()
+: <a class="el" href="classccp4srs_1_1_atom.html#a86606a9614641a62a9b477c0b90c3a87">ccp4srs::Atom</a>
+</li>
+<li>value()
+: <a class="el" href="classccp4srs_1_1_angle.html#a6ec0de44c0f607bcb5634a907fe9018a">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_torsion.html#a001451fd28649a8df65416d7e551b7a9">ccp4srs::Torsion</a>
+</li>
+<li>vdw_radius()
+: <a class="el" href="classccp4srs_1_1_atom.html#a2c283b644afb507ec45667611a685827">ccp4srs::Atom</a>
+</li>
+<li>vdwh_radius()
+: <a class="el" href="classccp4srs_1_1_atom.html#a2a2e411586e9a0be619a5ab5c634169d">ccp4srs::Atom</a>
+</li>
+<li>vdwhRadius
+: <a class="el" href="classccp4srs_1_1_atom.html#afd0adf07dd4f24e87acb6977335ff2ba">ccp4srs::Atom</a>
+</li>
+<li>vdwRadius
+: <a class="el" href="classccp4srs_1_1_atom.html#a74216b4c442b716656e5a55e908cea11">ccp4srs::Atom</a>
+</li>
+<li>volume_sign
+: <a class="el" href="classccp4srs_1_1_chi_center.html#a6fc568ab5bcd12bc56b58d6b9f2933a1">ccp4srs::ChiCenter</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x77.html ccp4srs/doc-html/html/functions_0x77.html
--- ccp4srs-old/doc-html/html/functions_0x77.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x77.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,147 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li class="current"><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_w"></a>- w -</h3><ul>
+<li>weight()
+: <a class="el" href="classccp4srs_1_1_atom.html#a4c6e0a23b45563f10657d839d4479961">ccp4srs::Atom</a>
+</li>
+<li>write()
+: <a class="el" href="classccp4srs_1_1_entry.html#a46d1eaa50c45f6e40ff054b30b93790d">ccp4srs::Entry</a>
+, <a class="el" href="classccp4srs_1_1_mem_i_o.html#ae2fd4e637343f3f9ac5ccfc3af085293">ccp4srs::MemIO</a>
+, <a class="el" href="classccp4srs_1_1_index.html#a2d6f487a5a3e945f92b90fc6f034f08b">ccp4srs::Index</a>
+, <a class="el" href="structccp4srs_1_1_m_p_file_pos.html#a6e1a52091171d7462c6b8334f1483998">ccp4srs::MPFilePos</a>
+</li>
+<li>write_buffer()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a98b3d03fd613c62e0d16bfda509aa630">ccp4srs::MemIO</a>
+</li>
+<li>write_mem()
+: <a class="el" href="classccp4srs_1_1_angle.html#a5fcc085237045429dd4a946595c1488f">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_plane.html#a759255f2b21b770caa535f129e5f60bb">ccp4srs::Plane</a>
+, <a class="el" href="classccp4srs_1_1_torsion.html#a9b4f1d2c543776a8e0412eae4c7db651">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_atom.html#adaebb2b3897e6758befc7c76d77c0420">ccp4srs::Atom</a>
+, <a class="el" href="classccp4srs_1_1_tree.html#a357b27f65ab5b653fc17a387e9653c4f">ccp4srs::Tree</a>
+, <a class="el" href="classccp4srs_1_1_monomer.html#ac0eb44f5d4ec3da57994cd741c8d6b0b">ccp4srs::Monomer</a>
+, <a class="el" href="classccp4srs_1_1_bond.html#aa44d448aa0181e6d51048beda35052f4">ccp4srs::Bond</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#ac36306727683e319c2282b936bd11d37">ccp4srs::ChiCenter</a>
+, <a class="el" href="classccp4srs_1_1_container.html#ae3d1a80023e670f0828814b887af5dc8">ccp4srs::Container&lt; T &gt;</a>
+, <a class="el" href="classccp4srs_1_1_entry.html#a817f6f566baf41280c5cee0fc3507871">ccp4srs::Entry</a>
+, <a class="el" href="classccp4srs_1_1_index.html#a5591c13f7296928d053492322b8bd02b">ccp4srs::Index</a>
+</li>
+<li>WriteError
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa29a865c4c24a0a158c5fc0514a29e517">ccp4srs::MemIO</a>
+</li>
+<li>writeToCIF()
+: <a class="el" href="classccp4srs_1_1_angle.html#a8a293c96f55ee3b13cc9b9db86d265cd">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_tree.html#ade370b24c17b2d47a4cb8f89c096e5c1">ccp4srs::Tree</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#a04b85d396a4ebc8d5163d3184206329d">ccp4srs::ChiCenter</a>
+, <a class="el" href="classccp4srs_1_1_bond.html#a89214f5f730f603bdd8dacea6317428f">ccp4srs::Bond</a>
+, <a class="el" href="classccp4srs_1_1_atom.html#ac83667146ec86aeab8fdcce133c2fea0">ccp4srs::Atom</a>
+, <a class="el" href="classccp4srs_1_1_torsion.html#ae53494ec218062be243d5e7b36f43dd0">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_plane.html#abd5b6df5e6d2bdafdd064a04974cf82a">ccp4srs::Plane</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x78.html ccp4srs/doc-html/html/functions_0x78.html
--- ccp4srs-old/doc-html/html/functions_0x78.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x78.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,119 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li class="current"><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_x"></a>- x -</h3><ul>
+<li>x()
+: <a class="el" href="classccp4srs_1_1_atom.html#a9af114ebe576f3a0af965579100da463">ccp4srs::Atom</a>
+</li>
+<li>x_mlib()
+: <a class="el" href="classccp4srs_1_1_atom.html#a7f9331955d7f98b1d2e869f8741a2188">ccp4srs::Atom</a>
+</li>
+<li>x_pdbx()
+: <a class="el" href="classccp4srs_1_1_atom.html#ac0fc0e47750a53f2be7ab60efc604d3b">ccp4srs::Atom</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
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+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x79.html ccp4srs/doc-html/html/functions_0x79.html
--- ccp4srs-old/doc-html/html/functions_0x79.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x79.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,119 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
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+<body onload='searchBox.OnSelectItem(0);'>
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+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
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+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li class="current"><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_y"></a>- y -</h3><ul>
+<li>y()
+: <a class="el" href="classccp4srs_1_1_atom.html#a10fc0f0f21af2cd5311c7d957b59f52b">ccp4srs::Atom</a>
+</li>
+<li>y_mlib()
+: <a class="el" href="classccp4srs_1_1_atom.html#acc50ad679a297a2626a6662cd0b61d3e">ccp4srs::Atom</a>
+</li>
+<li>y_pdbx()
+: <a class="el" href="classccp4srs_1_1_atom.html#a65cdadf3090a0fa712b6c47040adb578">ccp4srs::Atom</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x7a.html ccp4srs/doc-html/html/functions_0x7a.html
--- ccp4srs-old/doc-html/html/functions_0x7a.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x7a.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,119 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
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+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
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+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li class="current"><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_z"></a>- z -</h3><ul>
+<li>z()
+: <a class="el" href="classccp4srs_1_1_atom.html#a9d07e03f19613858142105d9f287466e">ccp4srs::Atom</a>
+</li>
+<li>z_mlib()
+: <a class="el" href="classccp4srs_1_1_atom.html#a73c4871fccf3ce91502449de659f835a">ccp4srs::Atom</a>
+</li>
+<li>z_pdbx()
+: <a class="el" href="classccp4srs_1_1_atom.html#aed837e19a61e89ce1e1eda0c35f10b2e">ccp4srs::Atom</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
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+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_0x7e.html ccp4srs/doc-html/html/functions_0x7e.html
--- ccp4srs-old/doc-html/html/functions_0x7e.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_0x7e.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,155 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
+      <li class="current"><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all class members with links to the classes they belong to:
+
+<h3><a class="anchor" id="index_0x7e"></a>- ~ -</h3><ul>
+<li>~Angle()
+: <a class="el" href="classccp4srs_1_1_angle.html#a8b6036ed3908589a9cee50f60f5e3806">ccp4srs::Angle</a>
+</li>
+<li>~Atom()
+: <a class="el" href="classccp4srs_1_1_atom.html#a27de39105bac03d49c949780edda55fd">ccp4srs::Atom</a>
+</li>
+<li>~Base()
+: <a class="el" href="classccp4srs_1_1_base.html#a2c46b036cb9701ac6a2d22fcec3fbdcf">ccp4srs::Base</a>
+</li>
+<li>~Bond()
+: <a class="el" href="classccp4srs_1_1_bond.html#a695a8236689b60df2ad108c7cc55eb1a">ccp4srs::Bond</a>
+</li>
+<li>~Chem()
+: <a class="el" href="classccp4srs_1_1_chem.html#a939cae4367e5e32664e60c725fabafbe">ccp4srs::Chem</a>
+</li>
+<li>~ChiCenter()
+: <a class="el" href="classccp4srs_1_1_chi_center.html#a051ae00e2cdb590a2dd7f4899c264cb9">ccp4srs::ChiCenter</a>
+</li>
+<li>~Container()
+: <a class="el" href="classccp4srs_1_1_container.html#a831fc7371918ff96de32b96c35fe31a2">ccp4srs::Container&lt; T &gt;</a>
+</li>
+<li>~Entry()
+: <a class="el" href="classccp4srs_1_1_entry.html#a191661efae468b8e2a62b69a247bcd3a">ccp4srs::Entry</a>
+</li>
+<li>~Index()
+: <a class="el" href="classccp4srs_1_1_index.html#a5a0d5db83db471eae5aa87dcfa6a151c">ccp4srs::Index</a>
+</li>
+<li>~Manager()
+: <a class="el" href="classccp4srs_1_1_manager.html#ac6d91d47cb19b9f6ea6c7b64a7f69bb5">ccp4srs::Manager</a>
+</li>
+<li>~MemIO()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#abb2d68b86867b62480e6f036a2f8bcbb">ccp4srs::MemIO</a>
+</li>
+<li>~Monomer()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a33207c3c799fe120851007002464e2e2">ccp4srs::Monomer</a>
+</li>
+<li>~Plane()
+: <a class="el" href="classccp4srs_1_1_plane.html#a521911d044ea2aa8ca4e769b9d8d4e58">ccp4srs::Plane</a>
+</li>
+<li>~Torsion()
+: <a class="el" href="classccp4srs_1_1_torsion.html#a45434048948cdf6fc5f01a6e3ca149a8">ccp4srs::Torsion</a>
+</li>
+<li>~Tree()
+: <a class="el" href="classccp4srs_1_1_tree.html#ab5a113a9574397dbb5e7679211ee3c24">ccp4srs::Tree</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_eval.html ccp4srs/doc-html/html/functions_eval.html
--- ccp4srs-old/doc-html/html/functions_eval.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_eval.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,147 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Enumerator</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li class="current"><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;<ul>
+<li>Aromatic
+: <a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba1511fd16010981add30c1e054980f193">ccp4srs::Bond</a>
+</li>
+<li>CantOpenFile
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaac65c121a2ac9e371d3e059cb480cf60d">ccp4srs::MemIO</a>
+</li>
+<li>CompressionError
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa6cf46f9d24d202ae6ac26ddb6aeb625d">ccp4srs::MemIO</a>
+</li>
+<li>Covalent
+: <a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795babaf2bbca3b364f84e83bbc9927b45e39">ccp4srs::Bond</a>
+</li>
+<li>Deloc
+: <a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba3e459a041fa6b33d363df5a335413e13">ccp4srs::Bond</a>
+</li>
+<li>Double
+: <a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba0311fe9d41fd3830910b1e4f93d9a83a">ccp4srs::Bond</a>
+</li>
+<li>EmptyFile
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa117fc645808ac4d9c4e53452bc608d51">ccp4srs::MemIO</a>
+</li>
+<li>EmptyLoop
+: <a class="el" href="classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5edad0a61a72f29321313e1bc19920df40f9">ccp4srs::Plane</a>
+</li>
+<li>Link
+: <a class="el" href="classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88cae7d526eebfeb15c8370f473885073095">ccp4srs::Entry</a>
+</li>
+<li>MemReadError
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaadf48b9ed60d08687c2fbd5271b328c70">ccp4srs::MemIO</a>
+</li>
+<li>Metal
+: <a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba1be67f1d82568ea8bb92f456440e7f01">ccp4srs::Bond</a>
+</li>
+<li>Monomer
+: <a class="el" href="classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88ca447bc9153594c5d2b79e47041f4982b6">ccp4srs::Entry</a>
+</li>
+<li>NoMorePlanes
+: <a class="el" href="classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5eda95f4f7898a15589a3db43827444d2692">ccp4srs::Plane</a>
+</li>
+<li>None
+: <a class="el" href="classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88ca616c951330c4d0b080622857146e2457">ccp4srs::Entry</a>
+</li>
+<li>noOrder
+: <a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba3a534360bb854109f0ad2d34f1858997">ccp4srs::Bond</a>
+</li>
+<li>Ok
+: <a class="el" href="classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5edae47dd3ee9591c478c387ddbe09f7ef34">ccp4srs::Plane</a>
+, <a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63">ccp4srs::MemIO</a>
+</li>
+<li>ReadError
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaab76082bd26e6e49c9c7794410cec3ca2">ccp4srs::MemIO</a>
+</li>
+<li>Single
+: <a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba338d16bbed971e9a0c912ff78efed793">ccp4srs::Bond</a>
+</li>
+<li>SizeError
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaaec9637fa3da0cf0cc0385a15d95af350">ccp4srs::MemIO</a>
+</li>
+<li>Triple
+: <a class="el" href="classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795baf6c5cfdf98463c48cd5772a18e49ad6f">ccp4srs::Bond</a>
+</li>
+<li>UncompressionError
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa63962a5b2f5046aa5e8a6b0b46271824">ccp4srs::MemIO</a>
+</li>
+<li>WriteError
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa29a865c4c24a0a158c5fc0514a29e517">ccp4srs::MemIO</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_func.html ccp4srs/doc-html/html/functions_func.html
--- ccp4srs-old/doc-html/html/functions_func.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_func.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,161 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li class="current"><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_a"></a>- a -</h3><ul>
+<li>add()
+: <a class="el" href="classccp4srs_1_1_container.html#a6caf1893b780f2cf196c85ee141baf18">ccp4srs::Container&lt; T &gt;</a>
+, <a class="el" href="classccp4srs_1_1_monomer.html#ae1c9221ebd49b62830621cd40524d215">ccp4srs::Monomer</a>
+</li>
+<li>addHydrogens()
+: <a class="el" href="classccp4srs_1_1_chem.html#acada705ca803ac2b68bb2c787a83fcb1">ccp4srs::Chem</a>
+, <a class="el" href="classccp4srs_1_1_monomer.html#a67a965eb782472588f1a5f4e693c509e">ccp4srs::Monomer</a>
+</li>
+<li>Angle()
+: <a class="el" href="classccp4srs_1_1_angle.html#a5ec6da380214e7100ff46e3e79898e15">ccp4srs::Angle</a>
+</li>
+<li>angle()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a61b179edff80a9d168997038093cc92f">ccp4srs::Monomer</a>
+</li>
+<li>at()
+: <a class="el" href="classccp4srs_1_1_container.html#ae9929d576289dd2313aaf4b2d9c377e9">ccp4srs::Container&lt; T &gt;</a>
+</li>
+<li>atom()
+: <a class="el" href="classccp4srs_1_1_monomer.html#ac3492a092c5436d182acae9b6712da7f">ccp4srs::Monomer</a>
+, <a class="el" href="classccp4srs_1_1_plane.html#ad1e544c70729b5a17dba23301ba6ca7e">ccp4srs::Plane</a>
+, <a class="el" href="classccp4srs_1_1_tree.html#aa05e210175e281b0b975b22040cbf45d">ccp4srs::Tree</a>
+</li>
+<li>Atom()
+: <a class="el" href="classccp4srs_1_1_atom.html#a66084d9a746b51608e8f0f8e28138e9d">ccp4srs::Atom</a>
+</li>
+<li>atom1()
+: <a class="el" href="classccp4srs_1_1_angle.html#a64770743097878619e8dccf787f93802">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_bond.html#a6ec052956ddec875a707d7e375ce0748">ccp4srs::Bond</a>
+, <a class="el" href="classccp4srs_1_1_torsion.html#af30f2e612259dedd1e569db13ff583fd">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#ae27490ac46e2f3904ee230fe0c5b80af">ccp4srs::ChiCenter</a>
+</li>
+<li>atom2()
+: <a class="el" href="classccp4srs_1_1_torsion.html#ae34ef1ddabf50dd732bf66336bb4a2eb">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_angle.html#a1be24203719da0b250775f7c0b5710ed">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#a5e1600b63a2e92494176dc328c6fc8a6">ccp4srs::ChiCenter</a>
+, <a class="el" href="classccp4srs_1_1_bond.html#a364bc6a611e192c07d0bf5236a3503b9">ccp4srs::Bond</a>
+</li>
+<li>atom3()
+: <a class="el" href="classccp4srs_1_1_angle.html#a6d62c8acfe549d3d439a061f2bbcada9">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_torsion.html#a37c594eb8a06aa962efd46c8d5c0e1b9">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#ac668dea1c66f203a26e46a1c87b37760">ccp4srs::ChiCenter</a>
+</li>
+<li>atom4()
+: <a class="el" href="classccp4srs_1_1_torsion.html#afb752f1836193a0af5befba252e16703">ccp4srs::Torsion</a>
+</li>
+<li>atom_no()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a9ac9e9e610a1a0450130d5e5c4242d34">ccp4srs::Monomer</a>
+</li>
+<li>atoms()
+: <a class="el" href="classccp4srs_1_1_plane.html#a91e4f55f473565e42c27b6aab5311222">ccp4srs::Plane</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
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+
+<!-- iframe showing the search results (closed by default) -->
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+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_func_0x62.html ccp4srs/doc-html/html/functions_func_0x62.html
--- ccp4srs-old/doc-html/html/functions_func_0x62.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_func_0x62.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,122 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
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+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
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+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li class="current"><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_b"></a>- b -</h3><ul>
+<li>backward()
+: <a class="el" href="classccp4srs_1_1_tree.html#a70a9e13b054276780039e0d6f0edcdd9">ccp4srs::Tree</a>
+</li>
+<li>Base()
+: <a class="el" href="classccp4srs_1_1_base.html#a0c37b44fe77e9f171d5f40281a6e82ae">ccp4srs::Base</a>
+</li>
+<li>bond()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a6b01e3fa4cb59dc507460ea0715823fa">ccp4srs::Monomer</a>
+</li>
+<li>Bond()
+: <a class="el" href="classccp4srs_1_1_bond.html#acd3c055b0b0827de95e44ca9a9ac972a">ccp4srs::Bond</a>
+</li>
+</ul>
+</div>
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+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
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+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_func_0x63.html ccp4srs/doc-html/html/functions_func_0x63.html
--- ccp4srs-old/doc-html/html/functions_func_0x63.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_func_0x63.html	2014-09-09 21:34:12.000000000 -0700
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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
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+<body onload='searchBox.OnSelectItem(0);'>
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+<script type="text/javascript"><!--
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+--></script>
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+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
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+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li class="current"><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_c"></a>- c -</h3><ul>
+<li>CalcHBonds()
+: <a class="el" href="classccp4srs_1_1_chem.html#ab5d4ff0f43b6785dc2c3cec72d4b8eec">ccp4srs::Chem</a>
+</li>
+<li>ccp4_chirality()
+: <a class="el" href="classccp4srs_1_1_atom.html#ac0274e4727f43cedf27380121215cbfa">ccp4srs::Atom</a>
+</li>
+<li>center()
+: <a class="el" href="classccp4srs_1_1_chi_center.html#a0264f7a5c26c795bda84de7b233e70ab">ccp4srs::ChiCenter</a>
+</li>
+<li>charge()
+: <a class="el" href="classccp4srs_1_1_atom.html#a199caf3c186d47d5ca6e13e235471a84">ccp4srs::Atom</a>
+</li>
+<li>Chem()
+: <a class="el" href="classccp4srs_1_1_chem.html#a6ca2d1c22ede07e88978645ab6a5887e">ccp4srs::Chem</a>
+</li>
+<li>chem_formula()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a6bbfc74c882e403c57984d7310d4fb98">ccp4srs::Monomer</a>
+</li>
+<li>chem_name()
+: <a class="el" href="classccp4srs_1_1_monomer.html#ab5a8d9361def2e547d1e65bf180f3252">ccp4srs::Monomer</a>
+</li>
+<li>chem_type()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a37432cca1867e01cd9af6d4569c2326a">ccp4srs::Monomer</a>
+</li>
+<li>chicenter()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a3c1ea4e271769745f01c8dc4146c683e">ccp4srs::Monomer</a>
+</li>
+<li>ChiCenter()
+: <a class="el" href="classccp4srs_1_1_chi_center.html#a536462552b25777be443867ec6a28b48">ccp4srs::ChiCenter</a>
+</li>
+<li>chirality()
+: <a class="el" href="classccp4srs_1_1_atom.html#a88df4aee528a9e551c126e9e8adab2f3">ccp4srs::Atom</a>
+</li>
+<li>compare()
+: <a class="el" href="classccp4srs_1_1_bond.html#acefa794143d2ab128897441895cdf562">ccp4srs::Bond</a>
+</li>
+<li>connect()
+: <a class="el" href="classccp4srs_1_1_tree.html#a9986231a0223ef6b62902823d119176f">ccp4srs::Tree</a>
+</li>
+<li>Container()
+: <a class="el" href="classccp4srs_1_1_container.html#acdff89dd6d441d731b517565021e3881">ccp4srs::Container&lt; T &gt;</a>
+</li>
+<li>copy()
+: <a class="el" href="classccp4srs_1_1_torsion.html#a2a6ff05c37b9ce514fe557ab3817a072">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_plane.html#a9db264baa4154922dfac882f4f437d34">ccp4srs::Plane</a>
+</li>
+<li>Copy()
+: <a class="el" href="structccp4srs_1_1_m_p_file_pos.html#a7f60e91b825a15d3def175dcdb71139d">ccp4srs::MPFilePos</a>
+</li>
+<li>copy()
+: <a class="el" href="classccp4srs_1_1_tree.html#acfc010d5d168bb288379e6b6721fb9fa">ccp4srs::Tree</a>
+, <a class="el" href="classccp4srs_1_1_bond.html#a0c6c410020c5fad46d2987d9fc8de65e">ccp4srs::Bond</a>
+, <a class="el" href="classccp4srs_1_1_angle.html#a085c530866442b6b3dfb8c969de2bfe8">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_bond.html#a4bb135bfcd9ee6078a2770fe9f15319c">ccp4srs::Bond</a>
+, <a class="el" href="classccp4srs_1_1_atom.html#a5aa8172f59efa4ac90359b2be7424d92">ccp4srs::Atom</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#ab3dc0fe1813d51055e829586a27ddd15">ccp4srs::ChiCenter</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
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+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_func_0x64.html ccp4srs/doc-html/html/functions_func_0x64.html
--- ccp4srs-old/doc-html/html/functions_func_0x64.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_func_0x64.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,113 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
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+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li class="current"><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_d"></a>- d -</h3><ul>
+<li>deleteSelections()
+: <a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a582873aa43d2c8708e99db1485013bef">ccp4srs::DASelHnds</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_func_0x65.html ccp4srs/doc-html/html/functions_func_0x65.html
--- ccp4srs-old/doc-html/html/functions_func_0x65.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_func_0x65.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,135 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
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+               onfocus="searchBox.OnSearchFieldFocus(true)" 
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+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li class="current"><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_e"></a>- e -</h3><ul>
+<li>element()
+: <a class="el" href="classccp4srs_1_1_atom.html#a78344a993072c3e8918a54c3259d55d8">ccp4srs::Atom</a>
+</li>
+<li>element_pdb()
+: <a class="el" href="classccp4srs_1_1_atom.html#a8d78d445f18a9f9e83d82f66e715b274">ccp4srs::Atom</a>
+</li>
+<li>empty()
+: <a class="el" href="classccp4srs_1_1_plane.html#a8da6c13ce79682d5f17e23f7c3e84849">ccp4srs::Plane</a>
+, <a class="el" href="classccp4srs_1_1_tree.html#a5f5e595cfdb5623cc59c0651ff7a25d3">ccp4srs::Tree</a>
+, <a class="el" href="classccp4srs_1_1_container.html#aeed888e25348f83a53021beaa21a0b1e">ccp4srs::Container&lt; T &gt;</a>
+</li>
+<li>energy_type()
+: <a class="el" href="classccp4srs_1_1_atom.html#af9d89db887cdbfc5523a79ece1c1e117">ccp4srs::Atom</a>
+</li>
+<li>Entry()
+: <a class="el" href="classccp4srs_1_1_entry.html#aa72cb70c4f1c115a2134e2da80b9bc34">ccp4srs::Entry</a>
+</li>
+<li>esd()
+: <a class="el" href="classccp4srs_1_1_torsion.html#a44095b8e5025c92a4b443a8715beceee">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_angle.html#a31b7030dec4dd77c0eefa3444c75901f">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_plane.html#ad9f1d004296b308a0955997695277ff4">ccp4srs::Plane</a>
+</li>
+<li>esds()
+: <a class="el" href="classccp4srs_1_1_plane.html#a4fd16b46609257ebe87c7b7347597b2b">ccp4srs::Plane</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_func_0x66.html ccp4srs/doc-html/html/functions_func_0x66.html
--- ccp4srs-old/doc-html/html/functions_func_0x66.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_func_0x66.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,119 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
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+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li class="current"><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_f"></a>- f -</h3><ul>
+<li>forward()
+: <a class="el" href="classccp4srs_1_1_tree.html#ad52fadb719ce7ca269b9f6875a9ce8e6">ccp4srs::Tree</a>
+</li>
+<li>free()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a4cda073662a49aa45b0c744ec88de39a">ccp4srs::MemIO</a>
+</li>
+<li>freeMemory()
+: <a class="el" href="classccp4srs_1_1_base.html#ab67f138edc7ae19791be69dde485c719">ccp4srs::Base</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_func_0x67.html ccp4srs/doc-html/html/functions_func_0x67.html
--- ccp4srs-old/doc-html/html/functions_func_0x67.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_func_0x67.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,229 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li class="current"><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_g"></a>- g -</h3><ul>
+<li>get_angles()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a8d4b4084ca5c0e0fa42075f59eaf3e08">ccp4srs::Monomer</a>
+</li>
+<li>get_atoms()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a1ca9838123fea51260be3c44abd6771f">ccp4srs::Monomer</a>
+</li>
+<li>get_bonds()
+: <a class="el" href="classccp4srs_1_1_monomer.html#af36aeb36b83f49d3b4fc28d4737b5efd">ccp4srs::Monomer</a>
+</li>
+<li>get_bool()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a0bbc28ba1593463385ae8f28b65225fa">ccp4srs::MemIO</a>
+</li>
+<li>get_bound()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a7b6acc92258007c15351989930e8672f">ccp4srs::Monomer</a>
+</li>
+<li>get_buffer()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#aa1d1ea86d64ee50cab284d4a18f55ab8">ccp4srs::MemIO</a>
+</li>
+<li>get_byte()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a296d38484504311f2773ff313298dda9">ccp4srs::MemIO</a>
+</li>
+<li>get_chicenters()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a591d5f8275f5b5756442d96221039ef3">ccp4srs::Monomer</a>
+</li>
+<li>get_chirality()
+: <a class="el" href="classccp4srs_1_1_chi_center.html#a1aa5ee605cdc3756abcb075279eeb8af">ccp4srs::ChiCenter</a>
+</li>
+<li>get_float()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#adf95c15823dd0fb1067002d2ee3d8095">ccp4srs::MemIO</a>
+</li>
+<li>get_ibyte()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a7bc9b6d871402f5b5601d05ad4012326">ccp4srs::MemIO</a>
+</li>
+<li>get_integer()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a2d311d3bf0798e1c2bcb1cbe7f5d622f">ccp4srs::MemIO</a>
+</li>
+<li>get_ishort()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a55e1b2e8f826ab2d6c0aef09f3beac9f">ccp4srs::MemIO</a>
+</li>
+<li>get_line()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a6cab031cef522531846e3ced7984f276">ccp4srs::MemIO</a>
+</li>
+<li>get_long()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a950878f651e3bb037cf7ddc4a9c00201">ccp4srs::MemIO</a>
+</li>
+<li>get_planes()
+: <a class="el" href="classccp4srs_1_1_monomer.html#aa454ac38a87c19006580a42bc38958fc">ccp4srs::Monomer</a>
+</li>
+<li>get_real()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#afcc2e5eede7a829347985f646f24dcb3">ccp4srs::MemIO</a>
+</li>
+<li>get_short()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#af2d1b382de42e06ce1dc5ae4ad6bb20f">ccp4srs::MemIO</a>
+</li>
+<li>get_shortreal()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a039402bc82d9d0de0bd3664769355573">ccp4srs::MemIO</a>
+</li>
+<li>get_string()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a22abd9cc96e80e4d3e71f0d1acbf1c4d">ccp4srs::MemIO</a>
+</li>
+<li>get_torsions()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a7b31b6675690c2edc0baa0e070d349ad">ccp4srs::Monomer</a>
+</li>
+<li>get_tree()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a351a18b323af41b74d1b415fcd1df640">ccp4srs::Monomer</a>
+</li>
+<li>get_word()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#ab932bc5aa0e98c9e681a3f3a9cc532c8">ccp4srs::MemIO</a>
+</li>
+<li>getAtNames()
+: <a class="el" href="classccp4srs_1_1_base.html#af9a1789b20b43e97a8eb6a56b4ef32c4">ccp4srs::Base</a>
+</li>
+<li>getAtomNameMatch()
+: <a class="el" href="classccp4srs_1_1_monomer.html#abb514ab63af7e9dbb68f59bc13551618">ccp4srs::Monomer</a>
+</li>
+<li>getAtoms()
+: <a class="el" href="classccp4srs_1_1_base.html#a7e47408dacc9bd80de046504e235cc06">ccp4srs::Base</a>
+</li>
+<li>getBonds()
+: <a class="el" href="classccp4srs_1_1_base.html#a8bb61486d7dd2df0566b8e3a1c7f1c89">ccp4srs::Base</a>
+</li>
+<li>getEnergyTypes()
+: <a class="el" href="classccp4srs_1_1_chem.html#a301341ad4a91bf6cc4e7641efeb56309">ccp4srs::Chem</a>
+</li>
+<li>getEntryNo()
+: <a class="el" href="classccp4srs_1_1_base.html#a57b706684f3e84c741099ff904e01152">ccp4srs::Base</a>
+</li>
+<li>getGraph()
+: <a class="el" href="classccp4srs_1_1_base.html#a418f3d4d079e0c4b93ebc6fff1fd0639">ccp4srs::Base</a>
+, <a class="el" href="classccp4srs_1_1_monomer.html#a9d1a2b0facb208344413158d74446755">ccp4srs::Monomer</a>
+, <a class="el" href="classccp4srs_1_1_base.html#af00d1ee772d045c048aa292457755b50">ccp4srs::Base</a>
+</li>
+<li>getGraphFile()
+: <a class="el" href="classccp4srs_1_1_base.html#a656b776b70ead2f8346b352b3bd1311e">ccp4srs::Base</a>
+</li>
+<li>getHetInfo()
+: <a class="el" href="classccp4srs_1_1_base.html#a88c88924e247250d08cc4795b345c66a">ccp4srs::Base</a>
+</li>
+<li>getIndex()
+: <a class="el" href="classccp4srs_1_1_base.html#a399ff3d49a14dd3bb8250058f6452f4f">ccp4srs::Base</a>
+</li>
+<li>getLeavingAtoms()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a6c3ad68f13fb779921605d0e696add1c">ccp4srs::Monomer</a>
+</li>
+<li>getMonomer()
+: <a class="el" href="classccp4srs_1_1_base.html#a6f3f6564a30198bfe82215bceb6806e2">ccp4srs::Base</a>
+</li>
+<li>getNewHandles()
+: <a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a3e8624665274bf47da9408f3b21f35d8">ccp4srs::DASelHnds</a>
+</li>
+<li>getNofAtoms()
+: <a class="el" href="classccp4srs_1_1_base.html#a646d2c4349be4a740f2121dfd2091150">ccp4srs::Base</a>
+</li>
+<li>getPath()
+: <a class="el" href="classccp4srs_1_1_base.html#ac5481a8eeeb26ead06d7df61f605dac9">ccp4srs::Base</a>
+</li>
+<li>getStructFile()
+: <a class="el" href="classccp4srs_1_1_base.html#a03eac100b52d1f2d2d13981799f928bb">ccp4srs::Base</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_func_0x68.html ccp4srs/doc-html/html/functions_func_0x68.html
--- ccp4srs-old/doc-html/html/functions_func_0x68.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_func_0x68.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,113 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li class="current"><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_h"></a>- h -</h3><ul>
+<li>hb_type()
+: <a class="el" href="classccp4srs_1_1_atom.html#ab45d65bdba2966ce382687548921cd56">ccp4srs::Atom</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_func_0x69.html ccp4srs/doc-html/html/functions_func_0x69.html
--- ccp4srs-old/doc-html/html/functions_func_0x69.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_func_0x69.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,146 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li class="current"><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_i"></a>- i -</h3><ul>
+<li>id()
+: <a class="el" href="classccp4srs_1_1_atom.html#a276b8b3e31130e6f0116af498e3a7766">ccp4srs::Atom</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#a9bd5958f4cb3519a6a745d1db16b135b">ccp4srs::ChiCenter</a>
+, <a class="el" href="classccp4srs_1_1_torsion.html#a63cbef738a4be2da8a46367802f83e3d">ccp4srs::Torsion</a>
+</li>
+<li>ID()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a1eca7f4a9537bddf81de26df20984183">ccp4srs::Monomer</a>
+</li>
+<li>id()
+: <a class="el" href="classccp4srs_1_1_plane.html#ac47f99cd6bf3190767da8fc85d01dc18">ccp4srs::Plane</a>
+</li>
+<li>index()
+: <a class="el" href="classccp4srs_1_1_container.html#a6afe8d51f68e07697d7362464e433cac">ccp4srs::Container&lt; T &gt;</a>
+</li>
+<li>Index()
+: <a class="el" href="classccp4srs_1_1_index.html#aaff51df26ae81aff0425bda97d6f7030">ccp4srs::Index</a>
+</li>
+<li>IndexInit()
+: <a class="el" href="classccp4srs_1_1_index.html#aedec88e9928356d4f7c913d449ca0d3e">ccp4srs::Index</a>
+</li>
+<li>Init()
+: <a class="el" href="classccp4srs_1_1_atom.html#ab6a22850541822e026c9d6a241079fd6">ccp4srs::Atom</a>
+, <a class="el" href="classccp4srs_1_1_monomer.html#a6a50cfb8d8e87162309106c66f5fc155">ccp4srs::Monomer</a>
+</li>
+<li>init_base()
+: <a class="el" href="classccp4srs_1_1_base.html#a9fb463b8df4034fefb6e136ab56d135b">ccp4srs::Base</a>
+</li>
+<li>init_chem()
+: <a class="el" href="classccp4srs_1_1_chem.html#a7ed4ac373981270bc1af2b8cc99b461d">ccp4srs::Chem</a>
+</li>
+<li>ion_radius()
+: <a class="el" href="classccp4srs_1_1_atom.html#a4cbbb8a7a4d9f69eca5caadfffa6c956">ccp4srs::Atom</a>
+</li>
+<li>isLeaving()
+: <a class="el" href="classccp4srs_1_1_atom.html#a7da89fae287dcf0c0838108fd442ec53">ccp4srs::Atom</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
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+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_func_0x6c.html ccp4srs/doc-html/html/functions_func_0x6c.html
--- ccp4srs-old/doc-html/html/functions_func_0x6c.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_func_0x6c.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,126 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
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+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li class="current"><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_l"></a>- l -</h3><ul>
+<li>leaving()
+: <a class="el" href="classccp4srs_1_1_atom.html#ac7f1f1f474b56199e70bb0dcd364bb4b">ccp4srs::Atom</a>
+</li>
+<li>length()
+: <a class="el" href="classccp4srs_1_1_bond.html#a3ebb971fa0af7886f076da460b4875e9">ccp4srs::Bond</a>
+, <a class="el" href="classccp4srs_1_1_mem_i_o.html#a5e4ae24f25179a720de85f185f8074ff">ccp4srs::MemIO</a>
+</li>
+<li>length_esd()
+: <a class="el" href="classccp4srs_1_1_bond.html#a28f3638c15b007dddaab637362635009">ccp4srs::Bond</a>
+</li>
+<li>loadIndex()
+: <a class="el" href="classccp4srs_1_1_base.html#ae95af9ff2fb5c9d0edb437be3bcbe016">ccp4srs::Base</a>
+</li>
+<li>loadStructure()
+: <a class="el" href="classccp4srs_1_1_base.html#a663ef26d53b80f6c8b1f9c9cdeb70d2c">ccp4srs::Base</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
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+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_func_0x6d.html ccp4srs/doc-html/html/functions_func_0x6d.html
--- ccp4srs-old/doc-html/html/functions_func_0x6d.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_func_0x6d.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,146 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li class="current"><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_m"></a>- m -</h3><ul>
+<li>makeAtom()
+: <a class="el" href="classccp4srs_1_1_atom.html#a40ec4d3c3ea0384ab4d2c56b3ee5389b">ccp4srs::Atom</a>
+</li>
+<li>makeBonds()
+: <a class="el" href="classccp4srs_1_1_chem.html#ad60a617bc151e054eb306e8c6bf592f4">ccp4srs::Chem</a>
+</li>
+<li>makeCIF()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a5e3fb1e64eab3e764cc83ff1e6c61fa3">ccp4srs::Monomer</a>
+</li>
+<li>makeCIFTags()
+: <a class="el" href="classccp4srs_1_1_chi_center.html#a93d09528c86718358137aaf48c1a8ce1">ccp4srs::ChiCenter</a>
+, <a class="el" href="classccp4srs_1_1_plane.html#a1ac0cfa095deac2bd97e99ce2b30de96">ccp4srs::Plane</a>
+, <a class="el" href="classccp4srs_1_1_angle.html#a257cefe6949d4371175d4c1573a1d40e">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_torsion.html#ae33b6fc8d12fdbd48a299cf488e16f0e">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_atom.html#ac1bcbe4ebfbf35c7d0369d41afa07714">ccp4srs::Atom</a>
+, <a class="el" href="classccp4srs_1_1_bond.html#a781542dae98140ea687a5d83a3e02e8e">ccp4srs::Bond</a>
+</li>
+<li>MakeCompositions()
+: <a class="el" href="classccp4srs_1_1_index.html#afda5436941f171c791be43b9d28f43a5">ccp4srs::Index</a>
+</li>
+<li>makeSelIndexes()
+: <a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#aaca5f89914d27b9869b6f082931c53d5">ccp4srs::DASelHnds</a>
+</li>
+<li>Manager()
+: <a class="el" href="classccp4srs_1_1_manager.html#a7b1bcc6f68308560b402c5b3f8533158">ccp4srs::Manager</a>
+</li>
+<li>MemIO()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#af2490447442255fa19b2a1c05c011f96">ccp4srs::MemIO</a>
+</li>
+<li>merge()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a6453406b0256cf9fbf74177a7db8770b">ccp4srs::Monomer</a>
+, <a class="el" href="classccp4srs_1_1_atom.html#af28439c95edf554364f29e988b47acd1">ccp4srs::Atom</a>
+</li>
+<li>Monomer()
+: <a class="el" href="classccp4srs_1_1_monomer.html#abd3a6efc83918f121e3e83165681ccd5">ccp4srs::Monomer</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_func_0x6e.html ccp4srs/doc-html/html/functions_func_0x6e.html
--- ccp4srs-old/doc-html/html/functions_func_0x6e.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_func_0x6e.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,140 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
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+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li class="current"><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_n"></a>- n -</h3><ul>
+<li>n_angles()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a832521f11b1adb4a0deb9fd92b4bc725">ccp4srs::Monomer</a>
+</li>
+<li>n_atoms()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a3e3e771e2d60581384b1169648b4d751">ccp4srs::Monomer</a>
+</li>
+<li>n_bonds()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a6a6e470c174fd570667bf43f95757c0d">ccp4srs::Monomer</a>
+</li>
+<li>n_chicenters()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a047ec20b44f73aa0027fdd071aa265d6">ccp4srs::Monomer</a>
+</li>
+<li>n_entries()
+: <a class="el" href="classccp4srs_1_1_base.html#aeb551e05e822e5eb3673aba1fa85bda6">ccp4srs::Base</a>
+</li>
+<li>n_planes()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a123cf02246e052730361055de3f0d477">ccp4srs::Monomer</a>
+</li>
+<li>n_torsions()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a0bf10d776d5d992424b99d88d884f101">ccp4srs::Monomer</a>
+</li>
+<li>name()
+: <a class="el" href="classccp4srs_1_1_atom.html#ad8288e82eeab398bf90da3f35ebe15c5">ccp4srs::Atom</a>
+</li>
+<li>name_pdb()
+: <a class="el" href="classccp4srs_1_1_atom.html#a357cfea9384684a64bb3220d02b3afa7">ccp4srs::Atom</a>
+</li>
+<li>numberOf()
+: <a class="el" href="classccp4srs_1_1_container.html#abbc5e6eeb9ea4d37b8d2025892ebd9ff">ccp4srs::Container&lt; T &gt;</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
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+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_func_0x6f.html ccp4srs/doc-html/html/functions_func_0x6f.html
--- ccp4srs-old/doc-html/html/functions_func_0x6f.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_func_0x6f.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,122 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
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+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li class="current"><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_o"></a>- o -</h3><ul>
+<li>old_name()
+: <a class="el" href="classccp4srs_1_1_atom.html#acda740ae967221e50f1d383ce70d58d9">ccp4srs::Atom</a>
+</li>
+<li>old_name_pdb()
+: <a class="el" href="classccp4srs_1_1_atom.html#abd73ea1b813b1321048f850b88914982">ccp4srs::Atom</a>
+</li>
+<li>oldID()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a271e6aaeed7ace67e36f2c5fea626d70">ccp4srs::Monomer</a>
+</li>
+<li>order()
+: <a class="el" href="classccp4srs_1_1_bond.html#ae18a9e08399e96910028f01a376d41f0">ccp4srs::Bond</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_func_0x70.html ccp4srs/doc-html/html/functions_func_0x70.html
--- ccp4srs-old/doc-html/html/functions_func_0x70.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_func_0x70.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,158 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li class="current"><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_p"></a>- p -</h3><ul>
+<li>period()
+: <a class="el" href="classccp4srs_1_1_torsion.html#a8fd30d637a8002a46ff4c50cadc8d34f">ccp4srs::Torsion</a>
+</li>
+<li>plane()
+: <a class="el" href="classccp4srs_1_1_monomer.html#afdebf230f6aa9bf2692a82b919d59918">ccp4srs::Monomer</a>
+</li>
+<li>Plane()
+: <a class="el" href="classccp4srs_1_1_plane.html#ab45260579cf6dd22ecdaa93ad3b5c183">ccp4srs::Plane</a>
+</li>
+<li>put_bool()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#ac3420c8a37ce57f324cf66eb4ccb9b13">ccp4srs::MemIO</a>
+</li>
+<li>put_byte()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a3c30e4f73927173a9ce5731fab39d170">ccp4srs::MemIO</a>
+</li>
+<li>put_float()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#ad82c1eca930cc9d5535f2da1ab3cde1a">ccp4srs::MemIO</a>
+</li>
+<li>put_ibyte()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a55ccb2d1a276365eadb422c75e982de3">ccp4srs::MemIO</a>
+</li>
+<li>put_integer()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a6c563469a6978a9c1c62a33457c90661">ccp4srs::MemIO</a>
+</li>
+<li>put_ishort()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a1a5cd9341de994fa17ae8efae3d61732">ccp4srs::MemIO</a>
+</li>
+<li>put_line()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a98548fca1e008178fef523b271db5423">ccp4srs::MemIO</a>
+</li>
+<li>put_long()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#af300f12e3fe4b3d878f80caf19b66341">ccp4srs::MemIO</a>
+</li>
+<li>put_real()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a1d8e03e12f2420c9650f4a8956a1c0a7">ccp4srs::MemIO</a>
+</li>
+<li>put_short()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a7117ff86d20006f7a693ea3a36035674">ccp4srs::MemIO</a>
+</li>
+<li>put_shortreal()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a4eb6ba2e97922bf9509d828ee075aa8e">ccp4srs::MemIO</a>
+</li>
+<li>put_string()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#aa35e6bbff841d942f793e50ee813fc97">ccp4srs::MemIO</a>
+</li>
+<li>put_word()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#abf6e925edc35b60fe7816223ceb7a15f">ccp4srs::MemIO</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_func_0x72.html ccp4srs/doc-html/html/functions_func_0x72.html
--- ccp4srs-old/doc-html/html/functions_func_0x72.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_func_0x72.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,168 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li class="current"><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_r"></a>- r -</h3><ul>
+<li>rcsb_chirality()
+: <a class="el" href="classccp4srs_1_1_atom.html#a1dc09ecc6dee155b93e5c3431d4c548e">ccp4srs::Atom</a>
+</li>
+<li>rcsb_name()
+: <a class="el" href="classccp4srs_1_1_atom.html#af0bbf72624e0f7de9900ec931b673410">ccp4srs::Atom</a>
+</li>
+<li>rcsb_name_pdb()
+: <a class="el" href="classccp4srs_1_1_atom.html#ace51a15043535b0fef9b2816dba48cdb">ccp4srs::Atom</a>
+</li>
+<li>read()
+: <a class="el" href="classccp4srs_1_1_entry.html#a262e2814d9a1bc35fbbfd75e46397343">ccp4srs::Entry</a>
+, <a class="el" href="structccp4srs_1_1_m_p_file_pos.html#a8351d37471b7cdab264a91bb1a92db1c">ccp4srs::MPFilePos</a>
+, <a class="el" href="classccp4srs_1_1_index.html#a17c3250780def030676fef212a19731c">ccp4srs::Index</a>
+, <a class="el" href="classccp4srs_1_1_mem_i_o.html#ad8c19ab9e2bd98b40caf95cc6d7e071e">ccp4srs::MemIO</a>
+</li>
+<li>read_buffer()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a7df5365c01565a15ac3bca748e46146b">ccp4srs::MemIO</a>
+</li>
+<li>read_mem()
+: <a class="el" href="classccp4srs_1_1_index.html#a06b50353c15a21a56688b3e00aad2e2d">ccp4srs::Index</a>
+, <a class="el" href="classccp4srs_1_1_monomer.html#ac12b93e766cfbcfd4288512df739a56e">ccp4srs::Monomer</a>
+, <a class="el" href="classccp4srs_1_1_plane.html#a148162145438f6f97414eee0aa72275a">ccp4srs::Plane</a>
+, <a class="el" href="classccp4srs_1_1_torsion.html#af65ef2e18a3b6494070300afec0099e1">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_angle.html#a2f34c77527204676236a28c863f5adee">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_tree.html#a7e39da9840cb8815e8854cd11552c3a9">ccp4srs::Tree</a>
+, <a class="el" href="classccp4srs_1_1_atom.html#a150503215d6820dda3726b107e8e1bc7">ccp4srs::Atom</a>
+, <a class="el" href="classccp4srs_1_1_bond.html#a47ad8a18d4c0363dc1f04f3cfbc670ec">ccp4srs::Bond</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#a64588b20c5010e22ad5d571343a7e6d0">ccp4srs::ChiCenter</a>
+, <a class="el" href="classccp4srs_1_1_container.html#a9f42bc8ec160490ba2dd8d7a8eeae15e">ccp4srs::Container&lt; T &gt;</a>
+, <a class="el" href="classccp4srs_1_1_entry.html#a2d3193b4e34c21b286526931e2e5b62d">ccp4srs::Entry</a>
+</li>
+<li>readFromCIF()
+: <a class="el" href="classccp4srs_1_1_monomer.html#aa9b0a99023e890070aec088182f8a65b">ccp4srs::Monomer</a>
+, <a class="el" href="classccp4srs_1_1_torsion.html#aaf9375ff9aeb22a2a148763276ec80d1">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_angle.html#a9a366216e8c07f33829fd26db9df4f00">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_atom.html#a94f5f81532b98126f3383f29c077473c">ccp4srs::Atom</a>
+, <a class="el" href="classccp4srs_1_1_bond.html#a24976c4962050d858ca00fa6f72684e2">ccp4srs::Bond</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#a8c038c3d35ef4effbe5e02db4cdf9f88">ccp4srs::ChiCenter</a>
+, <a class="el" href="classccp4srs_1_1_plane.html#a656a93b833de401dcac75db47b5bcf57">ccp4srs::Plane</a>
+, <a class="el" href="classccp4srs_1_1_tree.html#af50e009eb63e2bdf8da129afa193d637">ccp4srs::Tree</a>
+</li>
+<li>readFromCIF_ccp4()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a9e457d3f7633b79b598b66f382fa5c5c">ccp4srs::Monomer</a>
+, <a class="el" href="classccp4srs_1_1_atom.html#a0e4f39d4293b8e1907b0295e215c4230">ccp4srs::Atom</a>
+, <a class="el" href="classccp4srs_1_1_bond.html#ac6a267f1cb4e7553d746537cf36e5ea3">ccp4srs::Bond</a>
+</li>
+<li>readFromCIF_rcsb()
+: <a class="el" href="classccp4srs_1_1_atom.html#a12b7ff09ff7aa0cc7581a55e89ac9e0e">ccp4srs::Atom</a>
+, <a class="el" href="classccp4srs_1_1_bond.html#a54c6291defa953cc5f5750b0f116719c">ccp4srs::Bond</a>
+, <a class="el" href="classccp4srs_1_1_monomer.html#aaaec1b93dd1dcfe0e20484fd4bbc2a72">ccp4srs::Monomer</a>
+</li>
+<li>readMonIDFromCIF()
+: <a class="el" href="classccp4srs_1_1_monomer.html#acbe4714fc7593d649b5e8901668d5c5c">ccp4srs::Monomer</a>
+</li>
+<li>reset()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a42598d1f669c5e539cb024bb023e0551">ccp4srs::Monomer</a>
+, <a class="el" href="classccp4srs_1_1_mem_i_o.html#a855507e19582e7ab9b7236fb9d453da3">ccp4srs::MemIO</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
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+
+<!-- iframe showing the search results (closed by default) -->
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+        name="MSearchResults" id="MSearchResults">
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+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_func_0x73.html ccp4srs/doc-html/html/functions_func_0x73.html
--- ccp4srs-old/doc-html/html/functions_func_0x73.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_func_0x73.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,159 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
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+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li class="current"><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_s"></a>- s -</h3><ul>
+<li>set_buffer_length()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#ac84f72f62362171b812f386ef786a677">ccp4srs::MemIO</a>
+</li>
+<li>set_chirality()
+: <a class="el" href="classccp4srs_1_1_atom.html#a4839e285360f50dbe4dbfff765ece82c">ccp4srs::Atom</a>
+</li>
+<li>set_energy_type()
+: <a class="el" href="classccp4srs_1_1_atom.html#abab85177d8d15e5dfc51e12ed9af4d69">ccp4srs::Atom</a>
+</li>
+<li>set_hb_type()
+: <a class="el" href="classccp4srs_1_1_atom.html#a983a276a7821c272f3952f4edfb826c6">ccp4srs::Atom</a>
+</li>
+<li>set_ion_radius()
+: <a class="el" href="classccp4srs_1_1_atom.html#a132fd6895be46a1afa96bb0529c0a6ba">ccp4srs::Atom</a>
+</li>
+<li>set_old_name()
+: <a class="el" href="classccp4srs_1_1_atom.html#a67142fe2e03f768fea4dc3334826ef2e">ccp4srs::Atom</a>
+</li>
+<li>set_rcsb_chirality()
+: <a class="el" href="classccp4srs_1_1_atom.html#af46102bc6356f36610eda68ced6e9202">ccp4srs::Atom</a>
+</li>
+<li>set_sp()
+: <a class="el" href="classccp4srs_1_1_atom.html#aa9fe3297f6d6de92f1520a6631361861">ccp4srs::Atom</a>
+</li>
+<li>set_valency()
+: <a class="el" href="classccp4srs_1_1_atom.html#af50fcb98ad0f4a42768079e985adec5b">ccp4srs::Atom</a>
+</li>
+<li>set_vdw_radius()
+: <a class="el" href="classccp4srs_1_1_atom.html#aa2c293fa289d7a24bc8858578dd3357e">ccp4srs::Atom</a>
+</li>
+<li>set_vdwh_radius()
+: <a class="el" href="classccp4srs_1_1_atom.html#a8912626b88300dcb9e736cf1b4369f82">ccp4srs::Atom</a>
+</li>
+<li>setCompressionLevel()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#abfd614fba0e035434e9c7f1c4a58ad89">ccp4srs::MemIO</a>
+</li>
+<li>setOldID()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a3d9cd816f0e032e64e0d47ed7673ec63">ccp4srs::Monomer</a>
+</li>
+<li>sign()
+: <a class="el" href="classccp4srs_1_1_chi_center.html#a17574c6830e27efde72575acdf154d80">ccp4srs::ChiCenter</a>
+</li>
+<li>size()
+: <a class="el" href="classccp4srs_1_1_tree.html#a308ddfce7a902729218e39356db92cc0">ccp4srs::Tree</a>
+, <a class="el" href="classccp4srs_1_1_plane.html#a61ab65ef97a61c79d1190673a5a1b8e3">ccp4srs::Plane</a>
+</li>
+<li>sp()
+: <a class="el" href="classccp4srs_1_1_atom.html#a9ae7f9281596f659071394247d484ffb">ccp4srs::Atom</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_func_0x74.html ccp4srs/doc-html/html/functions_func_0x74.html
--- ccp4srs-old/doc-html/html/functions_func_0x74.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_func_0x74.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,126 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li class="current"><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_t"></a>- t -</h3><ul>
+<li>Torsion()
+: <a class="el" href="classccp4srs_1_1_torsion.html#a1939dda0f4d9e56c3762acade101e938">ccp4srs::Torsion</a>
+</li>
+<li>torsion()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a1fdc6bd34cea4b7ea59d5399a8367f70">ccp4srs::Monomer</a>
+</li>
+<li>tree()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a79a4445aa7279951aa8426dc79114ebf">ccp4srs::Monomer</a>
+</li>
+<li>Tree()
+: <a class="el" href="classccp4srs_1_1_tree.html#a342a1de215612310580d0cd6a06262cb">ccp4srs::Tree</a>
+</li>
+<li>type()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a01201fb01a7ed370e593563b129c74af">ccp4srs::Monomer</a>
+, <a class="el" href="classccp4srs_1_1_entry.html#a401d0e96699c34bef6b408e054f14540">ccp4srs::Entry</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_func_0x75.html ccp4srs/doc-html/html/functions_func_0x75.html
--- ccp4srs-old/doc-html/html/functions_func_0x75.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_func_0x75.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,113 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li class="current"><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_u"></a>- u -</h3><ul>
+<li>unloadStructure()
+: <a class="el" href="classccp4srs_1_1_base.html#a6d15803597f5a515c19848a5e8dbe164">ccp4srs::Base</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_func_0x76.html ccp4srs/doc-html/html/functions_func_0x76.html
--- ccp4srs-old/doc-html/html/functions_func_0x76.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_func_0x76.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,123 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li class="current"><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_v"></a>- v -</h3><ul>
+<li>valency()
+: <a class="el" href="classccp4srs_1_1_atom.html#a86606a9614641a62a9b477c0b90c3a87">ccp4srs::Atom</a>
+</li>
+<li>value()
+: <a class="el" href="classccp4srs_1_1_angle.html#a6ec0de44c0f607bcb5634a907fe9018a">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_torsion.html#a001451fd28649a8df65416d7e551b7a9">ccp4srs::Torsion</a>
+</li>
+<li>vdw_radius()
+: <a class="el" href="classccp4srs_1_1_atom.html#a2c283b644afb507ec45667611a685827">ccp4srs::Atom</a>
+</li>
+<li>vdwh_radius()
+: <a class="el" href="classccp4srs_1_1_atom.html#a2a2e411586e9a0be619a5ab5c634169d">ccp4srs::Atom</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_func_0x77.html ccp4srs/doc-html/html/functions_func_0x77.html
--- ccp4srs-old/doc-html/html/functions_func_0x77.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_func_0x77.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,144 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li class="current"><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_w"></a>- w -</h3><ul>
+<li>weight()
+: <a class="el" href="classccp4srs_1_1_atom.html#a4c6e0a23b45563f10657d839d4479961">ccp4srs::Atom</a>
+</li>
+<li>write()
+: <a class="el" href="classccp4srs_1_1_entry.html#a46d1eaa50c45f6e40ff054b30b93790d">ccp4srs::Entry</a>
+, <a class="el" href="classccp4srs_1_1_mem_i_o.html#ae2fd4e637343f3f9ac5ccfc3af085293">ccp4srs::MemIO</a>
+, <a class="el" href="classccp4srs_1_1_index.html#a2d6f487a5a3e945f92b90fc6f034f08b">ccp4srs::Index</a>
+, <a class="el" href="structccp4srs_1_1_m_p_file_pos.html#a6e1a52091171d7462c6b8334f1483998">ccp4srs::MPFilePos</a>
+</li>
+<li>write_buffer()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#a98b3d03fd613c62e0d16bfda509aa630">ccp4srs::MemIO</a>
+</li>
+<li>write_mem()
+: <a class="el" href="classccp4srs_1_1_angle.html#a5fcc085237045429dd4a946595c1488f">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_tree.html#a357b27f65ab5b653fc17a387e9653c4f">ccp4srs::Tree</a>
+, <a class="el" href="classccp4srs_1_1_plane.html#a759255f2b21b770caa535f129e5f60bb">ccp4srs::Plane</a>
+, <a class="el" href="classccp4srs_1_1_torsion.html#a9b4f1d2c543776a8e0412eae4c7db651">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_monomer.html#ac0eb44f5d4ec3da57994cd741c8d6b0b">ccp4srs::Monomer</a>
+, <a class="el" href="classccp4srs_1_1_atom.html#adaebb2b3897e6758befc7c76d77c0420">ccp4srs::Atom</a>
+, <a class="el" href="classccp4srs_1_1_bond.html#aa44d448aa0181e6d51048beda35052f4">ccp4srs::Bond</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#ac36306727683e319c2282b936bd11d37">ccp4srs::ChiCenter</a>
+, <a class="el" href="classccp4srs_1_1_container.html#ae3d1a80023e670f0828814b887af5dc8">ccp4srs::Container&lt; T &gt;</a>
+, <a class="el" href="classccp4srs_1_1_entry.html#a817f6f566baf41280c5cee0fc3507871">ccp4srs::Entry</a>
+, <a class="el" href="classccp4srs_1_1_index.html#a5591c13f7296928d053492322b8bd02b">ccp4srs::Index</a>
+</li>
+<li>writeToCIF()
+: <a class="el" href="classccp4srs_1_1_angle.html#a8a293c96f55ee3b13cc9b9db86d265cd">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_torsion.html#ae53494ec218062be243d5e7b36f43dd0">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_bond.html#a89214f5f730f603bdd8dacea6317428f">ccp4srs::Bond</a>
+, <a class="el" href="classccp4srs_1_1_atom.html#ac83667146ec86aeab8fdcce133c2fea0">ccp4srs::Atom</a>
+, <a class="el" href="classccp4srs_1_1_tree.html#ade370b24c17b2d47a4cb8f89c096e5c1">ccp4srs::Tree</a>
+, <a class="el" href="classccp4srs_1_1_plane.html#abd5b6df5e6d2bdafdd064a04974cf82a">ccp4srs::Plane</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#a04b85d396a4ebc8d5163d3184206329d">ccp4srs::ChiCenter</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
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+
+<!-- iframe showing the search results (closed by default) -->
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+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
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+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_func_0x78.html ccp4srs/doc-html/html/functions_func_0x78.html
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+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
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+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li class="current"><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
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+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_x"></a>- x -</h3><ul>
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+</li>
+<li>x_mlib()
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+</li>
+<li>x_pdbx()
+: <a class="el" href="classccp4srs_1_1_atom.html#ac0fc0e47750a53f2be7ab60efc604d3b">ccp4srs::Atom</a>
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+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
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diff -ruN ccp4srs-old/doc-html/html/functions_func_0x79.html ccp4srs/doc-html/html/functions_func_0x79.html
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+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
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+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li class="current"><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
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+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_y"></a>- y -</h3><ul>
+<li>y()
+: <a class="el" href="classccp4srs_1_1_atom.html#a10fc0f0f21af2cd5311c7d957b59f52b">ccp4srs::Atom</a>
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+<li>y_pdbx()
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+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
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diff -ruN ccp4srs-old/doc-html/html/functions_func_0x7a.html ccp4srs/doc-html/html/functions_func_0x7a.html
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+<title>ccp4srs: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
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+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
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+      <li id="searchli">
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+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li class="current"><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_z"></a>- z -</h3><ul>
+<li>z()
+: <a class="el" href="classccp4srs_1_1_atom.html#a9d07e03f19613858142105d9f287466e">ccp4srs::Atom</a>
+</li>
+<li>z_mlib()
+: <a class="el" href="classccp4srs_1_1_atom.html#a73c4871fccf3ce91502449de659f835a">ccp4srs::Atom</a>
+</li>
+<li>z_pdbx()
+: <a class="el" href="classccp4srs_1_1_atom.html#aed837e19a61e89ce1e1eda0c35f10b2e">ccp4srs::Atom</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_func_0x7e.html ccp4srs/doc-html/html/functions_func_0x7e.html
--- ccp4srs-old/doc-html/html/functions_func_0x7e.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_func_0x7e.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,155 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+      <li><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="functions_func.html#index_a"><span>a</span></a></li>
+      <li><a href="functions_func_0x62.html#index_b"><span>b</span></a></li>
+      <li><a href="functions_func_0x63.html#index_c"><span>c</span></a></li>
+      <li><a href="functions_func_0x64.html#index_d"><span>d</span></a></li>
+      <li><a href="functions_func_0x65.html#index_e"><span>e</span></a></li>
+      <li><a href="functions_func_0x66.html#index_f"><span>f</span></a></li>
+      <li><a href="functions_func_0x67.html#index_g"><span>g</span></a></li>
+      <li><a href="functions_func_0x68.html#index_h"><span>h</span></a></li>
+      <li><a href="functions_func_0x69.html#index_i"><span>i</span></a></li>
+      <li><a href="functions_func_0x6c.html#index_l"><span>l</span></a></li>
+      <li><a href="functions_func_0x6d.html#index_m"><span>m</span></a></li>
+      <li><a href="functions_func_0x6e.html#index_n"><span>n</span></a></li>
+      <li><a href="functions_func_0x6f.html#index_o"><span>o</span></a></li>
+      <li><a href="functions_func_0x70.html#index_p"><span>p</span></a></li>
+      <li><a href="functions_func_0x72.html#index_r"><span>r</span></a></li>
+      <li><a href="functions_func_0x73.html#index_s"><span>s</span></a></li>
+      <li><a href="functions_func_0x74.html#index_t"><span>t</span></a></li>
+      <li><a href="functions_func_0x75.html#index_u"><span>u</span></a></li>
+      <li><a href="functions_func_0x76.html#index_v"><span>v</span></a></li>
+      <li><a href="functions_func_0x77.html#index_w"><span>w</span></a></li>
+      <li><a href="functions_func_0x78.html#index_x"><span>x</span></a></li>
+      <li><a href="functions_func_0x79.html#index_y"><span>y</span></a></li>
+      <li><a href="functions_func_0x7a.html#index_z"><span>z</span></a></li>
+      <li class="current"><a href="functions_func_0x7e.html#index_0x7e"><span>~</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_0x7e"></a>- ~ -</h3><ul>
+<li>~Angle()
+: <a class="el" href="classccp4srs_1_1_angle.html#a8b6036ed3908589a9cee50f60f5e3806">ccp4srs::Angle</a>
+</li>
+<li>~Atom()
+: <a class="el" href="classccp4srs_1_1_atom.html#a27de39105bac03d49c949780edda55fd">ccp4srs::Atom</a>
+</li>
+<li>~Base()
+: <a class="el" href="classccp4srs_1_1_base.html#a2c46b036cb9701ac6a2d22fcec3fbdcf">ccp4srs::Base</a>
+</li>
+<li>~Bond()
+: <a class="el" href="classccp4srs_1_1_bond.html#a695a8236689b60df2ad108c7cc55eb1a">ccp4srs::Bond</a>
+</li>
+<li>~Chem()
+: <a class="el" href="classccp4srs_1_1_chem.html#a939cae4367e5e32664e60c725fabafbe">ccp4srs::Chem</a>
+</li>
+<li>~ChiCenter()
+: <a class="el" href="classccp4srs_1_1_chi_center.html#a051ae00e2cdb590a2dd7f4899c264cb9">ccp4srs::ChiCenter</a>
+</li>
+<li>~Container()
+: <a class="el" href="classccp4srs_1_1_container.html#a831fc7371918ff96de32b96c35fe31a2">ccp4srs::Container&lt; T &gt;</a>
+</li>
+<li>~Entry()
+: <a class="el" href="classccp4srs_1_1_entry.html#a191661efae468b8e2a62b69a247bcd3a">ccp4srs::Entry</a>
+</li>
+<li>~Index()
+: <a class="el" href="classccp4srs_1_1_index.html#a5a0d5db83db471eae5aa87dcfa6a151c">ccp4srs::Index</a>
+</li>
+<li>~Manager()
+: <a class="el" href="classccp4srs_1_1_manager.html#ac6d91d47cb19b9f6ea6c7b64a7f69bb5">ccp4srs::Manager</a>
+</li>
+<li>~MemIO()
+: <a class="el" href="classccp4srs_1_1_mem_i_o.html#abb2d68b86867b62480e6f036a2f8bcbb">ccp4srs::MemIO</a>
+</li>
+<li>~Monomer()
+: <a class="el" href="classccp4srs_1_1_monomer.html#a33207c3c799fe120851007002464e2e2">ccp4srs::Monomer</a>
+</li>
+<li>~Plane()
+: <a class="el" href="classccp4srs_1_1_plane.html#a521911d044ea2aa8ca4e769b9d8d4e58">ccp4srs::Plane</a>
+</li>
+<li>~Torsion()
+: <a class="el" href="classccp4srs_1_1_torsion.html#a45434048948cdf6fc5f01a6e3ca149a8">ccp4srs::Torsion</a>
+</li>
+<li>~Tree()
+: <a class="el" href="classccp4srs_1_1_tree.html#ab5a113a9574397dbb5e7679211ee3c24">ccp4srs::Tree</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/functions_vars.html ccp4srs/doc-html/html/functions_vars.html
--- ccp4srs-old/doc-html/html/functions_vars.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/functions_vars.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,435 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members - Variables</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="functions.html"><span>All</span></a></li>
+      <li><a href="functions_func.html"><span>Functions</span></a></li>
+      <li class="current"><a href="functions_vars.html"><span>Variables</span></a></li>
+      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="#index_a"><span>a</span></a></li>
+      <li><a href="#index_b"><span>b</span></a></li>
+      <li><a href="#index_c"><span>c</span></a></li>
+      <li><a href="#index_d"><span>d</span></a></li>
+      <li><a href="#index_e"><span>e</span></a></li>
+      <li><a href="#index_f"><span>f</span></a></li>
+      <li><a href="#index_i"><span>i</span></a></li>
+      <li><a href="#index_m"><span>m</span></a></li>
+      <li><a href="#index_n"><span>n</span></a></li>
+      <li><a href="#index_o"><span>o</span></a></li>
+      <li><a href="#index_p"><span>p</span></a></li>
+      <li><a href="#index_r"><span>r</span></a></li>
+      <li><a href="#index_s"><span>s</span></a></li>
+      <li><a href="#index_t"><span>t</span></a></li>
+      <li><a href="#index_v"><span>v</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_a"></a>- a -</h3><ul>
+<li>a1
+: <a class="el" href="structccp4srs_1_1_atom_pair.html#a0277f099acfa557ac20bf6fd3320bcaa">ccp4srs::AtomPair</a>
+</li>
+<li>a2
+: <a class="el" href="structccp4srs_1_1_atom_pair.html#a1f8f7df44905ac32088ccfcf1b80dda2">ccp4srs::AtomPair</a>
+</li>
+<li>angle
+: <a class="el" href="classccp4srs_1_1_angle.html#abf55314566cb2fa1d3764d0485284113">ccp4srs::Angle</a>
+</li>
+<li>angle_esd
+: <a class="el" href="classccp4srs_1_1_angle.html#a39e05de948ddbf9c944bf0b14123caf8">ccp4srs::Angle</a>
+</li>
+<li>angles
+: <a class="el" href="classccp4srs_1_1_monomer.html#a9177ec12ea5aeaa59228831d4127e592">ccp4srs::Monomer</a>
+</li>
+<li>atom_1
+: <a class="el" href="classccp4srs_1_1_chi_center.html#a246c77c96df7921a1d1c989de4a50f8f">ccp4srs::ChiCenter</a>
+, <a class="el" href="classccp4srs_1_1_torsion.html#ae6bb750e2ebd67defafc5bd38515e923">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_angle.html#ab59c639612d7dcae2b34213a647cdb45">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_bond.html#ad359689c475101246c6c3061d31c2541">ccp4srs::Bond</a>
+</li>
+<li>atom_2
+: <a class="el" href="classccp4srs_1_1_angle.html#a8a4fd7f9e6196f259b6ec0989b5cb64c">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_bond.html#a277aee984c745dcdfd338f19e7df1e48">ccp4srs::Bond</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#aa80d6d7fbec0a8497b62af13b16e2a12">ccp4srs::ChiCenter</a>
+, <a class="el" href="classccp4srs_1_1_torsion.html#aae803284861c24535f6ea3cab02f00b8">ccp4srs::Torsion</a>
+</li>
+<li>atom_3
+: <a class="el" href="classccp4srs_1_1_torsion.html#a16456310c79412ef19e6b3dd22baf3b3">ccp4srs::Torsion</a>
+, <a class="el" href="classccp4srs_1_1_angle.html#a545fb1039055e640aa938964b64c7d0a">ccp4srs::Angle</a>
+, <a class="el" href="classccp4srs_1_1_chi_center.html#a2b249cab1cc7c2ea80ea9259914fcd34">ccp4srs::ChiCenter</a>
+</li>
+<li>atom_4
+: <a class="el" href="classccp4srs_1_1_torsion.html#a73c5cc1a3f37ac0998b1316beb35c579">ccp4srs::Torsion</a>
+</li>
+<li>atom_backward
+: <a class="el" href="classccp4srs_1_1_tree.html#a612df27ef2431bf2ac087f7190e0f9d1">ccp4srs::Tree</a>
+</li>
+<li>atom_center
+: <a class="el" href="classccp4srs_1_1_chi_center.html#a5fe75db982419a5d7f3c3ff8b2e41f46">ccp4srs::ChiCenter</a>
+</li>
+<li>atom_forward
+: <a class="el" href="classccp4srs_1_1_tree.html#a3c63a71c2935da20a0feccad01d5ceaf">ccp4srs::Tree</a>
+</li>
+<li>atom_tree
+: <a class="el" href="classccp4srs_1_1_tree.html#a27d256081e9d371ff22a6644d9ee8a91">ccp4srs::Tree</a>
+</li>
+<li>atomCharge
+: <a class="el" href="classccp4srs_1_1_atom.html#a0e7a7e76f9fba1a8277dae436f900821">ccp4srs::Atom</a>
+</li>
+<li>atomName
+: <a class="el" href="classccp4srs_1_1_atom.html#a75168bfe9aa3e0e24ba5f81854323039">ccp4srs::Atom</a>
+</li>
+<li>atoms
+: <a class="el" href="classccp4srs_1_1_monomer.html#abd7decc2129038a1416f324fee53afa1">ccp4srs::Monomer</a>
+</li>
+<li>atomSP
+: <a class="el" href="classccp4srs_1_1_atom.html#acb4d50d536b22d4dd3f971072354f784">ccp4srs::Atom</a>
+</li>
+<li>atomValency
+: <a class="el" href="classccp4srs_1_1_atom.html#aeaa06e2eac23c671be3f49c0caaa7d12">ccp4srs::Atom</a>
+</li>
+<li>atomWeight
+: <a class="el" href="classccp4srs_1_1_atom.html#ac470c0fd96b775b2b1d979c353449ee4">ccp4srs::Atom</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_b"></a>- b -</h3><ul>
+<li>bond_length
+: <a class="el" href="classccp4srs_1_1_bond.html#a43513fb523b43f7f5f407a0bae151a95">ccp4srs::Bond</a>
+</li>
+<li>bond_length_esd
+: <a class="el" href="classccp4srs_1_1_bond.html#af438937a89d3cb3c7f2342ca6f38301c">ccp4srs::Bond</a>
+</li>
+<li>bond_order
+: <a class="el" href="classccp4srs_1_1_bond.html#ac6365bacbc07dd7cf914b6c7ad6cd5d7">ccp4srs::Bond</a>
+</li>
+<li>bonds
+: <a class="el" href="classccp4srs_1_1_monomer.html#a19495bb3c7e8d1c27f12f06729979d9e">ccp4srs::Monomer</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_c"></a>- c -</h3><ul>
+<li>chemElement
+: <a class="el" href="classccp4srs_1_1_atom.html#a621e19772fdb901353b6f60288afdb70">ccp4srs::Atom</a>
+</li>
+<li>chicenter_id
+: <a class="el" href="classccp4srs_1_1_chi_center.html#ac2387dc7a46c0c4451bcd08e23b25ae5">ccp4srs::ChiCenter</a>
+</li>
+<li>chicenters
+: <a class="el" href="classccp4srs_1_1_monomer.html#a96a126d39760ce281f8bf04186e29c13">ccp4srs::Monomer</a>
+</li>
+<li>chunkNo
+: <a class="el" href="structccp4srs_1_1_m_p_file_pos.html#ab84443c24cd9b322d81f2e165af4bd8a">ccp4srs::MPFilePos</a>
+</li>
+<li>Comp1
+: <a class="el" href="classccp4srs_1_1_index.html#af2a41a666517311e8877a3ec9e288916">ccp4srs::Index</a>
+</li>
+<li>Comp2
+: <a class="el" href="classccp4srs_1_1_index.html#af4ce5b42fe2cf6364f9916d0a42f08b2">ccp4srs::Index</a>
+</li>
+<li>connect_type
+: <a class="el" href="classccp4srs_1_1_tree.html#a97ee818b7a1b1724cfb712453be05743">ccp4srs::Tree</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_d"></a>- d -</h3><ul>
+<li>dist_esd
+: <a class="el" href="classccp4srs_1_1_plane.html#a5837e387b59c8d350271fd11a644ee8d">ccp4srs::Plane</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_e"></a>- e -</h3><ul>
+<li>energyType
+: <a class="el" href="classccp4srs_1_1_atom.html#ac429b2d0c02fe21432c4b651ad181fdb">ccp4srs::Atom</a>
+</li>
+<li>entryID
+: <a class="el" href="classccp4srs_1_1_index.html#a0bd1aedcf3b32bdd48d0de5cd2cc563e">ccp4srs::Index</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_f"></a>- f -</h3><ul>
+<li>fGraphPos
+: <a class="el" href="classccp4srs_1_1_index.html#a3be74bae1c6afc52ea36690b45ec5b96">ccp4srs::Index</a>
+</li>
+<li>fStructPos
+: <a class="el" href="classccp4srs_1_1_index.html#a21a1eddc77e99baf8df0b7450dee548b">ccp4srs::Index</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_i"></a>- i -</h3><ul>
+<li>index
+: <a class="el" href="classccp4srs_1_1_base.html#ada41928311fa3ba94bcb48a1ebf4b4df">ccp4srs::Base</a>
+</li>
+<li>ionRadius
+: <a class="el" href="classccp4srs_1_1_atom.html#aeb773fbdd5b04c0311969ad498622185">ccp4srs::Atom</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_m"></a>- m -</h3><ul>
+<li>maxDAAcos
+: <a class="el" href="classccp4srs_1_1_chem.html#aa32277562470e13dfe292f01bc269c17">ccp4srs::Chem</a>
+</li>
+<li>maxDAdist
+: <a class="el" href="classccp4srs_1_1_chem.html#a6655092e23b55ff3d6465a60101c135d">ccp4srs::Chem</a>
+</li>
+<li>maxDDAcos
+: <a class="el" href="classccp4srs_1_1_chem.html#aa5d2547bfa92f55c755aa57fce717a65">ccp4srs::Chem</a>
+</li>
+<li>maxDHAcos
+: <a class="el" href="classccp4srs_1_1_chem.html#a7408580f10d8868ae368f3faa1253577">ccp4srs::Chem</a>
+</li>
+<li>maxHAAcos
+: <a class="el" href="classccp4srs_1_1_chem.html#a71cea07257deb2795443e04e07ee4bed">ccp4srs::Chem</a>
+</li>
+<li>maxHAdist2
+: <a class="el" href="classccp4srs_1_1_chem.html#ada14781ad5390841304d35f262705c57">ccp4srs::Chem</a>
+</li>
+<li>maxSBdist
+: <a class="el" href="classccp4srs_1_1_chem.html#aeeb0e6bc6cc2e1a3f5ce78d59d8b496d">ccp4srs::Chem</a>
+</li>
+<li>memIO
+: <a class="el" href="classccp4srs_1_1_base.html#adf128b2adae954f6b25463c70ede5a58">ccp4srs::Base</a>
+</li>
+<li>minDAdist
+: <a class="el" href="classccp4srs_1_1_chem.html#a2e63b74dcf71dbf8583a64342de3848c">ccp4srs::Chem</a>
+</li>
+<li>mlib_x
+: <a class="el" href="classccp4srs_1_1_atom.html#a641d281e9661ff8ca51bc768b2db5628">ccp4srs::Atom</a>
+</li>
+<li>mlib_y
+: <a class="el" href="classccp4srs_1_1_atom.html#a92043cd1d43d17069c0c8f96020218b9">ccp4srs::Atom</a>
+</li>
+<li>mlib_z
+: <a class="el" href="classccp4srs_1_1_atom.html#a0b6c2ba6990da454ea672a64e285653f">ccp4srs::Atom</a>
+</li>
+<li>monFormula
+: <a class="el" href="classccp4srs_1_1_monomer.html#aeb6bee62372a765e8aca0c1496689b3a">ccp4srs::Monomer</a>
+</li>
+<li>monID
+: <a class="el" href="classccp4srs_1_1_monomer.html#a34240535a6e703495662936dba863026">ccp4srs::Monomer</a>
+</li>
+<li>monName
+: <a class="el" href="classccp4srs_1_1_monomer.html#a53b8d5232f3b2085d531eca33fb7c55a">ccp4srs::Monomer</a>
+</li>
+<li>monType
+: <a class="el" href="classccp4srs_1_1_monomer.html#af0a573429afbbea61647c9851f0deba7">ccp4srs::Monomer</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_n"></a>- n -</h3><ul>
+<li>n_atoms
+: <a class="el" href="classccp4srs_1_1_plane.html#aa76a845ff6abce3d2c8f40db13717842">ccp4srs::Plane</a>
+</li>
+<li>n_objects
+: <a class="el" href="classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748">ccp4srs::Container&lt; T &gt;</a>
+</li>
+<li>n_sections
+: <a class="el" href="classccp4srs_1_1_tree.html#a4056f0bb5ef8add5a55133eb8166c639">ccp4srs::Tree</a>
+</li>
+<li>nAtoms
+: <a class="el" href="classccp4srs_1_1_index.html#abba65d2d400f004fa3815a06101ac478">ccp4srs::Index</a>
+</li>
+<li>nBonds
+: <a class="el" href="classccp4srs_1_1_index.html#a5906658999e6e4e095589e0cdffabf11">ccp4srs::Index</a>
+</li>
+<li>nEntries
+: <a class="el" href="classccp4srs_1_1_base.html#a863fd5090d78f3bada7f351dd2f33859">ccp4srs::Base</a>
+</li>
+<li>nNonHAtoms
+: <a class="el" href="classccp4srs_1_1_index.html#aa97eb5251314eeb77e5acd2af72ce1aa">ccp4srs::Index</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_o"></a>- o -</h3><ul>
+<li>object
+: <a class="el" href="classccp4srs_1_1_container.html#a25a4ad3660f2ef6760c949be2c1372a8">ccp4srs::Container&lt; T &gt;</a>
+</li>
+<li>offset
+: <a class="el" href="structccp4srs_1_1_m_p_file_pos.html#afb6853252f03dbbc698dea44b425d2d9">ccp4srs::MPFilePos</a>
+</li>
+<li>oldAtomName
+: <a class="el" href="classccp4srs_1_1_atom.html#a45682b942f2f9262bc8fa1b5316a702b">ccp4srs::Atom</a>
+</li>
+<li>oldMonID
+: <a class="el" href="classccp4srs_1_1_monomer.html#a896cc0c3979b65913de25be2c2f75ec9">ccp4srs::Monomer</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_p"></a>- p -</h3><ul>
+<li>pdb_x
+: <a class="el" href="classccp4srs_1_1_atom.html#a49ff7aadab557a536541009606a2db12">ccp4srs::Atom</a>
+</li>
+<li>pdb_y
+: <a class="el" href="classccp4srs_1_1_atom.html#a901c15656be6fa36e191df297d25521d">ccp4srs::Atom</a>
+</li>
+<li>pdb_z
+: <a class="el" href="classccp4srs_1_1_atom.html#ae33b2033023270f96202151aed27a710">ccp4srs::Atom</a>
+</li>
+<li>pdbx_x
+: <a class="el" href="classccp4srs_1_1_atom.html#aec57c2566b6a42361a8215d7b15a7e29">ccp4srs::Atom</a>
+</li>
+<li>pdbx_y
+: <a class="el" href="classccp4srs_1_1_atom.html#a1d138de5fa3e222554a95b796c246d40">ccp4srs::Atom</a>
+</li>
+<li>pdbx_z
+: <a class="el" href="classccp4srs_1_1_atom.html#a424a6001bc93ea1c8256f9f1fb48a585">ccp4srs::Atom</a>
+</li>
+<li>plane_atoms
+: <a class="el" href="classccp4srs_1_1_plane.html#a4c8155332953ddb6cf79acf018c98c85">ccp4srs::Plane</a>
+</li>
+<li>plane_id
+: <a class="el" href="classccp4srs_1_1_plane.html#afdfdff5528e19537d834061022c2b2bf">ccp4srs::Plane</a>
+</li>
+<li>planes
+: <a class="el" href="classccp4srs_1_1_monomer.html#a2f927ab2a3e517f9fe6cba6e89954cfe">ccp4srs::Monomer</a>
+</li>
+<li>property
+: <a class="el" href="classccp4srs_1_1_atom.html#aa363093b5746f782b8c4e60a73ec6438">ccp4srs::Atom</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_r"></a>- r -</h3><ul>
+<li>rcsbAtomName
+: <a class="el" href="classccp4srs_1_1_atom.html#a198154f097c4f42a4ae1dd73d5394734">ccp4srs::Atom</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_s"></a>- s -</h3><ul>
+<li>selHndAcceptor
+: <a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a6df62532c19c06870cb386b3e1d4cc3c">ccp4srs::DASelHnds</a>
+</li>
+<li>selHndDonor
+: <a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a0291cf6e8fc47959f00d5dfa536d4d3c">ccp4srs::DASelHnds</a>
+</li>
+<li>selHndHydrogen
+: <a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a0dd02cde05c05d8d5f1c99c55aa6e251">ccp4srs::DASelHnds</a>
+</li>
+<li>selKey
+: <a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#ab9e53854d32fb72fb9003efc870354df">ccp4srs::DASelHnds</a>
+</li>
+<li>srsDir
+: <a class="el" href="classccp4srs_1_1_base.html#af3caa0403ce8a1c4489948fa4fc62b0c">ccp4srs::Base</a>
+</li>
+<li>srsVersion
+: <a class="el" href="classccp4srs_1_1_base.html#ad18087156761086530c1f01f3078f869">ccp4srs::Base</a>
+</li>
+<li>struct_tree
+: <a class="el" href="classccp4srs_1_1_monomer.html#aef8794097a333f1e4e20dd3d876f1432">ccp4srs::Monomer</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_t"></a>- t -</h3><ul>
+<li>torsion
+: <a class="el" href="classccp4srs_1_1_torsion.html#a68b1d2a3529f1b153db01830a6cde818">ccp4srs::Torsion</a>
+</li>
+<li>torsion_esd
+: <a class="el" href="classccp4srs_1_1_torsion.html#a34011e29f9c0faa8bc15a31274dd27c3">ccp4srs::Torsion</a>
+</li>
+<li>torsion_id
+: <a class="el" href="classccp4srs_1_1_torsion.html#ab82fe72dc4fb966139befa1636f0c4bd">ccp4srs::Torsion</a>
+</li>
+<li>torsion_period
+: <a class="el" href="classccp4srs_1_1_torsion.html#a681cd0d538d13fa8d30dee2eb0c7df20">ccp4srs::Torsion</a>
+</li>
+<li>torsions
+: <a class="el" href="classccp4srs_1_1_monomer.html#a70123373bff5c842e122856fb75634ab">ccp4srs::Monomer</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_v"></a>- v -</h3><ul>
+<li>vdwhRadius
+: <a class="el" href="classccp4srs_1_1_atom.html#afd0adf07dd4f24e87acb6977335ff2ba">ccp4srs::Atom</a>
+</li>
+<li>vdwRadius
+: <a class="el" href="classccp4srs_1_1_atom.html#a74216b4c442b716656e5a55e908cea11">ccp4srs::Atom</a>
+</li>
+<li>volume_sign
+: <a class="el" href="classccp4srs_1_1_chi_center.html#a6fc568ab5bcd12bc56b58d6b9f2933a1">ccp4srs::ChiCenter</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/globals.html ccp4srs/doc-html/html/globals.html
--- ccp4srs-old/doc-html/html/globals.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/globals.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,244 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li class="current"><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="files.html"><span>File&#160;List</span></a></li>
+      <li class="current"><a href="globals.html"><span>File&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="globals.html"><span>All</span></a></li>
+      <li><a href="globals_defs.html"><span>Defines</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="#index_m"><span>m</span></a></li>
+      <li><a href="#index_v"><span>v</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all file members with links to the files they belong to:
+
+<h3><a class="anchor" id="index_m"></a>- m -</h3><ul>
+<li>MMCIF_COMP
+: <a class="el" href="ccp4srs__defs_8h.html#aefbf24090a7fbe6109d4e58390f1aae4">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_LOOP_CHEM_COMP_ANGLE
+: <a class="el" href="ccp4srs__defs_8h.html#ad95350f455f90a8b546d688a1b7604d2">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_LOOP_CHEM_COMP_ATOM
+: <a class="el" href="ccp4srs__defs_8h.html#a96f3d7ae6d26ccb1b693b687f85ff382">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_LOOP_CHEM_COMP_BOND
+: <a class="el" href="ccp4srs__defs_8h.html#a442e6c574a7a90cf6955d1ca8e4cf18f">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_LOOP_CHEM_COMP_CHIR
+: <a class="el" href="ccp4srs__defs_8h.html#a745441f40029534d9996304227bc0d5c">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_LOOP_CHEM_COMP_PLANE_ATOM
+: <a class="el" href="ccp4srs__defs_8h.html#a66aec28ad11df2c52c17f89e854d3717">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_LOOP_CHEM_COMP_TOR
+: <a class="el" href="ccp4srs__defs_8h.html#aed5250676b70b953e859e148a46d26b2">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_LOOP_CHEM_COMP_TREE
+: <a class="el" href="ccp4srs__defs_8h.html#ab82eb4b740280944b8fbe74362121d2f">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_STRUCT_CHEM_COMP
+: <a class="el" href="ccp4srs__defs_8h.html#ae071049f6b4c72d884d50a7fb00c796b">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_ALT_ATOM_ID
+: <a class="el" href="ccp4srs__defs_8h.html#abf103686dc23d212a4dd43ebe9883f36">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_ATOM_BACK
+: <a class="el" href="ccp4srs__defs_8h.html#a2fc723c8a3cb4d9aecd670de41e006e5">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_ATOM_FORWARD
+: <a class="el" href="ccp4srs__defs_8h.html#a07c7f15b018109563b8dde9b59484568">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_ATOM_ID
+: <a class="el" href="ccp4srs__defs_8h.html#a0063d4d4b2407acb4c5e962e937d987c">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_ATOM_ID_1
+: <a class="el" href="ccp4srs__defs_8h.html#a379e5bcb509192bb36b833265f32ff9b">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_ATOM_ID_2
+: <a class="el" href="ccp4srs__defs_8h.html#ac01791d945ab084eecb5cb33e9d0232c">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_ATOM_ID_3
+: <a class="el" href="ccp4srs__defs_8h.html#a5a61b6835d1309e469feb356e2695388">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_ATOM_ID_4
+: <a class="el" href="ccp4srs__defs_8h.html#a0c93c9f5f166a7c389a0d6a6be3fd3b4">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_ATOM_ID_CENTRE
+: <a class="el" href="ccp4srs__defs_8h.html#a20c0ca81595c8d02438d80c53033f99d">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_COMP_ID
+: <a class="el" href="ccp4srs__defs_8h.html#a70bb9ac01714d5ddf96f030e39fc925d">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_CONNECT_TYPE
+: <a class="el" href="ccp4srs__defs_8h.html#aaf8c20eee68a9718052502c7ddb35c16">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_DIST_ESD
+: <a class="el" href="ccp4srs__defs_8h.html#a410537d70cb039747f3bd8a36a52f553">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_Formula
+: <a class="el" href="ccp4srs__defs_8h.html#a5cf744094676b0bd89430c485933f6fb">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_ID
+: <a class="el" href="ccp4srs__defs_8h.html#acb2e2c33e267f4d67aa3550454a6400c">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_MODEL_CARTN_X
+: <a class="el" href="ccp4srs__defs_8h.html#a84559f7c12aa9f1a387b8f530264ab16">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_MODEL_CARTN_Y
+: <a class="el" href="ccp4srs__defs_8h.html#af0b16d01af53acaed091894e08162b54">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_MODEL_CARTN_Z
+: <a class="el" href="ccp4srs__defs_8h.html#a252481f6fc180b9d746ef063c9a3609c">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_Name
+: <a class="el" href="ccp4srs__defs_8h.html#a0f3964efb8ec1746a152fa5aac689273">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_PARTIAL_CHARGE
+: <a class="el" href="ccp4srs__defs_8h.html#a2b31545950368db39b67371d64cbbef7">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_PDBX_AROMATIC_FLAG
+: <a class="el" href="ccp4srs__defs_8h.html#a9207204b4fac4b0f5587e33a56d6aca5">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_PDBX_LEAVING_ATOM_FLAG
+: <a class="el" href="ccp4srs__defs_8h.html#a3a906be28069a81e9429b36c1cfc2edc">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_PDBX_MODEL_CARTN_X
+: <a class="el" href="ccp4srs__defs_8h.html#a0993df52ba1ecc98ca2591a8392ffee6">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_PDBX_MODEL_CARTN_Y
+: <a class="el" href="ccp4srs__defs_8h.html#a56fcc86c982c756f3573ecd213c149d9">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_PDBX_MODEL_CARTN_Z
+: <a class="el" href="ccp4srs__defs_8h.html#a5cbd04910c2725cdc0c72531dfd38cac">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_PDBX_STEREO_CONFIG
+: <a class="el" href="ccp4srs__defs_8h.html#ad753a24e5bb150fc4cc1161dcc31111a">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_PERIOD
+: <a class="el" href="ccp4srs__defs_8h.html#ad7d263713c3571c9b1597ac2ffdceb8c">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_PLANE_ID
+: <a class="el" href="ccp4srs__defs_8h.html#a727023c5a08af92c674e88a97d3361f1">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_TYPE
+: <a class="el" href="ccp4srs__defs_8h.html#af5de8de3a7e69bd50f9c8ee2a7c9c53a">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_Type
+: <a class="el" href="ccp4srs__defs_8h.html#a20179e20def570d67ea892e8cd3bd666">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_TYPE_ENERGY
+: <a class="el" href="ccp4srs__defs_8h.html#a9e64e930d30f442af1eb427927297fad">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_TYPE_SYMBOL
+: <a class="el" href="ccp4srs__defs_8h.html#a681fa0489227ecf64eee279db3a2f21b">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_VALUE_ANGLE
+: <a class="el" href="ccp4srs__defs_8h.html#ac8d6aed8f4893094ad1dac7790505a30">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_VALUE_ANGLE_ESD
+: <a class="el" href="ccp4srs__defs_8h.html#a63fccdc102c24817b6dcef20a4135187">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_VALUE_DIST
+: <a class="el" href="ccp4srs__defs_8h.html#a36bc56204ef3bc3ab0b33754e8e791fb">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_VALUE_DIST_ESD
+: <a class="el" href="ccp4srs__defs_8h.html#a773a38551554ef102c997ba5e391c101">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_VALUE_ORDER
+: <a class="el" href="ccp4srs__defs_8h.html#a7b962f3e20a4c60f50b720aaaf483080">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_VOLUME_SIGN
+: <a class="el" href="ccp4srs__defs_8h.html#ace32f1cd1f6052d3cd1d78c18835016c">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_X
+: <a class="el" href="ccp4srs__defs_8h.html#ae9e78e9a02868061bee6c1a6b45453ca">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_Y
+: <a class="el" href="ccp4srs__defs_8h.html#ac08945b8f7b2dabe39335c716edc8266">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_Z
+: <a class="el" href="ccp4srs__defs_8h.html#ab3af4414a670e8553431994f5ba24aab">ccp4srs_defs.h</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_v"></a>- v -</h3><ul>
+<li>VOLUME_SIGN_BOTH
+: <a class="el" href="ccp4srs__chicenter_8cpp.html#a0876b7b066ef447a65ca374d8dc86417">ccp4srs_chicenter.cpp</a>
+</li>
+<li>VOLUME_SIGN_NEGATIVE
+: <a class="el" href="ccp4srs__chicenter_8cpp.html#a5e50b082b9f721d74d142b1a564358c8">ccp4srs_chicenter.cpp</a>
+</li>
+<li>VOLUME_SIGN_POSITIVE
+: <a class="el" href="ccp4srs__chicenter_8cpp.html#ab5d2d0dcd4a9adac0699b5e37132fcae">ccp4srs_chicenter.cpp</a>
+</li>
+</ul>
+</div>
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+
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+        name="MSearchResults" id="MSearchResults">
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+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/globals_defs.html ccp4srs/doc-html/html/globals_defs.html
--- ccp4srs-old/doc-html/html/globals_defs.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/globals_defs.html	2014-09-09 21:34:12.000000000 -0700
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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
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+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li class="current"><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
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+               onfocus="searchBox.OnSearchFieldFocus(true)" 
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+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="files.html"><span>File&#160;List</span></a></li>
+      <li class="current"><a href="globals.html"><span>File&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="globals.html"><span>All</span></a></li>
+      <li class="current"><a href="globals_defs.html"><span>Defines</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="#index_m"><span>m</span></a></li>
+      <li><a href="#index_v"><span>v</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;
+
+<h3><a class="anchor" id="index_m"></a>- m -</h3><ul>
+<li>MMCIF_COMP
+: <a class="el" href="ccp4srs__defs_8h.html#aefbf24090a7fbe6109d4e58390f1aae4">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_LOOP_CHEM_COMP_ANGLE
+: <a class="el" href="ccp4srs__defs_8h.html#ad95350f455f90a8b546d688a1b7604d2">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_LOOP_CHEM_COMP_ATOM
+: <a class="el" href="ccp4srs__defs_8h.html#a96f3d7ae6d26ccb1b693b687f85ff382">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_LOOP_CHEM_COMP_BOND
+: <a class="el" href="ccp4srs__defs_8h.html#a442e6c574a7a90cf6955d1ca8e4cf18f">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_LOOP_CHEM_COMP_CHIR
+: <a class="el" href="ccp4srs__defs_8h.html#a745441f40029534d9996304227bc0d5c">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_LOOP_CHEM_COMP_PLANE_ATOM
+: <a class="el" href="ccp4srs__defs_8h.html#a66aec28ad11df2c52c17f89e854d3717">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_LOOP_CHEM_COMP_TOR
+: <a class="el" href="ccp4srs__defs_8h.html#aed5250676b70b953e859e148a46d26b2">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_LOOP_CHEM_COMP_TREE
+: <a class="el" href="ccp4srs__defs_8h.html#ab82eb4b740280944b8fbe74362121d2f">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_STRUCT_CHEM_COMP
+: <a class="el" href="ccp4srs__defs_8h.html#ae071049f6b4c72d884d50a7fb00c796b">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_ALT_ATOM_ID
+: <a class="el" href="ccp4srs__defs_8h.html#abf103686dc23d212a4dd43ebe9883f36">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_ATOM_BACK
+: <a class="el" href="ccp4srs__defs_8h.html#a2fc723c8a3cb4d9aecd670de41e006e5">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_ATOM_FORWARD
+: <a class="el" href="ccp4srs__defs_8h.html#a07c7f15b018109563b8dde9b59484568">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_ATOM_ID
+: <a class="el" href="ccp4srs__defs_8h.html#a0063d4d4b2407acb4c5e962e937d987c">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_ATOM_ID_1
+: <a class="el" href="ccp4srs__defs_8h.html#a379e5bcb509192bb36b833265f32ff9b">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_ATOM_ID_2
+: <a class="el" href="ccp4srs__defs_8h.html#ac01791d945ab084eecb5cb33e9d0232c">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_ATOM_ID_3
+: <a class="el" href="ccp4srs__defs_8h.html#a5a61b6835d1309e469feb356e2695388">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_ATOM_ID_4
+: <a class="el" href="ccp4srs__defs_8h.html#a0c93c9f5f166a7c389a0d6a6be3fd3b4">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_ATOM_ID_CENTRE
+: <a class="el" href="ccp4srs__defs_8h.html#a20c0ca81595c8d02438d80c53033f99d">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_COMP_ID
+: <a class="el" href="ccp4srs__defs_8h.html#a70bb9ac01714d5ddf96f030e39fc925d">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_CONNECT_TYPE
+: <a class="el" href="ccp4srs__defs_8h.html#aaf8c20eee68a9718052502c7ddb35c16">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_DIST_ESD
+: <a class="el" href="ccp4srs__defs_8h.html#a410537d70cb039747f3bd8a36a52f553">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_Formula
+: <a class="el" href="ccp4srs__defs_8h.html#a5cf744094676b0bd89430c485933f6fb">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_ID
+: <a class="el" href="ccp4srs__defs_8h.html#acb2e2c33e267f4d67aa3550454a6400c">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_MODEL_CARTN_X
+: <a class="el" href="ccp4srs__defs_8h.html#a84559f7c12aa9f1a387b8f530264ab16">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_MODEL_CARTN_Y
+: <a class="el" href="ccp4srs__defs_8h.html#af0b16d01af53acaed091894e08162b54">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_MODEL_CARTN_Z
+: <a class="el" href="ccp4srs__defs_8h.html#a252481f6fc180b9d746ef063c9a3609c">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_Name
+: <a class="el" href="ccp4srs__defs_8h.html#a0f3964efb8ec1746a152fa5aac689273">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_PARTIAL_CHARGE
+: <a class="el" href="ccp4srs__defs_8h.html#a2b31545950368db39b67371d64cbbef7">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_PDBX_AROMATIC_FLAG
+: <a class="el" href="ccp4srs__defs_8h.html#a9207204b4fac4b0f5587e33a56d6aca5">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_PDBX_LEAVING_ATOM_FLAG
+: <a class="el" href="ccp4srs__defs_8h.html#a3a906be28069a81e9429b36c1cfc2edc">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_PDBX_MODEL_CARTN_X
+: <a class="el" href="ccp4srs__defs_8h.html#a0993df52ba1ecc98ca2591a8392ffee6">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_PDBX_MODEL_CARTN_Y
+: <a class="el" href="ccp4srs__defs_8h.html#a56fcc86c982c756f3573ecd213c149d9">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_PDBX_MODEL_CARTN_Z
+: <a class="el" href="ccp4srs__defs_8h.html#a5cbd04910c2725cdc0c72531dfd38cac">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_PDBX_STEREO_CONFIG
+: <a class="el" href="ccp4srs__defs_8h.html#ad753a24e5bb150fc4cc1161dcc31111a">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_PERIOD
+: <a class="el" href="ccp4srs__defs_8h.html#ad7d263713c3571c9b1597ac2ffdceb8c">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_PLANE_ID
+: <a class="el" href="ccp4srs__defs_8h.html#a727023c5a08af92c674e88a97d3361f1">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_TYPE
+: <a class="el" href="ccp4srs__defs_8h.html#af5de8de3a7e69bd50f9c8ee2a7c9c53a">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_Type
+: <a class="el" href="ccp4srs__defs_8h.html#a20179e20def570d67ea892e8cd3bd666">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_TYPE_ENERGY
+: <a class="el" href="ccp4srs__defs_8h.html#a9e64e930d30f442af1eb427927297fad">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_TYPE_SYMBOL
+: <a class="el" href="ccp4srs__defs_8h.html#a681fa0489227ecf64eee279db3a2f21b">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_VALUE_ANGLE
+: <a class="el" href="ccp4srs__defs_8h.html#ac8d6aed8f4893094ad1dac7790505a30">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_VALUE_ANGLE_ESD
+: <a class="el" href="ccp4srs__defs_8h.html#a63fccdc102c24817b6dcef20a4135187">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_VALUE_DIST
+: <a class="el" href="ccp4srs__defs_8h.html#a36bc56204ef3bc3ab0b33754e8e791fb">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_VALUE_DIST_ESD
+: <a class="el" href="ccp4srs__defs_8h.html#a773a38551554ef102c997ba5e391c101">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_VALUE_ORDER
+: <a class="el" href="ccp4srs__defs_8h.html#a7b962f3e20a4c60f50b720aaaf483080">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_VOLUME_SIGN
+: <a class="el" href="ccp4srs__defs_8h.html#ace32f1cd1f6052d3cd1d78c18835016c">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_X
+: <a class="el" href="ccp4srs__defs_8h.html#ae9e78e9a02868061bee6c1a6b45453ca">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_Y
+: <a class="el" href="ccp4srs__defs_8h.html#ac08945b8f7b2dabe39335c716edc8266">ccp4srs_defs.h</a>
+</li>
+<li>MMCIF_TAG_Z
+: <a class="el" href="ccp4srs__defs_8h.html#ab3af4414a670e8553431994f5ba24aab">ccp4srs_defs.h</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_v"></a>- v -</h3><ul>
+<li>VOLUME_SIGN_BOTH
+: <a class="el" href="ccp4srs__chicenter_8cpp.html#a0876b7b066ef447a65ca374d8dc86417">ccp4srs_chicenter.cpp</a>
+</li>
+<li>VOLUME_SIGN_NEGATIVE
+: <a class="el" href="ccp4srs__chicenter_8cpp.html#a5e50b082b9f721d74d142b1a564358c8">ccp4srs_chicenter.cpp</a>
+</li>
+<li>VOLUME_SIGN_POSITIVE
+: <a class="el" href="ccp4srs__chicenter_8cpp.html#ab5d2d0dcd4a9adac0699b5e37132fcae">ccp4srs_chicenter.cpp</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/graph_legend.html ccp4srs/doc-html/html/graph_legend.html
--- ccp4srs-old/doc-html/html/graph_legend.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/graph_legend.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,130 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Graph Legend</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>Graph Legend</h1>  </div>
+</div>
+<div class="contents">
+<p>This page explains how to interpret the graphs that are generated by doxygen.</p>
+<p>Consider the following example: </p>
+<div class="fragment"><pre class="fragment"><span class="comment">/*! Invisible class because of truncation */</span>
+<span class="keyword">class </span>Invisible { };
+<span class="comment"></span>
+<span class="comment">/*! Truncated class, inheritance relation is hidden */</span>
+<span class="keyword">class </span>Truncated : <span class="keyword">public</span> Invisible { };
+
+<span class="comment">/* Class not documented with doxygen comments */</span>
+<span class="keyword">class </span>Undocumented { };
+<span class="comment"></span>
+<span class="comment">/*! Class that is inherited using public inheritance */</span>
+<span class="keyword">class </span>PublicBase : <span class="keyword">public</span> Truncated { };
+<span class="comment"></span>
+<span class="comment">/*! A template class */</span>
+<span class="keyword">template</span>&lt;<span class="keyword">class</span> T&gt; <span class="keyword">class </span>Templ { };
+<span class="comment"></span>
+<span class="comment">/*! Class that is inherited using protected inheritance */</span>
+<span class="keyword">class </span>ProtectedBase { };
+<span class="comment"></span>
+<span class="comment">/*! Class that is inherited using private inheritance */</span>
+<span class="keyword">class </span>PrivateBase { };
+<span class="comment"></span>
+<span class="comment">/*! Class that is used by the Inherited class */</span>
+<span class="keyword">class </span>Used { };
+<span class="comment"></span>
+<span class="comment">/*! Super class that inherits a number of other classes */</span>
+<span class="keyword">class </span>Inherited : <span class="keyword">public</span> PublicBase,
+                  <span class="keyword">protected</span> ProtectedBase,
+                  <span class="keyword">private</span> PrivateBase,
+                  <span class="keyword">public</span> Undocumented,
+                  <span class="keyword">public</span> Templ&lt;int&gt;
+{
+  <span class="keyword">private</span>:
+    Used *m_usedClass;
+};
+</pre></div><p> This will result in the following graph:</p>
+<center><div align="center">
+<img src="graph_legend.png" alt="graph_legend.png"/>
+</div>
+</center> <p>The boxes in the above graph have the following meaning:  </p>
+<ul>
+<li>
+A filled gray box represents the struct or class for which the graph is generated. </li>
+<li>
+A box with a black border denotes a documented struct or class. </li>
+<li>
+A box with a grey border denotes an undocumented struct or class. </li>
+<li>
+A box with a red border denotes a documented struct or class forwhich not all inheritance/containment relations are shown. A graph is truncated if it does not fit within the specified boundaries. </li>
+</ul>
+<p>The arrows have the following meaning:  </p>
+<ul>
+<li>
+A dark blue arrow is used to visualize a public inheritance relation between two classes. </li>
+<li>
+A dark green arrow is used for protected inheritance. </li>
+<li>
+A dark red arrow is used for private inheritance. </li>
+<li>
+A purple dashed arrow is used if a class is contained or used by another class. The arrow is labeled with the variable(s) through which the pointed class or struct is accessible. </li>
+<li>
+A yellow dashed arrow denotes a relation between a template instance and the template class it was instantiated from. The arrow is labeled with the template parameters of the instance. </li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/graph_legend.md5 ccp4srs/doc-html/html/graph_legend.md5
--- ccp4srs-old/doc-html/html/graph_legend.md5	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/graph_legend.md5	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1 @@
+c43a1e38a88c7de97805a9273dc43584
\ No newline at end of file
Binary files ccp4srs-old/doc-html/html/graph_legend.png and ccp4srs/doc-html/html/graph_legend.png differ
diff -ruN ccp4srs-old/doc-html/html/hierarchy.html ccp4srs/doc-html/html/hierarchy.html
--- ccp4srs-old/doc-html/html/hierarchy.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/hierarchy.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,102 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Hierarchical Index</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li class="current"><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>Class Hierarchy</h1>  </div>
+</div>
+<div class="contents">
+
+<p><a href="inherits.html">Go to the graphical class hierarchy</a></p>
+This inheritance list is sorted roughly, but not completely, alphabetically:<ul>
+<li><a class="el" href="classccp4srs_1_1_angle.html">ccp4srs::Angle</a></li>
+<li><a class="el" href="classccp4srs_1_1_atom.html">ccp4srs::Atom</a></li>
+<li><a class="el" href="structccp4srs_1_1_atom_pair.html">ccp4srs::AtomPair</a></li>
+<li><a class="el" href="classccp4srs_1_1_base.html">ccp4srs::Base</a><ul>
+<li><a class="el" href="classccp4srs_1_1_chem.html">ccp4srs::Chem</a><ul>
+<li><a class="el" href="classccp4srs_1_1_manager.html">ccp4srs::Manager</a></li>
+</ul>
+</li>
+</ul>
+</li>
+<li><a class="el" href="classccp4srs_1_1_bond.html">ccp4srs::Bond</a></li>
+<li><a class="el" href="classccp4srs_1_1_chi_center.html">ccp4srs::ChiCenter</a></li>
+<li><a class="el" href="classccp4srs_1_1_container.html">ccp4srs::Container&lt; T &gt;</a></li>
+<li><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html">ccp4srs::DASelHnds</a></li>
+<li><a class="el" href="classccp4srs_1_1_entry.html">ccp4srs::Entry</a><ul>
+<li><a class="el" href="classccp4srs_1_1_monomer.html">ccp4srs::Monomer</a></li>
+</ul>
+</li>
+<li><a class="el" href="classccp4srs_1_1_index.html">ccp4srs::Index</a></li>
+<li><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></li>
+<li><a class="el" href="structccp4srs_1_1_m_p_file_pos.html">ccp4srs::MPFilePos</a></li>
+<li><a class="el" href="classccp4srs_1_1_plane.html">ccp4srs::Plane</a></li>
+<li><a class="el" href="classccp4srs_1_1_torsion.html">ccp4srs::Torsion</a></li>
+<li><a class="el" href="classccp4srs_1_1_tree.html">ccp4srs::Tree</a></li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/index.hhc ccp4srs/doc-html/html/index.hhc
--- ccp4srs-old/doc-html/html/index.hhc	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/index.hhc	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,103 @@
+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
+<HTML><HEAD></HEAD><BODY>
+<OBJECT type="text/site properties">
+<param name="FrameName" value="right">
+</OBJECT>
+<UL>
+<LI><OBJECT type="text/sitemap"><param name="Name" value="Class List"><param name="Local" value="annotated.html"><param name="ImageNumber" value="1"></OBJECT>
+  <UL>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Angle"><param name="Local" value="classccp4srs_1_1_angle.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Atom"><param name="Local" value="classccp4srs_1_1_atom.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::AtomPair"><param name="Local" value="structccp4srs_1_1_atom_pair.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Base"><param name="Local" value="classccp4srs_1_1_base.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Bond"><param name="Local" value="classccp4srs_1_1_bond.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Chem"><param name="Local" value="classccp4srs_1_1_chem.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::ChiCenter"><param name="Local" value="classccp4srs_1_1_chi_center.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Container< T >"><param name="Local" value="classccp4srs_1_1_container.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::DASelHnds"><param name="Local" value="structccp4srs_1_1_d_a_sel_hnds.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Entry"><param name="Local" value="classccp4srs_1_1_entry.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Index"><param name="Local" value="classccp4srs_1_1_index.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Manager"><param name="Local" value="classccp4srs_1_1_manager.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::MemIO"><param name="Local" value="classccp4srs_1_1_mem_i_o.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Monomer"><param name="Local" value="classccp4srs_1_1_monomer.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::MPFilePos"><param name="Local" value="structccp4srs_1_1_m_p_file_pos.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Plane"><param name="Local" value="classccp4srs_1_1_plane.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Torsion"><param name="Local" value="classccp4srs_1_1_torsion.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Tree"><param name="Local" value="classccp4srs_1_1_tree.html"><param name="ImageNumber" value="11"></OBJECT>
+  </UL>
+<LI><OBJECT type="text/sitemap"><param name="Name" value="Class Hierarchy"><param name="Local" value="hierarchy.html"><param name="ImageNumber" value="1"></OBJECT>
+  <UL>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Angle"><param name="Local" value="classccp4srs_1_1_angle.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Atom"><param name="Local" value="classccp4srs_1_1_atom.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::AtomPair"><param name="Local" value="structccp4srs_1_1_atom_pair.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Base"><param name="Local" value="classccp4srs_1_1_base.html"><param name="ImageNumber" value="1"></OBJECT>
+    <UL>
+    <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Chem"><param name="Local" value="classccp4srs_1_1_chem.html"><param name="ImageNumber" value="1"></OBJECT>
+      <UL>
+      <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Manager"><param name="Local" value="classccp4srs_1_1_manager.html"><param name="ImageNumber" value="11"></OBJECT>
+      </UL>
+    </UL>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Bond"><param name="Local" value="classccp4srs_1_1_bond.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::ChiCenter"><param name="Local" value="classccp4srs_1_1_chi_center.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Container< T >"><param name="Local" value="classccp4srs_1_1_container.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::DASelHnds"><param name="Local" value="structccp4srs_1_1_d_a_sel_hnds.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Entry"><param name="Local" value="classccp4srs_1_1_entry.html"><param name="ImageNumber" value="1"></OBJECT>
+    <UL>
+    <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Monomer"><param name="Local" value="classccp4srs_1_1_monomer.html"><param name="ImageNumber" value="11"></OBJECT>
+    </UL>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Index"><param name="Local" value="classccp4srs_1_1_index.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::MemIO"><param name="Local" value="classccp4srs_1_1_mem_i_o.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::MPFilePos"><param name="Local" value="structccp4srs_1_1_m_p_file_pos.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Plane"><param name="Local" value="classccp4srs_1_1_plane.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Torsion"><param name="Local" value="classccp4srs_1_1_torsion.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs::Tree"><param name="Local" value="classccp4srs_1_1_tree.html"><param name="ImageNumber" value="11"></OBJECT>
+  </UL>
+<LI><OBJECT type="text/sitemap"><param name="Name" value="Class Members"><param name="Local" value="functions.html"><param name="ImageNumber" value="11"></OBJECT>
+<LI><OBJECT type="text/sitemap"><param name="Name" value="Graphical Class Hierarchy"><param name="Local" value="inherits.html"><param name="ImageNumber" value="11"></OBJECT>
+<LI><OBJECT type="text/sitemap"><param name="Name" value="Namespace List"><param name="Local" value="namespaces.html"><param name="ImageNumber" value="1"></OBJECT>
+  <UL>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="ccp4srs"><param name="Local" value="namespaceccp4srs.html"><param name="ImageNumber" value="11"></OBJECT>
+  </UL>
+<LI><OBJECT type="text/sitemap"><param name="Name" value="Namespace Members"><param name="Local" value="namespacemembers.html"><param name="ImageNumber" value="11"></OBJECT>
+<LI><OBJECT type="text/sitemap"><param name="Name" value="File List"><param name="Local" value="files.html"><param name="ImageNumber" value="1"></OBJECT>
+  <UL>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_angle.cpp"><param name="Local" value="ccp4srs__angle_8cpp.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_angle.h"><param name="Local" value="ccp4srs__angle_8h.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_atom.cpp"><param name="Local" value="ccp4srs__atom_8cpp.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_atom.h"><param name="Local" value="ccp4srs__atom_8h.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_base.cpp"><param name="Local" value="ccp4srs__base_8cpp.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_base.h"><param name="Local" value="ccp4srs__base_8h.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_bond.cpp"><param name="Local" value="ccp4srs__bond_8cpp.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_bond.h"><param name="Local" value="ccp4srs__bond_8h.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_chem.cpp"><param name="Local" value="ccp4srs__chem_8cpp.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_chem.h"><param name="Local" value="ccp4srs__chem_8h.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_chicenter.cpp"><param name="Local" value="ccp4srs__chicenter_8cpp.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_chicenter.h"><param name="Local" value="ccp4srs__chicenter_8h.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_container.cpp"><param name="Local" value="ccp4srs__container_8cpp.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_container.h"><param name="Local" value="ccp4srs__container_8h.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_defs.h"><param name="Local" value="ccp4srs__defs_8h.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_entry.cpp"><param name="Local" value="ccp4srs__entry_8cpp.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_entry.h"><param name="Local" value="ccp4srs__entry_8h.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_index.cpp"><param name="Local" value="ccp4srs__index_8cpp.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_index.h"><param name="Local" value="ccp4srs__index_8h.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_manager.cpp"><param name="Local" value="ccp4srs__manager_8cpp.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_manager.h"><param name="Local" value="ccp4srs__manager_8h.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_monomer.cpp"><param name="Local" value="ccp4srs__monomer_8cpp.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_monomer.h"><param name="Local" value="ccp4srs__monomer_8h.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_plane.cpp"><param name="Local" value="ccp4srs__plane_8cpp.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_plane.h"><param name="Local" value="ccp4srs__plane_8h.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_torsion.cpp"><param name="Local" value="ccp4srs__torsion_8cpp.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_torsion.h"><param name="Local" value="ccp4srs__torsion_8h.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_tree.cpp"><param name="Local" value="ccp4srs__tree_8cpp.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_tree.h"><param name="Local" value="ccp4srs__tree_8h.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_types.cpp"><param name="Local" value="ccp4srs__types_8cpp.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/ccp4srs_types.h"><param name="Local" value="ccp4srs__types_8h.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/memio_.cpp"><param name="Local" value="memio___8cpp.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/memio_.h"><param name="Local" value="memio___8h.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/mpfile_.cpp"><param name="Local" value="mpfile___8cpp.html"><param name="ImageNumber" value="11"></OBJECT>
+  <LI><OBJECT type="text/sitemap"><param name="Name" value="src/mpfile_.h"><param name="Local" value="mpfile___8h.html"><param name="ImageNumber" value="11"></OBJECT>
+  </UL>
+<LI><OBJECT type="text/sitemap"><param name="Name" value="File Members"><param name="Local" value="globals.html"><param name="ImageNumber" value="11"></OBJECT>
+</UL>
+</BODY>
+</HTML>
diff -ruN ccp4srs-old/doc-html/html/index.hhk ccp4srs/doc-html/html/index.hhk
--- ccp4srs-old/doc-html/html/index.hhk	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/index.hhk	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,1358 @@
+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
+<HTML><HEAD></HEAD><BODY>
+<OBJECT type="text/site properties">
+<param name="FrameName" value="right">
+</OBJECT>
+<UL>
+  <LI><OBJECT type="text/sitemap"><param name="Local" value="namespaceccp4srs.html#a50bab1a74a6f5ebde0253478a4964b24"><param name="Name" value="_addAtomPair"></OBJECT>
+  <UL>
+    <LI><OBJECT type="text/sitemap"><param name="Local" value="namespaceccp4srs.html#a50bab1a74a6f5ebde0253478a4964b24"><param name="Name" value="ccp4srs"></OBJECT>
+    <LI><OBJECT type="text/sitemap"><param name="Local" value="namespaceccp4srs.html#a50bab1a74a6f5ebde0253478a4964b24"><param name="Name" value="ccp4srs_chem.cpp"></OBJECT>
+  </UL>
+  <LI><OBJECT type="text/sitemap"><param name="Local" value="namespaceccp4srs.html#adf196969f21a33865d5f6c0f2f32cb7f"><param name="Name" value="_findName"></OBJECT>
+  <UL>
+    <LI><OBJECT type="text/sitemap"><param name="Local" value="namespaceccp4srs.html#adf196969f21a33865d5f6c0f2f32cb7f"><param name="Name" value="ccp4srs"></OBJECT>
+    <LI><OBJECT type="text/sitemap"><param name="Local" value="namespaceccp4srs.html#adf196969f21a33865d5f6c0f2f32cb7f"><param name="Name" value="ccp4srs_base.cpp"></OBJECT>
+  </UL>
+  <LI><OBJECT type="text/sitemap"><param name="Local" value="namespaceccp4srs.html#a99ea9b07a217ceb6c0645faaea831c82"><param name="Name" value="_makeChirInd"></OBJECT>
+  <UL>
+    <LI><OBJECT type="text/sitemap"><param name="Local" value="namespaceccp4srs.html#a99ea9b07a217ceb6c0645faaea831c82"><param name="Name" value="ccp4srs"></OBJECT>
+    <LI><OBJECT type="text/sitemap"><param name="Local" value="namespaceccp4srs.html#a99ea9b07a217ceb6c0645faaea831c82"><param name="Name" value="ccp4srs_base.cpp"></OBJECT>
+  </UL>
+  <LI><OBJECT type="text/sitemap"><param name="Local" value="structccp4srs_1_1_atom_pair.html#a0277f099acfa557ac20bf6fd3320bcaa"><param name="Name" value="a1"></OBJECT>
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+  <LI><OBJECT type="text/sitemap"><param name="Local" value="classccp4srs_1_1_container.html#a6caf1893b780f2cf196c85ee141baf18"><param name="Name" value="add"></OBJECT>
+  <UL>
+    <LI><OBJECT type="text/sitemap"><param name="Local" value="classccp4srs_1_1_container.html#a6caf1893b780f2cf196c85ee141baf18"><param name="Name" value="ccp4srs::Container"></OBJECT>
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+  </UL>
+  <LI><OBJECT type="text/sitemap"><param name="Local" value="namespaceccp4srs.html#af3c63726e6eb75b06c5b1c33a3acb608"><param name="Name" value="add_atom_to_cif"></OBJECT>
+  <UL>
+    <LI><OBJECT type="text/sitemap"><param name="Local" value="namespaceccp4srs.html#af3c63726e6eb75b06c5b1c33a3acb608"><param name="Name" value="ccp4srs"></OBJECT>
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+  <LI><OBJECT type="text/sitemap"><param name="Local" value="namespaceccp4srs.html#aaf4dd7dc419cfe6ae4f5a162bf528bf3"><param name="Name" value="add_bond_type_to_cif"></OBJECT>
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+    <LI><OBJECT type="text/sitemap"><param name="Local" value="namespaceccp4srs.html#aaf4dd7dc419cfe6ae4f5a162bf528bf3"><param name="Name" value="ccp4srs"></OBJECT>
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diff -ruN ccp4srs-old/doc-html/html/index.hhp ccp4srs/doc-html/html/index.hhp
--- ccp4srs-old/doc-html/html/index.hhp	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/index.hhp	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,178 @@
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+namespacemembers_enum.html
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--- ccp4srs-old/doc-html/html/index.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/index.html	2014-09-09 21:34:12.000000000 -0700
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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Main Page</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li class="current"><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
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+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
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+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
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+        </div>
+      </li>
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+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>ccp4srs Documentation</h1>  </div>
+</div>
+<div class="contents">
+<h3 class="version">Version 1.0.0 </h3></div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
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+
+<!-- iframe showing the search results (closed by default) -->
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+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
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+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
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--- ccp4srs-old/doc-html/html/inherit__graph__8.md5	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/inherit__graph__8.md5	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1 @@
+c11d34adee5c07d05814385e0f96bcf7
\ No newline at end of file
Binary files ccp4srs-old/doc-html/html/inherit__graph__8.png and ccp4srs/doc-html/html/inherit__graph__8.png differ
diff -ruN ccp4srs-old/doc-html/html/inherit__graph__9.map ccp4srs/doc-html/html/inherit__graph__9.map
--- ccp4srs-old/doc-html/html/inherit__graph__9.map	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/inherit__graph__9.map	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,3 @@
+<map id="G" name="G">
+<area shape="rect" href="$classccp4srs_1_1_index.html" title="ccp4srs::Index" alt="" coords="5,5,128,32"/>
+</map>
diff -ruN ccp4srs-old/doc-html/html/inherit__graph__9.md5 ccp4srs/doc-html/html/inherit__graph__9.md5
--- ccp4srs-old/doc-html/html/inherit__graph__9.md5	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/inherit__graph__9.md5	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1 @@
+39191fd31138e7ccc6430b70b7cd7d99
\ No newline at end of file
Binary files ccp4srs-old/doc-html/html/inherit__graph__9.png and ccp4srs/doc-html/html/inherit__graph__9.png differ
diff -ruN ccp4srs-old/doc-html/html/inherits.html ccp4srs/doc-html/html/inherits.html
--- ccp4srs-old/doc-html/html/inherits.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/inherits.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,138 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Graphical Class Hierarchy</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li class="current"><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>Graphical Class Hierarchy</h1>  </div>
+</div>
+<div class="contents">
+
+<p><a href="hierarchy.html">Go to the textual class hierarchy</a></p>
+<table border="0" cellspacing="10" cellpadding="0">
+<tr><td><img src="inherit__graph__0.png" border="0" alt="" usemap="#ccp4srs_1_1_angle"/>
+<map name="ccp4srs_1_1_angle" id="ccp4srs_1_1_angle">
+<area shape="rect" href="classccp4srs_1_1_angle.html" title="ccp4srs::Angle" alt="" coords="7,5,129,32"/></map>
+</td></tr>
+<tr><td><img src="inherit__graph__1.png" border="0" alt="" usemap="#ccp4srs_1_1_atom"/>
+<map name="ccp4srs_1_1_atom" id="ccp4srs_1_1_atom">
+<area shape="rect" href="classccp4srs_1_1_atom.html" title="ccp4srs::Atom" alt="" coords="7,5,127,32"/></map>
+</td></tr>
+<tr><td><img src="inherit__graph__2.png" border="0" alt="" usemap="#ccp4srs_1_1_atom_pair"/>
+<map name="ccp4srs_1_1_atom_pair" id="ccp4srs_1_1_atom_pair">
+<area shape="rect" href="structccp4srs_1_1_atom_pair.html" title="ccp4srs::AtomPair" alt="" coords="7,5,153,32"/></map>
+</td></tr>
+<tr><td><img src="inherit__graph__3.png" border="0" alt="" usemap="#ccp4srs_1_1_base"/>
+<map name="ccp4srs_1_1_base" id="ccp4srs_1_1_base">
+<area shape="rect" href="classccp4srs_1_1_base.html" title="ccp4srs::Base" alt="" coords="5,5,123,32"/><area shape="rect" href="classccp4srs_1_1_chem.html" title="ccp4srs::Chem" alt="" coords="172,5,297,32"/><area shape="rect" href="classccp4srs_1_1_manager.html" title="ccp4srs::Manager" alt="" coords="347,5,493,32"/></map>
+</td></tr>
+<tr><td><img src="inherit__graph__4.png" border="0" alt="" usemap="#ccp4srs_1_1_bond"/>
+<map name="ccp4srs_1_1_bond" id="ccp4srs_1_1_bond">
+<area shape="rect" href="classccp4srs_1_1_bond.html" title="ccp4srs::Bond" alt="" coords="5,5,125,32"/></map>
+</td></tr>
+<tr><td><img src="inherit__graph__5.png" border="0" alt="" usemap="#ccp4srs_1_1_chi_center"/>
+<map name="ccp4srs_1_1_chi_center" id="ccp4srs_1_1_chi_center">
+<area shape="rect" href="classccp4srs_1_1_chi_center.html" title="ccp4srs::ChiCenter" alt="" coords="7,5,161,32"/></map>
+</td></tr>
+<tr><td><img src="inherit__graph__6.png" border="0" alt="" usemap="#ccp4srs_1_1_container_3_01_t_01_4"/>
+<map name="ccp4srs_1_1_container_3_01_t_01_4" id="ccp4srs_1_1_container_3_01_t_01_4">
+<area shape="rect" href="classccp4srs_1_1_container.html" title="ccp4srs::Container\&lt; T \&gt;" alt="" coords="7,5,201,32"/></map>
+</td></tr>
+<tr><td><img src="inherit__graph__7.png" border="0" alt="" usemap="#ccp4srs_1_1_d_a_sel_hnds"/>
+<map name="ccp4srs_1_1_d_a_sel_hnds" id="ccp4srs_1_1_d_a_sel_hnds">
+<area shape="rect" href="structccp4srs_1_1_d_a_sel_hnds.html" title="ccp4srs::DASelHnds" alt="" coords="7,5,167,32"/></map>
+</td></tr>
+<tr><td><img src="inherit__graph__8.png" border="0" alt="" usemap="#ccp4srs_1_1_entry"/>
+<map name="ccp4srs_1_1_entry" id="ccp4srs_1_1_entry">
+<area shape="rect" href="classccp4srs_1_1_entry.html" title="ccp4srs::Entry" alt="" coords="7,5,124,32"/><area shape="rect" href="classccp4srs_1_1_monomer.html" title="ccp4srs::Monomer" alt="" coords="173,5,325,32"/></map>
+</td></tr>
+<tr><td><img src="inherit__graph__9.png" border="0" alt="" usemap="#ccp4srs_1_1_index"/>
+<map name="ccp4srs_1_1_index" id="ccp4srs_1_1_index">
+<area shape="rect" href="classccp4srs_1_1_index.html" title="ccp4srs::Index" alt="" coords="5,5,128,32"/></map>
+</td></tr>
+<tr><td><img src="inherit__graph__10.png" border="0" alt="" usemap="#ccp4srs_1_1_mem_i_o"/>
+<map name="ccp4srs_1_1_mem_i_o" id="ccp4srs_1_1_mem_i_o">
+<area shape="rect" href="classccp4srs_1_1_mem_i_o.html" title="ccp4srs::MemIO" alt="" coords="7,5,140,32"/></map>
+</td></tr>
+<tr><td><img src="inherit__graph__11.png" border="0" alt="" usemap="#ccp4srs_1_1_m_p_file_pos"/>
+<map name="ccp4srs_1_1_m_p_file_pos" id="ccp4srs_1_1_m_p_file_pos">
+<area shape="rect" href="structccp4srs_1_1_m_p_file_pos.html" title="ccp4srs::MPFilePos" alt="" coords="5,5,157,32"/></map>
+</td></tr>
+<tr><td><img src="inherit__graph__12.png" border="0" alt="" usemap="#ccp4srs_1_1_plane"/>
+<map name="ccp4srs_1_1_plane" id="ccp4srs_1_1_plane">
+<area shape="rect" href="classccp4srs_1_1_plane.html" title="ccp4srs::Plane" alt="" coords="5,5,128,32"/></map>
+</td></tr>
+<tr><td><img src="inherit__graph__13.png" border="0" alt="" usemap="#ccp4srs_1_1_torsion"/>
+<map name="ccp4srs_1_1_torsion" id="ccp4srs_1_1_torsion">
+<area shape="rect" href="classccp4srs_1_1_torsion.html" title="ccp4srs::Torsion" alt="" coords="7,5,140,32"/></map>
+</td></tr>
+<tr><td><img src="inherit__graph__14.png" border="0" alt="" usemap="#ccp4srs_1_1_tree"/>
+<map name="ccp4srs_1_1_tree" id="ccp4srs_1_1_tree">
+<area shape="rect" href="classccp4srs_1_1_tree.html" title="ccp4srs::Tree" alt="" coords="5,5,120,32"/></map>
+</td></tr>
+</table>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/installdox ccp4srs/doc-html/html/installdox
--- ccp4srs-old/doc-html/html/installdox	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/installdox	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,117 @@
+#!/usr/bin/perl
+
+%subst = ( );
+$quiet   = 0;
+
+if (open(F,"search.cfg"))
+{
+  $_=<F> ; s/[ \t\n]*$//g ; $subst{"_doc"} = $_;
+  $_=<F> ; s/[ \t\n]*$//g ; $subst{"_cgi"} = $_;
+}
+
+while ( @ARGV ) {
+  $_ = shift @ARGV;
+  if ( s/^-// ) {
+    if ( /^l(.*)/ ) {
+      $v = ($1 eq "") ? shift @ARGV : $1;
+      ($v =~ /\/$/) || ($v .= "/");
+      $_ = $v;
+      if ( /(.+)\@(.+)/ ) {
+        if ( exists $subst{$1} ) {
+          $subst{$1} = $2;
+        } else {
+          print STDERR "Unknown tag file $1 given with option -l\n";
+          &usage();
+        }
+      } else {
+        print STDERR "Argument $_ is invalid for option -l\n";
+        &usage();
+      }
+    }
+    elsif ( /^q/ ) {
+      $quiet = 1;
+    }
+    elsif ( /^\?|^h/ ) {
+      &usage();
+    }
+    else {
+      print STDERR "Illegal option -$_\n";
+      &usage();
+    }
+  }
+  else {
+    push (@files, $_ );
+  }
+}
+
+foreach $sub (keys %subst)
+{
+  if ( $subst{$sub} eq "" ) 
+  {
+    print STDERR "No substitute given for tag file `$sub'\n";
+    &usage();
+  }
+  elsif ( ! $quiet && $sub ne "_doc" && $sub ne "_cgi" )
+  {
+    print "Substituting $subst{$sub} for each occurrence of tag file $sub\n"; 
+  }
+}
+
+if ( ! @files ) {
+  if (opendir(D,".")) {
+    foreach $file ( readdir(D) ) {
+      $match = ".html";
+      next if ( $file =~ /^\.\.?$/ );
+      ($file =~ /$match/) && (push @files, $file);
+      ($file =~ "tree.js") && (push @files, $file);
+    }
+    closedir(D);
+  }
+}
+
+if ( ! @files ) {
+  print STDERR "Warning: No input files given and none found!\n";
+}
+
+foreach $f (@files)
+{
+  if ( ! $quiet ) {
+    print "Editing: $f...\n";
+  }
+  $oldf = $f;
+  $f   .= ".bak";
+  unless (rename $oldf,$f) {
+    print STDERR "Error: cannot rename file $oldf\n";
+    exit 1;
+  }
+  if (open(F,"<$f")) {
+    unless (open(G,">$oldf")) {
+      print STDERR "Error: opening file $oldf for writing\n";
+      exit 1;
+    }
+    if ($oldf ne "tree.js") {
+      while (<F>) {
+        s/doxygen\=\"([^ \"\:\t\>\<]*)\:([^ \"\t\>\<]*)\" (href|src)=\"\2/doxygen\=\"$1:$subst{$1}\" \3=\"$subst{$1}/g;
+        print G "$_";
+      }
+    }
+    else {
+      while (<F>) {
+        s/\"([^ \"\:\t\>\<]*)\:([^ \"\t\>\<]*)\", \"\2/\"$1:$subst{$1}\" ,\"$subst{$1}/g;
+        print G "$_";
+      }
+    }
+  } 
+  else {
+    print STDERR "Warning file $f does not exist\n";
+  }
+  unlink $f;
+}
+
+sub usage {
+  print STDERR "Usage: installdox [options] [html-file [html-file ...]]\n";
+  print STDERR "Options:\n";
+  print STDERR "     -l tagfile\@linkName   tag file + URL or directory \n";
+  print STDERR "     -q                    Quiet mode\n\n";
+  exit 1;
+}
diff -ruN ccp4srs-old/doc-html/html/memio___8cpp.html ccp4srs/doc-html/html/memio___8cpp.html
--- ccp4srs-old/doc-html/html/memio___8cpp.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/memio___8cpp.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,82 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/memio_.cpp File Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li class="current"><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="files.html"><span>File&#160;List</span></a></li>
+      <li><a href="globals.html"><span>File&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="summary">
+<a href="#namespaces">Namespaces</a>  </div>
+  <div class="headertitle">
+<h1>src/memio_.cpp File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &lt;string.h&gt;</code><br/>
+<code>#include &lt;zlib.h&gt;</code><br/>
+<code>#include &quot;<a class="el" href="memio___8h_source.html">memio_.h</a>&quot;</code><br/>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+</table>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/memio___8h.html ccp4srs/doc-html/html/memio___8h.html
--- ccp4srs-old/doc-html/html/memio___8h.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/memio___8h.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,90 @@
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+<a href="#nested-classes">Classes</a> &#124;
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+<h1>src/memio_.h File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &quot;mmdb/mmdb_io_file.h&quot;</code><br/>
+
+<p><a href="memio___8h_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="nested-classes"></a>
+Classes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html">ccp4srs::MemIO</a></td></tr>
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+<tr><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a64bcbd2282ebaf1613021bf317bdf0cb">ccp4srs::DefineClass</a> (MemIO)</td></tr>
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+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
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diff -ruN ccp4srs-old/doc-html/html/memio___8h_source.html ccp4srs/doc-html/html/memio___8h_source.html
--- ccp4srs-old/doc-html/html/memio___8h_source.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/memio___8h_source.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,191 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/memio_.h Source File</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
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+<div class="header">
+  <div class="headertitle">
+<h1>src/memio_.h</h1>  </div>
+</div>
+<div class="contents">
+<a href="memio___8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">//  $Id: memio_.h $</span>
+<a name="l00002"></a>00002 <span class="comment">//  =================================================================</span>
+<a name="l00003"></a>00003 <span class="comment">//</span>
+<a name="l00004"></a>00004 <span class="comment">//   CCP4 SRS Library: Storage, Retrievak and Search support for</span>
+<a name="l00005"></a>00005 <span class="comment">//   CCP4 ligand data.</span>
+<a name="l00006"></a>00006 <span class="comment">//</span>
+<a name="l00007"></a>00007 <span class="comment">//   Copyright (C) Eugene Krissinel 2010-2013.</span>
+<a name="l00008"></a>00008 <span class="comment">//</span>
+<a name="l00009"></a>00009 <span class="comment">//   This library is free software: you can redistribute it and/or</span>
+<a name="l00010"></a>00010 <span class="comment">//   modify it under the terms of the GNU Lesser General Public</span>
+<a name="l00011"></a>00011 <span class="comment">//   License version 3, modified in accordance with the provisions</span>
+<a name="l00012"></a>00012 <span class="comment">//   of the license to address the requirements of UK law.</span>
+<a name="l00013"></a>00013 <span class="comment">//</span>
+<a name="l00014"></a>00014 <span class="comment">//   You should have received a copy of the modified GNU Lesser</span>
+<a name="l00015"></a>00015 <span class="comment">//   General Public License along with this library. If not, copies</span>
+<a name="l00016"></a>00016 <span class="comment">//   may be downloaded from http://www.ccp4.ac.uk/ccp4license.php</span>
+<a name="l00017"></a>00017 <span class="comment">//</span>
+<a name="l00018"></a>00018 <span class="comment">//   This program is distributed in the hope that it will be useful,</span>
+<a name="l00019"></a>00019 <span class="comment">//   but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
+<a name="l00020"></a>00020 <span class="comment">//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
+<a name="l00021"></a>00021 <span class="comment">//   GNU Lesser General Public License for more details.</span>
+<a name="l00022"></a>00022 <span class="comment">//</span>
+<a name="l00023"></a>00023 <span class="comment">//  =================================================================</span>
+<a name="l00024"></a>00024 <span class="comment">//</span>
+<a name="l00025"></a>00025 <span class="comment">//    18.09.13   &lt;--  Date of Last Modification.</span>
+<a name="l00026"></a>00026 <span class="comment">//                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
+<a name="l00027"></a>00027 <span class="comment">//  -----------------------------------------------------------------</span>
+<a name="l00028"></a>00028 <span class="comment">//</span>
+<a name="l00029"></a>00029 <span class="comment">//  **** Module  :  memio_  &lt;interface&gt;</span>
+<a name="l00030"></a>00030 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00031"></a>00031 <span class="comment">//  **** Classes :  ccp4srs::MemIO  - buffered I/O</span>
+<a name="l00032"></a>00032 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00033"></a>00033 <span class="comment">//</span>
+<a name="l00034"></a>00034 <span class="comment">//  (C) E. Krissinel 2010-2013</span>
+<a name="l00035"></a>00035 <span class="comment">//</span>
+<a name="l00036"></a>00036 <span class="comment">//  =================================================================</span>
+<a name="l00037"></a>00037 <span class="comment">//</span>
+<a name="l00038"></a>00038 
+<a name="l00039"></a>00039 <span class="preprocessor">#ifndef MEMIO_H</span>
+<a name="l00040"></a>00040 <span class="preprocessor"></span><span class="preprocessor">#define MEMIO_H</span>
+<a name="l00041"></a>00041 <span class="preprocessor"></span>
+<a name="l00042"></a>00042 <span class="preprocessor">#include &quot;mmdb/mmdb_io_file.h&quot;</span>
+<a name="l00043"></a>00043 
+<a name="l00044"></a>00044 <span class="keyword">namespace </span>ccp4srs  {
+<a name="l00045"></a>00045 
+<a name="l00046"></a>00046   <a class="code" href="namespaceccp4srs.html#afbb5df60616f08fcf36926a3585c185f">DefineClass</a>(MemIO);
+<a name="l00047"></a>00047 
+<a name="l00048"></a><a class="code" href="classccp4srs_1_1_mem_i_o.html">00048</a>   <span class="keyword">class </span><a class="code" href="classccp4srs_1_1_mem_i_o.html">MemIO</a>  {
+<a name="l00049"></a>00049 
+<a name="l00050"></a>00050     <span class="keyword">public</span>:
+<a name="l00051"></a>00051 
+<a name="l00052"></a><a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa29a865c4c24a0a158c5fc0514a29e517">00052</a>       <span class="keyword">enum</span> { <a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63">Ok</a>,<a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaac65c121a2ac9e371d3e059cb480cf60d">CantOpenFile</a>,<a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa117fc645808ac4d9c4e53452bc608d51">EmptyFile</a>,<a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaab76082bd26e6e49c9c7794410cec3ca2">ReadError</a>,<a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa29a865c4c24a0a158c5fc0514a29e517">WriteError</a>,<a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaadf48b9ed60d08687c2fbd5271b328c70">MemReadError</a>,
+<a name="l00053"></a><a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa63962a5b2f5046aa5e8a6b0b46271824">00053</a>              <a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa6cf46f9d24d202ae6ac26ddb6aeb625d">CompressionError</a>,<a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa63962a5b2f5046aa5e8a6b0b46271824">UncompressionError</a>,<a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaaec9637fa3da0cf0cc0385a15d95af350">SizeError</a> };
+<a name="l00054"></a>00054 
+<a name="l00055"></a>00055       <a class="code" href="classccp4srs_1_1_mem_i_o.html#af2490447442255fa19b2a1c05c011f96">MemIO</a>();
+<a name="l00056"></a>00056       <span class="keyword">virtual</span> <a class="code" href="classccp4srs_1_1_mem_i_o.html#abb2d68b86867b62480e6f036a2f8bcbb">~MemIO</a>();
+<a name="l00057"></a>00057 
+<a name="l00058"></a>00058       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#abfd614fba0e035434e9c7f1c4a58ad89">setCompressionLevel</a> ( <span class="keywordtype">int</span> compressionLevel ); <span class="comment">// 0,1,2,3</span>
+<a name="l00059"></a>00059 
+<a name="l00060"></a>00060       <span class="keywordtype">int</span>   <a class="code" href="classccp4srs_1_1_mem_i_o.html#ad8c19ab9e2bd98b40caf95cc6d7e071e">read</a>  ( mmdb::cpstr  fileName,
+<a name="l00061"></a>00061                     mmdb::io::GZ_MODE gzMode=mmdb::io::GZM_NONE );
+<a name="l00062"></a>00062       <span class="keywordtype">int</span>   <a class="code" href="classccp4srs_1_1_mem_i_o.html#ad8c19ab9e2bd98b40caf95cc6d7e071e">read</a>  ( mmdb::io::RFile f );
+<a name="l00063"></a>00063 
+<a name="l00064"></a>00064       <span class="keywordtype">int</span>   <a class="code" href="classccp4srs_1_1_mem_i_o.html#ae2fd4e637343f3f9ac5ccfc3af085293">write</a> ( mmdb::cpstr  fileName,
+<a name="l00065"></a>00065                     mmdb::io::GZ_MODE gzMode=mmdb::io::GZM_NONE );
+<a name="l00066"></a>00066       <span class="keywordtype">int</span>   <a class="code" href="classccp4srs_1_1_mem_i_o.html#ae2fd4e637343f3f9ac5ccfc3af085293">write</a> ( mmdb::io::RFile f );
+<a name="l00067"></a>00067 
+<a name="l00068"></a><a class="code" href="classccp4srs_1_1_mem_i_o.html#a5e4ae24f25179a720de85f185f8074ff">00068</a>       <span class="keywordtype">int</span>   <a class="code" href="classccp4srs_1_1_mem_i_o.html#a5e4ae24f25179a720de85f185f8074ff">length</a>() { <span class="keywordflow">return</span> buffer_length; }
+<a name="l00069"></a>00069 
+<a name="l00070"></a>00070       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#a855507e19582e7ab9b7236fb9d453da3">reset</a>();
+<a name="l00071"></a>00071       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#a4cda073662a49aa45b0c744ec88de39a">free</a> ();
+<a name="l00072"></a>00072 
+<a name="l00073"></a>00073       <span class="keywordtype">void</span> * <a class="code" href="classccp4srs_1_1_mem_i_o.html#aa1d1ea86d64ee50cab284d4a18f55ab8">get_buffer</a>        ( <span class="keyword">const</span> <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_mem_i_o.html#a5e4ae24f25179a720de85f185f8074ff">length</a> );
+<a name="l00074"></a><a class="code" href="classccp4srs_1_1_mem_i_o.html#ac84f72f62362171b812f386ef786a677">00074</a>       <span class="keywordtype">void</span>   <a class="code" href="classccp4srs_1_1_mem_i_o.html#ac84f72f62362171b812f386ef786a677">set_buffer_length</a> ( <span class="keyword">const</span> <span class="keywordtype">int</span> len )  { buffer_length = len; }
+<a name="l00075"></a>00075       <span class="keywordtype">void</span>   <a class="code" href="classccp4srs_1_1_mem_i_o.html#aa1d1ea86d64ee50cab284d4a18f55ab8">get_buffer</a>        ( mmdb::pstr * buf, <span class="keywordtype">int</span> * <a class="code" href="classccp4srs_1_1_mem_i_o.html#a5e4ae24f25179a720de85f185f8074ff">length</a> );
+<a name="l00076"></a>00076 
+<a name="l00077"></a>00077       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#a98b3d03fd613c62e0d16bfda509aa630">write_buffer</a> ( <span class="keyword">const</span> <span class="keywordtype">void</span> * src,  <span class="keyword">const</span> <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_mem_i_o.html#a5e4ae24f25179a720de85f185f8074ff">length</a>  );
+<a name="l00078"></a>00078       <span class="keywordtype">bool</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#a7df5365c01565a15ac3bca748e46146b">read_buffer</a>  ( <span class="keywordtype">void</span>       * dest, <span class="keyword">const</span> <span class="keywordtype">int</span> <a class="code" href="classccp4srs_1_1_mem_i_o.html#a5e4ae24f25179a720de85f185f8074ff">length</a>,
+<a name="l00079"></a>00079                            <span class="keywordtype">bool</span> * <a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63">Ok</a> = NULL);
+<a name="l00080"></a>00080 
+<a name="l00081"></a>00081       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#a6c563469a6978a9c1c62a33457c90661">put_integer</a>   ( <span class="keywordtype">int</span>        I );
+<a name="l00082"></a>00082       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#a1a5cd9341de994fa17ae8efae3d61732">put_ishort</a>    ( <span class="keywordtype">int</span>        I );  <span class="comment">// saves as short</span>
+<a name="l00083"></a>00083       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#a55ccb2d1a276365eadb422c75e982de3">put_ibyte</a>     ( <span class="keywordtype">int</span>        I );  <span class="comment">// saves as byte</span>
+<a name="l00084"></a>00084       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#a3c30e4f73927173a9ce5731fab39d170">put_byte</a>      ( mmdb::byte B );
+<a name="l00085"></a>00085       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#a7117ff86d20006f7a693ea3a36035674">put_short</a>     ( <span class="keywordtype">short</span>      I );
+<a name="l00086"></a>00086       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#af300f12e3fe4b3d878f80caf19b66341">put_long</a>      ( <span class="keywordtype">long</span>       I );
+<a name="l00087"></a>00087       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#abf6e925edc35b60fe7816223ceb7a15f">put_word</a>      ( mmdb::word W );
+<a name="l00088"></a>00088       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#a1d8e03e12f2420c9650f4a8956a1c0a7">put_real</a>      ( mmdb::realtype  R );
+<a name="l00089"></a>00089       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#ad82c1eca930cc9d5535f2da1ab3cde1a">put_float</a>     ( mmdb::realtype  R );  <span class="comment">// stores single precision</span>
+<a name="l00090"></a>00090       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#a4eb6ba2e97922bf9509d828ee075aa8e">put_shortreal</a> ( mmdb::shortreal R );
+<a name="l00091"></a>00091       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#a98548fca1e008178fef523b271db5423">put_line</a>      ( mmdb::cpstr     L );  <span class="comment">// for static strings</span>
+<a name="l00092"></a>00092       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#aa35e6bbff841d942f793e50ee813fc97">put_string</a>    ( mmdb::cpstr     L );  <span class="comment">// for dynamic strings</span>
+<a name="l00093"></a>00093       <span class="keywordtype">void</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#ac3420c8a37ce57f324cf66eb4ccb9b13">put_bool</a>      ( <span class="keywordtype">bool</span>   B );
+<a name="l00094"></a>00094 
+<a name="l00095"></a>00095       <span class="keywordtype">bool</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#a2d311d3bf0798e1c2bcb1cbe7f5d622f">get_integer</a>   ( <span class="keywordtype">int</span>        &amp; I, <span class="keywordtype">bool</span> * <a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63">Ok</a> = NULL );
+<a name="l00096"></a>00096       <span class="keywordtype">bool</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#a55e1b2e8f826ab2d6c0aef09f3beac9f">get_ishort</a>    ( <span class="keywordtype">int</span>        &amp; I, <span class="keywordtype">bool</span> * <a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63">Ok</a> = NULL );
+<a name="l00097"></a>00097       <span class="keywordtype">bool</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#a7bc9b6d871402f5b5601d05ad4012326">get_ibyte</a>     ( <span class="keywordtype">int</span>        &amp; I, <span class="keywordtype">bool</span> * <a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63">Ok</a> = NULL );
+<a name="l00098"></a>00098       <span class="keywordtype">bool</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#a296d38484504311f2773ff313298dda9">get_byte</a>      ( mmdb::byte &amp; B, <span class="keywordtype">bool</span> * <a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63">Ok</a> = NULL );
+<a name="l00099"></a>00099       <span class="keywordtype">bool</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#af2d1b382de42e06ce1dc5ae4ad6bb20f">get_short</a>     ( <span class="keywordtype">short</span>      &amp; I, <span class="keywordtype">bool</span> * <a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63">Ok</a> = NULL );
+<a name="l00100"></a>00100       <span class="keywordtype">bool</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#a950878f651e3bb037cf7ddc4a9c00201">get_long</a>      ( <span class="keywordtype">long</span>       &amp; I, <span class="keywordtype">bool</span> * <a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63">Ok</a> = NULL );
+<a name="l00101"></a>00101       <span class="keywordtype">bool</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#ab932bc5aa0e98c9e681a3f3a9cc532c8">get_word</a>      ( mmdb::word      &amp; W, <span class="keywordtype">bool</span> * <a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63">Ok</a> = NULL );
+<a name="l00102"></a>00102       <span class="keywordtype">bool</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#afcc2e5eede7a829347985f646f24dcb3">get_real</a>      ( mmdb::realtype  &amp; R, <span class="keywordtype">bool</span> * <a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63">Ok</a> = NULL );
+<a name="l00103"></a>00103       <span class="keywordtype">bool</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#adf95c15823dd0fb1067002d2ee3d8095">get_float</a>     ( mmdb::realtype  &amp; R, <span class="keywordtype">bool</span> * <a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63">Ok</a> = NULL );
+<a name="l00104"></a>00104       <span class="keywordtype">bool</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#a039402bc82d9d0de0bd3664769355573">get_shortreal</a> ( mmdb::shortreal &amp; R, <span class="keywordtype">bool</span> * <a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63">Ok</a> = NULL );
+<a name="l00105"></a>00105       <span class="keywordtype">bool</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#a6cab031cef522531846e3ced7984f276">get_line</a>      ( mmdb::pstr        L, <span class="keywordtype">bool</span> * <a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63">Ok</a> = NULL );
+<a name="l00106"></a>00106       <span class="keywordtype">bool</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#a22abd9cc96e80e4d3e71f0d1acbf1c4d">get_string</a>    ( mmdb::pstr      &amp; L, <span class="keywordtype">bool</span> * <a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63">Ok</a> = NULL );
+<a name="l00107"></a>00107       <span class="keywordtype">bool</span>  <a class="code" href="classccp4srs_1_1_mem_i_o.html#a0bbc28ba1593463385ae8f28b65225fa">get_bool</a>      ( <span class="keywordtype">bool</span>   &amp; B, <span class="keywordtype">bool</span> * <a class="code" href="classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63">Ok</a> = NULL );
+<a name="l00108"></a>00108 
+<a name="l00109"></a>00109     <span class="keyword">private</span>:
+<a name="l00110"></a>00110       <span class="keywordtype">int</span>           compression_level;
+<a name="l00111"></a>00111       mmdb::bvector buffer,compression_buffer;
+<a name="l00112"></a>00112       <span class="keywordtype">int</span>           buffer_length,buffer_pos,alloc_length,chunk_size;
+<a name="l00113"></a>00113       <span class="keywordtype">int</span>           compression_alloc;
+<a name="l00114"></a>00114 
+<a name="l00115"></a>00115   };
+<a name="l00116"></a>00116 
+<a name="l00117"></a>00117 }  <span class="comment">// namespace ccp4srs</span>
+<a name="l00118"></a>00118 
+<a name="l00119"></a>00119 <span class="preprocessor">#endif // MEMIO_H</span>
+</pre></div></div>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
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diff -ruN ccp4srs-old/doc-html/html/mpfile___8cpp.html ccp4srs/doc-html/html/mpfile___8cpp.html
--- ccp4srs-old/doc-html/html/mpfile___8cpp.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/mpfile___8cpp.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,80 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<h1>src/mpfile_.cpp File Reference</h1>  </div>
+</div>
+<div class="contents">
+<code>#include &quot;<a class="el" href="mpfile___8h_source.html">mpfile_.h</a>&quot;</code><br/>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
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diff -ruN ccp4srs-old/doc-html/html/mpfile___8h.html ccp4srs/doc-html/html/mpfile___8h.html
--- ccp4srs-old/doc-html/html/mpfile___8h.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/mpfile___8h.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,91 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: src/mpfile_.h File Reference</title>
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+<h1>src/mpfile_.h File Reference</h1>  </div>
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+<div class="contents">
+<code>#include &quot;mmdb/mmdb_io_file.h&quot;</code><br/>
+
+<p><a href="mpfile___8h_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="nested-classes"></a>
+Classes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structccp4srs_1_1_m_p_file_pos.html">ccp4srs::MPFilePos</a></td></tr>
+<tr><td colspan="2"><h2><a name="namespaces"></a>
+Namespaces</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">namespace &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td></tr>
+<tr><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#aad79147ea920868ed625a8f693277d56">ccp4srs::DefineStructure</a> (MPFilePos)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#aed1408df12f28bc4a3dd772230255597">ccp4srs::DefineClass</a> (MPFile) class MPFile</td></tr>
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diff -ruN ccp4srs-old/doc-html/html/mpfile___8h_source.html ccp4srs/doc-html/html/mpfile___8h_source.html
--- ccp4srs-old/doc-html/html/mpfile___8h_source.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/mpfile___8h_source.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,172 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+  <div class="headertitle">
+<h1>src/mpfile_.h</h1>  </div>
+</div>
+<div class="contents">
+<a href="mpfile___8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">//  $Id: mpfile_.h $</span>
+<a name="l00002"></a>00002 <span class="comment">//  =================================================================</span>
+<a name="l00003"></a>00003 <span class="comment">//</span>
+<a name="l00004"></a>00004 <span class="comment">//   CCP4 SRS Library: Storage, Retrieval and Search support for</span>
+<a name="l00005"></a>00005 <span class="comment">//   CCP4 ligand data.</span>
+<a name="l00006"></a>00006 <span class="comment">//</span>
+<a name="l00007"></a>00007 <span class="comment">//   Copyright (C) Eugene Krissinel 2010-2013.</span>
+<a name="l00008"></a>00008 <span class="comment">//</span>
+<a name="l00009"></a>00009 <span class="comment">//   This library is free software: you can redistribute it and/or</span>
+<a name="l00010"></a>00010 <span class="comment">//   modify it under the terms of the GNU Lesser General Public</span>
+<a name="l00011"></a>00011 <span class="comment">//   License version 3, modified in accordance with the provisions</span>
+<a name="l00012"></a>00012 <span class="comment">//   of the license to address the requirements of UK law.</span>
+<a name="l00013"></a>00013 <span class="comment">//</span>
+<a name="l00014"></a>00014 <span class="comment">//   You should have received a copy of the modified GNU Lesser</span>
+<a name="l00015"></a>00015 <span class="comment">//   General Public License along with this library. If not, copies</span>
+<a name="l00016"></a>00016 <span class="comment">//   may be downloaded from http://www.ccp4.ac.uk/ccp4license.php</span>
+<a name="l00017"></a>00017 <span class="comment">//</span>
+<a name="l00018"></a>00018 <span class="comment">//   This program is distributed in the hope that it will be useful,</span>
+<a name="l00019"></a>00019 <span class="comment">//   but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
+<a name="l00020"></a>00020 <span class="comment">//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
+<a name="l00021"></a>00021 <span class="comment">//   GNU Lesser General Public License for more details.</span>
+<a name="l00022"></a>00022 <span class="comment">//</span>
+<a name="l00023"></a>00023 <span class="comment">//  =================================================================</span>
+<a name="l00024"></a>00024 <span class="comment">//</span>
+<a name="l00025"></a>00025 <span class="comment">//    18.09.13   &lt;--  Date of Last Modification.</span>
+<a name="l00026"></a>00026 <span class="comment">//                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
+<a name="l00027"></a>00027 <span class="comment">//  -----------------------------------------------------------------</span>
+<a name="l00028"></a>00028 <span class="comment">//</span>
+<a name="l00029"></a>00029 <span class="comment">//  **** Module  :  mpfile_  &lt;interface&gt;</span>
+<a name="l00030"></a>00030 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00031"></a>00031 <span class="comment">//  **** Classes :  ccp4srs::MPFile  - multi-part file support</span>
+<a name="l00032"></a>00032 <span class="comment">//       ~~~~~~~~~</span>
+<a name="l00033"></a>00033 <span class="comment">//</span>
+<a name="l00034"></a>00034 <span class="comment">//  (C) E. Krissinel 2010-2013</span>
+<a name="l00035"></a>00035 <span class="comment">//</span>
+<a name="l00036"></a>00036 <span class="comment">//  =================================================================</span>
+<a name="l00037"></a>00037 <span class="comment">//</span>
+<a name="l00038"></a>00038 
+<a name="l00039"></a>00039 <span class="preprocessor">#ifndef  MPFILE_H</span>
+<a name="l00040"></a>00040 <span class="preprocessor"></span><span class="preprocessor">#define  MPFILE_H</span>
+<a name="l00041"></a>00041 <span class="preprocessor"></span>
+<a name="l00042"></a>00042 <span class="preprocessor">#include &quot;mmdb/mmdb_io_file.h&quot;</span>
+<a name="l00043"></a>00043 
+<a name="l00044"></a>00044 <span class="keyword">namespace </span>ccp4srs  {
+<a name="l00045"></a>00045 
+<a name="l00046"></a>00046   <span class="comment">//  ===========================  MPFile  ===========================</span>
+<a name="l00047"></a>00047 
+<a name="l00048"></a>00048   <a class="code" href="namespaceccp4srs.html#a38fd31a76e47d65dbd8f9343fdc2f001">DefineStructure</a>(MPFilePos);
+<a name="l00049"></a>00049 
+<a name="l00050"></a><a class="code" href="structccp4srs_1_1_m_p_file_pos.html">00050</a>   <span class="keyword">struct </span><a class="code" href="structccp4srs_1_1_m_p_file_pos.html">MPFilePos</a>  {
+<a name="l00051"></a><a class="code" href="structccp4srs_1_1_m_p_file_pos.html#ab84443c24cd9b322d81f2e165af4bd8a">00051</a>     mmdb::byte <a class="code" href="structccp4srs_1_1_m_p_file_pos.html#ab84443c24cd9b322d81f2e165af4bd8a">chunkNo</a>;   <span class="comment">// file part number (1-254)</span>
+<a name="l00052"></a><a class="code" href="structccp4srs_1_1_m_p_file_pos.html#afb6853252f03dbbc698dea44b425d2d9">00052</a>     <span class="keywordtype">long</span>       <a class="code" href="structccp4srs_1_1_m_p_file_pos.html#afb6853252f03dbbc698dea44b425d2d9">offset</a>;    <span class="comment">// offset in chunk</span>
+<a name="l00053"></a>00053     <span class="keywordtype">void</span> <a class="code" href="structccp4srs_1_1_m_p_file_pos.html#a7f60e91b825a15d3def175dcdb71139d">Copy</a>  ( RMPFilePos dbf_pos );
+<a name="l00054"></a>00054     <span class="keywordtype">void</span> <a class="code" href="structccp4srs_1_1_m_p_file_pos.html#a6e1a52091171d7462c6b8334f1483998">write</a> ( mmdb::io::RFile f );
+<a name="l00055"></a>00055     <span class="keywordtype">void</span> <a class="code" href="structccp4srs_1_1_m_p_file_pos.html#a8351d37471b7cdab264a91bb1a92db1c">read</a>  ( mmdb::io::RFile f );
+<a name="l00056"></a>00056   };
+<a name="l00057"></a>00057 
+<a name="l00058"></a><a class="code" href="namespaceccp4srs.html#aed1408df12f28bc4a3dd772230255597">00058</a>   <a class="code" href="namespaceccp4srs.html#afbb5df60616f08fcf36926a3585c185f">DefineClass</a>(MPFile)
+<a name="l00059"></a>00059 
+<a name="l00060"></a>00060   class MPFile  {
+<a name="l00061"></a>00061 
+<a name="l00062"></a>00062     <span class="keyword">public</span> :
+<a name="l00063"></a>00063       MPFile ();
+<a name="l00064"></a>00064       ~MPFile();
+<a name="l00065"></a>00065 
+<a name="l00066"></a>00066       <span class="keywordtype">void</span>  assign  ( mmdb::cpstr FName, <span class="keywordtype">bool</span> UniB=<span class="keyword">true</span> );
+<a name="l00067"></a>00067       <span class="keywordtype">bool</span>  reset   ( <span class="keywordtype">bool</span> readOnly=<span class="keyword">false</span> );
+<a name="l00068"></a>00068       <span class="keywordtype">bool</span>  rewrite ( <span class="keywordtype">long</span> chunk_size=1000000000  );
+<a name="l00069"></a>00069       <span class="keywordtype">bool</span>  append  ( <span class="keywordtype">long</span> chunk_size=1000000000  );
+<a name="l00070"></a>00070 
+<a name="l00071"></a>00071       mmdb::pstr FileName    () { <span class="keywordflow">return</span> fpath; }
+<a name="l00072"></a>00072       <span class="keywordtype">void</span>  getPosition ( RMPFilePos <a class="code" href="structccp4srs_1_1_m_p_file_pos.html">MPFilePos</a> );
+<a name="l00073"></a>00073       <span class="keywordtype">bool</span>  seek        ( RMPFilePos MPFilePos );
+<a name="l00074"></a>00074       <span class="keywordtype">bool</span>  MPFileEnd   ();
+<a name="l00075"></a>00075       <span class="keywordtype">bool</span>  Success     ();
+<a name="l00076"></a>00076       <span class="keywordtype">void</span>  shut        ();
+<a name="l00077"></a>00077 
+<a name="l00078"></a>00078       mmdb::io::PFile   getChunkRead ();
+<a name="l00079"></a>00079       mmdb::io::PFile   getChunkWrite();
+<a name="l00080"></a>00080 
+<a name="l00081"></a>00081     <span class="keyword">protected</span> :
+<a name="l00082"></a>00082       mmdb::io::PPFile f;
+<a name="l00083"></a>00083       mmdb::pstr       fpath;
+<a name="l00084"></a>00084       <span class="keywordtype">long</span>             chunkSize;
+<a name="l00085"></a>00085       mmdb::byte       chunkNo;
+<a name="l00086"></a>00086       <span class="keywordtype">bool</span>             uniBinary,readOnly;
+<a name="l00087"></a>00087 
+<a name="l00088"></a>00088       mmdb::pstr getChunkPath  ();
+<a name="l00089"></a>00089       <span class="keywordtype">bool</span> getChunk      ( <span class="keywordtype">int</span> toChunkNo, <span class="keywordtype">bool</span> onRead );
+<a name="l00090"></a>00090       <span class="keywordtype">bool</span> checkChunkEnd ( <span class="keywordtype">bool</span> onRead );
+<a name="l00091"></a>00091 
+<a name="l00092"></a>00092     <span class="keyword">private</span> :
+<a name="l00093"></a>00093       mmdb::pstr chunkPath;
+<a name="l00094"></a>00094       <span class="keywordtype">int</span>        nchunks;
+<a name="l00095"></a>00095 
+<a name="l00096"></a>00096   };
+<a name="l00097"></a>00097 
+<a name="l00098"></a>00098 }  <span class="comment">// namespace ccp4srs</span>
+<a name="l00099"></a>00099 
+<a name="l00100"></a>00100 <span class="preprocessor">#endif  //  MPFILE_H</span>
+</pre></div></div>
+</div>
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@@ -0,0 +1,1144 @@
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+<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_atom.html">Atom</a></td></tr>
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+<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_tree.html">Tree</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structccp4srs_1_1_atom_pair.html">AtomPair</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html">DASelHnds</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classccp4srs_1_1_mem_i_o.html">MemIO</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structccp4srs_1_1_m_p_file_pos.html">MPFilePos</a></td></tr>
+<tr><td colspan="2"><h2><a name="typedef-members"></a>
+Typedefs</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">typedef char&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#ae91f970060d687d02ccfb78cbd6222bb">ChiCenterID</a> [20]</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">typedef char&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#ac768cc62149be89b81a30d88a09f0166">PlaneID</a> [20]</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">typedef char&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a192f47d1deb71790866bce922f50bba1">TorsionID</a> [20]</td></tr>
+<tr><td colspan="2"><h2><a name="enum-members"></a>
+Enumerations</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40d">CCP4SRS_VERSION</a> { <a class="el" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40da70b6b61e66afecc14062283f4ab22165">MAJOR_VERSION</a> =  1, 
+<a class="el" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40da629c96b840f87c056420011f99867b11">MINOR_VERSION</a> =  0, 
+<a class="el" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40dafef3f6fb9926961d5bb1c2c5f5464228">MICRO_VERSION</a> =  0
+ }</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">CCP4SRS_RC</a> { <br/>
+&#160;&#160;<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa9f7a70887f053cb4ce97d321d477ac81">CCP4SRS_noDonors</a> =  4, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa2d2f9ebfa39ac8c445aaa789d3f7d73c">CCP4SRS_noAcceptors</a> =  3, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aae4c2a57f461a7c55fcdbf5f5256b633c">CCP4SRS_noHBonds</a> =  2, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa376037f37a8f3b5a5822abe08b8a2775">CCP4SRS_Incomplete</a> =  1, 
+<br/>
+&#160;&#160;<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa09553d9a0822e1b3ab31018c2a12cbbb">CCP4SRS_Ok</a> =  0, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa0f4cab4ac6672344d9c17addef3a5c2c">CCP4SRS_WrongBondType</a> =  -1, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa4513ed69439ddf6233fd9311675d3ec3">CCP4SRS_IndexCorrupt</a> =  -2, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aaf8be04ede882dccdaab276915605e785">CCP4SRS_FileNotFound</a> =  -3, 
+<br/>
+&#160;&#160;<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa0f0128ede6fa588e9e90ab7d96e3395d">CCP4SRS_EntryNotFound</a> =  -4, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa3f7eda4d59140c81cd5ca9224b569146">CCP4SRS_ReadErrors</a> =  -5, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aacec935441561de176dbd7b29c608a960">CCP4SRS_EmptyResidue</a> =  -6, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa6ce76e69c4e7c9b8ae5f28fcb6279c13">CCP4SRS_NoAtomsFound</a> =  -7, 
+<br/>
+&#160;&#160;<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aaf41577d27e0b8306dc1dfaebbffe3a85">CCP4SRS_NoBonds</a> =  -8, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa36de44e9555882901e32ff002491b4c1">CCP4SRS_EmptyResSet</a> =  -9, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa770346796e3fd0232458a3dd9709d735">CCP4SRS_Fail</a> =  -10, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aafabbc088bd534a406ce2a155b7c7be34">CCP4SRS_SVD_Fail</a> =  -11, 
+<br/>
+&#160;&#160;<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa86978a692503eda1577d1250f402e4d4">CCP4SRS_noCoordHierarchy</a> =  -12, 
+<a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa785ce210fda24a93bd0df60e0a612698">CCP4SRS_BrokenBonds</a> =  -13
+<br/>
+ }</td></tr>
+<tr><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#afbb5df60616f08fcf36926a3585c185f">DefineClass</a> (<a class="el" href="classccp4srs_1_1_angle.html">Angle</a>)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#adead0e638933d7d2949df9bb7b44f910">get_atom_from_cif</a> (int &amp;index, mmdb::mmcif::PLoop loop, mmdb::cpstr Tag, int row, <a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;atoms, int &amp;rc)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a012e980439f3fcbb1844abf82ab2e95e">get_atom_from_cif</a> (int &amp;index, mmdb::mmcif::PStruct mmCIFStruct, mmdb::cpstr Tag, <a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;atoms, int &amp;rc)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#af3c63726e6eb75b06c5b1c33a3acb608">add_atom_to_cif</a> (mmdb::mmcif::PLoop loop, int atom_no, <a class="el" href="classccp4srs_1_1_container.html">Container</a>&lt; <a class="el" href="classccp4srs_1_1_atom.html">Atom</a> &gt; &amp;atoms)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#aaacc6a8b59c08ac1bbfd9305ee663a1b">DefineClass</a> (<a class="el" href="classccp4srs_1_1_atom.html">Atom</a>)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a99ea9b07a217ceb6c0645faaea831c82">_makeChirInd</a> (char chirality)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#adf196969f21a33865d5f6c0f2f32cb7f">_findName</a> (mmdb::PAtomName Nams, mmdb::cpstr N, int len)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a4c159612746fffa9c8740ead5f891bb4">DefineClass</a> (<a class="el" href="classccp4srs_1_1_base.html">Base</a>)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a134be7dad55bde913e9bbb02825064e0">get_bond_type_from_cif_ccp4</a> (int &amp;type, mmdb::mmcif::PLoop loop, mmdb::cpstr Tag, int row, int &amp;rc)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a2fc315dbfb7012f8e39ff3a2f440a5d6">get_bond_type_from_cif_rcsb</a> (int &amp;type, mmdb::mmcif::PLoop loop, mmdb::cpstr Tag, int row, int &amp;rc)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a66b5a7cbf87409e898be86c84505275a">get_bond_type_from_cif</a> (int &amp;type, mmdb::mmcif::PStruct mmCIFStruct, mmdb::cpstr Tag, int &amp;rc)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#aaf4dd7dc419cfe6ae4f5a162bf528bf3">add_bond_type_to_cif</a> (mmdb::mmcif::PLoop loop, int type)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a156f31d96da750c94e75880a12fd5523">DefineClass</a> (<a class="el" href="classccp4srs_1_1_bond.html">Bond</a>)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a50bab1a74a6f5ebde0253478a4964b24">_addAtomPair</a> (mmdb::PAtom a1, mmdb::PAtom a2, PAtomPair &amp;Pair, int &amp;nPairs, int &amp;nPAlloc)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#abe82012e7a8178ae1069f381769da72d">DefineClass</a> (<a class="el" href="classccp4srs_1_1_chem.html">Chem</a>)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#aed1b87fee568c115c3bbdb07ad9a5bd7">DefineClass</a> (<a class="el" href="classccp4srs_1_1_chi_center.html">ChiCenter</a>)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#aa72ee17a81ce821f1c37483a10153ae7">DefineClass</a> (<a class="el" href="classccp4srs_1_1_entry.html">Entry</a>)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#afeba477403b4f346ef1c74ab27c0a797">DefineClass</a> (<a class="el" href="classccp4srs_1_1_index.html">Index</a>)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a8c36728a6d09c1cb65fe3168735979cb">DefineClass</a> (<a class="el" href="classccp4srs_1_1_manager.html">Manager</a>)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#ab9a709bd669d7de2cf530774f80905c7">superpose_atoms</a> (mmdb::mat44 &amp;T, PPAtom A1, mmdb::PPAtom A2, int nAtoms, mmdb::rmatrix &amp;A, mmdb::rmatrix &amp;U, mmdb::rmatrix &amp;V, mmdb::rvector &amp;W, mmdb::rvector &amp;RV1)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a8b4dcaee4f20949271ceaadfb7b5a96f">makeElementType</a> (int ElType, char chirality)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#aea118bfa214275496e94e42beca05c35">DefineClass</a> (<a class="el" href="classccp4srs_1_1_monomer.html">Monomer</a>)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a299f5fc0ddc551524a80fe756cf2525d">DefineClass</a> (<a class="el" href="classccp4srs_1_1_plane.html">Plane</a>)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a3e61bdd34189f80843c0e565ce68e628">DefineClass</a> (<a class="el" href="classccp4srs_1_1_torsion.html">Torsion</a>)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a6d1229e1b71f24fdb95a8700d402c6f8">DefineClass</a> (<a class="el" href="classccp4srs_1_1_tree.html">Tree</a>)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a38fd31a76e47d65dbd8f9343fdc2f001">DefineStructure</a> (<a class="el" href="structccp4srs_1_1_atom_pair.html">AtomPair</a>)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#af0f84ef74e24251a016c6d27c196fe2e">DefineStructure</a> (<a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html">DASelHnds</a>)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a64bcbd2282ebaf1613021bf317bdf0cb">DefineClass</a> (<a class="el" href="classccp4srs_1_1_mem_i_o.html">MemIO</a>)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#aad79147ea920868ed625a8f693277d56">DefineStructure</a> (<a class="el" href="structccp4srs_1_1_m_p_file_pos.html">MPFilePos</a>)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#aed1408df12f28bc4a3dd772230255597">DefineClass</a> (MPFile) class MPFile</td></tr>
+<tr><td colspan="2"><h2><a name="var-members"></a>
+Variables</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">const int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a4938160ce6172269adc59b8077014f7c">CCP4SRS_file_version</a> = 2</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a3f27798432992515be969c17425412d3">srsIndexFile</a> = &quot;index.srs&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#a4132afa4ce21fdcd2ff268bf6e980cfc">srsGraphFile</a> = &quot;graph.srs&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::cpstr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#af51e5a096118e643d5fcf5490d44c6db">srsStructFile</a> = &quot;struct.srs&quot;</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">const int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceccp4srs.html#aa44a92ce883cd1c525381111cd1a4ab3">AtomID_NA</a> = -10000</td></tr>
+</table>
+<hr/><h2>Typedef Documentation</h2>
+<a class="anchor" id="ae91f970060d687d02ccfb78cbd6222bb"></a><!-- doxytag: member="ccp4srs::ChiCenterID" ref="ae91f970060d687d02ccfb78cbd6222bb" args="[20]" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">typedef char <a class="el" href="namespaceccp4srs.html#ae91f970060d687d02ccfb78cbd6222bb">ccp4srs::ChiCenterID</a>[20]</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ac768cc62149be89b81a30d88a09f0166"></a><!-- doxytag: member="ccp4srs::PlaneID" ref="ac768cc62149be89b81a30d88a09f0166" args="[20]" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">typedef char <a class="el" href="namespaceccp4srs.html#ac768cc62149be89b81a30d88a09f0166">ccp4srs::PlaneID</a>[20]</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a192f47d1deb71790866bce922f50bba1"></a><!-- doxytag: member="ccp4srs::TorsionID" ref="a192f47d1deb71790866bce922f50bba1" args="[20]" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">typedef char <a class="el" href="namespaceccp4srs.html#a192f47d1deb71790866bce922f50bba1">ccp4srs::TorsionID</a>[20]</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Enumeration Type Documentation</h2>
+<a class="anchor" id="a058dffb1d0d0c445ac789e7e7b15b84a"></a><!-- doxytag: member="ccp4srs::CCP4SRS_RC" ref="a058dffb1d0d0c445ac789e7e7b15b84a" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">enum <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">ccp4srs::CCP4SRS_RC</a></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+<dl><dt><b>Enumerator: </b></dt><dd><table border="0" cellspacing="2" cellpadding="0">
+<tr><td valign="top"><em><a class="anchor" id="a058dffb1d0d0c445ac789e7e7b15b84aa9f7a70887f053cb4ce97d321d477ac81"></a><!-- doxytag: member="CCP4SRS_noDonors" ref="a058dffb1d0d0c445ac789e7e7b15b84aa9f7a70887f053cb4ce97d321d477ac81" args="" -->CCP4SRS_noDonors</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a058dffb1d0d0c445ac789e7e7b15b84aa2d2f9ebfa39ac8c445aaa789d3f7d73c"></a><!-- doxytag: member="CCP4SRS_noAcceptors" ref="a058dffb1d0d0c445ac789e7e7b15b84aa2d2f9ebfa39ac8c445aaa789d3f7d73c" args="" -->CCP4SRS_noAcceptors</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a058dffb1d0d0c445ac789e7e7b15b84aae4c2a57f461a7c55fcdbf5f5256b633c"></a><!-- doxytag: member="CCP4SRS_noHBonds" ref="a058dffb1d0d0c445ac789e7e7b15b84aae4c2a57f461a7c55fcdbf5f5256b633c" args="" -->CCP4SRS_noHBonds</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a058dffb1d0d0c445ac789e7e7b15b84aa376037f37a8f3b5a5822abe08b8a2775"></a><!-- doxytag: member="CCP4SRS_Incomplete" ref="a058dffb1d0d0c445ac789e7e7b15b84aa376037f37a8f3b5a5822abe08b8a2775" args="" -->CCP4SRS_Incomplete</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a058dffb1d0d0c445ac789e7e7b15b84aa09553d9a0822e1b3ab31018c2a12cbbb"></a><!-- doxytag: member="CCP4SRS_Ok" ref="a058dffb1d0d0c445ac789e7e7b15b84aa09553d9a0822e1b3ab31018c2a12cbbb" args="" -->CCP4SRS_Ok</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a058dffb1d0d0c445ac789e7e7b15b84aa0f4cab4ac6672344d9c17addef3a5c2c"></a><!-- doxytag: member="CCP4SRS_WrongBondType" ref="a058dffb1d0d0c445ac789e7e7b15b84aa0f4cab4ac6672344d9c17addef3a5c2c" args="" -->CCP4SRS_WrongBondType</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a058dffb1d0d0c445ac789e7e7b15b84aa4513ed69439ddf6233fd9311675d3ec3"></a><!-- doxytag: member="CCP4SRS_IndexCorrupt" ref="a058dffb1d0d0c445ac789e7e7b15b84aa4513ed69439ddf6233fd9311675d3ec3" args="" -->CCP4SRS_IndexCorrupt</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a058dffb1d0d0c445ac789e7e7b15b84aaf8be04ede882dccdaab276915605e785"></a><!-- doxytag: member="CCP4SRS_FileNotFound" ref="a058dffb1d0d0c445ac789e7e7b15b84aaf8be04ede882dccdaab276915605e785" args="" -->CCP4SRS_FileNotFound</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a058dffb1d0d0c445ac789e7e7b15b84aa0f0128ede6fa588e9e90ab7d96e3395d"></a><!-- doxytag: member="CCP4SRS_EntryNotFound" ref="a058dffb1d0d0c445ac789e7e7b15b84aa0f0128ede6fa588e9e90ab7d96e3395d" args="" -->CCP4SRS_EntryNotFound</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a058dffb1d0d0c445ac789e7e7b15b84aa3f7eda4d59140c81cd5ca9224b569146"></a><!-- doxytag: member="CCP4SRS_ReadErrors" ref="a058dffb1d0d0c445ac789e7e7b15b84aa3f7eda4d59140c81cd5ca9224b569146" args="" -->CCP4SRS_ReadErrors</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a058dffb1d0d0c445ac789e7e7b15b84aacec935441561de176dbd7b29c608a960"></a><!-- doxytag: member="CCP4SRS_EmptyResidue" ref="a058dffb1d0d0c445ac789e7e7b15b84aacec935441561de176dbd7b29c608a960" args="" -->CCP4SRS_EmptyResidue</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a058dffb1d0d0c445ac789e7e7b15b84aa6ce76e69c4e7c9b8ae5f28fcb6279c13"></a><!-- doxytag: member="CCP4SRS_NoAtomsFound" ref="a058dffb1d0d0c445ac789e7e7b15b84aa6ce76e69c4e7c9b8ae5f28fcb6279c13" args="" -->CCP4SRS_NoAtomsFound</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a058dffb1d0d0c445ac789e7e7b15b84aaf41577d27e0b8306dc1dfaebbffe3a85"></a><!-- doxytag: member="CCP4SRS_NoBonds" ref="a058dffb1d0d0c445ac789e7e7b15b84aaf41577d27e0b8306dc1dfaebbffe3a85" args="" -->CCP4SRS_NoBonds</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a058dffb1d0d0c445ac789e7e7b15b84aa36de44e9555882901e32ff002491b4c1"></a><!-- doxytag: member="CCP4SRS_EmptyResSet" ref="a058dffb1d0d0c445ac789e7e7b15b84aa36de44e9555882901e32ff002491b4c1" args="" -->CCP4SRS_EmptyResSet</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a058dffb1d0d0c445ac789e7e7b15b84aa770346796e3fd0232458a3dd9709d735"></a><!-- doxytag: member="CCP4SRS_Fail" ref="a058dffb1d0d0c445ac789e7e7b15b84aa770346796e3fd0232458a3dd9709d735" args="" -->CCP4SRS_Fail</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a058dffb1d0d0c445ac789e7e7b15b84aafabbc088bd534a406ce2a155b7c7be34"></a><!-- doxytag: member="CCP4SRS_SVD_Fail" ref="a058dffb1d0d0c445ac789e7e7b15b84aafabbc088bd534a406ce2a155b7c7be34" args="" -->CCP4SRS_SVD_Fail</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a058dffb1d0d0c445ac789e7e7b15b84aa86978a692503eda1577d1250f402e4d4"></a><!-- doxytag: member="CCP4SRS_noCoordHierarchy" ref="a058dffb1d0d0c445ac789e7e7b15b84aa86978a692503eda1577d1250f402e4d4" args="" -->CCP4SRS_noCoordHierarchy</em>&nbsp;</td><td>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a058dffb1d0d0c445ac789e7e7b15b84aa785ce210fda24a93bd0df60e0a612698"></a><!-- doxytag: member="CCP4SRS_BrokenBonds" ref="a058dffb1d0d0c445ac789e7e7b15b84aa785ce210fda24a93bd0df60e0a612698" args="" -->CCP4SRS_BrokenBonds</em>&nbsp;</td><td>
+</td></tr>
+</table>
+</dd>
+</dl>
+
+</div>
+</div>
+<a class="anchor" id="a82cd9b00128081b168cca2ba2e3af40d"></a><!-- doxytag: member="ccp4srs::CCP4SRS_VERSION" ref="a82cd9b00128081b168cca2ba2e3af40d" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">enum <a class="el" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40d">ccp4srs::CCP4SRS_VERSION</a></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+<dl><dt><b>Enumerator: </b></dt><dd><table border="0" cellspacing="2" cellpadding="0">
+<tr><td valign="top"><em><a class="anchor" id="a82cd9b00128081b168cca2ba2e3af40da70b6b61e66afecc14062283f4ab22165"></a><!-- doxytag: member="MAJOR_VERSION" ref="a82cd9b00128081b168cca2ba2e3af40da70b6b61e66afecc14062283f4ab22165" args="" -->MAJOR_VERSION</em>&nbsp;</td><td>
+<p>major version </p>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a82cd9b00128081b168cca2ba2e3af40da629c96b840f87c056420011f99867b11"></a><!-- doxytag: member="MINOR_VERSION" ref="a82cd9b00128081b168cca2ba2e3af40da629c96b840f87c056420011f99867b11" args="" -->MINOR_VERSION</em>&nbsp;</td><td>
+<p>minor version </p>
+</td></tr>
+<tr><td valign="top"><em><a class="anchor" id="a82cd9b00128081b168cca2ba2e3af40dafef3f6fb9926961d5bb1c2c5f5464228"></a><!-- doxytag: member="MICRO_VERSION" ref="a82cd9b00128081b168cca2ba2e3af40dafef3f6fb9926961d5bb1c2c5f5464228" args="" -->MICRO_VERSION</em>&nbsp;</td><td>
+<p>micro version </p>
+</td></tr>
+</table>
+</dd>
+</dl>
+
+</div>
+</div>
+<hr/><h2>Function Documentation</h2>
+<a class="anchor" id="a50bab1a74a6f5ebde0253478a4964b24"></a><!-- doxytag: member="ccp4srs::_addAtomPair" ref="a50bab1a74a6f5ebde0253478a4964b24" args="(mmdb::PAtom a1, mmdb::PAtom a2, PAtomPair &amp;Pair, int &amp;nPairs, int &amp;nPAlloc)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::_addAtomPair </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::PAtom&#160;</td>
+          <td class="paramname"> <em>a1</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::PAtom&#160;</td>
+          <td class="paramname"> <em>a2</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">PAtomPair &amp;&#160;</td>
+          <td class="paramname"> <em>Pair</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>nPairs</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>nPAlloc</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="adf196969f21a33865d5f6c0f2f32cb7f"></a><!-- doxytag: member="ccp4srs::_findName" ref="adf196969f21a33865d5f6c0f2f32cb7f" args="(mmdb::PAtomName Nams, mmdb::cpstr N, int len)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::_findName </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::PAtomName&#160;</td>
+          <td class="paramname"> <em>Nams</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>N</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>len</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a99ea9b07a217ceb6c0645faaea831c82"></a><!-- doxytag: member="ccp4srs::_makeChirInd" ref="a99ea9b07a217ceb6c0645faaea831c82" args="(char chirality)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::_makeChirInd </td>
+          <td>(</td>
+          <td class="paramtype">char&#160;</td>
+          <td class="paramname"> <em>chirality</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="af3c63726e6eb75b06c5b1c33a3acb608"></a><!-- doxytag: member="ccp4srs::add_atom_to_cif" ref="af3c63726e6eb75b06c5b1c33a3acb608" args="(mmdb::mmcif::PLoop loop, int atom_no, Container&lt; Atom &gt; &amp;atoms)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::add_atom_to_cif </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>loop</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>atom_no</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">Container&lt; Atom &gt; &amp;&#160;</td>
+          <td class="paramname"> <em>atoms</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aaf4dd7dc419cfe6ae4f5a162bf528bf3"></a><!-- doxytag: member="ccp4srs::add_bond_type_to_cif" ref="aaf4dd7dc419cfe6ae4f5a162bf528bf3" args="(mmdb::mmcif::PLoop loop, int type)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::add_bond_type_to_cif </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>loop</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>type</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="afbb5df60616f08fcf36926a3585c185f"></a><!-- doxytag: member="ccp4srs::DefineClass" ref="afbb5df60616f08fcf36926a3585c185f" args="(Angle)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::DefineClass </td>
+          <td>(</td>
+          <td class="paramtype">Angle&#160;</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a4c159612746fffa9c8740ead5f891bb4"></a><!-- doxytag: member="ccp4srs::DefineClass" ref="a4c159612746fffa9c8740ead5f891bb4" args="(Base)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::DefineClass </td>
+          <td>(</td>
+          <td class="paramtype">Base&#160;</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aed1b87fee568c115c3bbdb07ad9a5bd7"></a><!-- doxytag: member="ccp4srs::DefineClass" ref="aed1b87fee568c115c3bbdb07ad9a5bd7" args="(ChiCenter)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::DefineClass </td>
+          <td>(</td>
+          <td class="paramtype">ChiCenter&#160;</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a299f5fc0ddc551524a80fe756cf2525d"></a><!-- doxytag: member="ccp4srs::DefineClass" ref="a299f5fc0ddc551524a80fe756cf2525d" args="(Plane)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::DefineClass </td>
+          <td>(</td>
+          <td class="paramtype">Plane&#160;</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aa72ee17a81ce821f1c37483a10153ae7"></a><!-- doxytag: member="ccp4srs::DefineClass" ref="aa72ee17a81ce821f1c37483a10153ae7" args="(Entry)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::DefineClass </td>
+          <td>(</td>
+          <td class="paramtype">Entry&#160;</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="afeba477403b4f346ef1c74ab27c0a797"></a><!-- doxytag: member="ccp4srs::DefineClass" ref="afeba477403b4f346ef1c74ab27c0a797" args="(Index)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::DefineClass </td>
+          <td>(</td>
+          <td class="paramtype">Index&#160;</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a8c36728a6d09c1cb65fe3168735979cb"></a><!-- doxytag: member="ccp4srs::DefineClass" ref="a8c36728a6d09c1cb65fe3168735979cb" args="(Manager)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::DefineClass </td>
+          <td>(</td>
+          <td class="paramtype">Manager&#160;</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aaacc6a8b59c08ac1bbfd9305ee663a1b"></a><!-- doxytag: member="ccp4srs::DefineClass" ref="aaacc6a8b59c08ac1bbfd9305ee663a1b" args="(Atom)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::DefineClass </td>
+          <td>(</td>
+          <td class="paramtype">Atom&#160;</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aea118bfa214275496e94e42beca05c35"></a><!-- doxytag: member="ccp4srs::DefineClass" ref="aea118bfa214275496e94e42beca05c35" args="(Monomer)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::DefineClass </td>
+          <td>(</td>
+          <td class="paramtype">Monomer&#160;</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a3e61bdd34189f80843c0e565ce68e628"></a><!-- doxytag: member="ccp4srs::DefineClass" ref="a3e61bdd34189f80843c0e565ce68e628" args="(Torsion)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::DefineClass </td>
+          <td>(</td>
+          <td class="paramtype">Torsion&#160;</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
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+          <td>(</td>
+          <td class="paramtype">Tree&#160;</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
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+        <tr>
+          <td class="memname">ccp4srs::DefineClass </td>
+          <td>(</td>
+          <td class="paramtype">Chem&#160;</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
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+</div>
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+        <tr>
+          <td class="memname">ccp4srs::DefineClass </td>
+          <td>(</td>
+          <td class="paramtype">MemIO&#160;</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a156f31d96da750c94e75880a12fd5523"></a><!-- doxytag: member="ccp4srs::DefineClass" ref="a156f31d96da750c94e75880a12fd5523" args="(Bond)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::DefineClass </td>
+          <td>(</td>
+          <td class="paramtype">Bond&#160;</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aed1408df12f28bc4a3dd772230255597"></a><!-- doxytag: member="ccp4srs::DefineClass" ref="aed1408df12f28bc4a3dd772230255597" args="(MPFile) class MPFile" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::DefineClass </td>
+          <td>(</td>
+          <td class="paramtype">MPFile&#160;</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aad79147ea920868ed625a8f693277d56"></a><!-- doxytag: member="ccp4srs::DefineStructure" ref="aad79147ea920868ed625a8f693277d56" args="(MPFilePos)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::DefineStructure </td>
+          <td>(</td>
+          <td class="paramtype">MPFilePos&#160;</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a38fd31a76e47d65dbd8f9343fdc2f001"></a><!-- doxytag: member="ccp4srs::DefineStructure" ref="a38fd31a76e47d65dbd8f9343fdc2f001" args="(AtomPair)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::DefineStructure </td>
+          <td>(</td>
+          <td class="paramtype">AtomPair&#160;</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="af0f84ef74e24251a016c6d27c196fe2e"></a><!-- doxytag: member="ccp4srs::DefineStructure" ref="af0f84ef74e24251a016c6d27c196fe2e" args="(DASelHnds)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">ccp4srs::DefineStructure </td>
+          <td>(</td>
+          <td class="paramtype">DASelHnds&#160;</td>
+          <td class="paramname">&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="adead0e638933d7d2949df9bb7b44f910"></a><!-- doxytag: member="ccp4srs::get_atom_from_cif" ref="adead0e638933d7d2949df9bb7b44f910" args="(int &amp;index, mmdb::mmcif::PLoop loop, mmdb::cpstr Tag, int row, Container&lt; Atom &gt; &amp;atoms, int &amp;rc)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::get_atom_from_cif </td>
+          <td>(</td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>index</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>loop</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>Tag</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>row</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">Container&lt; Atom &gt; &amp;&#160;</td>
+          <td class="paramname"> <em>atoms</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>rc</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a012e980439f3fcbb1844abf82ab2e95e"></a><!-- doxytag: member="ccp4srs::get_atom_from_cif" ref="a012e980439f3fcbb1844abf82ab2e95e" args="(int &amp;index, mmdb::mmcif::PStruct mmCIFStruct, mmdb::cpstr Tag, Container&lt; Atom &gt; &amp;atoms, int &amp;rc)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::get_atom_from_cif </td>
+          <td>(</td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>index</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::mmcif::PStruct&#160;</td>
+          <td class="paramname"> <em>mmCIFStruct</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>Tag</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">Container&lt; Atom &gt; &amp;&#160;</td>
+          <td class="paramname"> <em>atoms</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>rc</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a66b5a7cbf87409e898be86c84505275a"></a><!-- doxytag: member="ccp4srs::get_bond_type_from_cif" ref="a66b5a7cbf87409e898be86c84505275a" args="(int &amp;type, mmdb::mmcif::PStruct mmCIFStruct, mmdb::cpstr Tag, int &amp;rc)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::get_bond_type_from_cif </td>
+          <td>(</td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>type</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::mmcif::PStruct&#160;</td>
+          <td class="paramname"> <em>mmCIFStruct</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>Tag</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>rc</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a134be7dad55bde913e9bbb02825064e0"></a><!-- doxytag: member="ccp4srs::get_bond_type_from_cif_ccp4" ref="a134be7dad55bde913e9bbb02825064e0" args="(int &amp;type, mmdb::mmcif::PLoop loop, mmdb::cpstr Tag, int row, int &amp;rc)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::get_bond_type_from_cif_ccp4 </td>
+          <td>(</td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>type</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>loop</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>Tag</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>row</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>rc</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a2fc315dbfb7012f8e39ff3a2f440a5d6"></a><!-- doxytag: member="ccp4srs::get_bond_type_from_cif_rcsb" ref="a2fc315dbfb7012f8e39ff3a2f440a5d6" args="(int &amp;type, mmdb::mmcif::PLoop loop, mmdb::cpstr Tag, int row, int &amp;rc)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::get_bond_type_from_cif_rcsb </td>
+          <td>(</td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>type</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::mmcif::PLoop&#160;</td>
+          <td class="paramname"> <em>loop</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::cpstr&#160;</td>
+          <td class="paramname"> <em>Tag</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>row</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int &amp;&#160;</td>
+          <td class="paramname"> <em>rc</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a8b4dcaee4f20949271ceaadfb7b5a96f"></a><!-- doxytag: member="ccp4srs::makeElementType" ref="a8b4dcaee4f20949271ceaadfb7b5a96f" args="(int ElType, char chirality)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::makeElementType </td>
+          <td>(</td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>ElType</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">char&#160;</td>
+          <td class="paramname"> <em>chirality</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ab9a709bd669d7de2cf530774f80905c7"></a><!-- doxytag: member="ccp4srs::superpose_atoms" ref="ab9a709bd669d7de2cf530774f80905c7" args="(mmdb::mat44 &amp;T, PPAtom A1, mmdb::PPAtom A2, int nAtoms, mmdb::rmatrix &amp;A, mmdb::rmatrix &amp;U, mmdb::rmatrix &amp;V, mmdb::rvector &amp;W, mmdb::rvector &amp;RV1)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int ccp4srs::superpose_atoms </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::mat44 &amp;&#160;</td>
+          <td class="paramname"> <em>T</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">PPAtom&#160;</td>
+          <td class="paramname"> <em>A1</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::PPAtom&#160;</td>
+          <td class="paramname"> <em>A2</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">int&#160;</td>
+          <td class="paramname"> <em>nAtoms</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::rmatrix &amp;&#160;</td>
+          <td class="paramname"> <em>A</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::rmatrix &amp;&#160;</td>
+          <td class="paramname"> <em>U</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::rmatrix &amp;&#160;</td>
+          <td class="paramname"> <em>V</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::rvector &amp;&#160;</td>
+          <td class="paramname"> <em>W</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">mmdb::rvector &amp;&#160;</td>
+          <td class="paramname"> <em>RV1</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Variable Documentation</h2>
+<a class="anchor" id="aa44a92ce883cd1c525381111cd1a4ab3"></a><!-- doxytag: member="ccp4srs::AtomID_NA" ref="aa44a92ce883cd1c525381111cd1a4ab3" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">const int <a class="el" href="namespaceccp4srs.html#aa44a92ce883cd1c525381111cd1a4ab3">ccp4srs::AtomID_NA</a> = -10000</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a4938160ce6172269adc59b8077014f7c"></a><!-- doxytag: member="ccp4srs::CCP4SRS_file_version" ref="a4938160ce6172269adc59b8077014f7c" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">const int <a class="el" href="namespaceccp4srs.html#a4938160ce6172269adc59b8077014f7c">ccp4srs::CCP4SRS_file_version</a> = 2</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a4132afa4ce21fdcd2ff268bf6e980cfc"></a><!-- doxytag: member="ccp4srs::srsGraphFile" ref="a4132afa4ce21fdcd2ff268bf6e980cfc" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::cpstr <a class="el" href="namespaceccp4srs.html#a4132afa4ce21fdcd2ff268bf6e980cfc">ccp4srs::srsGraphFile</a> = &quot;graph.srs&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a3f27798432992515be969c17425412d3"></a><!-- doxytag: member="ccp4srs::srsIndexFile" ref="a3f27798432992515be969c17425412d3" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::cpstr <a class="el" href="namespaceccp4srs.html#a3f27798432992515be969c17425412d3">ccp4srs::srsIndexFile</a> = &quot;index.srs&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="af51e5a096118e643d5fcf5490d44c6db"></a><!-- doxytag: member="ccp4srs::srsStructFile" ref="af51e5a096118e643d5fcf5490d44c6db" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::cpstr <a class="el" href="namespaceccp4srs.html#af51e5a096118e643d5fcf5490d44c6db">ccp4srs::srsStructFile</a> = &quot;struct.srs&quot;</td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/namespacemembers.html ccp4srs/doc-html/html/namespacemembers.html
--- ccp4srs-old/doc-html/html/namespacemembers.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/namespacemembers.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,259 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li class="current"><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="namespaces.html"><span>Namespace&#160;List</span></a></li>
+      <li class="current"><a href="namespacemembers.html"><span>Namespace&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="namespacemembers.html"><span>All</span></a></li>
+      <li><a href="namespacemembers_func.html"><span>Functions</span></a></li>
+      <li><a href="namespacemembers_vars.html"><span>Variables</span></a></li>
+      <li><a href="namespacemembers_type.html"><span>Typedefs</span></a></li>
+      <li><a href="namespacemembers_enum.html"><span>Enumerations</span></a></li>
+      <li><a href="namespacemembers_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs3">
+    <ul class="tablist">
+      <li><a href="#index__"><span>_</span></a></li>
+      <li><a href="#index_a"><span>a</span></a></li>
+      <li><a href="#index_c"><span>c</span></a></li>
+      <li><a href="#index_d"><span>d</span></a></li>
+      <li><a href="#index_g"><span>g</span></a></li>
+      <li><a href="#index_m"><span>m</span></a></li>
+      <li><a href="#index_p"><span>p</span></a></li>
+      <li><a href="#index_s"><span>s</span></a></li>
+      <li><a href="#index_t"><span>t</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+Here is a list of all namespace members with links to the namespace documentation for each member:
+
+<h3><a class="anchor" id="index__"></a>- _ -</h3><ul>
+<li>_addAtomPair()
+: <a class="el" href="namespaceccp4srs.html#a50bab1a74a6f5ebde0253478a4964b24">ccp4srs</a>
+</li>
+<li>_findName()
+: <a class="el" href="namespaceccp4srs.html#adf196969f21a33865d5f6c0f2f32cb7f">ccp4srs</a>
+</li>
+<li>_makeChirInd()
+: <a class="el" href="namespaceccp4srs.html#a99ea9b07a217ceb6c0645faaea831c82">ccp4srs</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_a"></a>- a -</h3><ul>
+<li>add_atom_to_cif()
+: <a class="el" href="namespaceccp4srs.html#af3c63726e6eb75b06c5b1c33a3acb608">ccp4srs</a>
+</li>
+<li>add_bond_type_to_cif()
+: <a class="el" href="namespaceccp4srs.html#aaf4dd7dc419cfe6ae4f5a162bf528bf3">ccp4srs</a>
+</li>
+<li>AtomID_NA
+: <a class="el" href="namespaceccp4srs.html#aa44a92ce883cd1c525381111cd1a4ab3">ccp4srs</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_c"></a>- c -</h3><ul>
+<li>CCP4SRS_BrokenBonds
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa785ce210fda24a93bd0df60e0a612698">ccp4srs</a>
+</li>
+<li>CCP4SRS_EmptyResidue
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aacec935441561de176dbd7b29c608a960">ccp4srs</a>
+</li>
+<li>CCP4SRS_EmptyResSet
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa36de44e9555882901e32ff002491b4c1">ccp4srs</a>
+</li>
+<li>CCP4SRS_EntryNotFound
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa0f0128ede6fa588e9e90ab7d96e3395d">ccp4srs</a>
+</li>
+<li>CCP4SRS_Fail
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa770346796e3fd0232458a3dd9709d735">ccp4srs</a>
+</li>
+<li>CCP4SRS_file_version
+: <a class="el" href="namespaceccp4srs.html#a4938160ce6172269adc59b8077014f7c">ccp4srs</a>
+</li>
+<li>CCP4SRS_FileNotFound
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aaf8be04ede882dccdaab276915605e785">ccp4srs</a>
+</li>
+<li>CCP4SRS_Incomplete
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa376037f37a8f3b5a5822abe08b8a2775">ccp4srs</a>
+</li>
+<li>CCP4SRS_IndexCorrupt
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa4513ed69439ddf6233fd9311675d3ec3">ccp4srs</a>
+</li>
+<li>CCP4SRS_noAcceptors
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa2d2f9ebfa39ac8c445aaa789d3f7d73c">ccp4srs</a>
+</li>
+<li>CCP4SRS_NoAtomsFound
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa6ce76e69c4e7c9b8ae5f28fcb6279c13">ccp4srs</a>
+</li>
+<li>CCP4SRS_NoBonds
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aaf41577d27e0b8306dc1dfaebbffe3a85">ccp4srs</a>
+</li>
+<li>CCP4SRS_noCoordHierarchy
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa86978a692503eda1577d1250f402e4d4">ccp4srs</a>
+</li>
+<li>CCP4SRS_noDonors
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa9f7a70887f053cb4ce97d321d477ac81">ccp4srs</a>
+</li>
+<li>CCP4SRS_noHBonds
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aae4c2a57f461a7c55fcdbf5f5256b633c">ccp4srs</a>
+</li>
+<li>CCP4SRS_Ok
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa09553d9a0822e1b3ab31018c2a12cbbb">ccp4srs</a>
+</li>
+<li>CCP4SRS_RC
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">ccp4srs</a>
+</li>
+<li>CCP4SRS_ReadErrors
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa3f7eda4d59140c81cd5ca9224b569146">ccp4srs</a>
+</li>
+<li>CCP4SRS_SVD_Fail
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aafabbc088bd534a406ce2a155b7c7be34">ccp4srs</a>
+</li>
+<li>CCP4SRS_VERSION
+: <a class="el" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40d">ccp4srs</a>
+</li>
+<li>CCP4SRS_WrongBondType
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa0f4cab4ac6672344d9c17addef3a5c2c">ccp4srs</a>
+</li>
+<li>ChiCenterID
+: <a class="el" href="namespaceccp4srs.html#ae91f970060d687d02ccfb78cbd6222bb">ccp4srs</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_d"></a>- d -</h3><ul>
+<li>DefineClass()
+: <a class="el" href="namespaceccp4srs.html#afbb5df60616f08fcf36926a3585c185f">ccp4srs</a>
+</li>
+<li>DefineStructure()
+: <a class="el" href="namespaceccp4srs.html#a38fd31a76e47d65dbd8f9343fdc2f001">ccp4srs</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_g"></a>- g -</h3><ul>
+<li>get_atom_from_cif()
+: <a class="el" href="namespaceccp4srs.html#adead0e638933d7d2949df9bb7b44f910">ccp4srs</a>
+</li>
+<li>get_bond_type_from_cif()
+: <a class="el" href="namespaceccp4srs.html#a66b5a7cbf87409e898be86c84505275a">ccp4srs</a>
+</li>
+<li>get_bond_type_from_cif_ccp4()
+: <a class="el" href="namespaceccp4srs.html#a134be7dad55bde913e9bbb02825064e0">ccp4srs</a>
+</li>
+<li>get_bond_type_from_cif_rcsb()
+: <a class="el" href="namespaceccp4srs.html#a2fc315dbfb7012f8e39ff3a2f440a5d6">ccp4srs</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_m"></a>- m -</h3><ul>
+<li>MAJOR_VERSION
+: <a class="el" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40da70b6b61e66afecc14062283f4ab22165">ccp4srs</a>
+</li>
+<li>makeElementType()
+: <a class="el" href="namespaceccp4srs.html#a8b4dcaee4f20949271ceaadfb7b5a96f">ccp4srs</a>
+</li>
+<li>MICRO_VERSION
+: <a class="el" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40dafef3f6fb9926961d5bb1c2c5f5464228">ccp4srs</a>
+</li>
+<li>MINOR_VERSION
+: <a class="el" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40da629c96b840f87c056420011f99867b11">ccp4srs</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_p"></a>- p -</h3><ul>
+<li>PlaneID
+: <a class="el" href="namespaceccp4srs.html#ac768cc62149be89b81a30d88a09f0166">ccp4srs</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_s"></a>- s -</h3><ul>
+<li>srsGraphFile
+: <a class="el" href="namespaceccp4srs.html#a4132afa4ce21fdcd2ff268bf6e980cfc">ccp4srs</a>
+</li>
+<li>srsIndexFile
+: <a class="el" href="namespaceccp4srs.html#a3f27798432992515be969c17425412d3">ccp4srs</a>
+</li>
+<li>srsStructFile
+: <a class="el" href="namespaceccp4srs.html#af51e5a096118e643d5fcf5490d44c6db">ccp4srs</a>
+</li>
+<li>superpose_atoms()
+: <a class="el" href="namespaceccp4srs.html#ab9a709bd669d7de2cf530774f80905c7">ccp4srs</a>
+</li>
+</ul>
+
+
+<h3><a class="anchor" id="index_t"></a>- t -</h3><ul>
+<li>TorsionID
+: <a class="el" href="namespaceccp4srs.html#a192f47d1deb71790866bce922f50bba1">ccp4srs</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/namespacemembers_enum.html ccp4srs/doc-html/html/namespacemembers_enum.html
--- ccp4srs-old/doc-html/html/namespacemembers_enum.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/namespacemembers_enum.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,86 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li class="current"><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="namespaces.html"><span>Namespace&#160;List</span></a></li>
+      <li class="current"><a href="namespacemembers.html"><span>Namespace&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="namespacemembers.html"><span>All</span></a></li>
+      <li><a href="namespacemembers_func.html"><span>Functions</span></a></li>
+      <li><a href="namespacemembers_vars.html"><span>Variables</span></a></li>
+      <li><a href="namespacemembers_type.html"><span>Typedefs</span></a></li>
+      <li class="current"><a href="namespacemembers_enum.html"><span>Enumerations</span></a></li>
+      <li><a href="namespacemembers_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;<ul>
+<li>CCP4SRS_RC
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a">ccp4srs</a>
+</li>
+<li>CCP4SRS_VERSION
+: <a class="el" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40d">ccp4srs</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/namespacemembers_eval.html ccp4srs/doc-html/html/namespacemembers_eval.html
--- ccp4srs-old/doc-html/html/namespacemembers_eval.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/namespacemembers_eval.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,143 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li class="current"><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="namespaces.html"><span>Namespace&#160;List</span></a></li>
+      <li class="current"><a href="namespacemembers.html"><span>Namespace&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="namespacemembers.html"><span>All</span></a></li>
+      <li><a href="namespacemembers_func.html"><span>Functions</span></a></li>
+      <li><a href="namespacemembers_vars.html"><span>Variables</span></a></li>
+      <li><a href="namespacemembers_type.html"><span>Typedefs</span></a></li>
+      <li><a href="namespacemembers_enum.html"><span>Enumerations</span></a></li>
+      <li class="current"><a href="namespacemembers_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;<ul>
+<li>CCP4SRS_BrokenBonds
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa785ce210fda24a93bd0df60e0a612698">ccp4srs</a>
+</li>
+<li>CCP4SRS_EmptyResidue
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aacec935441561de176dbd7b29c608a960">ccp4srs</a>
+</li>
+<li>CCP4SRS_EmptyResSet
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa36de44e9555882901e32ff002491b4c1">ccp4srs</a>
+</li>
+<li>CCP4SRS_EntryNotFound
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa0f0128ede6fa588e9e90ab7d96e3395d">ccp4srs</a>
+</li>
+<li>CCP4SRS_Fail
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa770346796e3fd0232458a3dd9709d735">ccp4srs</a>
+</li>
+<li>CCP4SRS_FileNotFound
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aaf8be04ede882dccdaab276915605e785">ccp4srs</a>
+</li>
+<li>CCP4SRS_Incomplete
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa376037f37a8f3b5a5822abe08b8a2775">ccp4srs</a>
+</li>
+<li>CCP4SRS_IndexCorrupt
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa4513ed69439ddf6233fd9311675d3ec3">ccp4srs</a>
+</li>
+<li>CCP4SRS_noAcceptors
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa2d2f9ebfa39ac8c445aaa789d3f7d73c">ccp4srs</a>
+</li>
+<li>CCP4SRS_NoAtomsFound
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa6ce76e69c4e7c9b8ae5f28fcb6279c13">ccp4srs</a>
+</li>
+<li>CCP4SRS_NoBonds
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aaf41577d27e0b8306dc1dfaebbffe3a85">ccp4srs</a>
+</li>
+<li>CCP4SRS_noCoordHierarchy
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa86978a692503eda1577d1250f402e4d4">ccp4srs</a>
+</li>
+<li>CCP4SRS_noDonors
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa9f7a70887f053cb4ce97d321d477ac81">ccp4srs</a>
+</li>
+<li>CCP4SRS_noHBonds
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aae4c2a57f461a7c55fcdbf5f5256b633c">ccp4srs</a>
+</li>
+<li>CCP4SRS_Ok
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa09553d9a0822e1b3ab31018c2a12cbbb">ccp4srs</a>
+</li>
+<li>CCP4SRS_ReadErrors
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa3f7eda4d59140c81cd5ca9224b569146">ccp4srs</a>
+</li>
+<li>CCP4SRS_SVD_Fail
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aafabbc088bd534a406ce2a155b7c7be34">ccp4srs</a>
+</li>
+<li>CCP4SRS_WrongBondType
+: <a class="el" href="namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa0f4cab4ac6672344d9c17addef3a5c2c">ccp4srs</a>
+</li>
+<li>MAJOR_VERSION
+: <a class="el" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40da70b6b61e66afecc14062283f4ab22165">ccp4srs</a>
+</li>
+<li>MICRO_VERSION
+: <a class="el" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40dafef3f6fb9926961d5bb1c2c5f5464228">ccp4srs</a>
+</li>
+<li>MINOR_VERSION
+: <a class="el" href="namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40da629c96b840f87c056420011f99867b11">ccp4srs</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/namespacemembers_func.html ccp4srs/doc-html/html/namespacemembers_func.html
--- ccp4srs-old/doc-html/html/namespacemembers_func.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/namespacemembers_func.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,119 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li class="current"><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="namespaces.html"><span>Namespace&#160;List</span></a></li>
+      <li class="current"><a href="namespacemembers.html"><span>Namespace&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="namespacemembers.html"><span>All</span></a></li>
+      <li class="current"><a href="namespacemembers_func.html"><span>Functions</span></a></li>
+      <li><a href="namespacemembers_vars.html"><span>Variables</span></a></li>
+      <li><a href="namespacemembers_type.html"><span>Typedefs</span></a></li>
+      <li><a href="namespacemembers_enum.html"><span>Enumerations</span></a></li>
+      <li><a href="namespacemembers_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;<ul>
+<li>_addAtomPair()
+: <a class="el" href="namespaceccp4srs.html#a50bab1a74a6f5ebde0253478a4964b24">ccp4srs</a>
+</li>
+<li>_findName()
+: <a class="el" href="namespaceccp4srs.html#adf196969f21a33865d5f6c0f2f32cb7f">ccp4srs</a>
+</li>
+<li>_makeChirInd()
+: <a class="el" href="namespaceccp4srs.html#a99ea9b07a217ceb6c0645faaea831c82">ccp4srs</a>
+</li>
+<li>add_atom_to_cif()
+: <a class="el" href="namespaceccp4srs.html#af3c63726e6eb75b06c5b1c33a3acb608">ccp4srs</a>
+</li>
+<li>add_bond_type_to_cif()
+: <a class="el" href="namespaceccp4srs.html#aaf4dd7dc419cfe6ae4f5a162bf528bf3">ccp4srs</a>
+</li>
+<li>DefineClass()
+: <a class="el" href="namespaceccp4srs.html#afbb5df60616f08fcf36926a3585c185f">ccp4srs</a>
+</li>
+<li>DefineStructure()
+: <a class="el" href="namespaceccp4srs.html#a38fd31a76e47d65dbd8f9343fdc2f001">ccp4srs</a>
+</li>
+<li>get_atom_from_cif()
+: <a class="el" href="namespaceccp4srs.html#adead0e638933d7d2949df9bb7b44f910">ccp4srs</a>
+</li>
+<li>get_bond_type_from_cif()
+: <a class="el" href="namespaceccp4srs.html#a66b5a7cbf87409e898be86c84505275a">ccp4srs</a>
+</li>
+<li>get_bond_type_from_cif_ccp4()
+: <a class="el" href="namespaceccp4srs.html#a134be7dad55bde913e9bbb02825064e0">ccp4srs</a>
+</li>
+<li>get_bond_type_from_cif_rcsb()
+: <a class="el" href="namespaceccp4srs.html#a2fc315dbfb7012f8e39ff3a2f440a5d6">ccp4srs</a>
+</li>
+<li>makeElementType()
+: <a class="el" href="namespaceccp4srs.html#a8b4dcaee4f20949271ceaadfb7b5a96f">ccp4srs</a>
+</li>
+<li>superpose_atoms()
+: <a class="el" href="namespaceccp4srs.html#ab9a709bd669d7de2cf530774f80905c7">ccp4srs</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/namespacemembers_type.html ccp4srs/doc-html/html/namespacemembers_type.html
--- ccp4srs-old/doc-html/html/namespacemembers_type.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/namespacemembers_type.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,89 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li class="current"><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="namespaces.html"><span>Namespace&#160;List</span></a></li>
+      <li class="current"><a href="namespacemembers.html"><span>Namespace&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="namespacemembers.html"><span>All</span></a></li>
+      <li><a href="namespacemembers_func.html"><span>Functions</span></a></li>
+      <li><a href="namespacemembers_vars.html"><span>Variables</span></a></li>
+      <li class="current"><a href="namespacemembers_type.html"><span>Typedefs</span></a></li>
+      <li><a href="namespacemembers_enum.html"><span>Enumerations</span></a></li>
+      <li><a href="namespacemembers_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;<ul>
+<li>ChiCenterID
+: <a class="el" href="namespaceccp4srs.html#ae91f970060d687d02ccfb78cbd6222bb">ccp4srs</a>
+</li>
+<li>PlaneID
+: <a class="el" href="namespaceccp4srs.html#ac768cc62149be89b81a30d88a09f0166">ccp4srs</a>
+</li>
+<li>TorsionID
+: <a class="el" href="namespaceccp4srs.html#a192f47d1deb71790866bce922f50bba1">ccp4srs</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/namespacemembers_vars.html ccp4srs/doc-html/html/namespacemembers_vars.html
--- ccp4srs-old/doc-html/html/namespacemembers_vars.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/namespacemembers_vars.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,95 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li class="current"><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
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+        <span class="left">
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+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
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+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="namespaces.html"><span>Namespace&#160;List</span></a></li>
+      <li class="current"><a href="namespacemembers.html"><span>Namespace&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="namespacemembers.html"><span>All</span></a></li>
+      <li><a href="namespacemembers_func.html"><span>Functions</span></a></li>
+      <li class="current"><a href="namespacemembers_vars.html"><span>Variables</span></a></li>
+      <li><a href="namespacemembers_type.html"><span>Typedefs</span></a></li>
+      <li><a href="namespacemembers_enum.html"><span>Enumerations</span></a></li>
+      <li><a href="namespacemembers_eval.html"><span>Enumerator</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="contents">
+&#160;<ul>
+<li>AtomID_NA
+: <a class="el" href="namespaceccp4srs.html#aa44a92ce883cd1c525381111cd1a4ab3">ccp4srs</a>
+</li>
+<li>CCP4SRS_file_version
+: <a class="el" href="namespaceccp4srs.html#a4938160ce6172269adc59b8077014f7c">ccp4srs</a>
+</li>
+<li>srsGraphFile
+: <a class="el" href="namespaceccp4srs.html#a4132afa4ce21fdcd2ff268bf6e980cfc">ccp4srs</a>
+</li>
+<li>srsIndexFile
+: <a class="el" href="namespaceccp4srs.html#a3f27798432992515be969c17425412d3">ccp4srs</a>
+</li>
+<li>srsStructFile
+: <a class="el" href="namespaceccp4srs.html#af51e5a096118e643d5fcf5490d44c6db">ccp4srs</a>
+</li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/namespaces.html ccp4srs/doc-html/html/namespaces.html
--- ccp4srs-old/doc-html/html/namespaces.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/namespaces.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,75 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Namespace Index</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li class="current"><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
+          </span><span class="right">
+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li class="current"><a href="namespaces.html"><span>Namespace&#160;List</span></a></li>
+      <li><a href="namespacemembers.html"><span>Namespace&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>Namespace List</h1>  </div>
+</div>
+<div class="contents">
+Here is a list of all namespaces with brief descriptions:<table>
+  <tr><td class="indexkey"><a class="el" href="namespaceccp4srs.html">ccp4srs</a></td><td class="indexvalue"></td></tr>
+</table>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="" frameborder="0" 
+        name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
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--- ccp4srs-old/doc-html/html/search/all_5f.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_5f.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,38 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR__5faddatompair">
+ <div class="SREntry">
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+  <span class="SRScope">ccp4srs</span>
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+  <span class="SRScope">ccp4srs</span>
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+  <span class="SRScope">ccp4srs</span>
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+</div>
+</body>
+</html>
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--- ccp4srs-old/doc-html/html/search/all_61.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_61.html	2014-09-09 21:34:12.000000000 -0700
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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_a1">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../structccp4srs_1_1_atom_pair.html#a0277f099acfa557ac20bf6fd3320bcaa" target="_parent">a1</a>
+  <span class="SRScope">ccp4srs::AtomPair</span>
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+ <div class="SREntry">
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+  <span class="SRScope">ccp4srs::AtomPair</span>
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+<div class="SRResult" id="SR_add">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_add')">add</a>
+  <div class="SRChildren">
+    <a id="Item2_c0" onkeydown="return searchResults.NavChild(event,2,0)" onkeypress="return searchResults.NavChild(event,2,0)" onkeyup="return searchResults.NavChild(event,2,0)" class="SRScope" href="../classccp4srs_1_1_container.html#a6caf1893b780f2cf196c85ee141baf18" target="_parent">ccp4srs::Container::add()</a>
+    <a id="Item2_c1" onkeydown="return searchResults.NavChild(event,2,1)" onkeypress="return searchResults.NavChild(event,2,1)" onkeyup="return searchResults.NavChild(event,2,1)" class="SRScope" href="../classccp4srs_1_1_monomer.html#ae1c9221ebd49b62830621cd40524d215" target="_parent">ccp4srs::Monomer::add(PAtom atom)</a>
+    <a id="Item2_c2" onkeydown="return searchResults.NavChild(event,2,2)" onkeypress="return searchResults.NavChild(event,2,2)" onkeyup="return searchResults.NavChild(event,2,2)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a88d4f2d1f97364930fed4bf349b23cb1" target="_parent">ccp4srs::Monomer::add(PBond bond)</a>
+    <a id="Item2_c3" onkeydown="return searchResults.NavChild(event,2,3)" onkeypress="return searchResults.NavChild(event,2,3)" onkeyup="return searchResults.NavChild(event,2,3)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a3eab75471f83c2c92834a1e30400642e" target="_parent">ccp4srs::Monomer::add(PAngle angle)</a>
+    <a id="Item2_c4" onkeydown="return searchResults.NavChild(event,2,4)" onkeypress="return searchResults.NavChild(event,2,4)" onkeyup="return searchResults.NavChild(event,2,4)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a394b2b32b99cd3c6e0b3654593436a2f" target="_parent">ccp4srs::Monomer::add(PPlane plane)</a>
+    <a id="Item2_c5" onkeydown="return searchResults.NavChild(event,2,5)" onkeypress="return searchResults.NavChild(event,2,5)" onkeyup="return searchResults.NavChild(event,2,5)" class="SRScope" href="../classccp4srs_1_1_monomer.html#acdfa8628139cfb914f2aecdb1e2f37d2" target="_parent">ccp4srs::Monomer::add(PTree stree)</a>
+    <a id="Item2_c6" onkeydown="return searchResults.NavChild(event,2,6)" onkeypress="return searchResults.NavChild(event,2,6)" onkeyup="return searchResults.NavChild(event,2,6)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a555cba2de4ecd6d3d7c192a52a9d44a3" target="_parent">ccp4srs::Monomer::add(PTorsion torsion)</a>
+    <a id="Item2_c7" onkeydown="return searchResults.NavChild(event,2,7)" onkeypress="return searchResults.NavChild(event,2,7)" onkeyup="return searchResults.NavChild(event,2,7)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a1820529a0bee358372e53ea0fb0c0a56" target="_parent">ccp4srs::Monomer::add(PChiCenter chicenter)</a>
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+<div class="SRResult" id="SR_add_5fatom_5fto_5fcif">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../namespaceccp4srs.html#af3c63726e6eb75b06c5b1c33a3acb608" target="_parent">add_atom_to_cif</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_add_5fbond_5ftype_5fto_5fcif">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../namespaceccp4srs.html#aaf4dd7dc419cfe6ae4f5a162bf528bf3" target="_parent">add_bond_type_to_cif</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_addhydrogens">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_addhydrogens')">addHydrogens</a>
+  <div class="SRChildren">
+    <a id="Item5_c0" onkeydown="return searchResults.NavChild(event,5,0)" onkeypress="return searchResults.NavChild(event,5,0)" onkeyup="return searchResults.NavChild(event,5,0)" class="SRScope" href="../classccp4srs_1_1_chem.html#acada705ca803ac2b68bb2c787a83fcb1" target="_parent">ccp4srs::Chem::addHydrogens(mmdb::PResidue R, mmdb::io::PFile structFile)</a>
+    <a id="Item5_c1" onkeydown="return searchResults.NavChild(event,5,1)" onkeypress="return searchResults.NavChild(event,5,1)" onkeyup="return searchResults.NavChild(event,5,1)" class="SRScope" href="../classccp4srs_1_1_chem.html#ac1ae2d0c6f7f79b3f5b02a6a3b082b81" target="_parent">ccp4srs::Chem::addHydrogens(mmdb::PChain chain, mmdb::io::PFile structFile)</a>
+    <a id="Item5_c2" onkeydown="return searchResults.NavChild(event,5,2)" onkeypress="return searchResults.NavChild(event,5,2)" onkeyup="return searchResults.NavChild(event,5,2)" class="SRScope" href="../classccp4srs_1_1_chem.html#a75fb480c106432f52d7301eae93d2942" target="_parent">ccp4srs::Chem::addHydrogens(mmdb::PModel model, mmdb::io::PFile structFile)</a>
+    <a id="Item5_c3" onkeydown="return searchResults.NavChild(event,5,3)" onkeypress="return searchResults.NavChild(event,5,3)" onkeyup="return searchResults.NavChild(event,5,3)" class="SRScope" href="../classccp4srs_1_1_chem.html#a45ea7718ea3dea244ba51f6f318d3623" target="_parent">ccp4srs::Chem::addHydrogens(mmdb::PManager MMDB, mmdb::io::PFile structFile)</a>
+    <a id="Item5_c4" onkeydown="return searchResults.NavChild(event,5,4)" onkeypress="return searchResults.NavChild(event,5,4)" onkeyup="return searchResults.NavChild(event,5,4)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a67a965eb782472588f1a5f4e693c509e" target="_parent">ccp4srs::Monomer::addHydrogens()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_angle">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_angle')">Angle</a>
+  <div class="SRChildren">
+    <a id="Item6_c0" onkeydown="return searchResults.NavChild(event,6,0)" onkeypress="return searchResults.NavChild(event,6,0)" onkeyup="return searchResults.NavChild(event,6,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a5ec6da380214e7100ff46e3e79898e15" target="_parent">ccp4srs::Angle::Angle()</a>
+    <a id="Item6_c1" onkeydown="return searchResults.NavChild(event,6,1)" onkeypress="return searchResults.NavChild(event,6,1)" onkeyup="return searchResults.NavChild(event,6,1)" class="SRScope" href="../classccp4srs_1_1_angle.html#abf55314566cb2fa1d3764d0485284113" target="_parent">ccp4srs::Angle::angle()</a>
+    <a id="Item6_c2" onkeydown="return searchResults.NavChild(event,6,2)" onkeypress="return searchResults.NavChild(event,6,2)" onkeyup="return searchResults.NavChild(event,6,2)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a61b179edff80a9d168997038093cc92f" target="_parent">ccp4srs::Monomer::angle()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_angle">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_angle.html" target="_parent">Angle</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_angle_5fesd">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="../classccp4srs_1_1_angle.html#a39e05de948ddbf9c944bf0b14123caf8" target="_parent">angle_esd</a>
+  <span class="SRScope">ccp4srs::Angle</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_angles">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a9177ec12ea5aeaa59228831d4127e592" target="_parent">angles</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_aromatic">
+ <div class="SREntry">
+  <a id="Item10" onkeydown="return searchResults.Nav(event,10)" onkeypress="return searchResults.Nav(event,10)" onkeyup="return searchResults.Nav(event,10)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba1511fd16010981add30c1e054980f193" target="_parent">Aromatic</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_at">
+ <div class="SREntry">
+  <a id="Item11" onkeydown="return searchResults.Nav(event,11)" onkeypress="return searchResults.Nav(event,11)" onkeyup="return searchResults.Nav(event,11)" class="SRSymbol" href="../classccp4srs_1_1_container.html#ae9929d576289dd2313aaf4b2d9c377e9" target="_parent">at</a>
+  <span class="SRScope">ccp4srs::Container</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom">
+ <div class="SREntry">
+  <a id="Item12" onkeydown="return searchResults.Nav(event,12)" onkeypress="return searchResults.Nav(event,12)" onkeyup="return searchResults.Nav(event,12)" class="SRSymbol" href="../classccp4srs_1_1_atom.html" target="_parent">Atom</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom">
+ <div class="SREntry">
+  <a id="Item13" onkeydown="return searchResults.Nav(event,13)" onkeypress="return searchResults.Nav(event,13)" onkeyup="return searchResults.Nav(event,13)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_atom')">atom</a>
+  <div class="SRChildren">
+    <a id="Item13_c0" onkeydown="return searchResults.NavChild(event,13,0)" onkeypress="return searchResults.NavChild(event,13,0)" onkeyup="return searchResults.NavChild(event,13,0)" class="SRScope" href="../classccp4srs_1_1_monomer.html#ac3492a092c5436d182acae9b6712da7f" target="_parent">ccp4srs::Monomer::atom()</a>
+    <a id="Item13_c1" onkeydown="return searchResults.NavChild(event,13,1)" onkeypress="return searchResults.NavChild(event,13,1)" onkeyup="return searchResults.NavChild(event,13,1)" class="SRScope" href="../classccp4srs_1_1_plane.html#ad1e544c70729b5a17dba23301ba6ca7e" target="_parent">ccp4srs::Plane::atom()</a>
+    <a id="Item13_c2" onkeydown="return searchResults.NavChild(event,13,2)" onkeypress="return searchResults.NavChild(event,13,2)" onkeyup="return searchResults.NavChild(event,13,2)" class="SRScope" href="../classccp4srs_1_1_tree.html#aa05e210175e281b0b975b22040cbf45d" target="_parent">ccp4srs::Tree::atom()</a>
+    <a id="Item13_c3" onkeydown="return searchResults.NavChild(event,13,3)" onkeypress="return searchResults.NavChild(event,13,3)" onkeyup="return searchResults.NavChild(event,13,3)" class="SRScope" href="../classccp4srs_1_1_atom.html#a66084d9a746b51608e8f0f8e28138e9d" target="_parent">ccp4srs::Atom::Atom()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom1">
+ <div class="SREntry">
+  <a id="Item14" onkeydown="return searchResults.Nav(event,14)" onkeypress="return searchResults.Nav(event,14)" onkeyup="return searchResults.Nav(event,14)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_atom1')">atom1</a>
+  <div class="SRChildren">
+    <a id="Item14_c0" onkeydown="return searchResults.NavChild(event,14,0)" onkeypress="return searchResults.NavChild(event,14,0)" onkeyup="return searchResults.NavChild(event,14,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a64770743097878619e8dccf787f93802" target="_parent">ccp4srs::Angle::atom1()</a>
+    <a id="Item14_c1" onkeydown="return searchResults.NavChild(event,14,1)" onkeypress="return searchResults.NavChild(event,14,1)" onkeyup="return searchResults.NavChild(event,14,1)" class="SRScope" href="../classccp4srs_1_1_bond.html#a6ec052956ddec875a707d7e375ce0748" target="_parent">ccp4srs::Bond::atom1()</a>
+    <a id="Item14_c2" onkeydown="return searchResults.NavChild(event,14,2)" onkeypress="return searchResults.NavChild(event,14,2)" onkeyup="return searchResults.NavChild(event,14,2)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#ae27490ac46e2f3904ee230fe0c5b80af" target="_parent">ccp4srs::ChiCenter::atom1()</a>
+    <a id="Item14_c3" onkeydown="return searchResults.NavChild(event,14,3)" onkeypress="return searchResults.NavChild(event,14,3)" onkeyup="return searchResults.NavChild(event,14,3)" class="SRScope" href="../classccp4srs_1_1_torsion.html#af30f2e612259dedd1e569db13ff583fd" target="_parent">ccp4srs::Torsion::atom1()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom2">
+ <div class="SREntry">
+  <a id="Item15" onkeydown="return searchResults.Nav(event,15)" onkeypress="return searchResults.Nav(event,15)" onkeyup="return searchResults.Nav(event,15)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_atom2')">atom2</a>
+  <div class="SRChildren">
+    <a id="Item15_c0" onkeydown="return searchResults.NavChild(event,15,0)" onkeypress="return searchResults.NavChild(event,15,0)" onkeyup="return searchResults.NavChild(event,15,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a1be24203719da0b250775f7c0b5710ed" target="_parent">ccp4srs::Angle::atom2()</a>
+    <a id="Item15_c1" onkeydown="return searchResults.NavChild(event,15,1)" onkeypress="return searchResults.NavChild(event,15,1)" onkeyup="return searchResults.NavChild(event,15,1)" class="SRScope" href="../classccp4srs_1_1_bond.html#a364bc6a611e192c07d0bf5236a3503b9" target="_parent">ccp4srs::Bond::atom2()</a>
+    <a id="Item15_c2" onkeydown="return searchResults.NavChild(event,15,2)" onkeypress="return searchResults.NavChild(event,15,2)" onkeyup="return searchResults.NavChild(event,15,2)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#a5e1600b63a2e92494176dc328c6fc8a6" target="_parent">ccp4srs::ChiCenter::atom2()</a>
+    <a id="Item15_c3" onkeydown="return searchResults.NavChild(event,15,3)" onkeypress="return searchResults.NavChild(event,15,3)" onkeyup="return searchResults.NavChild(event,15,3)" class="SRScope" href="../classccp4srs_1_1_torsion.html#ae34ef1ddabf50dd732bf66336bb4a2eb" target="_parent">ccp4srs::Torsion::atom2()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom3">
+ <div class="SREntry">
+  <a id="Item16" onkeydown="return searchResults.Nav(event,16)" onkeypress="return searchResults.Nav(event,16)" onkeyup="return searchResults.Nav(event,16)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_atom3')">atom3</a>
+  <div class="SRChildren">
+    <a id="Item16_c0" onkeydown="return searchResults.NavChild(event,16,0)" onkeypress="return searchResults.NavChild(event,16,0)" onkeyup="return searchResults.NavChild(event,16,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a6d62c8acfe549d3d439a061f2bbcada9" target="_parent">ccp4srs::Angle::atom3()</a>
+    <a id="Item16_c1" onkeydown="return searchResults.NavChild(event,16,1)" onkeypress="return searchResults.NavChild(event,16,1)" onkeyup="return searchResults.NavChild(event,16,1)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#ac668dea1c66f203a26e46a1c87b37760" target="_parent">ccp4srs::ChiCenter::atom3()</a>
+    <a id="Item16_c2" onkeydown="return searchResults.NavChild(event,16,2)" onkeypress="return searchResults.NavChild(event,16,2)" onkeyup="return searchResults.NavChild(event,16,2)" class="SRScope" href="../classccp4srs_1_1_torsion.html#a37c594eb8a06aa962efd46c8d5c0e1b9" target="_parent">ccp4srs::Torsion::atom3()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom4">
+ <div class="SREntry">
+  <a id="Item17" onkeydown="return searchResults.Nav(event,17)" onkeypress="return searchResults.Nav(event,17)" onkeyup="return searchResults.Nav(event,17)" class="SRSymbol" href="../classccp4srs_1_1_torsion.html#afb752f1836193a0af5befba252e16703" target="_parent">atom4</a>
+  <span class="SRScope">ccp4srs::Torsion</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom_5f1">
+ <div class="SREntry">
+  <a id="Item18" onkeydown="return searchResults.Nav(event,18)" onkeypress="return searchResults.Nav(event,18)" onkeyup="return searchResults.Nav(event,18)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_atom_5f1')">atom_1</a>
+  <div class="SRChildren">
+    <a id="Item18_c0" onkeydown="return searchResults.NavChild(event,18,0)" onkeypress="return searchResults.NavChild(event,18,0)" onkeyup="return searchResults.NavChild(event,18,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#ab59c639612d7dcae2b34213a647cdb45" target="_parent">ccp4srs::Angle::atom_1()</a>
+    <a id="Item18_c1" onkeydown="return searchResults.NavChild(event,18,1)" onkeypress="return searchResults.NavChild(event,18,1)" onkeyup="return searchResults.NavChild(event,18,1)" class="SRScope" href="../classccp4srs_1_1_bond.html#ad359689c475101246c6c3061d31c2541" target="_parent">ccp4srs::Bond::atom_1()</a>
+    <a id="Item18_c2" onkeydown="return searchResults.NavChild(event,18,2)" onkeypress="return searchResults.NavChild(event,18,2)" onkeyup="return searchResults.NavChild(event,18,2)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#a246c77c96df7921a1d1c989de4a50f8f" target="_parent">ccp4srs::ChiCenter::atom_1()</a>
+    <a id="Item18_c3" onkeydown="return searchResults.NavChild(event,18,3)" onkeypress="return searchResults.NavChild(event,18,3)" onkeyup="return searchResults.NavChild(event,18,3)" class="SRScope" href="../classccp4srs_1_1_torsion.html#ae6bb750e2ebd67defafc5bd38515e923" target="_parent">ccp4srs::Torsion::atom_1()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom_5f2">
+ <div class="SREntry">
+  <a id="Item19" onkeydown="return searchResults.Nav(event,19)" onkeypress="return searchResults.Nav(event,19)" onkeyup="return searchResults.Nav(event,19)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_atom_5f2')">atom_2</a>
+  <div class="SRChildren">
+    <a id="Item19_c0" onkeydown="return searchResults.NavChild(event,19,0)" onkeypress="return searchResults.NavChild(event,19,0)" onkeyup="return searchResults.NavChild(event,19,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a8a4fd7f9e6196f259b6ec0989b5cb64c" target="_parent">ccp4srs::Angle::atom_2()</a>
+    <a id="Item19_c1" onkeydown="return searchResults.NavChild(event,19,1)" onkeypress="return searchResults.NavChild(event,19,1)" onkeyup="return searchResults.NavChild(event,19,1)" class="SRScope" href="../classccp4srs_1_1_bond.html#a277aee984c745dcdfd338f19e7df1e48" target="_parent">ccp4srs::Bond::atom_2()</a>
+    <a id="Item19_c2" onkeydown="return searchResults.NavChild(event,19,2)" onkeypress="return searchResults.NavChild(event,19,2)" onkeyup="return searchResults.NavChild(event,19,2)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#aa80d6d7fbec0a8497b62af13b16e2a12" target="_parent">ccp4srs::ChiCenter::atom_2()</a>
+    <a id="Item19_c3" onkeydown="return searchResults.NavChild(event,19,3)" onkeypress="return searchResults.NavChild(event,19,3)" onkeyup="return searchResults.NavChild(event,19,3)" class="SRScope" href="../classccp4srs_1_1_torsion.html#aae803284861c24535f6ea3cab02f00b8" target="_parent">ccp4srs::Torsion::atom_2()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom_5f3">
+ <div class="SREntry">
+  <a id="Item20" onkeydown="return searchResults.Nav(event,20)" onkeypress="return searchResults.Nav(event,20)" onkeyup="return searchResults.Nav(event,20)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_atom_5f3')">atom_3</a>
+  <div class="SRChildren">
+    <a id="Item20_c0" onkeydown="return searchResults.NavChild(event,20,0)" onkeypress="return searchResults.NavChild(event,20,0)" onkeyup="return searchResults.NavChild(event,20,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a545fb1039055e640aa938964b64c7d0a" target="_parent">ccp4srs::Angle::atom_3()</a>
+    <a id="Item20_c1" onkeydown="return searchResults.NavChild(event,20,1)" onkeypress="return searchResults.NavChild(event,20,1)" onkeyup="return searchResults.NavChild(event,20,1)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#a2b249cab1cc7c2ea80ea9259914fcd34" target="_parent">ccp4srs::ChiCenter::atom_3()</a>
+    <a id="Item20_c2" onkeydown="return searchResults.NavChild(event,20,2)" onkeypress="return searchResults.NavChild(event,20,2)" onkeyup="return searchResults.NavChild(event,20,2)" class="SRScope" href="../classccp4srs_1_1_torsion.html#a16456310c79412ef19e6b3dd22baf3b3" target="_parent">ccp4srs::Torsion::atom_3()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom_5f4">
+ <div class="SREntry">
+  <a id="Item21" onkeydown="return searchResults.Nav(event,21)" onkeypress="return searchResults.Nav(event,21)" onkeyup="return searchResults.Nav(event,21)" class="SRSymbol" href="../classccp4srs_1_1_torsion.html#a73c5cc1a3f37ac0998b1316beb35c579" target="_parent">atom_4</a>
+  <span class="SRScope">ccp4srs::Torsion</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom_5fbackward">
+ <div class="SREntry">
+  <a id="Item22" onkeydown="return searchResults.Nav(event,22)" onkeypress="return searchResults.Nav(event,22)" onkeyup="return searchResults.Nav(event,22)" class="SRSymbol" href="../classccp4srs_1_1_tree.html#a612df27ef2431bf2ac087f7190e0f9d1" target="_parent">atom_backward</a>
+  <span class="SRScope">ccp4srs::Tree</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom_5fcenter">
+ <div class="SREntry">
+  <a id="Item23" onkeydown="return searchResults.Nav(event,23)" onkeypress="return searchResults.Nav(event,23)" onkeyup="return searchResults.Nav(event,23)" class="SRSymbol" href="../classccp4srs_1_1_chi_center.html#a5fe75db982419a5d7f3c3ff8b2e41f46" target="_parent">atom_center</a>
+  <span class="SRScope">ccp4srs::ChiCenter</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom_5fforward">
+ <div class="SREntry">
+  <a id="Item24" onkeydown="return searchResults.Nav(event,24)" onkeypress="return searchResults.Nav(event,24)" onkeyup="return searchResults.Nav(event,24)" class="SRSymbol" href="../classccp4srs_1_1_tree.html#a3c63a71c2935da20a0feccad01d5ceaf" target="_parent">atom_forward</a>
+  <span class="SRScope">ccp4srs::Tree</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom_5fno">
+ <div class="SREntry">
+  <a id="Item25" onkeydown="return searchResults.Nav(event,25)" onkeypress="return searchResults.Nav(event,25)" onkeyup="return searchResults.Nav(event,25)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a9ac9e9e610a1a0450130d5e5c4242d34" target="_parent">atom_no</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom_5ftree">
+ <div class="SREntry">
+  <a id="Item26" onkeydown="return searchResults.Nav(event,26)" onkeypress="return searchResults.Nav(event,26)" onkeyup="return searchResults.Nav(event,26)" class="SRSymbol" href="../classccp4srs_1_1_tree.html#a27d256081e9d371ff22a6644d9ee8a91" target="_parent">atom_tree</a>
+  <span class="SRScope">ccp4srs::Tree</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atomcharge">
+ <div class="SREntry">
+  <a id="Item27" onkeydown="return searchResults.Nav(event,27)" onkeypress="return searchResults.Nav(event,27)" onkeyup="return searchResults.Nav(event,27)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a0e7a7e76f9fba1a8277dae436f900821" target="_parent">atomCharge</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atomid_5fna">
+ <div class="SREntry">
+  <a id="Item28" onkeydown="return searchResults.Nav(event,28)" onkeypress="return searchResults.Nav(event,28)" onkeyup="return searchResults.Nav(event,28)" class="SRSymbol" href="../namespaceccp4srs.html#aa44a92ce883cd1c525381111cd1a4ab3" target="_parent">AtomID_NA</a>
+  <span class="SRScope">ccp4srs</span>
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+</div>
+<div class="SRResult" id="SR_atomname">
+ <div class="SREntry">
+  <a id="Item29" onkeydown="return searchResults.Nav(event,29)" onkeypress="return searchResults.Nav(event,29)" onkeyup="return searchResults.Nav(event,29)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a75168bfe9aa3e0e24ba5f81854323039" target="_parent">atomName</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atompair">
+ <div class="SREntry">
+  <a id="Item30" onkeydown="return searchResults.Nav(event,30)" onkeypress="return searchResults.Nav(event,30)" onkeyup="return searchResults.Nav(event,30)" class="SRSymbol" href="../structccp4srs_1_1_atom_pair.html" target="_parent">AtomPair</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atoms">
+ <div class="SREntry">
+  <a id="Item31" onkeydown="return searchResults.Nav(event,31)" onkeypress="return searchResults.Nav(event,31)" onkeyup="return searchResults.Nav(event,31)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_atoms')">atoms</a>
+  <div class="SRChildren">
+    <a id="Item31_c0" onkeydown="return searchResults.NavChild(event,31,0)" onkeypress="return searchResults.NavChild(event,31,0)" onkeyup="return searchResults.NavChild(event,31,0)" class="SRScope" href="../classccp4srs_1_1_monomer.html#abd7decc2129038a1416f324fee53afa1" target="_parent">ccp4srs::Monomer::atoms()</a>
+    <a id="Item31_c1" onkeydown="return searchResults.NavChild(event,31,1)" onkeypress="return searchResults.NavChild(event,31,1)" onkeyup="return searchResults.NavChild(event,31,1)" class="SRScope" href="../classccp4srs_1_1_plane.html#a91e4f55f473565e42c27b6aab5311222" target="_parent">ccp4srs::Plane::atoms()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_atomsp">
+ <div class="SREntry">
+  <a id="Item32" onkeydown="return searchResults.Nav(event,32)" onkeypress="return searchResults.Nav(event,32)" onkeyup="return searchResults.Nav(event,32)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#acb4d50d536b22d4dd3f971072354f784" target="_parent">atomSP</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atomvalency">
+ <div class="SREntry">
+  <a id="Item33" onkeydown="return searchResults.Nav(event,33)" onkeypress="return searchResults.Nav(event,33)" onkeyup="return searchResults.Nav(event,33)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#aeaa06e2eac23c671be3f49c0caaa7d12" target="_parent">atomValency</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atomweight">
+ <div class="SREntry">
+  <a id="Item34" onkeydown="return searchResults.Nav(event,34)" onkeypress="return searchResults.Nav(event,34)" onkeyup="return searchResults.Nav(event,34)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#ac470c0fd96b775b2b1d979c353449ee4" target="_parent">atomWeight</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_62.html ccp4srs/doc-html/html/search/all_62.html
--- ccp4srs-old/doc-html/html/search/all_62.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_62.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,77 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_backward">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_tree.html#a70a9e13b054276780039e0d6f0edcdd9" target="_parent">backward</a>
+  <span class="SRScope">ccp4srs::Tree</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_base">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a0c37b44fe77e9f171d5f40281a6e82ae" target="_parent">Base</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_base">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_base.html" target="_parent">Base</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_bond">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_bond.html" target="_parent">Bond</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_bond">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_bond')">bond</a>
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+    <a id="Item4_c1" onkeydown="return searchResults.NavChild(event,4,1)" onkeypress="return searchResults.NavChild(event,4,1)" onkeyup="return searchResults.NavChild(event,4,1)" class="SRScope" href="../classccp4srs_1_1_bond.html#acd3c055b0b0827de95e44ca9a9ac972a" target="_parent">ccp4srs::Bond::Bond()</a>
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+<div class="SRResult" id="SR_bond_5flength">
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+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#a43513fb523b43f7f5f407a0bae151a95" target="_parent">bond_length</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_bond_5flength_5fesd">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#af438937a89d3cb3c7f2342ca6f38301c" target="_parent">bond_length_esd</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_bond_5forder">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#ac6365bacbc07dd7cf914b6c7ad6cd5d7" target="_parent">bond_order</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_bonds">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a19495bb3c7e8d1c27f12f06729979d9e" target="_parent">bonds</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
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+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_63.html ccp4srs/doc-html/html/search/all_63.html
--- ccp4srs-old/doc-html/html/search/all_63.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_63.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,523 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_calchbonds">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_chem.html#ab5d4ff0f43b6785dc2c3cec72d4b8eec" target="_parent">CalcHBonds</a>
+  <span class="SRScope">ccp4srs::Chem</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_cantopenfile">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaac65c121a2ac9e371d3e059cb480cf60d" target="_parent">CantOpenFile</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_ccp4_5fchirality">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#ac0274e4727f43cedf27380121215cbfa" target="_parent">ccp4_chirality</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_ccp4srs">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../namespaceccp4srs.html" target="_parent">ccp4srs</a>
+ </div>
+</div>
+<div class="SRResult" id="SR_ccp4srs_5fangle_2ecpp">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../ccp4srs__angle_8cpp.html" target="_parent">ccp4srs_angle.cpp</a>
+ </div>
+</div>
+<div class="SRResult" id="SR_ccp4srs_5fangle_2eh">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../ccp4srs__angle_8h.html" target="_parent">ccp4srs_angle.h</a>
+ </div>
+</div>
+<div class="SRResult" id="SR_ccp4srs_5fatom_2ecpp">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../ccp4srs__atom_8cpp.html" target="_parent">ccp4srs_atom.cpp</a>
+ </div>
+</div>
+<div class="SRResult" id="SR_ccp4srs_5fatom_2eh">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../ccp4srs__atom_8h.html" target="_parent">ccp4srs_atom.h</a>
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+</div>
+<div class="SRResult" id="SR_ccp4srs_5fbase_2ecpp">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="../ccp4srs__base_8cpp.html" target="_parent">ccp4srs_base.cpp</a>
+ </div>
+</div>
+<div class="SRResult" id="SR_ccp4srs_5fbase_2eh">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="../ccp4srs__base_8h.html" target="_parent">ccp4srs_base.h</a>
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+</div>
+<div class="SRResult" id="SR_ccp4srs_5fbond_2ecpp">
+ <div class="SREntry">
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+</div>
+<div class="SRResult" id="SR_ccp4srs_5fbond_2eh">
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+<div class="SRResult" id="SR_ccp4srs_5fbrokenbonds">
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+<div class="SRResult" id="SR_ccp4srs_5fchem_2ecpp">
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+</div>
+<div class="SRResult" id="SR_ccp4srs_5fchem_2eh">
+ <div class="SREntry">
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+</div>
+<div class="SRResult" id="SR_ccp4srs_5fchicenter_2ecpp">
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+</div>
+<div class="SRResult" id="SR_ccp4srs_5fchicenter_2eh">
+ <div class="SREntry">
+  <a id="Item16" onkeydown="return searchResults.Nav(event,16)" onkeypress="return searchResults.Nav(event,16)" onkeyup="return searchResults.Nav(event,16)" class="SRSymbol" href="../ccp4srs__chicenter_8h.html" target="_parent">ccp4srs_chicenter.h</a>
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+</div>
+<div class="SRResult" id="SR_ccp4srs_5fcontainer_2ecpp">
+ <div class="SREntry">
+  <a id="Item17" onkeydown="return searchResults.Nav(event,17)" onkeypress="return searchResults.Nav(event,17)" onkeyup="return searchResults.Nav(event,17)" class="SRSymbol" href="../ccp4srs__container_8cpp.html" target="_parent">ccp4srs_container.cpp</a>
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+</div>
+<div class="SRResult" id="SR_ccp4srs_5fcontainer_2eh">
+ <div class="SREntry">
+  <a id="Item18" onkeydown="return searchResults.Nav(event,18)" onkeypress="return searchResults.Nav(event,18)" onkeyup="return searchResults.Nav(event,18)" class="SRSymbol" href="../ccp4srs__container_8h.html" target="_parent">ccp4srs_container.h</a>
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+</div>
+<div class="SRResult" id="SR_ccp4srs_5fdefs_2eh">
+ <div class="SREntry">
+  <a id="Item19" onkeydown="return searchResults.Nav(event,19)" onkeypress="return searchResults.Nav(event,19)" onkeyup="return searchResults.Nav(event,19)" class="SRSymbol" href="../ccp4srs__defs_8h.html" target="_parent">ccp4srs_defs.h</a>
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+</div>
+<div class="SRResult" id="SR_ccp4srs_5femptyresidue">
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+<div class="SRResult" id="SR_ccp4srs_5femptyresset">
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+<div class="SRResult" id="SR_ccp4srs_5fentry_2ecpp">
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+<div class="SRResult" id="SR_ccp4srs_5fentry_2eh">
+ <div class="SREntry">
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+</div>
+<div class="SRResult" id="SR_ccp4srs_5fentrynotfound">
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+<div class="SRResult" id="SR_ccp4srs_5ffail">
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+<div class="SRResult" id="SR_ccp4srs_5fmanager_2ecpp">
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+<div class="SRResult" id="SR_ccp4srs_5fnohbonds">
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+<div class="SRResult" id="SR_ccp4srs_5frc">
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+  <span class="SRScope">ccp4srs</span>
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+<div class="SRResult" id="SR_ccp4srs_5freaderrors">
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+<div class="SRResult" id="SR_ccp4srs_5ftree_2eh">
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+<div class="SRResult" id="SR_ccp4srs_5fversion">
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+<div class="SRResult" id="SR_chunkno">
+ <div class="SREntry">
+  <a id="Item70" onkeydown="return searchResults.Nav(event,70)" onkeypress="return searchResults.Nav(event,70)" onkeyup="return searchResults.Nav(event,70)" class="SRSymbol" href="../structccp4srs_1_1_m_p_file_pos.html#ab84443c24cd9b322d81f2e165af4bd8a" target="_parent">chunkNo</a>
+  <span class="SRScope">ccp4srs::MPFilePos</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_comp1">
+ <div class="SREntry">
+  <a id="Item71" onkeydown="return searchResults.Nav(event,71)" onkeypress="return searchResults.Nav(event,71)" onkeyup="return searchResults.Nav(event,71)" class="SRSymbol" href="../classccp4srs_1_1_index.html#af2a41a666517311e8877a3ec9e288916" target="_parent">Comp1</a>
+  <span class="SRScope">ccp4srs::Index</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_comp2">
+ <div class="SREntry">
+  <a id="Item72" onkeydown="return searchResults.Nav(event,72)" onkeypress="return searchResults.Nav(event,72)" onkeyup="return searchResults.Nav(event,72)" class="SRSymbol" href="../classccp4srs_1_1_index.html#af4ce5b42fe2cf6364f9916d0a42f08b2" target="_parent">Comp2</a>
+  <span class="SRScope">ccp4srs::Index</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_compare">
+ <div class="SREntry">
+  <a id="Item73" onkeydown="return searchResults.Nav(event,73)" onkeypress="return searchResults.Nav(event,73)" onkeyup="return searchResults.Nav(event,73)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#acefa794143d2ab128897441895cdf562" target="_parent">compare</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_compressionerror">
+ <div class="SREntry">
+  <a id="Item74" onkeydown="return searchResults.Nav(event,74)" onkeypress="return searchResults.Nav(event,74)" onkeyup="return searchResults.Nav(event,74)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa6cf46f9d24d202ae6ac26ddb6aeb625d" target="_parent">CompressionError</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_connect">
+ <div class="SREntry">
+  <a id="Item75" onkeydown="return searchResults.Nav(event,75)" onkeypress="return searchResults.Nav(event,75)" onkeyup="return searchResults.Nav(event,75)" class="SRSymbol" href="../classccp4srs_1_1_tree.html#a9986231a0223ef6b62902823d119176f" target="_parent">connect</a>
+  <span class="SRScope">ccp4srs::Tree</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_connect_5ftype">
+ <div class="SREntry">
+  <a id="Item76" onkeydown="return searchResults.Nav(event,76)" onkeypress="return searchResults.Nav(event,76)" onkeyup="return searchResults.Nav(event,76)" class="SRSymbol" href="../classccp4srs_1_1_tree.html#a97ee818b7a1b1724cfb712453be05743" target="_parent">connect_type</a>
+  <span class="SRScope">ccp4srs::Tree</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_container">
+ <div class="SREntry">
+  <a id="Item77" onkeydown="return searchResults.Nav(event,77)" onkeypress="return searchResults.Nav(event,77)" onkeyup="return searchResults.Nav(event,77)" class="SRSymbol" href="../classccp4srs_1_1_container.html#acdff89dd6d441d731b517565021e3881" target="_parent">Container</a>
+  <span class="SRScope">ccp4srs::Container</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_container">
+ <div class="SREntry">
+  <a id="Item78" onkeydown="return searchResults.Nav(event,78)" onkeypress="return searchResults.Nav(event,78)" onkeyup="return searchResults.Nav(event,78)" class="SRSymbol" href="../classccp4srs_1_1_container.html" target="_parent">Container</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_container_3c_20angle_20_3e">
+ <div class="SREntry">
+  <a id="Item79" onkeydown="return searchResults.Nav(event,79)" onkeypress="return searchResults.Nav(event,79)" onkeyup="return searchResults.Nav(event,79)" class="SRSymbol" href="../classccp4srs_1_1_container.html" target="_parent">Container&lt; Angle &gt;</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_container_3c_20atom_20_3e">
+ <div class="SREntry">
+  <a id="Item80" onkeydown="return searchResults.Nav(event,80)" onkeypress="return searchResults.Nav(event,80)" onkeyup="return searchResults.Nav(event,80)" class="SRSymbol" href="../classccp4srs_1_1_container.html" target="_parent">Container&lt; Atom &gt;</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_container_3c_20bond_20_3e">
+ <div class="SREntry">
+  <a id="Item81" onkeydown="return searchResults.Nav(event,81)" onkeypress="return searchResults.Nav(event,81)" onkeyup="return searchResults.Nav(event,81)" class="SRSymbol" href="../classccp4srs_1_1_container.html" target="_parent">Container&lt; Bond &gt;</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_container_3c_20chicenter_20_3e">
+ <div class="SREntry">
+  <a id="Item82" onkeydown="return searchResults.Nav(event,82)" onkeypress="return searchResults.Nav(event,82)" onkeyup="return searchResults.Nav(event,82)" class="SRSymbol" href="../classccp4srs_1_1_container.html" target="_parent">Container&lt; ChiCenter &gt;</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_container_3c_20plane_20_3e">
+ <div class="SREntry">
+  <a id="Item83" onkeydown="return searchResults.Nav(event,83)" onkeypress="return searchResults.Nav(event,83)" onkeyup="return searchResults.Nav(event,83)" class="SRSymbol" href="../classccp4srs_1_1_container.html" target="_parent">Container&lt; Plane &gt;</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_container_3c_20torsion_20_3e">
+ <div class="SREntry">
+  <a id="Item84" onkeydown="return searchResults.Nav(event,84)" onkeypress="return searchResults.Nav(event,84)" onkeyup="return searchResults.Nav(event,84)" class="SRSymbol" href="../classccp4srs_1_1_container.html" target="_parent">Container&lt; Torsion &gt;</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_copy">
+ <div class="SREntry">
+  <a id="Item85" onkeydown="return searchResults.Nav(event,85)" onkeypress="return searchResults.Nav(event,85)" onkeyup="return searchResults.Nav(event,85)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_copy')">copy</a>
+  <div class="SRChildren">
+    <a id="Item85_c0" onkeydown="return searchResults.NavChild(event,85,0)" onkeypress="return searchResults.NavChild(event,85,0)" onkeyup="return searchResults.NavChild(event,85,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a085c530866442b6b3dfb8c969de2bfe8" target="_parent">ccp4srs::Angle::copy()</a>
+    <a id="Item85_c1" onkeydown="return searchResults.NavChild(event,85,1)" onkeypress="return searchResults.NavChild(event,85,1)" onkeyup="return searchResults.NavChild(event,85,1)" class="SRScope" href="../classccp4srs_1_1_atom.html#a5aa8172f59efa4ac90359b2be7424d92" target="_parent">ccp4srs::Atom::copy()</a>
+    <a id="Item85_c2" onkeydown="return searchResults.NavChild(event,85,2)" onkeypress="return searchResults.NavChild(event,85,2)" onkeyup="return searchResults.NavChild(event,85,2)" class="SRScope" href="../classccp4srs_1_1_bond.html#a4bb135bfcd9ee6078a2770fe9f15319c" target="_parent">ccp4srs::Bond::copy(Container&lt; Atom &gt; &amp;atoms, PBond bond, Container&lt; Atom &gt; &amp;bond_atoms)</a>
+    <a id="Item85_c3" onkeydown="return searchResults.NavChild(event,85,3)" onkeypress="return searchResults.NavChild(event,85,3)" onkeyup="return searchResults.NavChild(event,85,3)" class="SRScope" href="../classccp4srs_1_1_bond.html#a0c6c410020c5fad46d2987d9fc8de65e" target="_parent">ccp4srs::Bond::copy(PBond bond, mmdb::ivector anmatch=NULL)</a>
+    <a id="Item85_c4" onkeydown="return searchResults.NavChild(event,85,4)" onkeypress="return searchResults.NavChild(event,85,4)" onkeyup="return searchResults.NavChild(event,85,4)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#ab3dc0fe1813d51055e829586a27ddd15" target="_parent">ccp4srs::ChiCenter::copy()</a>
+    <a id="Item85_c5" onkeydown="return searchResults.NavChild(event,85,5)" onkeypress="return searchResults.NavChild(event,85,5)" onkeyup="return searchResults.NavChild(event,85,5)" class="SRScope" href="../classccp4srs_1_1_plane.html#a9db264baa4154922dfac882f4f437d34" target="_parent">ccp4srs::Plane::copy()</a>
+    <a id="Item85_c6" onkeydown="return searchResults.NavChild(event,85,6)" onkeypress="return searchResults.NavChild(event,85,6)" onkeyup="return searchResults.NavChild(event,85,6)" class="SRScope" href="../classccp4srs_1_1_torsion.html#a2a6ff05c37b9ce514fe557ab3817a072" target="_parent">ccp4srs::Torsion::copy()</a>
+    <a id="Item85_c7" onkeydown="return searchResults.NavChild(event,85,7)" onkeypress="return searchResults.NavChild(event,85,7)" onkeyup="return searchResults.NavChild(event,85,7)" class="SRScope" href="../classccp4srs_1_1_tree.html#acfc010d5d168bb288379e6b6721fb9fa" target="_parent">ccp4srs::Tree::copy()</a>
+    <a id="Item85_c8" onkeydown="return searchResults.NavChild(event,85,8)" onkeypress="return searchResults.NavChild(event,85,8)" onkeyup="return searchResults.NavChild(event,85,8)" class="SRScope" href="../structccp4srs_1_1_m_p_file_pos.html#a7f60e91b825a15d3def175dcdb71139d" target="_parent">ccp4srs::MPFilePos::Copy()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_covalent">
+ <div class="SREntry">
+  <a id="Item86" onkeydown="return searchResults.Nav(event,86)" onkeypress="return searchResults.Nav(event,86)" onkeyup="return searchResults.Nav(event,86)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795babaf2bbca3b364f84e83bbc9927b45e39" target="_parent">Covalent</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_64.html ccp4srs/doc-html/html/search/all_64.html
--- ccp4srs-old/doc-html/html/search/all_64.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_64.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,82 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_daselhnds">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../structccp4srs_1_1_d_a_sel_hnds.html" target="_parent">DASelHnds</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_defineclass">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_defineclass')">DefineClass</a>
+  <div class="SRChildren">
+    <a id="Item1_c0" onkeydown="return searchResults.NavChild(event,1,0)" onkeypress="return searchResults.NavChild(event,1,0)" onkeyup="return searchResults.NavChild(event,1,0)" class="SRScope" href="../namespaceccp4srs.html#afbb5df60616f08fcf36926a3585c185f" target="_parent">ccp4srs::DefineClass(Angle)</a>
+    <a id="Item1_c1" onkeydown="return searchResults.NavChild(event,1,1)" onkeypress="return searchResults.NavChild(event,1,1)" onkeyup="return searchResults.NavChild(event,1,1)" class="SRScope" href="../namespaceccp4srs.html#aaacc6a8b59c08ac1bbfd9305ee663a1b" target="_parent">ccp4srs::DefineClass(Atom)</a>
+    <a id="Item1_c2" onkeydown="return searchResults.NavChild(event,1,2)" onkeypress="return searchResults.NavChild(event,1,2)" onkeyup="return searchResults.NavChild(event,1,2)" class="SRScope" href="../namespaceccp4srs.html#a4c159612746fffa9c8740ead5f891bb4" target="_parent">ccp4srs::DefineClass(Base)</a>
+    <a id="Item1_c3" onkeydown="return searchResults.NavChild(event,1,3)" onkeypress="return searchResults.NavChild(event,1,3)" onkeyup="return searchResults.NavChild(event,1,3)" class="SRScope" href="../namespaceccp4srs.html#a156f31d96da750c94e75880a12fd5523" target="_parent">ccp4srs::DefineClass(Bond)</a>
+    <a id="Item1_c4" onkeydown="return searchResults.NavChild(event,1,4)" onkeypress="return searchResults.NavChild(event,1,4)" onkeyup="return searchResults.NavChild(event,1,4)" class="SRScope" href="../namespaceccp4srs.html#abe82012e7a8178ae1069f381769da72d" target="_parent">ccp4srs::DefineClass(Chem)</a>
+    <a id="Item1_c5" onkeydown="return searchResults.NavChild(event,1,5)" onkeypress="return searchResults.NavChild(event,1,5)" onkeyup="return searchResults.NavChild(event,1,5)" class="SRScope" href="../namespaceccp4srs.html#aed1b87fee568c115c3bbdb07ad9a5bd7" target="_parent">ccp4srs::DefineClass(ChiCenter)</a>
+    <a id="Item1_c6" onkeydown="return searchResults.NavChild(event,1,6)" onkeypress="return searchResults.NavChild(event,1,6)" onkeyup="return searchResults.NavChild(event,1,6)" class="SRScope" href="../namespaceccp4srs.html#aa72ee17a81ce821f1c37483a10153ae7" target="_parent">ccp4srs::DefineClass(Entry)</a>
+    <a id="Item1_c7" onkeydown="return searchResults.NavChild(event,1,7)" onkeypress="return searchResults.NavChild(event,1,7)" onkeyup="return searchResults.NavChild(event,1,7)" class="SRScope" href="../namespaceccp4srs.html#afeba477403b4f346ef1c74ab27c0a797" target="_parent">ccp4srs::DefineClass(Index)</a>
+    <a id="Item1_c8" onkeydown="return searchResults.NavChild(event,1,8)" onkeypress="return searchResults.NavChild(event,1,8)" onkeyup="return searchResults.NavChild(event,1,8)" class="SRScope" href="../namespaceccp4srs.html#a8c36728a6d09c1cb65fe3168735979cb" target="_parent">ccp4srs::DefineClass(Manager)</a>
+    <a id="Item1_c9" onkeydown="return searchResults.NavChild(event,1,9)" onkeypress="return searchResults.NavChild(event,1,9)" onkeyup="return searchResults.NavChild(event,1,9)" class="SRScope" href="../namespaceccp4srs.html#aea118bfa214275496e94e42beca05c35" target="_parent">ccp4srs::DefineClass(Monomer)</a>
+    <a id="Item1_c10" onkeydown="return searchResults.NavChild(event,1,10)" onkeypress="return searchResults.NavChild(event,1,10)" onkeyup="return searchResults.NavChild(event,1,10)" class="SRScope" href="../namespaceccp4srs.html#a299f5fc0ddc551524a80fe756cf2525d" target="_parent">ccp4srs::DefineClass(Plane)</a>
+    <a id="Item1_c11" onkeydown="return searchResults.NavChild(event,1,11)" onkeypress="return searchResults.NavChild(event,1,11)" onkeyup="return searchResults.NavChild(event,1,11)" class="SRScope" href="../namespaceccp4srs.html#a3e61bdd34189f80843c0e565ce68e628" target="_parent">ccp4srs::DefineClass(Torsion)</a>
+    <a id="Item1_c12" onkeydown="return searchResults.NavChild(event,1,12)" onkeypress="return searchResults.NavChild(event,1,12)" onkeyup="return searchResults.NavChild(event,1,12)" class="SRScope" href="../namespaceccp4srs.html#a6d1229e1b71f24fdb95a8700d402c6f8" target="_parent">ccp4srs::DefineClass(Tree)</a>
+    <a id="Item1_c13" onkeydown="return searchResults.NavChild(event,1,13)" onkeypress="return searchResults.NavChild(event,1,13)" onkeyup="return searchResults.NavChild(event,1,13)" class="SRScope" href="../namespaceccp4srs.html#a64bcbd2282ebaf1613021bf317bdf0cb" target="_parent">ccp4srs::DefineClass(MemIO)</a>
+    <a id="Item1_c14" onkeydown="return searchResults.NavChild(event,1,14)" onkeypress="return searchResults.NavChild(event,1,14)" onkeyup="return searchResults.NavChild(event,1,14)" class="SRScope" href="../namespaceccp4srs.html#aed1408df12f28bc4a3dd772230255597" target="_parent">ccp4srs::DefineClass(MPFile) class MPFile</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_definestructure">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_definestructure')">DefineStructure</a>
+  <div class="SRChildren">
+    <a id="Item2_c0" onkeydown="return searchResults.NavChild(event,2,0)" onkeypress="return searchResults.NavChild(event,2,0)" onkeyup="return searchResults.NavChild(event,2,0)" class="SRScope" href="../namespaceccp4srs.html#a38fd31a76e47d65dbd8f9343fdc2f001" target="_parent">ccp4srs::DefineStructure(AtomPair)</a>
+    <a id="Item2_c1" onkeydown="return searchResults.NavChild(event,2,1)" onkeypress="return searchResults.NavChild(event,2,1)" onkeyup="return searchResults.NavChild(event,2,1)" class="SRScope" href="../namespaceccp4srs.html#af0f84ef74e24251a016c6d27c196fe2e" target="_parent">ccp4srs::DefineStructure(DASelHnds)</a>
+    <a id="Item2_c2" onkeydown="return searchResults.NavChild(event,2,2)" onkeypress="return searchResults.NavChild(event,2,2)" onkeyup="return searchResults.NavChild(event,2,2)" class="SRScope" href="../namespaceccp4srs.html#aad79147ea920868ed625a8f693277d56" target="_parent">ccp4srs::DefineStructure(MPFilePos)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_deleteselections">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../structccp4srs_1_1_d_a_sel_hnds.html#a582873aa43d2c8708e99db1485013bef" target="_parent">deleteSelections</a>
+  <span class="SRScope">ccp4srs::DASelHnds</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_deloc">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba3e459a041fa6b33d363df5a335413e13" target="_parent">Deloc</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_dist_5fesd">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_plane.html#a5837e387b59c8d350271fd11a644ee8d" target="_parent">dist_esd</a>
+  <span class="SRScope">ccp4srs::Plane</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_double">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba0311fe9d41fd3830910b1e4f93d9a83a" target="_parent">Double</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_65.html ccp4srs/doc-html/html/search/all_65.html
--- ccp4srs-old/doc-html/html/search/all_65.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_65.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,100 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_element">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a78344a993072c3e8918a54c3259d55d8" target="_parent">element</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_element_5fpdb">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a8d78d445f18a9f9e83d82f66e715b274" target="_parent">element_pdb</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_empty">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_empty')">empty</a>
+  <div class="SRChildren">
+    <a id="Item2_c0" onkeydown="return searchResults.NavChild(event,2,0)" onkeypress="return searchResults.NavChild(event,2,0)" onkeyup="return searchResults.NavChild(event,2,0)" class="SRScope" href="../classccp4srs_1_1_container.html#aeed888e25348f83a53021beaa21a0b1e" target="_parent">ccp4srs::Container::empty()</a>
+    <a id="Item2_c1" onkeydown="return searchResults.NavChild(event,2,1)" onkeypress="return searchResults.NavChild(event,2,1)" onkeyup="return searchResults.NavChild(event,2,1)" class="SRScope" href="../classccp4srs_1_1_plane.html#a8da6c13ce79682d5f17e23f7c3e84849" target="_parent">ccp4srs::Plane::empty()</a>
+    <a id="Item2_c2" onkeydown="return searchResults.NavChild(event,2,2)" onkeypress="return searchResults.NavChild(event,2,2)" onkeyup="return searchResults.NavChild(event,2,2)" class="SRScope" href="../classccp4srs_1_1_tree.html#a5f5e595cfdb5623cc59c0651ff7a25d3" target="_parent">ccp4srs::Tree::empty()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_emptyfile">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa117fc645808ac4d9c4e53452bc608d51" target="_parent">EmptyFile</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_emptyloop">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5edad0a61a72f29321313e1bc19920df40f9" target="_parent">EmptyLoop</a>
+  <span class="SRScope">ccp4srs::Plane</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_energy_5ftype">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#af9d89db887cdbfc5523a79ece1c1e117" target="_parent">energy_type</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_energytype">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#ac429b2d0c02fe21432c4b651ad181fdb" target="_parent">energyType</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_entry">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_entry.html" target="_parent">Entry</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_entry">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="../classccp4srs_1_1_entry.html#aa72cb70c4f1c115a2134e2da80b9bc34" target="_parent">Entry</a>
+  <span class="SRScope">ccp4srs::Entry</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_entryid">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="../classccp4srs_1_1_index.html#a0bd1aedcf3b32bdd48d0de5cd2cc563e" target="_parent">entryID</a>
+  <span class="SRScope">ccp4srs::Index</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_esd">
+ <div class="SREntry">
+  <a id="Item10" onkeydown="return searchResults.Nav(event,10)" onkeypress="return searchResults.Nav(event,10)" onkeyup="return searchResults.Nav(event,10)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_esd')">esd</a>
+  <div class="SRChildren">
+    <a id="Item10_c0" onkeydown="return searchResults.NavChild(event,10,0)" onkeypress="return searchResults.NavChild(event,10,0)" onkeyup="return searchResults.NavChild(event,10,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a31b7030dec4dd77c0eefa3444c75901f" target="_parent">ccp4srs::Angle::esd()</a>
+    <a id="Item10_c1" onkeydown="return searchResults.NavChild(event,10,1)" onkeypress="return searchResults.NavChild(event,10,1)" onkeyup="return searchResults.NavChild(event,10,1)" class="SRScope" href="../classccp4srs_1_1_plane.html#ad9f1d004296b308a0955997695277ff4" target="_parent">ccp4srs::Plane::esd()</a>
+    <a id="Item10_c2" onkeydown="return searchResults.NavChild(event,10,2)" onkeypress="return searchResults.NavChild(event,10,2)" onkeyup="return searchResults.NavChild(event,10,2)" class="SRScope" href="../classccp4srs_1_1_torsion.html#a44095b8e5025c92a4b443a8715beceee" target="_parent">ccp4srs::Torsion::esd()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_esds">
+ <div class="SREntry">
+  <a id="Item11" onkeydown="return searchResults.Nav(event,11)" onkeypress="return searchResults.Nav(event,11)" onkeyup="return searchResults.Nav(event,11)" class="SRSymbol" href="../classccp4srs_1_1_plane.html#a4fd16b46609257ebe87c7b7347597b2b" target="_parent">esds</a>
+  <span class="SRScope">ccp4srs::Plane</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_66.html ccp4srs/doc-html/html/search/all_66.html
--- ccp4srs-old/doc-html/html/search/all_66.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_66.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,50 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_fgraphpos">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_index.html#a3be74bae1c6afc52ea36690b45ec5b96" target="_parent">fGraphPos</a>
+  <span class="SRScope">ccp4srs::Index</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_forward">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_tree.html#ad52fadb719ce7ca269b9f6875a9ce8e6" target="_parent">forward</a>
+  <span class="SRScope">ccp4srs::Tree</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_free">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a4cda073662a49aa45b0c744ec88de39a" target="_parent">free</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_freememory">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_base.html#ab67f138edc7ae19791be69dde485c719" target="_parent">freeMemory</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_fstructpos">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_index.html#a21a1eddc77e99baf8df0b7450dee548b" target="_parent">fStructPos</a>
+  <span class="SRScope">ccp4srs::Index</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_67.html ccp4srs/doc-html/html/search/all_67.html
--- ccp4srs-old/doc-html/html/search/all_67.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_67.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,318 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_get_5fangles">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a8d4b4084ca5c0e0fa42075f59eaf3e08" target="_parent">get_angles</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fatom_5ffrom_5fcif">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_get_5fatom_5ffrom_5fcif')">get_atom_from_cif</a>
+  <div class="SRChildren">
+    <a id="Item1_c0" onkeydown="return searchResults.NavChild(event,1,0)" onkeypress="return searchResults.NavChild(event,1,0)" onkeyup="return searchResults.NavChild(event,1,0)" class="SRScope" href="../namespaceccp4srs.html#adead0e638933d7d2949df9bb7b44f910" target="_parent">ccp4srs::get_atom_from_cif(int &amp;index, mmdb::mmcif::PLoop loop, mmdb::cpstr Tag, int row, Container&lt; Atom &gt; &amp;atoms, int &amp;rc)</a>
+    <a id="Item1_c1" onkeydown="return searchResults.NavChild(event,1,1)" onkeypress="return searchResults.NavChild(event,1,1)" onkeyup="return searchResults.NavChild(event,1,1)" class="SRScope" href="../namespaceccp4srs.html#a012e980439f3fcbb1844abf82ab2e95e" target="_parent">ccp4srs::get_atom_from_cif(int &amp;index, mmdb::mmcif::PStruct mmCIFStruct, mmdb::cpstr Tag, Container&lt; Atom &gt; &amp;atoms, int &amp;rc)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fatoms">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a1ca9838123fea51260be3c44abd6771f" target="_parent">get_atoms</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fbond_5ftype_5ffrom_5fcif">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../namespaceccp4srs.html#a66b5a7cbf87409e898be86c84505275a" target="_parent">get_bond_type_from_cif</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fbond_5ftype_5ffrom_5fcif_5fccp4">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../namespaceccp4srs.html#a134be7dad55bde913e9bbb02825064e0" target="_parent">get_bond_type_from_cif_ccp4</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fbond_5ftype_5ffrom_5fcif_5frcsb">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../namespaceccp4srs.html#a2fc315dbfb7012f8e39ff3a2f440a5d6" target="_parent">get_bond_type_from_cif_rcsb</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fbonds">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#af36aeb36b83f49d3b4fc28d4737b5efd" target="_parent">get_bonds</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fbool">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a0bbc28ba1593463385ae8f28b65225fa" target="_parent">get_bool</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fbound">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_get_5fbound')">get_bound</a>
+  <div class="SRChildren">
+    <a id="Item8_c0" onkeydown="return searchResults.NavChild(event,8,0)" onkeypress="return searchResults.NavChild(event,8,0)" onkeyup="return searchResults.NavChild(event,8,0)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a7b6acc92258007c15351989930e8672f" target="_parent">ccp4srs::Monomer::get_bound(int atomNo, mmdb::cpstr elem, int serNo)</a>
+    <a id="Item8_c1" onkeydown="return searchResults.NavChild(event,8,1)" onkeypress="return searchResults.NavChild(event,8,1)" onkeyup="return searchResults.NavChild(event,8,1)" class="SRScope" href="../classccp4srs_1_1_monomer.html#ae60200771fdf1a869023dacebfb98278" target="_parent">ccp4srs::Monomer::get_bound(int atomNo, int n)</a>
+    <a id="Item8_c2" onkeydown="return searchResults.NavChild(event,8,2)" onkeypress="return searchResults.NavChild(event,8,2)" onkeyup="return searchResults.NavChild(event,8,2)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a8ae0097e0e9950fc3f443f373a0a9359" target="_parent">ccp4srs::Monomer::get_bound(mmdb::cpstr aname, int n)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fbuffer">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_get_5fbuffer')">get_buffer</a>
+  <div class="SRChildren">
+    <a id="Item9_c0" onkeydown="return searchResults.NavChild(event,9,0)" onkeypress="return searchResults.NavChild(event,9,0)" onkeyup="return searchResults.NavChild(event,9,0)" class="SRScope" href="../classccp4srs_1_1_mem_i_o.html#aa1d1ea86d64ee50cab284d4a18f55ab8" target="_parent">ccp4srs::MemIO::get_buffer(const int length)</a>
+    <a id="Item9_c1" onkeydown="return searchResults.NavChild(event,9,1)" onkeypress="return searchResults.NavChild(event,9,1)" onkeyup="return searchResults.NavChild(event,9,1)" class="SRScope" href="../classccp4srs_1_1_mem_i_o.html#adad4a428c7530e61362f46d37b87d524" target="_parent">ccp4srs::MemIO::get_buffer(mmdb::pstr *buf, int *length)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fbyte">
+ <div class="SREntry">
+  <a id="Item10" onkeydown="return searchResults.Nav(event,10)" onkeypress="return searchResults.Nav(event,10)" onkeyup="return searchResults.Nav(event,10)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a296d38484504311f2773ff313298dda9" target="_parent">get_byte</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fchicenters">
+ <div class="SREntry">
+  <a id="Item11" onkeydown="return searchResults.Nav(event,11)" onkeypress="return searchResults.Nav(event,11)" onkeyup="return searchResults.Nav(event,11)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a591d5f8275f5b5756442d96221039ef3" target="_parent">get_chicenters</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fchirality">
+ <div class="SREntry">
+  <a id="Item12" onkeydown="return searchResults.Nav(event,12)" onkeypress="return searchResults.Nav(event,12)" onkeyup="return searchResults.Nav(event,12)" class="SRSymbol" href="../classccp4srs_1_1_chi_center.html#a1aa5ee605cdc3756abcb075279eeb8af" target="_parent">get_chirality</a>
+  <span class="SRScope">ccp4srs::ChiCenter</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5ffloat">
+ <div class="SREntry">
+  <a id="Item13" onkeydown="return searchResults.Nav(event,13)" onkeypress="return searchResults.Nav(event,13)" onkeyup="return searchResults.Nav(event,13)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#adf95c15823dd0fb1067002d2ee3d8095" target="_parent">get_float</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fibyte">
+ <div class="SREntry">
+  <a id="Item14" onkeydown="return searchResults.Nav(event,14)" onkeypress="return searchResults.Nav(event,14)" onkeyup="return searchResults.Nav(event,14)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a7bc9b6d871402f5b5601d05ad4012326" target="_parent">get_ibyte</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5finteger">
+ <div class="SREntry">
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+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fishort">
+ <div class="SREntry">
+  <a id="Item16" onkeydown="return searchResults.Nav(event,16)" onkeypress="return searchResults.Nav(event,16)" onkeyup="return searchResults.Nav(event,16)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a55e1b2e8f826ab2d6c0aef09f3beac9f" target="_parent">get_ishort</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fline">
+ <div class="SREntry">
+  <a id="Item17" onkeydown="return searchResults.Nav(event,17)" onkeypress="return searchResults.Nav(event,17)" onkeyup="return searchResults.Nav(event,17)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a6cab031cef522531846e3ced7984f276" target="_parent">get_line</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5flong">
+ <div class="SREntry">
+  <a id="Item18" onkeydown="return searchResults.Nav(event,18)" onkeypress="return searchResults.Nav(event,18)" onkeyup="return searchResults.Nav(event,18)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a950878f651e3bb037cf7ddc4a9c00201" target="_parent">get_long</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fplanes">
+ <div class="SREntry">
+  <a id="Item19" onkeydown="return searchResults.Nav(event,19)" onkeypress="return searchResults.Nav(event,19)" onkeyup="return searchResults.Nav(event,19)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#aa454ac38a87c19006580a42bc38958fc" target="_parent">get_planes</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5freal">
+ <div class="SREntry">
+  <a id="Item20" onkeydown="return searchResults.Nav(event,20)" onkeypress="return searchResults.Nav(event,20)" onkeyup="return searchResults.Nav(event,20)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#afcc2e5eede7a829347985f646f24dcb3" target="_parent">get_real</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fshort">
+ <div class="SREntry">
+  <a id="Item21" onkeydown="return searchResults.Nav(event,21)" onkeypress="return searchResults.Nav(event,21)" onkeyup="return searchResults.Nav(event,21)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#af2d1b382de42e06ce1dc5ae4ad6bb20f" target="_parent">get_short</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fshortreal">
+ <div class="SREntry">
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+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fstring">
+ <div class="SREntry">
+  <a id="Item23" onkeydown="return searchResults.Nav(event,23)" onkeypress="return searchResults.Nav(event,23)" onkeyup="return searchResults.Nav(event,23)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a22abd9cc96e80e4d3e71f0d1acbf1c4d" target="_parent">get_string</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5ftorsions">
+ <div class="SREntry">
+  <a id="Item24" onkeydown="return searchResults.Nav(event,24)" onkeypress="return searchResults.Nav(event,24)" onkeyup="return searchResults.Nav(event,24)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a7b31b6675690c2edc0baa0e070d349ad" target="_parent">get_torsions</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5ftree">
+ <div class="SREntry">
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+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fword">
+ <div class="SREntry">
+  <a id="Item26" onkeydown="return searchResults.Nav(event,26)" onkeypress="return searchResults.Nav(event,26)" onkeyup="return searchResults.Nav(event,26)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#ab932bc5aa0e98c9e681a3f3a9cc532c8" target="_parent">get_word</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_getatnames">
+ <div class="SREntry">
+  <a id="Item27" onkeydown="return searchResults.Nav(event,27)" onkeypress="return searchResults.Nav(event,27)" onkeyup="return searchResults.Nav(event,27)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_getatnames')">getAtNames</a>
+  <div class="SRChildren">
+    <a id="Item27_c0" onkeydown="return searchResults.NavChild(event,27,0)" onkeypress="return searchResults.NavChild(event,27,0)" onkeyup="return searchResults.NavChild(event,27,0)" class="SRScope" href="../classccp4srs_1_1_base.html#af9a1789b20b43e97a8eb6a56b4ef32c4" target="_parent">ccp4srs::Base::getAtNames(int entryNo, mmdb::PAtomName AtName, int &amp;nAtoms, int &amp;nH)</a>
+    <a id="Item27_c1" onkeydown="return searchResults.NavChild(event,27,1)" onkeypress="return searchResults.NavChild(event,27,1)" onkeyup="return searchResults.NavChild(event,27,1)" class="SRScope" href="../classccp4srs_1_1_base.html#afbe234eef9c84fde630b72fbcfe27946" target="_parent">ccp4srs::Base::getAtNames(mmdb::io::PFile structFile, int entryNo, mmdb::PAtomName AtName, int &amp;nAtoms, int &amp;nH)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_getatomnamematch">
+ <div class="SREntry">
+  <a id="Item28" onkeydown="return searchResults.Nav(event,28)" onkeypress="return searchResults.Nav(event,28)" onkeyup="return searchResults.Nav(event,28)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_getatomnamematch')">getAtomNameMatch</a>
+  <div class="SRChildren">
+    <a id="Item28_c0" onkeydown="return searchResults.NavChild(event,28,0)" onkeypress="return searchResults.NavChild(event,28,0)" onkeyup="return searchResults.NavChild(event,28,0)" class="SRScope" href="../classccp4srs_1_1_monomer.html#abb514ab63af7e9dbb68f59bc13551618" target="_parent">ccp4srs::Monomer::getAtomNameMatch(mmdb::PPAtom A, int nat, mmdb::pstr altLoc, mmdb::ivector anmatch)</a>
+    <a id="Item28_c1" onkeydown="return searchResults.NavChild(event,28,1)" onkeypress="return searchResults.NavChild(event,28,1)" onkeyup="return searchResults.NavChild(event,28,1)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a17d26aa3a5b3b637cf6148499013c345" target="_parent">ccp4srs::Monomer::getAtomNameMatch(Container&lt; Atom &gt; *A, mmdb::ivector anmatch)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_getatoms">
+ <div class="SREntry">
+  <a id="Item29" onkeydown="return searchResults.Nav(event,29)" onkeypress="return searchResults.Nav(event,29)" onkeyup="return searchResults.Nav(event,29)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a7e47408dacc9bd80de046504e235cc06" target="_parent">getAtoms</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_getbonds">
+ <div class="SREntry">
+  <a id="Item30" onkeydown="return searchResults.Nav(event,30)" onkeypress="return searchResults.Nav(event,30)" onkeyup="return searchResults.Nav(event,30)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a8bb61486d7dd2df0566b8e3a1c7f1c89" target="_parent">getBonds</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_getenergytypes">
+ <div class="SREntry">
+  <a id="Item31" onkeydown="return searchResults.Nav(event,31)" onkeypress="return searchResults.Nav(event,31)" onkeyup="return searchResults.Nav(event,31)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_getenergytypes')">getEnergyTypes</a>
+  <div class="SRChildren">
+    <a id="Item31_c0" onkeydown="return searchResults.NavChild(event,31,0)" onkeypress="return searchResults.NavChild(event,31,0)" onkeyup="return searchResults.NavChild(event,31,0)" class="SRScope" href="../classccp4srs_1_1_chem.html#a301341ad4a91bf6cc4e7641efeb56309" target="_parent">ccp4srs::Chem::getEnergyTypes(mmdb::PResidue R, mmdb::io::PFile structFile)</a>
+    <a id="Item31_c1" onkeydown="return searchResults.NavChild(event,31,1)" onkeypress="return searchResults.NavChild(event,31,1)" onkeyup="return searchResults.NavChild(event,31,1)" class="SRScope" href="../classccp4srs_1_1_chem.html#acb540af5e9036d7765dfdaa762fb6b2f" target="_parent">ccp4srs::Chem::getEnergyTypes(mmdb::PPResidue R, int nRes, mmdb::io::PFile structFile)</a>
+    <a id="Item31_c2" onkeydown="return searchResults.NavChild(event,31,2)" onkeypress="return searchResults.NavChild(event,31,2)" onkeyup="return searchResults.NavChild(event,31,2)" class="SRScope" href="../classccp4srs_1_1_chem.html#a6993968f40984c210ffad03588321d70" target="_parent">ccp4srs::Chem::getEnergyTypes(mmdb::PChain chain, mmdb::io::PFile structFile)</a>
+    <a id="Item31_c3" onkeydown="return searchResults.NavChild(event,31,3)" onkeypress="return searchResults.NavChild(event,31,3)" onkeyup="return searchResults.NavChild(event,31,3)" class="SRScope" href="../classccp4srs_1_1_chem.html#a6a9f477d2484e2e2d71328934432e1f8" target="_parent">ccp4srs::Chem::getEnergyTypes(mmdb::PModel model, mmdb::io::PFile structFile)</a>
+    <a id="Item31_c4" onkeydown="return searchResults.NavChild(event,31,4)" onkeypress="return searchResults.NavChild(event,31,4)" onkeyup="return searchResults.NavChild(event,31,4)" class="SRScope" href="../classccp4srs_1_1_chem.html#a227201ea4eedc8464c764dd015b7b190" target="_parent">ccp4srs::Chem::getEnergyTypes(mmdb::PManager MMDB, mmdb::io::PFile structFile)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_getentryno">
+ <div class="SREntry">
+  <a id="Item32" onkeydown="return searchResults.Nav(event,32)" onkeypress="return searchResults.Nav(event,32)" onkeyup="return searchResults.Nav(event,32)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a57b706684f3e84c741099ff904e01152" target="_parent">getEntryNo</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_getgraph">
+ <div class="SREntry">
+  <a id="Item33" onkeydown="return searchResults.Nav(event,33)" onkeypress="return searchResults.Nav(event,33)" onkeyup="return searchResults.Nav(event,33)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_getgraph')">getGraph</a>
+  <div class="SRChildren">
+    <a id="Item33_c0" onkeydown="return searchResults.NavChild(event,33,0)" onkeypress="return searchResults.NavChild(event,33,0)" onkeyup="return searchResults.NavChild(event,33,0)" class="SRScope" href="../classccp4srs_1_1_base.html#a17b78139832b00d7025236171ab31b7e" target="_parent">ccp4srs::Base::getGraph(mmdb::io::PFile graphFile, mmdb::math::RPGraph G)</a>
+    <a id="Item33_c1" onkeydown="return searchResults.NavChild(event,33,1)" onkeypress="return searchResults.NavChild(event,33,1)" onkeyup="return searchResults.NavChild(event,33,1)" class="SRScope" href="../classccp4srs_1_1_base.html#a8421066e4a9117cd380ff4362c355986" target="_parent">ccp4srs::Base::getGraph(mmdb::io::PFile graphFile, int entryNo, mmdb::math::RPGraph G, int Hflag)</a>
+    <a id="Item33_c2" onkeydown="return searchResults.NavChild(event,33,2)" onkeypress="return searchResults.NavChild(event,33,2)" onkeyup="return searchResults.NavChild(event,33,2)" class="SRScope" href="../classccp4srs_1_1_base.html#af00d1ee772d045c048aa292457755b50" target="_parent">ccp4srs::Base::getGraph(mmdb::io::PFile graphFile, mmdb::math::RPGraph G, int Hflag)</a>
+    <a id="Item33_c3" onkeydown="return searchResults.NavChild(event,33,3)" onkeypress="return searchResults.NavChild(event,33,3)" onkeyup="return searchResults.NavChild(event,33,3)" class="SRScope" href="../classccp4srs_1_1_base.html#a418f3d4d079e0c4b93ebc6fff1fd0639" target="_parent">ccp4srs::Base::getGraph(int entryNo, mmdb::math::RPGraph G, int Hflag)</a>
+    <a id="Item33_c4" onkeydown="return searchResults.NavChild(event,33,4)" onkeypress="return searchResults.NavChild(event,33,4)" onkeyup="return searchResults.NavChild(event,33,4)" class="SRScope" href="../classccp4srs_1_1_base.html#a1f9dd08ea6c39fc0bb0a3885e6b3efac" target="_parent">ccp4srs::Base::getGraph(mmdb::cpstr entryID, mmdb::math::RPGraph G, int Hflag)</a>
+    <a id="Item33_c5" onkeydown="return searchResults.NavChild(event,33,5)" onkeypress="return searchResults.NavChild(event,33,5)" onkeyup="return searchResults.NavChild(event,33,5)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a9d1a2b0facb208344413158d74446755" target="_parent">ccp4srs::Monomer::getGraph()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_getgraphfile">
+ <div class="SREntry">
+  <a id="Item34" onkeydown="return searchResults.Nav(event,34)" onkeypress="return searchResults.Nav(event,34)" onkeyup="return searchResults.Nav(event,34)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a656b776b70ead2f8346b352b3bd1311e" target="_parent">getGraphFile</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_gethetinfo">
+ <div class="SREntry">
+  <a id="Item35" onkeydown="return searchResults.Nav(event,35)" onkeypress="return searchResults.Nav(event,35)" onkeyup="return searchResults.Nav(event,35)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a88c88924e247250d08cc4795b345c66a" target="_parent">getHetInfo</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_getindex">
+ <div class="SREntry">
+  <a id="Item36" onkeydown="return searchResults.Nav(event,36)" onkeypress="return searchResults.Nav(event,36)" onkeyup="return searchResults.Nav(event,36)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_getindex')">getIndex</a>
+  <div class="SRChildren">
+    <a id="Item36_c0" onkeydown="return searchResults.NavChild(event,36,0)" onkeypress="return searchResults.NavChild(event,36,0)" onkeyup="return searchResults.NavChild(event,36,0)" class="SRScope" href="../classccp4srs_1_1_base.html#affa058db2078bc7835e9c78ca3bdde81" target="_parent">ccp4srs::Base::getIndex(mmdb::cpstr entryID)</a>
+    <a id="Item36_c1" onkeydown="return searchResults.NavChild(event,36,1)" onkeypress="return searchResults.NavChild(event,36,1)" onkeyup="return searchResults.NavChild(event,36,1)" class="SRScope" href="../classccp4srs_1_1_base.html#a399ff3d49a14dd3bb8250058f6452f4f" target="_parent">ccp4srs::Base::getIndex(int n)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_getleavingatoms">
+ <div class="SREntry">
+  <a id="Item37" onkeydown="return searchResults.Nav(event,37)" onkeypress="return searchResults.Nav(event,37)" onkeyup="return searchResults.Nav(event,37)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a6c3ad68f13fb779921605d0e696add1c" target="_parent">getLeavingAtoms</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_getmonomer">
+ <div class="SREntry">
+  <a id="Item38" onkeydown="return searchResults.Nav(event,38)" onkeypress="return searchResults.Nav(event,38)" onkeyup="return searchResults.Nav(event,38)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_getmonomer')">getMonomer</a>
+  <div class="SRChildren">
+    <a id="Item38_c0" onkeydown="return searchResults.NavChild(event,38,0)" onkeypress="return searchResults.NavChild(event,38,0)" onkeyup="return searchResults.NavChild(event,38,0)" class="SRScope" href="../classccp4srs_1_1_base.html#a339033984c68dd221cd6db184b734694" target="_parent">ccp4srs::Base::getMonomer(mmdb::cpstr entryID)</a>
+    <a id="Item38_c1" onkeydown="return searchResults.NavChild(event,38,1)" onkeypress="return searchResults.NavChild(event,38,1)" onkeyup="return searchResults.NavChild(event,38,1)" class="SRScope" href="../classccp4srs_1_1_base.html#a6f3f6564a30198bfe82215bceb6806e2" target="_parent">ccp4srs::Base::getMonomer(int entryNo, mmdb::io::PFile structFile)</a>
+    <a id="Item38_c2" onkeydown="return searchResults.NavChild(event,38,2)" onkeypress="return searchResults.NavChild(event,38,2)" onkeyup="return searchResults.NavChild(event,38,2)" class="SRScope" href="../classccp4srs_1_1_base.html#ad25bf7474ec0574a39081ec5eeaefc5b" target="_parent">ccp4srs::Base::getMonomer(mmdb::cpstr entryID, mmdb::io::PFile structFile)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_getnewhandles">
+ <div class="SREntry">
+  <a id="Item39" onkeydown="return searchResults.Nav(event,39)" onkeypress="return searchResults.Nav(event,39)" onkeyup="return searchResults.Nav(event,39)" class="SRSymbol" href="../structccp4srs_1_1_d_a_sel_hnds.html#a3e8624665274bf47da9408f3b21f35d8" target="_parent">getNewHandles</a>
+  <span class="SRScope">ccp4srs::DASelHnds</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_getnofatoms">
+ <div class="SREntry">
+  <a id="Item40" onkeydown="return searchResults.Nav(event,40)" onkeypress="return searchResults.Nav(event,40)" onkeyup="return searchResults.Nav(event,40)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_getnofatoms')">getNofAtoms</a>
+  <div class="SRChildren">
+    <a id="Item40_c0" onkeydown="return searchResults.NavChild(event,40,0)" onkeypress="return searchResults.NavChild(event,40,0)" onkeyup="return searchResults.NavChild(event,40,0)" class="SRScope" href="../classccp4srs_1_1_base.html#a646d2c4349be4a740f2121dfd2091150" target="_parent">ccp4srs::Base::getNofAtoms(mmdb::cpstr entryID)</a>
+    <a id="Item40_c1" onkeydown="return searchResults.NavChild(event,40,1)" onkeypress="return searchResults.NavChild(event,40,1)" onkeyup="return searchResults.NavChild(event,40,1)" class="SRScope" href="../classccp4srs_1_1_base.html#a025a5622f0bfb83808cdad7cbf7af974" target="_parent">ccp4srs::Base::getNofAtoms(int entryNo)</a>
+    <a id="Item40_c2" onkeydown="return searchResults.NavChild(event,40,2)" onkeypress="return searchResults.NavChild(event,40,2)" onkeyup="return searchResults.NavChild(event,40,2)" class="SRScope" href="../classccp4srs_1_1_base.html#af0653379d9db757dcc64c44c0e9ce070" target="_parent">ccp4srs::Base::getNofAtoms(int entryNo, int &amp;nNonHAtoms, int &amp;nHAtoms)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_getpath">
+ <div class="SREntry">
+  <a id="Item41" onkeydown="return searchResults.Nav(event,41)" onkeypress="return searchResults.Nav(event,41)" onkeyup="return searchResults.Nav(event,41)" class="SRSymbol" href="../classccp4srs_1_1_base.html#ac5481a8eeeb26ead06d7df61f605dac9" target="_parent">getPath</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_getstructfile">
+ <div class="SREntry">
+  <a id="Item42" onkeydown="return searchResults.Nav(event,42)" onkeypress="return searchResults.Nav(event,42)" onkeyup="return searchResults.Nav(event,42)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a03eac100b52d1f2d2d13981799f928bb" target="_parent">getStructFile</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
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+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_68.html ccp4srs/doc-html/html/search/all_68.html
--- ccp4srs-old/doc-html/html/search/all_68.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_68.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,26 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_hb_5ftype">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#ab45d65bdba2966ce382687548921cd56" target="_parent">hb_type</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_69.html ccp4srs/doc-html/html/search/all_69.html
--- ccp4srs-old/doc-html/html/search/all_69.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_69.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,93 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_id">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_id')">id</a>
+  <div class="SRChildren">
+    <a id="Item0_c0" onkeydown="return searchResults.NavChild(event,0,0)" onkeypress="return searchResults.NavChild(event,0,0)" onkeyup="return searchResults.NavChild(event,0,0)" class="SRScope" href="../classccp4srs_1_1_atom.html#a276b8b3e31130e6f0116af498e3a7766" target="_parent">ccp4srs::Atom::id()</a>
+    <a id="Item0_c1" onkeydown="return searchResults.NavChild(event,0,1)" onkeypress="return searchResults.NavChild(event,0,1)" onkeyup="return searchResults.NavChild(event,0,1)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#a9bd5958f4cb3519a6a745d1db16b135b" target="_parent">ccp4srs::ChiCenter::id()</a>
+    <a id="Item0_c2" onkeydown="return searchResults.NavChild(event,0,2)" onkeypress="return searchResults.NavChild(event,0,2)" onkeyup="return searchResults.NavChild(event,0,2)" class="SRScope" href="../classccp4srs_1_1_plane.html#ac47f99cd6bf3190767da8fc85d01dc18" target="_parent">ccp4srs::Plane::id()</a>
+    <a id="Item0_c3" onkeydown="return searchResults.NavChild(event,0,3)" onkeypress="return searchResults.NavChild(event,0,3)" onkeyup="return searchResults.NavChild(event,0,3)" class="SRScope" href="../classccp4srs_1_1_torsion.html#a63cbef738a4be2da8a46367802f83e3d" target="_parent">ccp4srs::Torsion::id()</a>
+    <a id="Item0_c4" onkeydown="return searchResults.NavChild(event,0,4)" onkeypress="return searchResults.NavChild(event,0,4)" onkeyup="return searchResults.NavChild(event,0,4)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a1eca7f4a9537bddf81de26df20984183" target="_parent">ccp4srs::Monomer::ID()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_index">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_index.html" target="_parent">Index</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_index">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_index')">index</a>
+  <div class="SRChildren">
+    <a id="Item2_c0" onkeydown="return searchResults.NavChild(event,2,0)" onkeypress="return searchResults.NavChild(event,2,0)" onkeyup="return searchResults.NavChild(event,2,0)" class="SRScope" href="../classccp4srs_1_1_base.html#ada41928311fa3ba94bcb48a1ebf4b4df" target="_parent">ccp4srs::Base::index()</a>
+    <a id="Item2_c1" onkeydown="return searchResults.NavChild(event,2,1)" onkeypress="return searchResults.NavChild(event,2,1)" onkeyup="return searchResults.NavChild(event,2,1)" class="SRScope" href="../classccp4srs_1_1_container.html#a6afe8d51f68e07697d7362464e433cac" target="_parent">ccp4srs::Container::index()</a>
+    <a id="Item2_c2" onkeydown="return searchResults.NavChild(event,2,2)" onkeypress="return searchResults.NavChild(event,2,2)" onkeyup="return searchResults.NavChild(event,2,2)" class="SRScope" href="../classccp4srs_1_1_index.html#aaff51df26ae81aff0425bda97d6f7030" target="_parent">ccp4srs::Index::Index()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_indexinit">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_index.html#aedec88e9928356d4f7c913d449ca0d3e" target="_parent">IndexInit</a>
+  <span class="SRScope">ccp4srs::Index</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_init">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_init')">Init</a>
+  <div class="SRChildren">
+    <a id="Item4_c0" onkeydown="return searchResults.NavChild(event,4,0)" onkeypress="return searchResults.NavChild(event,4,0)" onkeyup="return searchResults.NavChild(event,4,0)" class="SRScope" href="../classccp4srs_1_1_atom.html#ab6a22850541822e026c9d6a241079fd6" target="_parent">ccp4srs::Atom::Init()</a>
+    <a id="Item4_c1" onkeydown="return searchResults.NavChild(event,4,1)" onkeypress="return searchResults.NavChild(event,4,1)" onkeyup="return searchResults.NavChild(event,4,1)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a6a50cfb8d8e87162309106c66f5fc155" target="_parent">ccp4srs::Monomer::Init()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_init_5fbase">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a9fb463b8df4034fefb6e136ab56d135b" target="_parent">init_base</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_init_5fchem">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_chem.html#a7ed4ac373981270bc1af2b8cc99b461d" target="_parent">init_chem</a>
+  <span class="SRScope">ccp4srs::Chem</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_ion_5fradius">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a4cbbb8a7a4d9f69eca5caadfffa6c956" target="_parent">ion_radius</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_ionradius">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#aeb773fbdd5b04c0311969ad498622185" target="_parent">ionRadius</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_isleaving">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a7da89fae287dcf0c0838108fd442ec53" target="_parent">isLeaving</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_6c.html ccp4srs/doc-html/html/search/all_6c.html
--- ccp4srs-old/doc-html/html/search/all_6c.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_6c.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,59 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_leaving">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#ac7f1f1f474b56199e70bb0dcd364bb4b" target="_parent">leaving</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_length">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_length')">length</a>
+  <div class="SRChildren">
+    <a id="Item1_c0" onkeydown="return searchResults.NavChild(event,1,0)" onkeypress="return searchResults.NavChild(event,1,0)" onkeyup="return searchResults.NavChild(event,1,0)" class="SRScope" href="../classccp4srs_1_1_bond.html#a3ebb971fa0af7886f076da460b4875e9" target="_parent">ccp4srs::Bond::length()</a>
+    <a id="Item1_c1" onkeydown="return searchResults.NavChild(event,1,1)" onkeypress="return searchResults.NavChild(event,1,1)" onkeyup="return searchResults.NavChild(event,1,1)" class="SRScope" href="../classccp4srs_1_1_mem_i_o.html#a5e4ae24f25179a720de85f185f8074ff" target="_parent">ccp4srs::MemIO::length()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_length_5fesd">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#a28f3638c15b007dddaab637362635009" target="_parent">length_esd</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_link">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88cae7d526eebfeb15c8370f473885073095" target="_parent">Link</a>
+  <span class="SRScope">ccp4srs::Entry</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_loadindex">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_base.html#ae95af9ff2fb5c9d0edb437be3bcbe016" target="_parent">loadIndex</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_loadstructure">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a663ef26d53b80f6c8b1f9c9cdeb70d2c" target="_parent">loadStructure</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_6d.html ccp4srs/doc-html/html/search/all_6d.html
--- ccp4srs-old/doc-html/html/search/all_6d.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_6d.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,560 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_major_5fversion">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40da70b6b61e66afecc14062283f4ab22165" target="_parent">MAJOR_VERSION</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_makeatom">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_makeatom')">makeAtom</a>
+  <div class="SRChildren">
+    <a id="Item1_c0" onkeydown="return searchResults.NavChild(event,1,0)" onkeypress="return searchResults.NavChild(event,1,0)" onkeyup="return searchResults.NavChild(event,1,0)" class="SRScope" href="../classccp4srs_1_1_atom.html#a40ec4d3c3ea0384ab4d2c56b3ee5389b" target="_parent">ccp4srs::Atom::makeAtom(mmdb::RPAtom a)</a>
+    <a id="Item1_c1" onkeydown="return searchResults.NavChild(event,1,1)" onkeypress="return searchResults.NavChild(event,1,1)" onkeyup="return searchResults.NavChild(event,1,1)" class="SRScope" href="../classccp4srs_1_1_atom.html#a2528b66c2480aa6e3db8d6cfba0c4586" target="_parent">ccp4srs::Atom::makeAtom()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_makebonds">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_chem.html#ad60a617bc151e054eb306e8c6bf592f4" target="_parent">makeBonds</a>
+  <span class="SRScope">ccp4srs::Chem</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_makecif">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a5e3fb1e64eab3e764cc83ff1e6c61fa3" target="_parent">makeCIF</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_makeciftags">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_makeciftags')">makeCIFTags</a>
+  <div class="SRChildren">
+    <a id="Item4_c0" onkeydown="return searchResults.NavChild(event,4,0)" onkeypress="return searchResults.NavChild(event,4,0)" onkeyup="return searchResults.NavChild(event,4,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a257cefe6949d4371175d4c1573a1d40e" target="_parent">ccp4srs::Angle::makeCIFTags()</a>
+    <a id="Item4_c1" onkeydown="return searchResults.NavChild(event,4,1)" onkeypress="return searchResults.NavChild(event,4,1)" onkeyup="return searchResults.NavChild(event,4,1)" class="SRScope" href="../classccp4srs_1_1_atom.html#ac1bcbe4ebfbf35c7d0369d41afa07714" target="_parent">ccp4srs::Atom::makeCIFTags()</a>
+    <a id="Item4_c2" onkeydown="return searchResults.NavChild(event,4,2)" onkeypress="return searchResults.NavChild(event,4,2)" onkeyup="return searchResults.NavChild(event,4,2)" class="SRScope" href="../classccp4srs_1_1_bond.html#a781542dae98140ea687a5d83a3e02e8e" target="_parent">ccp4srs::Bond::makeCIFTags()</a>
+    <a id="Item4_c3" onkeydown="return searchResults.NavChild(event,4,3)" onkeypress="return searchResults.NavChild(event,4,3)" onkeyup="return searchResults.NavChild(event,4,3)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#a93d09528c86718358137aaf48c1a8ce1" target="_parent">ccp4srs::ChiCenter::makeCIFTags()</a>
+    <a id="Item4_c4" onkeydown="return searchResults.NavChild(event,4,4)" onkeypress="return searchResults.NavChild(event,4,4)" onkeyup="return searchResults.NavChild(event,4,4)" class="SRScope" href="../classccp4srs_1_1_plane.html#a1ac0cfa095deac2bd97e99ce2b30de96" target="_parent">ccp4srs::Plane::makeCIFTags()</a>
+    <a id="Item4_c5" onkeydown="return searchResults.NavChild(event,4,5)" onkeypress="return searchResults.NavChild(event,4,5)" onkeyup="return searchResults.NavChild(event,4,5)" class="SRScope" href="../classccp4srs_1_1_torsion.html#ae33b6fc8d12fdbd48a299cf488e16f0e" target="_parent">ccp4srs::Torsion::makeCIFTags()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_makecompositions">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_index.html#afda5436941f171c791be43b9d28f43a5" target="_parent">MakeCompositions</a>
+  <span class="SRScope">ccp4srs::Index</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_makeelementtype">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../namespaceccp4srs.html#a8b4dcaee4f20949271ceaadfb7b5a96f" target="_parent">makeElementType</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_makeselindexes">
+ <div class="SREntry">
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+<div class="SRResult" id="SR_mmcif_5ftag_5ftype_5fenergy">
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+ <div class="SREntry">
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+ <div class="SREntry">
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+<div class="SRResult" id="SR_mmcif_5ftag_5fz">
+ <div class="SREntry">
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+  <span class="SRScope">ccp4srs_defs.h</span>
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+</div>
+<div class="SRResult" id="SR_monformula">
+ <div class="SREntry">
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+  <span class="SRScope">ccp4srs::Monomer</span>
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+</div>
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+  <span class="SRScope">ccp4srs::Monomer</span>
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+</div>
+<div class="SRResult" id="SR_monname">
+ <div class="SREntry">
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+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_monomer">
+ <div class="SREntry">
+  <a id="Item81" onkeydown="return searchResults.Nav(event,81)" onkeypress="return searchResults.Nav(event,81)" onkeyup="return searchResults.Nav(event,81)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_monomer')">Monomer</a>
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+ <div class="SREntry">
+  <a id="Item82" onkeydown="return searchResults.Nav(event,82)" onkeypress="return searchResults.Nav(event,82)" onkeyup="return searchResults.Nav(event,82)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html" target="_parent">Monomer</a>
+  <span class="SRScope">ccp4srs</span>
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+</div>
+<div class="SRResult" id="SR_montype">
+ <div class="SREntry">
+  <a id="Item83" onkeydown="return searchResults.Nav(event,83)" onkeypress="return searchResults.Nav(event,83)" onkeyup="return searchResults.Nav(event,83)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#af0a573429afbbea61647c9851f0deba7" target="_parent">monType</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
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+</div>
+<div class="SRResult" id="SR_mpfile_5f_2eh">
+ <div class="SREntry">
+  <a id="Item85" onkeydown="return searchResults.Nav(event,85)" onkeypress="return searchResults.Nav(event,85)" onkeyup="return searchResults.Nav(event,85)" class="SRSymbol" href="../mpfile___8h.html" target="_parent">mpfile_.h</a>
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+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
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+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_6e.html ccp4srs/doc-html/html/search/all_6e.html
--- ccp4srs-old/doc-html/html/search/all_6e.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_6e.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,137 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_n_5fangles">
+ <div class="SREntry">
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+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
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+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_n_5fatoms')">n_atoms</a>
+  <div class="SRChildren">
+    <a id="Item1_c0" onkeydown="return searchResults.NavChild(event,1,0)" onkeypress="return searchResults.NavChild(event,1,0)" onkeyup="return searchResults.NavChild(event,1,0)" class="SRScope" href="../classccp4srs_1_1_plane.html#aa76a845ff6abce3d2c8f40db13717842" target="_parent">ccp4srs::Plane::n_atoms()</a>
+    <a id="Item1_c1" onkeydown="return searchResults.NavChild(event,1,1)" onkeypress="return searchResults.NavChild(event,1,1)" onkeyup="return searchResults.NavChild(event,1,1)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a3e3e771e2d60581384b1169648b4d751" target="_parent">ccp4srs::Monomer::n_atoms()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_n_5fbonds">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a6a6e470c174fd570667bf43f95757c0d" target="_parent">n_bonds</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_n_5fchicenters">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a047ec20b44f73aa0027fdd071aa265d6" target="_parent">n_chicenters</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_n_5fentries">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_base.html#aeb551e05e822e5eb3673aba1fa85bda6" target="_parent">n_entries</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_n_5fobjects">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748" target="_parent">n_objects</a>
+  <span class="SRScope">ccp4srs::Container</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_n_5fplanes">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a123cf02246e052730361055de3f0d477" target="_parent">n_planes</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_n_5fsections">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_tree.html#a4056f0bb5ef8add5a55133eb8166c639" target="_parent">n_sections</a>
+  <span class="SRScope">ccp4srs::Tree</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_n_5ftorsions">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a0bf10d776d5d992424b99d88d884f101" target="_parent">n_torsions</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_name">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#ad8288e82eeab398bf90da3f35ebe15c5" target="_parent">name</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_name_5fpdb">
+ <div class="SREntry">
+  <a id="Item10" onkeydown="return searchResults.Nav(event,10)" onkeypress="return searchResults.Nav(event,10)" onkeyup="return searchResults.Nav(event,10)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a357cfea9384684a64bb3220d02b3afa7" target="_parent">name_pdb</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_natoms">
+ <div class="SREntry">
+  <a id="Item11" onkeydown="return searchResults.Nav(event,11)" onkeypress="return searchResults.Nav(event,11)" onkeyup="return searchResults.Nav(event,11)" class="SRSymbol" href="../classccp4srs_1_1_index.html#abba65d2d400f004fa3815a06101ac478" target="_parent">nAtoms</a>
+  <span class="SRScope">ccp4srs::Index</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_nbonds">
+ <div class="SREntry">
+  <a id="Item12" onkeydown="return searchResults.Nav(event,12)" onkeypress="return searchResults.Nav(event,12)" onkeyup="return searchResults.Nav(event,12)" class="SRSymbol" href="../classccp4srs_1_1_index.html#a5906658999e6e4e095589e0cdffabf11" target="_parent">nBonds</a>
+  <span class="SRScope">ccp4srs::Index</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_nentries">
+ <div class="SREntry">
+  <a id="Item13" onkeydown="return searchResults.Nav(event,13)" onkeypress="return searchResults.Nav(event,13)" onkeyup="return searchResults.Nav(event,13)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a863fd5090d78f3bada7f351dd2f33859" target="_parent">nEntries</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_nnonhatoms">
+ <div class="SREntry">
+  <a id="Item14" onkeydown="return searchResults.Nav(event,14)" onkeypress="return searchResults.Nav(event,14)" onkeyup="return searchResults.Nav(event,14)" class="SRSymbol" href="../classccp4srs_1_1_index.html#aa97eb5251314eeb77e5acd2af72ce1aa" target="_parent">nNonHAtoms</a>
+  <span class="SRScope">ccp4srs::Index</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_nomoreplanes">
+ <div class="SREntry">
+  <a id="Item15" onkeydown="return searchResults.Nav(event,15)" onkeypress="return searchResults.Nav(event,15)" onkeyup="return searchResults.Nav(event,15)" class="SRSymbol" href="../classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5eda95f4f7898a15589a3db43827444d2692" target="_parent">NoMorePlanes</a>
+  <span class="SRScope">ccp4srs::Plane</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_none">
+ <div class="SREntry">
+  <a id="Item16" onkeydown="return searchResults.Nav(event,16)" onkeypress="return searchResults.Nav(event,16)" onkeyup="return searchResults.Nav(event,16)" class="SRSymbol" href="../classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88ca616c951330c4d0b080622857146e2457" target="_parent">None</a>
+  <span class="SRScope">ccp4srs::Entry</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_noorder">
+ <div class="SREntry">
+  <a id="Item17" onkeydown="return searchResults.Nav(event,17)" onkeypress="return searchResults.Nav(event,17)" onkeyup="return searchResults.Nav(event,17)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba3a534360bb854109f0ad2d34f1858997" target="_parent">noOrder</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_numberof">
+ <div class="SREntry">
+  <a id="Item18" onkeydown="return searchResults.Nav(event,18)" onkeypress="return searchResults.Nav(event,18)" onkeyup="return searchResults.Nav(event,18)" class="SRSymbol" href="../classccp4srs_1_1_container.html#abbc5e6eeb9ea4d37b8d2025892ebd9ff" target="_parent">numberOf</a>
+  <span class="SRScope">ccp4srs::Container</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_6f.html ccp4srs/doc-html/html/search/all_6f.html
--- ccp4srs-old/doc-html/html/search/all_6f.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_6f.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,77 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_object">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_container.html#a25a4ad3660f2ef6760c949be2c1372a8" target="_parent">object</a>
+  <span class="SRScope">ccp4srs::Container</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_offset">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../structccp4srs_1_1_m_p_file_pos.html#afb6853252f03dbbc698dea44b425d2d9" target="_parent">offset</a>
+  <span class="SRScope">ccp4srs::MPFilePos</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_ok">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_ok')">Ok</a>
+  <div class="SRChildren">
+    <a id="Item2_c0" onkeydown="return searchResults.NavChild(event,2,0)" onkeypress="return searchResults.NavChild(event,2,0)" onkeyup="return searchResults.NavChild(event,2,0)" class="SRScope" href="../classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5edae47dd3ee9591c478c387ddbe09f7ef34" target="_parent">ccp4srs::Plane::Ok()</a>
+    <a id="Item2_c1" onkeydown="return searchResults.NavChild(event,2,1)" onkeypress="return searchResults.NavChild(event,2,1)" onkeyup="return searchResults.NavChild(event,2,1)" class="SRScope" href="../classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63" target="_parent">ccp4srs::MemIO::Ok()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_old_5fname">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#acda740ae967221e50f1d383ce70d58d9" target="_parent">old_name</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_old_5fname_5fpdb">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#abd73ea1b813b1321048f850b88914982" target="_parent">old_name_pdb</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_oldatomname">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a45682b942f2f9262bc8fa1b5316a702b" target="_parent">oldAtomName</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_oldid">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a271e6aaeed7ace67e36f2c5fea626d70" target="_parent">oldID</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_oldmonid">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a896cc0c3979b65913de25be2c2f75ec9" target="_parent">oldMonID</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_order">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#ae18a9e08399e96910028f01a376d41f0" target="_parent">order</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_70.html ccp4srs/doc-html/html/search/all_70.html
--- ccp4srs-old/doc-html/html/search/all_70.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_70.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,185 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_pdb_5fx">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a49ff7aadab557a536541009606a2db12" target="_parent">pdb_x</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_pdb_5fy">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a901c15656be6fa36e191df297d25521d" target="_parent">pdb_y</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_pdb_5fz">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#ae33b2033023270f96202151aed27a710" target="_parent">pdb_z</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_pdbx_5fx">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#aec57c2566b6a42361a8215d7b15a7e29" target="_parent">pdbx_x</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_pdbx_5fy">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a1d138de5fa3e222554a95b796c246d40" target="_parent">pdbx_y</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_pdbx_5fz">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a424a6001bc93ea1c8256f9f1fb48a585" target="_parent">pdbx_z</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_period">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_torsion.html#a8fd30d637a8002a46ff4c50cadc8d34f" target="_parent">period</a>
+  <span class="SRScope">ccp4srs::Torsion</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_plane">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_plane.html" target="_parent">Plane</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_plane">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_plane')">plane</a>
+  <div class="SRChildren">
+    <a id="Item8_c0" onkeydown="return searchResults.NavChild(event,8,0)" onkeypress="return searchResults.NavChild(event,8,0)" onkeyup="return searchResults.NavChild(event,8,0)" class="SRScope" href="../classccp4srs_1_1_monomer.html#afdebf230f6aa9bf2692a82b919d59918" target="_parent">ccp4srs::Monomer::plane()</a>
+    <a id="Item8_c1" onkeydown="return searchResults.NavChild(event,8,1)" onkeypress="return searchResults.NavChild(event,8,1)" onkeyup="return searchResults.NavChild(event,8,1)" class="SRScope" href="../classccp4srs_1_1_plane.html#ab45260579cf6dd22ecdaa93ad3b5c183" target="_parent">ccp4srs::Plane::Plane()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_plane_5fatoms">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="../classccp4srs_1_1_plane.html#a4c8155332953ddb6cf79acf018c98c85" target="_parent">plane_atoms</a>
+  <span class="SRScope">ccp4srs::Plane</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_plane_5fid">
+ <div class="SREntry">
+  <a id="Item10" onkeydown="return searchResults.Nav(event,10)" onkeypress="return searchResults.Nav(event,10)" onkeyup="return searchResults.Nav(event,10)" class="SRSymbol" href="../classccp4srs_1_1_plane.html#afdfdff5528e19537d834061022c2b2bf" target="_parent">plane_id</a>
+  <span class="SRScope">ccp4srs::Plane</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_planeid">
+ <div class="SREntry">
+  <a id="Item11" onkeydown="return searchResults.Nav(event,11)" onkeypress="return searchResults.Nav(event,11)" onkeyup="return searchResults.Nav(event,11)" class="SRSymbol" href="../namespaceccp4srs.html#ac768cc62149be89b81a30d88a09f0166" target="_parent">PlaneID</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_planes">
+ <div class="SREntry">
+  <a id="Item12" onkeydown="return searchResults.Nav(event,12)" onkeypress="return searchResults.Nav(event,12)" onkeyup="return searchResults.Nav(event,12)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a2f927ab2a3e517f9fe6cba6e89954cfe" target="_parent">planes</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
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+<div class="SRResult" id="SR_property">
+ <div class="SREntry">
+  <a id="Item13" onkeydown="return searchResults.Nav(event,13)" onkeypress="return searchResults.Nav(event,13)" onkeyup="return searchResults.Nav(event,13)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#aa363093b5746f782b8c4e60a73ec6438" target="_parent">property</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5fbool">
+ <div class="SREntry">
+  <a id="Item14" onkeydown="return searchResults.Nav(event,14)" onkeypress="return searchResults.Nav(event,14)" onkeyup="return searchResults.Nav(event,14)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#ac3420c8a37ce57f324cf66eb4ccb9b13" target="_parent">put_bool</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5fbyte">
+ <div class="SREntry">
+  <a id="Item15" onkeydown="return searchResults.Nav(event,15)" onkeypress="return searchResults.Nav(event,15)" onkeyup="return searchResults.Nav(event,15)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a3c30e4f73927173a9ce5731fab39d170" target="_parent">put_byte</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5ffloat">
+ <div class="SREntry">
+  <a id="Item16" onkeydown="return searchResults.Nav(event,16)" onkeypress="return searchResults.Nav(event,16)" onkeyup="return searchResults.Nav(event,16)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#ad82c1eca930cc9d5535f2da1ab3cde1a" target="_parent">put_float</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5fibyte">
+ <div class="SREntry">
+  <a id="Item17" onkeydown="return searchResults.Nav(event,17)" onkeypress="return searchResults.Nav(event,17)" onkeyup="return searchResults.Nav(event,17)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a55ccb2d1a276365eadb422c75e982de3" target="_parent">put_ibyte</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5finteger">
+ <div class="SREntry">
+  <a id="Item18" onkeydown="return searchResults.Nav(event,18)" onkeypress="return searchResults.Nav(event,18)" onkeyup="return searchResults.Nav(event,18)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a6c563469a6978a9c1c62a33457c90661" target="_parent">put_integer</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5fishort">
+ <div class="SREntry">
+  <a id="Item19" onkeydown="return searchResults.Nav(event,19)" onkeypress="return searchResults.Nav(event,19)" onkeyup="return searchResults.Nav(event,19)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a1a5cd9341de994fa17ae8efae3d61732" target="_parent">put_ishort</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5fline">
+ <div class="SREntry">
+  <a id="Item20" onkeydown="return searchResults.Nav(event,20)" onkeypress="return searchResults.Nav(event,20)" onkeyup="return searchResults.Nav(event,20)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a98548fca1e008178fef523b271db5423" target="_parent">put_line</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5flong">
+ <div class="SREntry">
+  <a id="Item21" onkeydown="return searchResults.Nav(event,21)" onkeypress="return searchResults.Nav(event,21)" onkeyup="return searchResults.Nav(event,21)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#af300f12e3fe4b3d878f80caf19b66341" target="_parent">put_long</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5freal">
+ <div class="SREntry">
+  <a id="Item22" onkeydown="return searchResults.Nav(event,22)" onkeypress="return searchResults.Nav(event,22)" onkeyup="return searchResults.Nav(event,22)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a1d8e03e12f2420c9650f4a8956a1c0a7" target="_parent">put_real</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5fshort">
+ <div class="SREntry">
+  <a id="Item23" onkeydown="return searchResults.Nav(event,23)" onkeypress="return searchResults.Nav(event,23)" onkeyup="return searchResults.Nav(event,23)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a7117ff86d20006f7a693ea3a36035674" target="_parent">put_short</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5fshortreal">
+ <div class="SREntry">
+  <a id="Item24" onkeydown="return searchResults.Nav(event,24)" onkeypress="return searchResults.Nav(event,24)" onkeyup="return searchResults.Nav(event,24)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a4eb6ba2e97922bf9509d828ee075aa8e" target="_parent">put_shortreal</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5fstring">
+ <div class="SREntry">
+  <a id="Item25" onkeydown="return searchResults.Nav(event,25)" onkeypress="return searchResults.Nav(event,25)" onkeyup="return searchResults.Nav(event,25)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#aa35e6bbff841d942f793e50ee813fc97" target="_parent">put_string</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5fword">
+ <div class="SREntry">
+  <a id="Item26" onkeydown="return searchResults.Nav(event,26)" onkeypress="return searchResults.Nav(event,26)" onkeyup="return searchResults.Nav(event,26)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#abf6e925edc35b60fe7816223ceb7a15f" target="_parent">put_word</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
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+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_72.html ccp4srs/doc-html/html/search/all_72.html
--- ccp4srs-old/doc-html/html/search/all_72.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_72.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,139 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_rcsb_5fchirality">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a1dc09ecc6dee155b93e5c3431d4c548e" target="_parent">rcsb_chirality</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_rcsb_5fname">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#af0bbf72624e0f7de9900ec931b673410" target="_parent">rcsb_name</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_rcsb_5fname_5fpdb">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#ace51a15043535b0fef9b2816dba48cdb" target="_parent">rcsb_name_pdb</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_rcsbatomname">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a198154f097c4f42a4ae1dd73d5394734" target="_parent">rcsbAtomName</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_read">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_read')">read</a>
+  <div class="SRChildren">
+    <a id="Item4_c0" onkeydown="return searchResults.NavChild(event,4,0)" onkeypress="return searchResults.NavChild(event,4,0)" onkeyup="return searchResults.NavChild(event,4,0)" class="SRScope" href="../classccp4srs_1_1_entry.html#a262e2814d9a1bc35fbbfd75e46397343" target="_parent">ccp4srs::Entry::read()</a>
+    <a id="Item4_c1" onkeydown="return searchResults.NavChild(event,4,1)" onkeypress="return searchResults.NavChild(event,4,1)" onkeyup="return searchResults.NavChild(event,4,1)" class="SRScope" href="../classccp4srs_1_1_index.html#a17c3250780def030676fef212a19731c" target="_parent">ccp4srs::Index::read()</a>
+    <a id="Item4_c2" onkeydown="return searchResults.NavChild(event,4,2)" onkeypress="return searchResults.NavChild(event,4,2)" onkeyup="return searchResults.NavChild(event,4,2)" class="SRScope" href="../classccp4srs_1_1_mem_i_o.html#ad8c19ab9e2bd98b40caf95cc6d7e071e" target="_parent">ccp4srs::MemIO::read(mmdb::cpstr fileName, mmdb::io::GZ_MODE gzMode=mmdb::io::GZM_NONE)</a>
+    <a id="Item4_c3" onkeydown="return searchResults.NavChild(event,4,3)" onkeypress="return searchResults.NavChild(event,4,3)" onkeyup="return searchResults.NavChild(event,4,3)" class="SRScope" href="../classccp4srs_1_1_mem_i_o.html#aebd3a0d6614c77b533433bc75de6d069" target="_parent">ccp4srs::MemIO::read(mmdb::io::RFile f)</a>
+    <a id="Item4_c4" onkeydown="return searchResults.NavChild(event,4,4)" onkeypress="return searchResults.NavChild(event,4,4)" onkeyup="return searchResults.NavChild(event,4,4)" class="SRScope" href="../structccp4srs_1_1_m_p_file_pos.html#a8351d37471b7cdab264a91bb1a92db1c" target="_parent">ccp4srs::MPFilePos::read()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_read_5fbuffer">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a7df5365c01565a15ac3bca748e46146b" target="_parent">read_buffer</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_read_5fmem">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_read_5fmem')">read_mem</a>
+  <div class="SRChildren">
+    <a id="Item6_c0" onkeydown="return searchResults.NavChild(event,6,0)" onkeypress="return searchResults.NavChild(event,6,0)" onkeyup="return searchResults.NavChild(event,6,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a2f34c77527204676236a28c863f5adee" target="_parent">ccp4srs::Angle::read_mem()</a>
+    <a id="Item6_c1" onkeydown="return searchResults.NavChild(event,6,1)" onkeypress="return searchResults.NavChild(event,6,1)" onkeyup="return searchResults.NavChild(event,6,1)" class="SRScope" href="../classccp4srs_1_1_atom.html#a150503215d6820dda3726b107e8e1bc7" target="_parent">ccp4srs::Atom::read_mem()</a>
+    <a id="Item6_c2" onkeydown="return searchResults.NavChild(event,6,2)" onkeypress="return searchResults.NavChild(event,6,2)" onkeyup="return searchResults.NavChild(event,6,2)" class="SRScope" href="../classccp4srs_1_1_bond.html#a47ad8a18d4c0363dc1f04f3cfbc670ec" target="_parent">ccp4srs::Bond::read_mem()</a>
+    <a id="Item6_c3" onkeydown="return searchResults.NavChild(event,6,3)" onkeypress="return searchResults.NavChild(event,6,3)" onkeyup="return searchResults.NavChild(event,6,3)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#a64588b20c5010e22ad5d571343a7e6d0" target="_parent">ccp4srs::ChiCenter::read_mem()</a>
+    <a id="Item6_c4" onkeydown="return searchResults.NavChild(event,6,4)" onkeypress="return searchResults.NavChild(event,6,4)" onkeyup="return searchResults.NavChild(event,6,4)" class="SRScope" href="../classccp4srs_1_1_container.html#a9f42bc8ec160490ba2dd8d7a8eeae15e" target="_parent">ccp4srs::Container::read_mem()</a>
+    <a id="Item6_c5" onkeydown="return searchResults.NavChild(event,6,5)" onkeypress="return searchResults.NavChild(event,6,5)" onkeyup="return searchResults.NavChild(event,6,5)" class="SRScope" href="../classccp4srs_1_1_entry.html#a2d3193b4e34c21b286526931e2e5b62d" target="_parent">ccp4srs::Entry::read_mem()</a>
+    <a id="Item6_c6" onkeydown="return searchResults.NavChild(event,6,6)" onkeypress="return searchResults.NavChild(event,6,6)" onkeyup="return searchResults.NavChild(event,6,6)" class="SRScope" href="../classccp4srs_1_1_index.html#a06b50353c15a21a56688b3e00aad2e2d" target="_parent">ccp4srs::Index::read_mem()</a>
+    <a id="Item6_c7" onkeydown="return searchResults.NavChild(event,6,7)" onkeypress="return searchResults.NavChild(event,6,7)" onkeyup="return searchResults.NavChild(event,6,7)" class="SRScope" href="../classccp4srs_1_1_monomer.html#ac12b93e766cfbcfd4288512df739a56e" target="_parent">ccp4srs::Monomer::read_mem()</a>
+    <a id="Item6_c8" onkeydown="return searchResults.NavChild(event,6,8)" onkeypress="return searchResults.NavChild(event,6,8)" onkeyup="return searchResults.NavChild(event,6,8)" class="SRScope" href="../classccp4srs_1_1_plane.html#a148162145438f6f97414eee0aa72275a" target="_parent">ccp4srs::Plane::read_mem()</a>
+    <a id="Item6_c9" onkeydown="return searchResults.NavChild(event,6,9)" onkeypress="return searchResults.NavChild(event,6,9)" onkeyup="return searchResults.NavChild(event,6,9)" class="SRScope" href="../classccp4srs_1_1_torsion.html#af65ef2e18a3b6494070300afec0099e1" target="_parent">ccp4srs::Torsion::read_mem()</a>
+    <a id="Item6_c10" onkeydown="return searchResults.NavChild(event,6,10)" onkeypress="return searchResults.NavChild(event,6,10)" onkeyup="return searchResults.NavChild(event,6,10)" class="SRScope" href="../classccp4srs_1_1_tree.html#a7e39da9840cb8815e8854cd11552c3a9" target="_parent">ccp4srs::Tree::read_mem()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_readerror">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaab76082bd26e6e49c9c7794410cec3ca2" target="_parent">ReadError</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_readfromcif">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_readfromcif')">readFromCIF</a>
+  <div class="SRChildren">
+    <a id="Item8_c0" onkeydown="return searchResults.NavChild(event,8,0)" onkeypress="return searchResults.NavChild(event,8,0)" onkeyup="return searchResults.NavChild(event,8,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a9a366216e8c07f33829fd26db9df4f00" target="_parent">ccp4srs::Angle::readFromCIF()</a>
+    <a id="Item8_c1" onkeydown="return searchResults.NavChild(event,8,1)" onkeypress="return searchResults.NavChild(event,8,1)" onkeyup="return searchResults.NavChild(event,8,1)" class="SRScope" href="../classccp4srs_1_1_atom.html#a94f5f81532b98126f3383f29c077473c" target="_parent">ccp4srs::Atom::readFromCIF()</a>
+    <a id="Item8_c2" onkeydown="return searchResults.NavChild(event,8,2)" onkeypress="return searchResults.NavChild(event,8,2)" onkeyup="return searchResults.NavChild(event,8,2)" class="SRScope" href="../classccp4srs_1_1_bond.html#a24976c4962050d858ca00fa6f72684e2" target="_parent">ccp4srs::Bond::readFromCIF()</a>
+    <a id="Item8_c3" onkeydown="return searchResults.NavChild(event,8,3)" onkeypress="return searchResults.NavChild(event,8,3)" onkeyup="return searchResults.NavChild(event,8,3)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#a8c038c3d35ef4effbe5e02db4cdf9f88" target="_parent">ccp4srs::ChiCenter::readFromCIF()</a>
+    <a id="Item8_c4" onkeydown="return searchResults.NavChild(event,8,4)" onkeypress="return searchResults.NavChild(event,8,4)" onkeyup="return searchResults.NavChild(event,8,4)" class="SRScope" href="../classccp4srs_1_1_monomer.html#aa9b0a99023e890070aec088182f8a65b" target="_parent">ccp4srs::Monomer::readFromCIF()</a>
+    <a id="Item8_c5" onkeydown="return searchResults.NavChild(event,8,5)" onkeypress="return searchResults.NavChild(event,8,5)" onkeyup="return searchResults.NavChild(event,8,5)" class="SRScope" href="../classccp4srs_1_1_plane.html#a656a93b833de401dcac75db47b5bcf57" target="_parent">ccp4srs::Plane::readFromCIF()</a>
+    <a id="Item8_c6" onkeydown="return searchResults.NavChild(event,8,6)" onkeypress="return searchResults.NavChild(event,8,6)" onkeyup="return searchResults.NavChild(event,8,6)" class="SRScope" href="../classccp4srs_1_1_torsion.html#aaf9375ff9aeb22a2a148763276ec80d1" target="_parent">ccp4srs::Torsion::readFromCIF()</a>
+    <a id="Item8_c7" onkeydown="return searchResults.NavChild(event,8,7)" onkeypress="return searchResults.NavChild(event,8,7)" onkeyup="return searchResults.NavChild(event,8,7)" class="SRScope" href="../classccp4srs_1_1_tree.html#af50e009eb63e2bdf8da129afa193d637" target="_parent">ccp4srs::Tree::readFromCIF()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_readfromcif_5fccp4">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_readfromcif_5fccp4')">readFromCIF_ccp4</a>
+  <div class="SRChildren">
+    <a id="Item9_c0" onkeydown="return searchResults.NavChild(event,9,0)" onkeypress="return searchResults.NavChild(event,9,0)" onkeyup="return searchResults.NavChild(event,9,0)" class="SRScope" href="../classccp4srs_1_1_atom.html#a0e4f39d4293b8e1907b0295e215c4230" target="_parent">ccp4srs::Atom::readFromCIF_ccp4()</a>
+    <a id="Item9_c1" onkeydown="return searchResults.NavChild(event,9,1)" onkeypress="return searchResults.NavChild(event,9,1)" onkeyup="return searchResults.NavChild(event,9,1)" class="SRScope" href="../classccp4srs_1_1_bond.html#ac6a267f1cb4e7553d746537cf36e5ea3" target="_parent">ccp4srs::Bond::readFromCIF_ccp4()</a>
+    <a id="Item9_c2" onkeydown="return searchResults.NavChild(event,9,2)" onkeypress="return searchResults.NavChild(event,9,2)" onkeyup="return searchResults.NavChild(event,9,2)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a9e457d3f7633b79b598b66f382fa5c5c" target="_parent">ccp4srs::Monomer::readFromCIF_ccp4()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_readfromcif_5frcsb">
+ <div class="SREntry">
+  <a id="Item10" onkeydown="return searchResults.Nav(event,10)" onkeypress="return searchResults.Nav(event,10)" onkeyup="return searchResults.Nav(event,10)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_readfromcif_5frcsb')">readFromCIF_rcsb</a>
+  <div class="SRChildren">
+    <a id="Item10_c0" onkeydown="return searchResults.NavChild(event,10,0)" onkeypress="return searchResults.NavChild(event,10,0)" onkeyup="return searchResults.NavChild(event,10,0)" class="SRScope" href="../classccp4srs_1_1_atom.html#a12b7ff09ff7aa0cc7581a55e89ac9e0e" target="_parent">ccp4srs::Atom::readFromCIF_rcsb()</a>
+    <a id="Item10_c1" onkeydown="return searchResults.NavChild(event,10,1)" onkeypress="return searchResults.NavChild(event,10,1)" onkeyup="return searchResults.NavChild(event,10,1)" class="SRScope" href="../classccp4srs_1_1_bond.html#a54c6291defa953cc5f5750b0f116719c" target="_parent">ccp4srs::Bond::readFromCIF_rcsb()</a>
+    <a id="Item10_c2" onkeydown="return searchResults.NavChild(event,10,2)" onkeypress="return searchResults.NavChild(event,10,2)" onkeyup="return searchResults.NavChild(event,10,2)" class="SRScope" href="../classccp4srs_1_1_monomer.html#aaaec1b93dd1dcfe0e20484fd4bbc2a72" target="_parent">ccp4srs::Monomer::readFromCIF_rcsb()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_readmonidfromcif">
+ <div class="SREntry">
+  <a id="Item11" onkeydown="return searchResults.Nav(event,11)" onkeypress="return searchResults.Nav(event,11)" onkeyup="return searchResults.Nav(event,11)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_readmonidfromcif')">readMonIDFromCIF</a>
+  <div class="SRChildren">
+    <a id="Item11_c0" onkeydown="return searchResults.NavChild(event,11,0)" onkeypress="return searchResults.NavChild(event,11,0)" onkeyup="return searchResults.NavChild(event,11,0)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a4e12236b18de645dabd1afe57b46ebc0" target="_parent">ccp4srs::Monomer::readMonIDFromCIF(mmdb::mmcif::PLoop loop)</a>
+    <a id="Item11_c1" onkeydown="return searchResults.NavChild(event,11,1)" onkeypress="return searchResults.NavChild(event,11,1)" onkeyup="return searchResults.NavChild(event,11,1)" class="SRScope" href="../classccp4srs_1_1_monomer.html#acbe4714fc7593d649b5e8901668d5c5c" target="_parent">ccp4srs::Monomer::readMonIDFromCIF(mmdb::mmcif::PStruct mmCIFStruct)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_reset">
+ <div class="SREntry">
+  <a id="Item12" onkeydown="return searchResults.Nav(event,12)" onkeypress="return searchResults.Nav(event,12)" onkeyup="return searchResults.Nav(event,12)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_reset')">reset</a>
+  <div class="SRChildren">
+    <a id="Item12_c0" onkeydown="return searchResults.NavChild(event,12,0)" onkeypress="return searchResults.NavChild(event,12,0)" onkeyup="return searchResults.NavChild(event,12,0)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a42598d1f669c5e539cb024bb023e0551" target="_parent">ccp4srs::Monomer::reset()</a>
+    <a id="Item12_c1" onkeydown="return searchResults.NavChild(event,12,1)" onkeypress="return searchResults.NavChild(event,12,1)" onkeyup="return searchResults.NavChild(event,12,1)" class="SRScope" href="../classccp4srs_1_1_mem_i_o.html#a855507e19582e7ab9b7236fb9d453da3" target="_parent">ccp4srs::MemIO::reset()</a>
+  </div>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_73.html ccp4srs/doc-html/html/search/all_73.html
--- ccp4srs-old/doc-html/html/search/all_73.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_73.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,197 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_selhndacceptor">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../structccp4srs_1_1_d_a_sel_hnds.html#a6df62532c19c06870cb386b3e1d4cc3c" target="_parent">selHndAcceptor</a>
+  <span class="SRScope">ccp4srs::DASelHnds</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_selhnddonor">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../structccp4srs_1_1_d_a_sel_hnds.html#a0291cf6e8fc47959f00d5dfa536d4d3c" target="_parent">selHndDonor</a>
+  <span class="SRScope">ccp4srs::DASelHnds</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_selhndhydrogen">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../structccp4srs_1_1_d_a_sel_hnds.html#a0dd02cde05c05d8d5f1c99c55aa6e251" target="_parent">selHndHydrogen</a>
+  <span class="SRScope">ccp4srs::DASelHnds</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_selkey">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../structccp4srs_1_1_d_a_sel_hnds.html#ab9e53854d32fb72fb9003efc870354df" target="_parent">selKey</a>
+  <span class="SRScope">ccp4srs::DASelHnds</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_set_5fbuffer_5flength">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#ac84f72f62362171b812f386ef786a677" target="_parent">set_buffer_length</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_set_5fchirality">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a4839e285360f50dbe4dbfff765ece82c" target="_parent">set_chirality</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_set_5fenergy_5ftype">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#abab85177d8d15e5dfc51e12ed9af4d69" target="_parent">set_energy_type</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_set_5fhb_5ftype">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a983a276a7821c272f3952f4edfb826c6" target="_parent">set_hb_type</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_set_5fion_5fradius">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a132fd6895be46a1afa96bb0529c0a6ba" target="_parent">set_ion_radius</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_set_5fold_5fname">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a67142fe2e03f768fea4dc3334826ef2e" target="_parent">set_old_name</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_set_5frcsb_5fchirality">
+ <div class="SREntry">
+  <a id="Item10" onkeydown="return searchResults.Nav(event,10)" onkeypress="return searchResults.Nav(event,10)" onkeyup="return searchResults.Nav(event,10)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#af46102bc6356f36610eda68ced6e9202" target="_parent">set_rcsb_chirality</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_set_5fsp">
+ <div class="SREntry">
+  <a id="Item11" onkeydown="return searchResults.Nav(event,11)" onkeypress="return searchResults.Nav(event,11)" onkeyup="return searchResults.Nav(event,11)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#aa9fe3297f6d6de92f1520a6631361861" target="_parent">set_sp</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_set_5fvalency">
+ <div class="SREntry">
+  <a id="Item12" onkeydown="return searchResults.Nav(event,12)" onkeypress="return searchResults.Nav(event,12)" onkeyup="return searchResults.Nav(event,12)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#af50fcb98ad0f4a42768079e985adec5b" target="_parent">set_valency</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_set_5fvdw_5fradius">
+ <div class="SREntry">
+  <a id="Item13" onkeydown="return searchResults.Nav(event,13)" onkeypress="return searchResults.Nav(event,13)" onkeyup="return searchResults.Nav(event,13)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#aa2c293fa289d7a24bc8858578dd3357e" target="_parent">set_vdw_radius</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_set_5fvdwh_5fradius">
+ <div class="SREntry">
+  <a id="Item14" onkeydown="return searchResults.Nav(event,14)" onkeypress="return searchResults.Nav(event,14)" onkeyup="return searchResults.Nav(event,14)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a8912626b88300dcb9e736cf1b4369f82" target="_parent">set_vdwh_radius</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_setcompressionlevel">
+ <div class="SREntry">
+  <a id="Item15" onkeydown="return searchResults.Nav(event,15)" onkeypress="return searchResults.Nav(event,15)" onkeyup="return searchResults.Nav(event,15)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#abfd614fba0e035434e9c7f1c4a58ad89" target="_parent">setCompressionLevel</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_setoldid">
+ <div class="SREntry">
+  <a id="Item16" onkeydown="return searchResults.Nav(event,16)" onkeypress="return searchResults.Nav(event,16)" onkeyup="return searchResults.Nav(event,16)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a3d9cd816f0e032e64e0d47ed7673ec63" target="_parent">setOldID</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_sign">
+ <div class="SREntry">
+  <a id="Item17" onkeydown="return searchResults.Nav(event,17)" onkeypress="return searchResults.Nav(event,17)" onkeyup="return searchResults.Nav(event,17)" class="SRSymbol" href="../classccp4srs_1_1_chi_center.html#a17574c6830e27efde72575acdf154d80" target="_parent">sign</a>
+  <span class="SRScope">ccp4srs::ChiCenter</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_single">
+ <div class="SREntry">
+  <a id="Item18" onkeydown="return searchResults.Nav(event,18)" onkeypress="return searchResults.Nav(event,18)" onkeyup="return searchResults.Nav(event,18)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba338d16bbed971e9a0c912ff78efed793" target="_parent">Single</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_size">
+ <div class="SREntry">
+  <a id="Item19" onkeydown="return searchResults.Nav(event,19)" onkeypress="return searchResults.Nav(event,19)" onkeyup="return searchResults.Nav(event,19)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_size')">size</a>
+  <div class="SRChildren">
+    <a id="Item19_c0" onkeydown="return searchResults.NavChild(event,19,0)" onkeypress="return searchResults.NavChild(event,19,0)" onkeyup="return searchResults.NavChild(event,19,0)" class="SRScope" href="../classccp4srs_1_1_plane.html#a61ab65ef97a61c79d1190673a5a1b8e3" target="_parent">ccp4srs::Plane::size()</a>
+    <a id="Item19_c1" onkeydown="return searchResults.NavChild(event,19,1)" onkeypress="return searchResults.NavChild(event,19,1)" onkeyup="return searchResults.NavChild(event,19,1)" class="SRScope" href="../classccp4srs_1_1_tree.html#a308ddfce7a902729218e39356db92cc0" target="_parent">ccp4srs::Tree::size()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_sizeerror">
+ <div class="SREntry">
+  <a id="Item20" onkeydown="return searchResults.Nav(event,20)" onkeypress="return searchResults.Nav(event,20)" onkeyup="return searchResults.Nav(event,20)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaaec9637fa3da0cf0cc0385a15d95af350" target="_parent">SizeError</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_sp">
+ <div class="SREntry">
+  <a id="Item21" onkeydown="return searchResults.Nav(event,21)" onkeypress="return searchResults.Nav(event,21)" onkeyup="return searchResults.Nav(event,21)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a9ae7f9281596f659071394247d484ffb" target="_parent">sp</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_srsdir">
+ <div class="SREntry">
+  <a id="Item22" onkeydown="return searchResults.Nav(event,22)" onkeypress="return searchResults.Nav(event,22)" onkeyup="return searchResults.Nav(event,22)" class="SRSymbol" href="../classccp4srs_1_1_base.html#af3caa0403ce8a1c4489948fa4fc62b0c" target="_parent">srsDir</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_srsgraphfile">
+ <div class="SREntry">
+  <a id="Item23" onkeydown="return searchResults.Nav(event,23)" onkeypress="return searchResults.Nav(event,23)" onkeyup="return searchResults.Nav(event,23)" class="SRSymbol" href="../namespaceccp4srs.html#a4132afa4ce21fdcd2ff268bf6e980cfc" target="_parent">srsGraphFile</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_srsindexfile">
+ <div class="SREntry">
+  <a id="Item24" onkeydown="return searchResults.Nav(event,24)" onkeypress="return searchResults.Nav(event,24)" onkeyup="return searchResults.Nav(event,24)" class="SRSymbol" href="../namespaceccp4srs.html#a3f27798432992515be969c17425412d3" target="_parent">srsIndexFile</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_srsstructfile">
+ <div class="SREntry">
+  <a id="Item25" onkeydown="return searchResults.Nav(event,25)" onkeypress="return searchResults.Nav(event,25)" onkeyup="return searchResults.Nav(event,25)" class="SRSymbol" href="../namespaceccp4srs.html#af51e5a096118e643d5fcf5490d44c6db" target="_parent">srsStructFile</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_srsversion">
+ <div class="SREntry">
+  <a id="Item26" onkeydown="return searchResults.Nav(event,26)" onkeypress="return searchResults.Nav(event,26)" onkeyup="return searchResults.Nav(event,26)" class="SRSymbol" href="../classccp4srs_1_1_base.html#ad18087156761086530c1f01f3078f869" target="_parent">srsVersion</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_struct_5ftree">
+ <div class="SREntry">
+  <a id="Item27" onkeydown="return searchResults.Nav(event,27)" onkeypress="return searchResults.Nav(event,27)" onkeyup="return searchResults.Nav(event,27)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#aef8794097a333f1e4e20dd3d876f1432" target="_parent">struct_tree</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_superpose_5fatoms">
+ <div class="SREntry">
+  <a id="Item28" onkeydown="return searchResults.Nav(event,28)" onkeypress="return searchResults.Nav(event,28)" onkeyup="return searchResults.Nav(event,28)" class="SRSymbol" href="../namespaceccp4srs.html#ab9a709bd669d7de2cf530774f80905c7" target="_parent">superpose_atoms</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_74.html ccp4srs/doc-html/html/search/all_74.html
--- ccp4srs-old/doc-html/html/search/all_74.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_74.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,96 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_torsion">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_torsion.html" target="_parent">Torsion</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_torsion">
+ <div class="SREntry">
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+  <div class="SRChildren">
+    <a id="Item1_c0" onkeydown="return searchResults.NavChild(event,1,0)" onkeypress="return searchResults.NavChild(event,1,0)" onkeyup="return searchResults.NavChild(event,1,0)" class="SRScope" href="../classccp4srs_1_1_torsion.html#a1939dda0f4d9e56c3762acade101e938" target="_parent">ccp4srs::Torsion::Torsion()</a>
+    <a id="Item1_c1" onkeydown="return searchResults.NavChild(event,1,1)" onkeypress="return searchResults.NavChild(event,1,1)" onkeyup="return searchResults.NavChild(event,1,1)" class="SRScope" href="../classccp4srs_1_1_torsion.html#a68b1d2a3529f1b153db01830a6cde818" target="_parent">ccp4srs::Torsion::torsion()</a>
+    <a id="Item1_c2" onkeydown="return searchResults.NavChild(event,1,2)" onkeypress="return searchResults.NavChild(event,1,2)" onkeyup="return searchResults.NavChild(event,1,2)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a1fdc6bd34cea4b7ea59d5399a8367f70" target="_parent">ccp4srs::Monomer::torsion()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_torsion_5fesd">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_torsion.html#a34011e29f9c0faa8bc15a31274dd27c3" target="_parent">torsion_esd</a>
+  <span class="SRScope">ccp4srs::Torsion</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_torsion_5fid">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_torsion.html#ab82fe72dc4fb966139befa1636f0c4bd" target="_parent">torsion_id</a>
+  <span class="SRScope">ccp4srs::Torsion</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_torsion_5fperiod">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_torsion.html#a681cd0d538d13fa8d30dee2eb0c7df20" target="_parent">torsion_period</a>
+  <span class="SRScope">ccp4srs::Torsion</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_torsionid">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../namespaceccp4srs.html#a192f47d1deb71790866bce922f50bba1" target="_parent">TorsionID</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_torsions">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a70123373bff5c842e122856fb75634ab" target="_parent">torsions</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_tree">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_tree.html" target="_parent">Tree</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_tree">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_tree')">Tree</a>
+  <div class="SRChildren">
+    <a id="Item8_c0" onkeydown="return searchResults.NavChild(event,8,0)" onkeypress="return searchResults.NavChild(event,8,0)" onkeyup="return searchResults.NavChild(event,8,0)" class="SRScope" href="../classccp4srs_1_1_tree.html#a342a1de215612310580d0cd6a06262cb" target="_parent">ccp4srs::Tree::Tree()</a>
+    <a id="Item8_c1" onkeydown="return searchResults.NavChild(event,8,1)" onkeypress="return searchResults.NavChild(event,8,1)" onkeyup="return searchResults.NavChild(event,8,1)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a79a4445aa7279951aa8426dc79114ebf" target="_parent">ccp4srs::Monomer::tree()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_triple">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795baf6c5cfdf98463c48cd5772a18e49ad6f" target="_parent">Triple</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_type">
+ <div class="SREntry">
+  <a id="Item10" onkeydown="return searchResults.Nav(event,10)" onkeypress="return searchResults.Nav(event,10)" onkeyup="return searchResults.Nav(event,10)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_type')">type</a>
+  <div class="SRChildren">
+    <a id="Item10_c0" onkeydown="return searchResults.NavChild(event,10,0)" onkeypress="return searchResults.NavChild(event,10,0)" onkeyup="return searchResults.NavChild(event,10,0)" class="SRScope" href="../classccp4srs_1_1_entry.html#a401d0e96699c34bef6b408e054f14540" target="_parent">ccp4srs::Entry::type()</a>
+    <a id="Item10_c1" onkeydown="return searchResults.NavChild(event,10,1)" onkeypress="return searchResults.NavChild(event,10,1)" onkeyup="return searchResults.NavChild(event,10,1)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a01201fb01a7ed370e593563b129c74af" target="_parent">ccp4srs::Monomer::type()</a>
+  </div>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_75.html ccp4srs/doc-html/html/search/all_75.html
--- ccp4srs-old/doc-html/html/search/all_75.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_75.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,32 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_uncompressionerror">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa63962a5b2f5046aa5e8a6b0b46271824" target="_parent">UncompressionError</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_unloadstructure">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a6d15803597f5a515c19848a5e8dbe164" target="_parent">unloadStructure</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_76.html ccp4srs/doc-html/html/search/all_76.html
--- ccp4srs-old/doc-html/html/search/all_76.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_76.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,83 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_valency">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a86606a9614641a62a9b477c0b90c3a87" target="_parent">valency</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_value">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_value')">value</a>
+  <div class="SRChildren">
+    <a id="Item1_c0" onkeydown="return searchResults.NavChild(event,1,0)" onkeypress="return searchResults.NavChild(event,1,0)" onkeyup="return searchResults.NavChild(event,1,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a6ec0de44c0f607bcb5634a907fe9018a" target="_parent">ccp4srs::Angle::value()</a>
+    <a id="Item1_c1" onkeydown="return searchResults.NavChild(event,1,1)" onkeypress="return searchResults.NavChild(event,1,1)" onkeyup="return searchResults.NavChild(event,1,1)" class="SRScope" href="../classccp4srs_1_1_torsion.html#a001451fd28649a8df65416d7e551b7a9" target="_parent">ccp4srs::Torsion::value()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_vdw_5fradius">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a2c283b644afb507ec45667611a685827" target="_parent">vdw_radius</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_vdwh_5fradius">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a2a2e411586e9a0be619a5ab5c634169d" target="_parent">vdwh_radius</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_vdwhradius">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#afd0adf07dd4f24e87acb6977335ff2ba" target="_parent">vdwhRadius</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_vdwradius">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a74216b4c442b716656e5a55e908cea11" target="_parent">vdwRadius</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_volume_5fsign">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_chi_center.html#a6fc568ab5bcd12bc56b58d6b9f2933a1" target="_parent">volume_sign</a>
+  <span class="SRScope">ccp4srs::ChiCenter</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_volume_5fsign_5fboth">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../ccp4srs__chicenter_8cpp.html#a0876b7b066ef447a65ca374d8dc86417" target="_parent">VOLUME_SIGN_BOTH</a>
+  <span class="SRScope">ccp4srs_chicenter.cpp</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_volume_5fsign_5fnegative">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="../ccp4srs__chicenter_8cpp.html#a5e50b082b9f721d74d142b1a564358c8" target="_parent">VOLUME_SIGN_NEGATIVE</a>
+  <span class="SRScope">ccp4srs_chicenter.cpp</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_volume_5fsign_5fpositive">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="../ccp4srs__chicenter_8cpp.html#ab5d2d0dcd4a9adac0699b5e37132fcae" target="_parent">VOLUME_SIGN_POSITIVE</a>
+  <span class="SRScope">ccp4srs_chicenter.cpp</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_77.html ccp4srs/doc-html/html/search/all_77.html
--- ccp4srs-old/doc-html/html/search/all_77.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_77.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,82 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_weight">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a4c6e0a23b45563f10657d839d4479961" target="_parent">weight</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_write">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_write')">write</a>
+  <div class="SRChildren">
+    <a id="Item1_c0" onkeydown="return searchResults.NavChild(event,1,0)" onkeypress="return searchResults.NavChild(event,1,0)" onkeyup="return searchResults.NavChild(event,1,0)" class="SRScope" href="../classccp4srs_1_1_entry.html#a46d1eaa50c45f6e40ff054b30b93790d" target="_parent">ccp4srs::Entry::write()</a>
+    <a id="Item1_c1" onkeydown="return searchResults.NavChild(event,1,1)" onkeypress="return searchResults.NavChild(event,1,1)" onkeyup="return searchResults.NavChild(event,1,1)" class="SRScope" href="../classccp4srs_1_1_index.html#a2d6f487a5a3e945f92b90fc6f034f08b" target="_parent">ccp4srs::Index::write()</a>
+    <a id="Item1_c2" onkeydown="return searchResults.NavChild(event,1,2)" onkeypress="return searchResults.NavChild(event,1,2)" onkeyup="return searchResults.NavChild(event,1,2)" class="SRScope" href="../classccp4srs_1_1_mem_i_o.html#ae2fd4e637343f3f9ac5ccfc3af085293" target="_parent">ccp4srs::MemIO::write(mmdb::cpstr fileName, mmdb::io::GZ_MODE gzMode=mmdb::io::GZM_NONE)</a>
+    <a id="Item1_c3" onkeydown="return searchResults.NavChild(event,1,3)" onkeypress="return searchResults.NavChild(event,1,3)" onkeyup="return searchResults.NavChild(event,1,3)" class="SRScope" href="../classccp4srs_1_1_mem_i_o.html#a501f0773dd4ebb8f8f9b369cf59f07e0" target="_parent">ccp4srs::MemIO::write(mmdb::io::RFile f)</a>
+    <a id="Item1_c4" onkeydown="return searchResults.NavChild(event,1,4)" onkeypress="return searchResults.NavChild(event,1,4)" onkeyup="return searchResults.NavChild(event,1,4)" class="SRScope" href="../structccp4srs_1_1_m_p_file_pos.html#a6e1a52091171d7462c6b8334f1483998" target="_parent">ccp4srs::MPFilePos::write()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_write_5fbuffer">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a98b3d03fd613c62e0d16bfda509aa630" target="_parent">write_buffer</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_write_5fmem">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_write_5fmem')">write_mem</a>
+  <div class="SRChildren">
+    <a id="Item3_c0" onkeydown="return searchResults.NavChild(event,3,0)" onkeypress="return searchResults.NavChild(event,3,0)" onkeyup="return searchResults.NavChild(event,3,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a5fcc085237045429dd4a946595c1488f" target="_parent">ccp4srs::Angle::write_mem()</a>
+    <a id="Item3_c1" onkeydown="return searchResults.NavChild(event,3,1)" onkeypress="return searchResults.NavChild(event,3,1)" onkeyup="return searchResults.NavChild(event,3,1)" class="SRScope" href="../classccp4srs_1_1_atom.html#adaebb2b3897e6758befc7c76d77c0420" target="_parent">ccp4srs::Atom::write_mem()</a>
+    <a id="Item3_c2" onkeydown="return searchResults.NavChild(event,3,2)" onkeypress="return searchResults.NavChild(event,3,2)" onkeyup="return searchResults.NavChild(event,3,2)" class="SRScope" href="../classccp4srs_1_1_bond.html#aa44d448aa0181e6d51048beda35052f4" target="_parent">ccp4srs::Bond::write_mem()</a>
+    <a id="Item3_c3" onkeydown="return searchResults.NavChild(event,3,3)" onkeypress="return searchResults.NavChild(event,3,3)" onkeyup="return searchResults.NavChild(event,3,3)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#ac36306727683e319c2282b936bd11d37" target="_parent">ccp4srs::ChiCenter::write_mem()</a>
+    <a id="Item3_c4" onkeydown="return searchResults.NavChild(event,3,4)" onkeypress="return searchResults.NavChild(event,3,4)" onkeyup="return searchResults.NavChild(event,3,4)" class="SRScope" href="../classccp4srs_1_1_container.html#ae3d1a80023e670f0828814b887af5dc8" target="_parent">ccp4srs::Container::write_mem()</a>
+    <a id="Item3_c5" onkeydown="return searchResults.NavChild(event,3,5)" onkeypress="return searchResults.NavChild(event,3,5)" onkeyup="return searchResults.NavChild(event,3,5)" class="SRScope" href="../classccp4srs_1_1_entry.html#a817f6f566baf41280c5cee0fc3507871" target="_parent">ccp4srs::Entry::write_mem()</a>
+    <a id="Item3_c6" onkeydown="return searchResults.NavChild(event,3,6)" onkeypress="return searchResults.NavChild(event,3,6)" onkeyup="return searchResults.NavChild(event,3,6)" class="SRScope" href="../classccp4srs_1_1_index.html#a5591c13f7296928d053492322b8bd02b" target="_parent">ccp4srs::Index::write_mem()</a>
+    <a id="Item3_c7" onkeydown="return searchResults.NavChild(event,3,7)" onkeypress="return searchResults.NavChild(event,3,7)" onkeyup="return searchResults.NavChild(event,3,7)" class="SRScope" href="../classccp4srs_1_1_monomer.html#ac0eb44f5d4ec3da57994cd741c8d6b0b" target="_parent">ccp4srs::Monomer::write_mem()</a>
+    <a id="Item3_c8" onkeydown="return searchResults.NavChild(event,3,8)" onkeypress="return searchResults.NavChild(event,3,8)" onkeyup="return searchResults.NavChild(event,3,8)" class="SRScope" href="../classccp4srs_1_1_plane.html#a759255f2b21b770caa535f129e5f60bb" target="_parent">ccp4srs::Plane::write_mem()</a>
+    <a id="Item3_c9" onkeydown="return searchResults.NavChild(event,3,9)" onkeypress="return searchResults.NavChild(event,3,9)" onkeyup="return searchResults.NavChild(event,3,9)" class="SRScope" href="../classccp4srs_1_1_torsion.html#a9b4f1d2c543776a8e0412eae4c7db651" target="_parent">ccp4srs::Torsion::write_mem()</a>
+    <a id="Item3_c10" onkeydown="return searchResults.NavChild(event,3,10)" onkeypress="return searchResults.NavChild(event,3,10)" onkeyup="return searchResults.NavChild(event,3,10)" class="SRScope" href="../classccp4srs_1_1_tree.html#a357b27f65ab5b653fc17a387e9653c4f" target="_parent">ccp4srs::Tree::write_mem()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_writeerror">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa29a865c4c24a0a158c5fc0514a29e517" target="_parent">WriteError</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_writetocif">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_writetocif')">writeToCIF</a>
+  <div class="SRChildren">
+    <a id="Item5_c0" onkeydown="return searchResults.NavChild(event,5,0)" onkeypress="return searchResults.NavChild(event,5,0)" onkeyup="return searchResults.NavChild(event,5,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a8a293c96f55ee3b13cc9b9db86d265cd" target="_parent">ccp4srs::Angle::writeToCIF()</a>
+    <a id="Item5_c1" onkeydown="return searchResults.NavChild(event,5,1)" onkeypress="return searchResults.NavChild(event,5,1)" onkeyup="return searchResults.NavChild(event,5,1)" class="SRScope" href="../classccp4srs_1_1_atom.html#ac83667146ec86aeab8fdcce133c2fea0" target="_parent">ccp4srs::Atom::writeToCIF()</a>
+    <a id="Item5_c2" onkeydown="return searchResults.NavChild(event,5,2)" onkeypress="return searchResults.NavChild(event,5,2)" onkeyup="return searchResults.NavChild(event,5,2)" class="SRScope" href="../classccp4srs_1_1_bond.html#a89214f5f730f603bdd8dacea6317428f" target="_parent">ccp4srs::Bond::writeToCIF()</a>
+    <a id="Item5_c3" onkeydown="return searchResults.NavChild(event,5,3)" onkeypress="return searchResults.NavChild(event,5,3)" onkeyup="return searchResults.NavChild(event,5,3)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#a04b85d396a4ebc8d5163d3184206329d" target="_parent">ccp4srs::ChiCenter::writeToCIF()</a>
+    <a id="Item5_c4" onkeydown="return searchResults.NavChild(event,5,4)" onkeypress="return searchResults.NavChild(event,5,4)" onkeyup="return searchResults.NavChild(event,5,4)" class="SRScope" href="../classccp4srs_1_1_plane.html#abd5b6df5e6d2bdafdd064a04974cf82a" target="_parent">ccp4srs::Plane::writeToCIF()</a>
+    <a id="Item5_c5" onkeydown="return searchResults.NavChild(event,5,5)" onkeypress="return searchResults.NavChild(event,5,5)" onkeyup="return searchResults.NavChild(event,5,5)" class="SRScope" href="../classccp4srs_1_1_torsion.html#ae53494ec218062be243d5e7b36f43dd0" target="_parent">ccp4srs::Torsion::writeToCIF()</a>
+    <a id="Item5_c6" onkeydown="return searchResults.NavChild(event,5,6)" onkeypress="return searchResults.NavChild(event,5,6)" onkeyup="return searchResults.NavChild(event,5,6)" class="SRScope" href="../classccp4srs_1_1_tree.html#ade370b24c17b2d47a4cb8f89c096e5c1" target="_parent">ccp4srs::Tree::writeToCIF()</a>
+  </div>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_78.html ccp4srs/doc-html/html/search/all_78.html
--- ccp4srs-old/doc-html/html/search/all_78.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_78.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,38 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_x">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a9af114ebe576f3a0af965579100da463" target="_parent">x</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_x_5fmlib">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a7f9331955d7f98b1d2e869f8741a2188" target="_parent">x_mlib</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_x_5fpdbx">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#ac0fc0e47750a53f2be7ab60efc604d3b" target="_parent">x_pdbx</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_79.html ccp4srs/doc-html/html/search/all_79.html
--- ccp4srs-old/doc-html/html/search/all_79.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_79.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,38 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_y">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a10fc0f0f21af2cd5311c7d957b59f52b" target="_parent">y</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_y_5fmlib">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#acc50ad679a297a2626a6662cd0b61d3e" target="_parent">y_mlib</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_y_5fpdbx">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a65cdadf3090a0fa712b6c47040adb578" target="_parent">y_pdbx</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_7a.html ccp4srs/doc-html/html/search/all_7a.html
--- ccp4srs-old/doc-html/html/search/all_7a.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_7a.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,38 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_z">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a9d07e03f19613858142105d9f287466e" target="_parent">z</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_z_5fmlib">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a73c4871fccf3ce91502449de659f835a" target="_parent">z_mlib</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_z_5fpdbx">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#aed837e19a61e89ce1e1eda0c35f10b2e" target="_parent">z_pdbx</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/all_7e.html ccp4srs/doc-html/html/search/all_7e.html
--- ccp4srs-old/doc-html/html/search/all_7e.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/all_7e.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,110 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR__7eangle">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_angle.html#a8b6036ed3908589a9cee50f60f5e3806" target="_parent">~Angle</a>
+  <span class="SRScope">ccp4srs::Angle</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7eatom">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a27de39105bac03d49c949780edda55fd" target="_parent">~Atom</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7ebase">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a2c46b036cb9701ac6a2d22fcec3fbdcf" target="_parent">~Base</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7ebond">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#a695a8236689b60df2ad108c7cc55eb1a" target="_parent">~Bond</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7echem">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_chem.html#a939cae4367e5e32664e60c725fabafbe" target="_parent">~Chem</a>
+  <span class="SRScope">ccp4srs::Chem</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7echicenter">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_chi_center.html#a051ae00e2cdb590a2dd7f4899c264cb9" target="_parent">~ChiCenter</a>
+  <span class="SRScope">ccp4srs::ChiCenter</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7econtainer">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_container.html#a831fc7371918ff96de32b96c35fe31a2" target="_parent">~Container</a>
+  <span class="SRScope">ccp4srs::Container</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7eentry">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_entry.html#a191661efae468b8e2a62b69a247bcd3a" target="_parent">~Entry</a>
+  <span class="SRScope">ccp4srs::Entry</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7eindex">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="../classccp4srs_1_1_index.html#a5a0d5db83db471eae5aa87dcfa6a151c" target="_parent">~Index</a>
+  <span class="SRScope">ccp4srs::Index</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7emanager">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="../classccp4srs_1_1_manager.html#ac6d91d47cb19b9f6ea6c7b64a7f69bb5" target="_parent">~Manager</a>
+  <span class="SRScope">ccp4srs::Manager</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7ememio">
+ <div class="SREntry">
+  <a id="Item10" onkeydown="return searchResults.Nav(event,10)" onkeypress="return searchResults.Nav(event,10)" onkeyup="return searchResults.Nav(event,10)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#abb2d68b86867b62480e6f036a2f8bcbb" target="_parent">~MemIO</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7emonomer">
+ <div class="SREntry">
+  <a id="Item11" onkeydown="return searchResults.Nav(event,11)" onkeypress="return searchResults.Nav(event,11)" onkeyup="return searchResults.Nav(event,11)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a33207c3c799fe120851007002464e2e2" target="_parent">~Monomer</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7eplane">
+ <div class="SREntry">
+  <a id="Item12" onkeydown="return searchResults.Nav(event,12)" onkeypress="return searchResults.Nav(event,12)" onkeyup="return searchResults.Nav(event,12)" class="SRSymbol" href="../classccp4srs_1_1_plane.html#a521911d044ea2aa8ca4e769b9d8d4e58" target="_parent">~Plane</a>
+  <span class="SRScope">ccp4srs::Plane</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7etorsion">
+ <div class="SREntry">
+  <a id="Item13" onkeydown="return searchResults.Nav(event,13)" onkeypress="return searchResults.Nav(event,13)" onkeyup="return searchResults.Nav(event,13)" class="SRSymbol" href="../classccp4srs_1_1_torsion.html#a45434048948cdf6fc5f01a6e3ca149a8" target="_parent">~Torsion</a>
+  <span class="SRScope">ccp4srs::Torsion</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7etree">
+ <div class="SREntry">
+  <a id="Item14" onkeydown="return searchResults.Nav(event,14)" onkeypress="return searchResults.Nav(event,14)" onkeyup="return searchResults.Nav(event,14)" class="SRSymbol" href="../classccp4srs_1_1_tree.html#ab5a113a9574397dbb5e7679211ee3c24" target="_parent">~Tree</a>
+  <span class="SRScope">ccp4srs::Tree</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/classes_61.html ccp4srs/doc-html/html/search/classes_61.html
--- ccp4srs-old/doc-html/html/search/classes_61.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/classes_61.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,38 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_angle">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_angle.html" target="_parent">Angle</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_atom.html" target="_parent">Atom</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atompair">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../structccp4srs_1_1_atom_pair.html" target="_parent">AtomPair</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/classes_62.html ccp4srs/doc-html/html/search/classes_62.html
--- ccp4srs-old/doc-html/html/search/classes_62.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/classes_62.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,32 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_base">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_base.html" target="_parent">Base</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_bond">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_bond.html" target="_parent">Bond</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/classes_63.html ccp4srs/doc-html/html/search/classes_63.html
--- ccp4srs-old/doc-html/html/search/classes_63.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/classes_63.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,74 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_chem">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_chem.html" target="_parent">Chem</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_chicenter">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_chi_center.html" target="_parent">ChiCenter</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_container">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_container.html" target="_parent">Container</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_container_3c_20angle_20_3e">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_container.html" target="_parent">Container&lt; Angle &gt;</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_container_3c_20atom_20_3e">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_container.html" target="_parent">Container&lt; Atom &gt;</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_container_3c_20bond_20_3e">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_container.html" target="_parent">Container&lt; Bond &gt;</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_container_3c_20chicenter_20_3e">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_container.html" target="_parent">Container&lt; ChiCenter &gt;</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_container_3c_20plane_20_3e">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_container.html" target="_parent">Container&lt; Plane &gt;</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_container_3c_20torsion_20_3e">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="../classccp4srs_1_1_container.html" target="_parent">Container&lt; Torsion &gt;</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/classes_64.html ccp4srs/doc-html/html/search/classes_64.html
--- ccp4srs-old/doc-html/html/search/classes_64.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/classes_64.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,26 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_daselhnds">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../structccp4srs_1_1_d_a_sel_hnds.html" target="_parent">DASelHnds</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/classes_65.html ccp4srs/doc-html/html/search/classes_65.html
--- ccp4srs-old/doc-html/html/search/classes_65.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/classes_65.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,26 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_entry">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_entry.html" target="_parent">Entry</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/classes_69.html ccp4srs/doc-html/html/search/classes_69.html
--- ccp4srs-old/doc-html/html/search/classes_69.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/classes_69.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,26 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_index">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_index.html" target="_parent">Index</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/classes_6d.html ccp4srs/doc-html/html/search/classes_6d.html
--- ccp4srs-old/doc-html/html/search/classes_6d.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/classes_6d.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,44 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_manager">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_manager.html" target="_parent">Manager</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_memio">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html" target="_parent">MemIO</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_monomer">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html" target="_parent">Monomer</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_mpfilepos">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../structccp4srs_1_1_m_p_file_pos.html" target="_parent">MPFilePos</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/classes_70.html ccp4srs/doc-html/html/search/classes_70.html
--- ccp4srs-old/doc-html/html/search/classes_70.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/classes_70.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,26 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_plane">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_plane.html" target="_parent">Plane</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/classes_74.html ccp4srs/doc-html/html/search/classes_74.html
--- ccp4srs-old/doc-html/html/search/classes_74.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/classes_74.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,32 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_torsion">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_torsion.html" target="_parent">Torsion</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_tree">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_tree.html" target="_parent">Tree</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
Binary files ccp4srs-old/doc-html/html/search/close.png and ccp4srs/doc-html/html/search/close.png differ
diff -ruN ccp4srs-old/doc-html/html/search/defines_6d.html ccp4srs/doc-html/html/search/defines_6d.html
--- ccp4srs-old/doc-html/html/search/defines_6d.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/defines_6d.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,311 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_mmcif_5fcomp">
+ <div class="SREntry">
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+</div>
+<div class="SRResult" id="SR_mmcif_5ftag_5fvalue_5fdist">
+ <div class="SREntry">
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+<div class="SRResult" id="SR_mmcif_5ftag_5fvalue_5forder">
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+  <span class="SRScope">ccp4srs_defs.h</span>
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+<div class="SRResult" id="SR_mmcif_5ftag_5fx">
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+<div class="SRResult" id="SR_mmcif_5ftag_5fy">
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+<div class="SRResult" id="SR_mmcif_5ftag_5fz">
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+  <span class="SRScope">ccp4srs_defs.h</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
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+</html>
diff -ruN ccp4srs-old/doc-html/html/search/defines_76.html ccp4srs/doc-html/html/search/defines_76.html
--- ccp4srs-old/doc-html/html/search/defines_76.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/defines_76.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,38 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
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+<div class="SRResult" id="SR_volume_5fsign_5fboth">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../ccp4srs__chicenter_8cpp.html#a0876b7b066ef447a65ca374d8dc86417" target="_parent">VOLUME_SIGN_BOTH</a>
+  <span class="SRScope">ccp4srs_chicenter.cpp</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_volume_5fsign_5fnegative">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../ccp4srs__chicenter_8cpp.html#a5e50b082b9f721d74d142b1a564358c8" target="_parent">VOLUME_SIGN_NEGATIVE</a>
+  <span class="SRScope">ccp4srs_chicenter.cpp</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_volume_5fsign_5fpositive">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../ccp4srs__chicenter_8cpp.html#ab5d2d0dcd4a9adac0699b5e37132fcae" target="_parent">VOLUME_SIGN_POSITIVE</a>
+  <span class="SRScope">ccp4srs_chicenter.cpp</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
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+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/enums_63.html ccp4srs/doc-html/html/search/enums_63.html
--- ccp4srs-old/doc-html/html/search/enums_63.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/enums_63.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,32 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_ccp4srs_5frc">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84a" target="_parent">CCP4SRS_RC</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_ccp4srs_5fversion">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40d" target="_parent">CCP4SRS_VERSION</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
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+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/enumvalues_61.html ccp4srs/doc-html/html/search/enumvalues_61.html
--- ccp4srs-old/doc-html/html/search/enumvalues_61.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/enumvalues_61.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,26 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_aromatic">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba1511fd16010981add30c1e054980f193" target="_parent">Aromatic</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
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+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/enumvalues_63.html ccp4srs/doc-html/html/search/enumvalues_63.html
--- ccp4srs-old/doc-html/html/search/enumvalues_63.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/enumvalues_63.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,146 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_cantopenfile">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaac65c121a2ac9e371d3e059cb480cf60d" target="_parent">CantOpenFile</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_ccp4srs_5fbrokenbonds">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa785ce210fda24a93bd0df60e0a612698" target="_parent">CCP4SRS_BrokenBonds</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_ccp4srs_5femptyresidue">
+ <div class="SREntry">
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+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_ccp4srs_5femptyresset">
+ <div class="SREntry">
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+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_ccp4srs_5fentrynotfound">
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+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_ccp4srs_5ffail">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../namespaceccp4srs.html#a058dffb1d0d0c445ac789e7e7b15b84aa770346796e3fd0232458a3dd9709d735" target="_parent">CCP4SRS_Fail</a>
+  <span class="SRScope">ccp4srs</span>
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+<div class="SRResult" id="SR_ccp4srs_5ffilenotfound">
+ <div class="SREntry">
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+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_ccp4srs_5fincomplete">
+ <div class="SREntry">
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+<div class="SRResult" id="SR_ccp4srs_5findexcorrupt">
+ <div class="SREntry">
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+<div class="SRResult" id="SR_ccp4srs_5fnoacceptors">
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+<div class="SRResult" id="SR_ccp4srs_5fnobonds">
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+</div>
+<div class="SRResult" id="SR_ccp4srs_5fnocoordhierarchy">
+ <div class="SREntry">
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+</div>
+<div class="SRResult" id="SR_ccp4srs_5fnodonors">
+ <div class="SREntry">
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+<div class="SRResult" id="SR_ccp4srs_5fnohbonds">
+ <div class="SREntry">
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+</div>
+<div class="SRResult" id="SR_ccp4srs_5fok">
+ <div class="SREntry">
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+  <span class="SRScope">ccp4srs</span>
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+<div class="SRResult" id="SR_ccp4srs_5freaderrors">
+ <div class="SREntry">
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+<div class="SRResult" id="SR_ccp4srs_5fsvd_5ffail">
+ <div class="SREntry">
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+<div class="SRResult" id="SR_ccp4srs_5fwrongbondtype">
+ <div class="SREntry">
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+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_compressionerror">
+ <div class="SREntry">
+  <a id="Item19" onkeydown="return searchResults.Nav(event,19)" onkeypress="return searchResults.Nav(event,19)" onkeyup="return searchResults.Nav(event,19)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa6cf46f9d24d202ae6ac26ddb6aeb625d" target="_parent">CompressionError</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_covalent">
+ <div class="SREntry">
+  <a id="Item20" onkeydown="return searchResults.Nav(event,20)" onkeypress="return searchResults.Nav(event,20)" onkeyup="return searchResults.Nav(event,20)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795babaf2bbca3b364f84e83bbc9927b45e39" target="_parent">Covalent</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/enumvalues_64.html ccp4srs/doc-html/html/search/enumvalues_64.html
--- ccp4srs-old/doc-html/html/search/enumvalues_64.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/enumvalues_64.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,32 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_deloc">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba3e459a041fa6b33d363df5a335413e13" target="_parent">Deloc</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_double">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba0311fe9d41fd3830910b1e4f93d9a83a" target="_parent">Double</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/enumvalues_65.html ccp4srs/doc-html/html/search/enumvalues_65.html
--- ccp4srs-old/doc-html/html/search/enumvalues_65.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/enumvalues_65.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,32 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_emptyfile">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa117fc645808ac4d9c4e53452bc608d51" target="_parent">EmptyFile</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_emptyloop">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5edad0a61a72f29321313e1bc19920df40f9" target="_parent">EmptyLoop</a>
+  <span class="SRScope">ccp4srs::Plane</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/enumvalues_6c.html ccp4srs/doc-html/html/search/enumvalues_6c.html
--- ccp4srs-old/doc-html/html/search/enumvalues_6c.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/enumvalues_6c.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,26 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_link">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88cae7d526eebfeb15c8370f473885073095" target="_parent">Link</a>
+  <span class="SRScope">ccp4srs::Entry</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/enumvalues_6d.html ccp4srs/doc-html/html/search/enumvalues_6d.html
--- ccp4srs-old/doc-html/html/search/enumvalues_6d.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/enumvalues_6d.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,56 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_major_5fversion">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40da70b6b61e66afecc14062283f4ab22165" target="_parent">MAJOR_VERSION</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_memreaderror">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaadf48b9ed60d08687c2fbd5271b328c70" target="_parent">MemReadError</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_metal">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba1be67f1d82568ea8bb92f456440e7f01" target="_parent">Metal</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_micro_5fversion">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40dafef3f6fb9926961d5bb1c2c5f5464228" target="_parent">MICRO_VERSION</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_minor_5fversion">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../namespaceccp4srs.html#a82cd9b00128081b168cca2ba2e3af40da629c96b840f87c056420011f99867b11" target="_parent">MINOR_VERSION</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_monomer">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88ca447bc9153594c5d2b79e47041f4982b6" target="_parent">Monomer</a>
+  <span class="SRScope">ccp4srs::Entry</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/enumvalues_6e.html ccp4srs/doc-html/html/search/enumvalues_6e.html
--- ccp4srs-old/doc-html/html/search/enumvalues_6e.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/enumvalues_6e.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,38 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_nomoreplanes">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5eda95f4f7898a15589a3db43827444d2692" target="_parent">NoMorePlanes</a>
+  <span class="SRScope">ccp4srs::Plane</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_none">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_entry.html#a6167625e2b80805e2ba7e3f78a1cd88ca616c951330c4d0b080622857146e2457" target="_parent">None</a>
+  <span class="SRScope">ccp4srs::Entry</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_noorder">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba3a534360bb854109f0ad2d34f1858997" target="_parent">noOrder</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/enumvalues_6f.html ccp4srs/doc-html/html/search/enumvalues_6f.html
--- ccp4srs-old/doc-html/html/search/enumvalues_6f.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/enumvalues_6f.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,29 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_ok">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_ok')">Ok</a>
+  <div class="SRChildren">
+    <a id="Item0_c0" onkeydown="return searchResults.NavChild(event,0,0)" onkeypress="return searchResults.NavChild(event,0,0)" onkeyup="return searchResults.NavChild(event,0,0)" class="SRScope" href="../classccp4srs_1_1_plane.html#a629b7441d8798a5fc692feefd6cbe5edae47dd3ee9591c478c387ddbe09f7ef34" target="_parent">ccp4srs::Plane::Ok()</a>
+    <a id="Item0_c1" onkeydown="return searchResults.NavChild(event,0,1)" onkeypress="return searchResults.NavChild(event,0,1)" onkeyup="return searchResults.NavChild(event,0,1)" class="SRScope" href="../classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa61a20c0d573c1e2b3dff78cdd13baa63" target="_parent">ccp4srs::MemIO::Ok()</a>
+  </div>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/enumvalues_72.html ccp4srs/doc-html/html/search/enumvalues_72.html
--- ccp4srs-old/doc-html/html/search/enumvalues_72.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/enumvalues_72.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,26 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_readerror">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaab76082bd26e6e49c9c7794410cec3ca2" target="_parent">ReadError</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/enumvalues_73.html ccp4srs/doc-html/html/search/enumvalues_73.html
--- ccp4srs-old/doc-html/html/search/enumvalues_73.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/enumvalues_73.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,32 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_single">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#a85174d1fd8631c6fe1cf12d60ee8795ba338d16bbed971e9a0c912ff78efed793" target="_parent">Single</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_sizeerror">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaaec9637fa3da0cf0cc0385a15d95af350" target="_parent">SizeError</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/enumvalues_74.html ccp4srs/doc-html/html/search/enumvalues_74.html
--- ccp4srs-old/doc-html/html/search/enumvalues_74.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/enumvalues_74.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,26 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_triple">
+ <div class="SREntry">
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+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
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diff -ruN ccp4srs-old/doc-html/html/search/enumvalues_75.html ccp4srs/doc-html/html/search/enumvalues_75.html
--- ccp4srs-old/doc-html/html/search/enumvalues_75.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/enumvalues_75.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,26 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_uncompressionerror">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa63962a5b2f5046aa5e8a6b0b46271824" target="_parent">UncompressionError</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
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+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/enumvalues_77.html ccp4srs/doc-html/html/search/enumvalues_77.html
--- ccp4srs-old/doc-html/html/search/enumvalues_77.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/enumvalues_77.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,26 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_writeerror">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a58ea0e99940fe1f006ed20ecc2f35cbaa29a865c4c24a0a158c5fc0514a29e517" target="_parent">WriteError</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
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+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/files_63.html ccp4srs/doc-html/html/search/files_63.html
--- ccp4srs-old/doc-html/html/search/files_63.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/files_63.html	2014-09-09 21:34:12.000000000 -0700
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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
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+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_ccp4srs_5fangle_2ecpp">
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+</div>
+<div class="SRResult" id="SR_ccp4srs_5fangle_2eh">
+ <div class="SREntry">
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+</div>
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+</div>
+<div class="SRResult" id="SR_ccp4srs_5fatom_2eh">
+ <div class="SREntry">
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+<div class="SRResult" id="SR_ccp4srs_5findex_2eh">
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+<div class="SRResult" id="SR_ccp4srs_5fmanager_2ecpp">
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+<div class="SRResult" id="SR_ccp4srs_5fmanager_2eh">
+ <div class="SREntry">
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+</div>
+<div class="SRResult" id="SR_ccp4srs_5fmonomer_2ecpp">
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+ </div>
+</div>
+<div class="SRResult" id="SR_ccp4srs_5fmonomer_2eh">
+ <div class="SREntry">
+  <a id="Item22" onkeydown="return searchResults.Nav(event,22)" onkeypress="return searchResults.Nav(event,22)" onkeyup="return searchResults.Nav(event,22)" class="SRSymbol" href="../ccp4srs__monomer_8h.html" target="_parent">ccp4srs_monomer.h</a>
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+</div>
+<div class="SRResult" id="SR_ccp4srs_5fplane_2ecpp">
+ <div class="SREntry">
+  <a id="Item23" onkeydown="return searchResults.Nav(event,23)" onkeypress="return searchResults.Nav(event,23)" onkeyup="return searchResults.Nav(event,23)" class="SRSymbol" href="../ccp4srs__plane_8cpp.html" target="_parent">ccp4srs_plane.cpp</a>
+ </div>
+</div>
+<div class="SRResult" id="SR_ccp4srs_5fplane_2eh">
+ <div class="SREntry">
+  <a id="Item24" onkeydown="return searchResults.Nav(event,24)" onkeypress="return searchResults.Nav(event,24)" onkeyup="return searchResults.Nav(event,24)" class="SRSymbol" href="../ccp4srs__plane_8h.html" target="_parent">ccp4srs_plane.h</a>
+ </div>
+</div>
+<div class="SRResult" id="SR_ccp4srs_5ftorsion_2ecpp">
+ <div class="SREntry">
+  <a id="Item25" onkeydown="return searchResults.Nav(event,25)" onkeypress="return searchResults.Nav(event,25)" onkeyup="return searchResults.Nav(event,25)" class="SRSymbol" href="../ccp4srs__torsion_8cpp.html" target="_parent">ccp4srs_torsion.cpp</a>
+ </div>
+</div>
+<div class="SRResult" id="SR_ccp4srs_5ftorsion_2eh">
+ <div class="SREntry">
+  <a id="Item26" onkeydown="return searchResults.Nav(event,26)" onkeypress="return searchResults.Nav(event,26)" onkeyup="return searchResults.Nav(event,26)" class="SRSymbol" href="../ccp4srs__torsion_8h.html" target="_parent">ccp4srs_torsion.h</a>
+ </div>
+</div>
+<div class="SRResult" id="SR_ccp4srs_5ftree_2ecpp">
+ <div class="SREntry">
+  <a id="Item27" onkeydown="return searchResults.Nav(event,27)" onkeypress="return searchResults.Nav(event,27)" onkeyup="return searchResults.Nav(event,27)" class="SRSymbol" href="../ccp4srs__tree_8cpp.html" target="_parent">ccp4srs_tree.cpp</a>
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+</div>
+<div class="SRResult" id="SR_ccp4srs_5ftree_2eh">
+ <div class="SREntry">
+  <a id="Item28" onkeydown="return searchResults.Nav(event,28)" onkeypress="return searchResults.Nav(event,28)" onkeyup="return searchResults.Nav(event,28)" class="SRSymbol" href="../ccp4srs__tree_8h.html" target="_parent">ccp4srs_tree.h</a>
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+</div>
+<div class="SRResult" id="SR_ccp4srs_5ftypes_2ecpp">
+ <div class="SREntry">
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+ </div>
+</div>
+<div class="SRResult" id="SR_ccp4srs_5ftypes_2eh">
+ <div class="SREntry">
+  <a id="Item30" onkeydown="return searchResults.Nav(event,30)" onkeypress="return searchResults.Nav(event,30)" onkeyup="return searchResults.Nav(event,30)" class="SRSymbol" href="../ccp4srs__types_8h.html" target="_parent">ccp4srs_types.h</a>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
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+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/files_6d.html ccp4srs/doc-html/html/search/files_6d.html
--- ccp4srs-old/doc-html/html/search/files_6d.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/files_6d.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,40 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_memio_5f_2ecpp">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../memio___8cpp.html" target="_parent">memio_.cpp</a>
+ </div>
+</div>
+<div class="SRResult" id="SR_memio_5f_2eh">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../memio___8h.html" target="_parent">memio_.h</a>
+ </div>
+</div>
+<div class="SRResult" id="SR_mpfile_5f_2ecpp">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../mpfile___8cpp.html" target="_parent">mpfile_.cpp</a>
+ </div>
+</div>
+<div class="SRResult" id="SR_mpfile_5f_2eh">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../mpfile___8h.html" target="_parent">mpfile_.h</a>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_5f.html ccp4srs/doc-html/html/search/functions_5f.html
--- ccp4srs-old/doc-html/html/search/functions_5f.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_5f.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,38 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR__5faddatompair">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../namespaceccp4srs.html#a50bab1a74a6f5ebde0253478a4964b24" target="_parent">_addAtomPair</a>
+  <span class="SRScope">ccp4srs</span>
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+</div>
+<div class="SRResult" id="SR__5ffindname">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../namespaceccp4srs.html#adf196969f21a33865d5f6c0f2f32cb7f" target="_parent">_findName</a>
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+<div class="SRResult" id="SR__5fmakechirind">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../namespaceccp4srs.html#a99ea9b07a217ceb6c0645faaea831c82" target="_parent">_makeChirInd</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_61.html ccp4srs/doc-html/html/search/functions_61.html
--- ccp4srs-old/doc-html/html/search/functions_61.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_61.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,135 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_add">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_add')">add</a>
+  <div class="SRChildren">
+    <a id="Item0_c0" onkeydown="return searchResults.NavChild(event,0,0)" onkeypress="return searchResults.NavChild(event,0,0)" onkeyup="return searchResults.NavChild(event,0,0)" class="SRScope" href="../classccp4srs_1_1_container.html#a6caf1893b780f2cf196c85ee141baf18" target="_parent">ccp4srs::Container::add()</a>
+    <a id="Item0_c1" onkeydown="return searchResults.NavChild(event,0,1)" onkeypress="return searchResults.NavChild(event,0,1)" onkeyup="return searchResults.NavChild(event,0,1)" class="SRScope" href="../classccp4srs_1_1_monomer.html#ae1c9221ebd49b62830621cd40524d215" target="_parent">ccp4srs::Monomer::add(PAtom atom)</a>
+    <a id="Item0_c2" onkeydown="return searchResults.NavChild(event,0,2)" onkeypress="return searchResults.NavChild(event,0,2)" onkeyup="return searchResults.NavChild(event,0,2)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a88d4f2d1f97364930fed4bf349b23cb1" target="_parent">ccp4srs::Monomer::add(PBond bond)</a>
+    <a id="Item0_c3" onkeydown="return searchResults.NavChild(event,0,3)" onkeypress="return searchResults.NavChild(event,0,3)" onkeyup="return searchResults.NavChild(event,0,3)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a3eab75471f83c2c92834a1e30400642e" target="_parent">ccp4srs::Monomer::add(PAngle angle)</a>
+    <a id="Item0_c4" onkeydown="return searchResults.NavChild(event,0,4)" onkeypress="return searchResults.NavChild(event,0,4)" onkeyup="return searchResults.NavChild(event,0,4)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a394b2b32b99cd3c6e0b3654593436a2f" target="_parent">ccp4srs::Monomer::add(PPlane plane)</a>
+    <a id="Item0_c5" onkeydown="return searchResults.NavChild(event,0,5)" onkeypress="return searchResults.NavChild(event,0,5)" onkeyup="return searchResults.NavChild(event,0,5)" class="SRScope" href="../classccp4srs_1_1_monomer.html#acdfa8628139cfb914f2aecdb1e2f37d2" target="_parent">ccp4srs::Monomer::add(PTree stree)</a>
+    <a id="Item0_c6" onkeydown="return searchResults.NavChild(event,0,6)" onkeypress="return searchResults.NavChild(event,0,6)" onkeyup="return searchResults.NavChild(event,0,6)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a555cba2de4ecd6d3d7c192a52a9d44a3" target="_parent">ccp4srs::Monomer::add(PTorsion torsion)</a>
+    <a id="Item0_c7" onkeydown="return searchResults.NavChild(event,0,7)" onkeypress="return searchResults.NavChild(event,0,7)" onkeyup="return searchResults.NavChild(event,0,7)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a1820529a0bee358372e53ea0fb0c0a56" target="_parent">ccp4srs::Monomer::add(PChiCenter chicenter)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_add_5fatom_5fto_5fcif">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../namespaceccp4srs.html#af3c63726e6eb75b06c5b1c33a3acb608" target="_parent">add_atom_to_cif</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_add_5fbond_5ftype_5fto_5fcif">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../namespaceccp4srs.html#aaf4dd7dc419cfe6ae4f5a162bf528bf3" target="_parent">add_bond_type_to_cif</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_addhydrogens">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_addhydrogens')">addHydrogens</a>
+  <div class="SRChildren">
+    <a id="Item3_c0" onkeydown="return searchResults.NavChild(event,3,0)" onkeypress="return searchResults.NavChild(event,3,0)" onkeyup="return searchResults.NavChild(event,3,0)" class="SRScope" href="../classccp4srs_1_1_chem.html#acada705ca803ac2b68bb2c787a83fcb1" target="_parent">ccp4srs::Chem::addHydrogens(mmdb::PResidue R, mmdb::io::PFile structFile)</a>
+    <a id="Item3_c1" onkeydown="return searchResults.NavChild(event,3,1)" onkeypress="return searchResults.NavChild(event,3,1)" onkeyup="return searchResults.NavChild(event,3,1)" class="SRScope" href="../classccp4srs_1_1_chem.html#ac1ae2d0c6f7f79b3f5b02a6a3b082b81" target="_parent">ccp4srs::Chem::addHydrogens(mmdb::PChain chain, mmdb::io::PFile structFile)</a>
+    <a id="Item3_c2" onkeydown="return searchResults.NavChild(event,3,2)" onkeypress="return searchResults.NavChild(event,3,2)" onkeyup="return searchResults.NavChild(event,3,2)" class="SRScope" href="../classccp4srs_1_1_chem.html#a75fb480c106432f52d7301eae93d2942" target="_parent">ccp4srs::Chem::addHydrogens(mmdb::PModel model, mmdb::io::PFile structFile)</a>
+    <a id="Item3_c3" onkeydown="return searchResults.NavChild(event,3,3)" onkeypress="return searchResults.NavChild(event,3,3)" onkeyup="return searchResults.NavChild(event,3,3)" class="SRScope" href="../classccp4srs_1_1_chem.html#a45ea7718ea3dea244ba51f6f318d3623" target="_parent">ccp4srs::Chem::addHydrogens(mmdb::PManager MMDB, mmdb::io::PFile structFile)</a>
+    <a id="Item3_c4" onkeydown="return searchResults.NavChild(event,3,4)" onkeypress="return searchResults.NavChild(event,3,4)" onkeyup="return searchResults.NavChild(event,3,4)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a67a965eb782472588f1a5f4e693c509e" target="_parent">ccp4srs::Monomer::addHydrogens()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_angle">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_angle')">Angle</a>
+  <div class="SRChildren">
+    <a id="Item4_c0" onkeydown="return searchResults.NavChild(event,4,0)" onkeypress="return searchResults.NavChild(event,4,0)" onkeyup="return searchResults.NavChild(event,4,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a5ec6da380214e7100ff46e3e79898e15" target="_parent">ccp4srs::Angle::Angle()</a>
+    <a id="Item4_c1" onkeydown="return searchResults.NavChild(event,4,1)" onkeypress="return searchResults.NavChild(event,4,1)" onkeyup="return searchResults.NavChild(event,4,1)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a61b179edff80a9d168997038093cc92f" target="_parent">ccp4srs::Monomer::angle()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_at">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_container.html#ae9929d576289dd2313aaf4b2d9c377e9" target="_parent">at</a>
+  <span class="SRScope">ccp4srs::Container</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_atom')">atom</a>
+  <div class="SRChildren">
+    <a id="Item6_c0" onkeydown="return searchResults.NavChild(event,6,0)" onkeypress="return searchResults.NavChild(event,6,0)" onkeyup="return searchResults.NavChild(event,6,0)" class="SRScope" href="../classccp4srs_1_1_monomer.html#ac3492a092c5436d182acae9b6712da7f" target="_parent">ccp4srs::Monomer::atom()</a>
+    <a id="Item6_c1" onkeydown="return searchResults.NavChild(event,6,1)" onkeypress="return searchResults.NavChild(event,6,1)" onkeyup="return searchResults.NavChild(event,6,1)" class="SRScope" href="../classccp4srs_1_1_plane.html#ad1e544c70729b5a17dba23301ba6ca7e" target="_parent">ccp4srs::Plane::atom()</a>
+    <a id="Item6_c2" onkeydown="return searchResults.NavChild(event,6,2)" onkeypress="return searchResults.NavChild(event,6,2)" onkeyup="return searchResults.NavChild(event,6,2)" class="SRScope" href="../classccp4srs_1_1_tree.html#aa05e210175e281b0b975b22040cbf45d" target="_parent">ccp4srs::Tree::atom()</a>
+    <a id="Item6_c3" onkeydown="return searchResults.NavChild(event,6,3)" onkeypress="return searchResults.NavChild(event,6,3)" onkeyup="return searchResults.NavChild(event,6,3)" class="SRScope" href="../classccp4srs_1_1_atom.html#a66084d9a746b51608e8f0f8e28138e9d" target="_parent">ccp4srs::Atom::Atom()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom1">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_atom1')">atom1</a>
+  <div class="SRChildren">
+    <a id="Item7_c0" onkeydown="return searchResults.NavChild(event,7,0)" onkeypress="return searchResults.NavChild(event,7,0)" onkeyup="return searchResults.NavChild(event,7,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a64770743097878619e8dccf787f93802" target="_parent">ccp4srs::Angle::atom1()</a>
+    <a id="Item7_c1" onkeydown="return searchResults.NavChild(event,7,1)" onkeypress="return searchResults.NavChild(event,7,1)" onkeyup="return searchResults.NavChild(event,7,1)" class="SRScope" href="../classccp4srs_1_1_bond.html#a6ec052956ddec875a707d7e375ce0748" target="_parent">ccp4srs::Bond::atom1()</a>
+    <a id="Item7_c2" onkeydown="return searchResults.NavChild(event,7,2)" onkeypress="return searchResults.NavChild(event,7,2)" onkeyup="return searchResults.NavChild(event,7,2)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#ae27490ac46e2f3904ee230fe0c5b80af" target="_parent">ccp4srs::ChiCenter::atom1()</a>
+    <a id="Item7_c3" onkeydown="return searchResults.NavChild(event,7,3)" onkeypress="return searchResults.NavChild(event,7,3)" onkeyup="return searchResults.NavChild(event,7,3)" class="SRScope" href="../classccp4srs_1_1_torsion.html#af30f2e612259dedd1e569db13ff583fd" target="_parent">ccp4srs::Torsion::atom1()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom2">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_atom2')">atom2</a>
+  <div class="SRChildren">
+    <a id="Item8_c0" onkeydown="return searchResults.NavChild(event,8,0)" onkeypress="return searchResults.NavChild(event,8,0)" onkeyup="return searchResults.NavChild(event,8,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a1be24203719da0b250775f7c0b5710ed" target="_parent">ccp4srs::Angle::atom2()</a>
+    <a id="Item8_c1" onkeydown="return searchResults.NavChild(event,8,1)" onkeypress="return searchResults.NavChild(event,8,1)" onkeyup="return searchResults.NavChild(event,8,1)" class="SRScope" href="../classccp4srs_1_1_bond.html#a364bc6a611e192c07d0bf5236a3503b9" target="_parent">ccp4srs::Bond::atom2()</a>
+    <a id="Item8_c2" onkeydown="return searchResults.NavChild(event,8,2)" onkeypress="return searchResults.NavChild(event,8,2)" onkeyup="return searchResults.NavChild(event,8,2)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#a5e1600b63a2e92494176dc328c6fc8a6" target="_parent">ccp4srs::ChiCenter::atom2()</a>
+    <a id="Item8_c3" onkeydown="return searchResults.NavChild(event,8,3)" onkeypress="return searchResults.NavChild(event,8,3)" onkeyup="return searchResults.NavChild(event,8,3)" class="SRScope" href="../classccp4srs_1_1_torsion.html#ae34ef1ddabf50dd732bf66336bb4a2eb" target="_parent">ccp4srs::Torsion::atom2()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom3">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_atom3')">atom3</a>
+  <div class="SRChildren">
+    <a id="Item9_c0" onkeydown="return searchResults.NavChild(event,9,0)" onkeypress="return searchResults.NavChild(event,9,0)" onkeyup="return searchResults.NavChild(event,9,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a6d62c8acfe549d3d439a061f2bbcada9" target="_parent">ccp4srs::Angle::atom3()</a>
+    <a id="Item9_c1" onkeydown="return searchResults.NavChild(event,9,1)" onkeypress="return searchResults.NavChild(event,9,1)" onkeyup="return searchResults.NavChild(event,9,1)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#ac668dea1c66f203a26e46a1c87b37760" target="_parent">ccp4srs::ChiCenter::atom3()</a>
+    <a id="Item9_c2" onkeydown="return searchResults.NavChild(event,9,2)" onkeypress="return searchResults.NavChild(event,9,2)" onkeyup="return searchResults.NavChild(event,9,2)" class="SRScope" href="../classccp4srs_1_1_torsion.html#a37c594eb8a06aa962efd46c8d5c0e1b9" target="_parent">ccp4srs::Torsion::atom3()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom4">
+ <div class="SREntry">
+  <a id="Item10" onkeydown="return searchResults.Nav(event,10)" onkeypress="return searchResults.Nav(event,10)" onkeyup="return searchResults.Nav(event,10)" class="SRSymbol" href="../classccp4srs_1_1_torsion.html#afb752f1836193a0af5befba252e16703" target="_parent">atom4</a>
+  <span class="SRScope">ccp4srs::Torsion</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom_5fno">
+ <div class="SREntry">
+  <a id="Item11" onkeydown="return searchResults.Nav(event,11)" onkeypress="return searchResults.Nav(event,11)" onkeyup="return searchResults.Nav(event,11)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a9ac9e9e610a1a0450130d5e5c4242d34" target="_parent">atom_no</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atoms">
+ <div class="SREntry">
+  <a id="Item12" onkeydown="return searchResults.Nav(event,12)" onkeypress="return searchResults.Nav(event,12)" onkeyup="return searchResults.Nav(event,12)" class="SRSymbol" href="../classccp4srs_1_1_plane.html#a91e4f55f473565e42c27b6aab5311222" target="_parent">atoms</a>
+  <span class="SRScope">ccp4srs::Plane</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_62.html ccp4srs/doc-html/html/search/functions_62.html
--- ccp4srs-old/doc-html/html/search/functions_62.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_62.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,41 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_backward">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_tree.html#a70a9e13b054276780039e0d6f0edcdd9" target="_parent">backward</a>
+  <span class="SRScope">ccp4srs::Tree</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_base">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a0c37b44fe77e9f171d5f40281a6e82ae" target="_parent">Base</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_bond">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_bond')">bond</a>
+  <div class="SRChildren">
+    <a id="Item2_c0" onkeydown="return searchResults.NavChild(event,2,0)" onkeypress="return searchResults.NavChild(event,2,0)" onkeyup="return searchResults.NavChild(event,2,0)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a6b01e3fa4cb59dc507460ea0715823fa" target="_parent">ccp4srs::Monomer::bond()</a>
+    <a id="Item2_c1" onkeydown="return searchResults.NavChild(event,2,1)" onkeypress="return searchResults.NavChild(event,2,1)" onkeyup="return searchResults.NavChild(event,2,1)" class="SRScope" href="../classccp4srs_1_1_bond.html#acd3c055b0b0827de95e44ca9a9ac972a" target="_parent">ccp4srs::Bond::Bond()</a>
+  </div>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_63.html ccp4srs/doc-html/html/search/functions_63.html
--- ccp4srs-old/doc-html/html/search/functions_63.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_63.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,117 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_calchbonds">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_chem.html#ab5d4ff0f43b6785dc2c3cec72d4b8eec" target="_parent">CalcHBonds</a>
+  <span class="SRScope">ccp4srs::Chem</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_ccp4_5fchirality">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#ac0274e4727f43cedf27380121215cbfa" target="_parent">ccp4_chirality</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_center">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_chi_center.html#a0264f7a5c26c795bda84de7b233e70ab" target="_parent">center</a>
+  <span class="SRScope">ccp4srs::ChiCenter</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_charge">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a199caf3c186d47d5ca6e13e235471a84" target="_parent">charge</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_chem">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_chem.html#a6ca2d1c22ede07e88978645ab6a5887e" target="_parent">Chem</a>
+  <span class="SRScope">ccp4srs::Chem</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_chem_5fformula">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a6bbfc74c882e403c57984d7310d4fb98" target="_parent">chem_formula</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_chem_5fname">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#ab5a8d9361def2e547d1e65bf180f3252" target="_parent">chem_name</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_chem_5ftype">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a37432cca1867e01cd9af6d4569c2326a" target="_parent">chem_type</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_chicenter">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_chicenter')">chicenter</a>
+  <div class="SRChildren">
+    <a id="Item8_c0" onkeydown="return searchResults.NavChild(event,8,0)" onkeypress="return searchResults.NavChild(event,8,0)" onkeyup="return searchResults.NavChild(event,8,0)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a3c1ea4e271769745f01c8dc4146c683e" target="_parent">ccp4srs::Monomer::chicenter()</a>
+    <a id="Item8_c1" onkeydown="return searchResults.NavChild(event,8,1)" onkeypress="return searchResults.NavChild(event,8,1)" onkeyup="return searchResults.NavChild(event,8,1)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#a536462552b25777be443867ec6a28b48" target="_parent">ccp4srs::ChiCenter::ChiCenter()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_chirality">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a88df4aee528a9e551c126e9e8adab2f3" target="_parent">chirality</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_compare">
+ <div class="SREntry">
+  <a id="Item10" onkeydown="return searchResults.Nav(event,10)" onkeypress="return searchResults.Nav(event,10)" onkeyup="return searchResults.Nav(event,10)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#acefa794143d2ab128897441895cdf562" target="_parent">compare</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_connect">
+ <div class="SREntry">
+  <a id="Item11" onkeydown="return searchResults.Nav(event,11)" onkeypress="return searchResults.Nav(event,11)" onkeyup="return searchResults.Nav(event,11)" class="SRSymbol" href="../classccp4srs_1_1_tree.html#a9986231a0223ef6b62902823d119176f" target="_parent">connect</a>
+  <span class="SRScope">ccp4srs::Tree</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_container">
+ <div class="SREntry">
+  <a id="Item12" onkeydown="return searchResults.Nav(event,12)" onkeypress="return searchResults.Nav(event,12)" onkeyup="return searchResults.Nav(event,12)" class="SRSymbol" href="../classccp4srs_1_1_container.html#acdff89dd6d441d731b517565021e3881" target="_parent">Container</a>
+  <span class="SRScope">ccp4srs::Container</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_copy">
+ <div class="SREntry">
+  <a id="Item13" onkeydown="return searchResults.Nav(event,13)" onkeypress="return searchResults.Nav(event,13)" onkeyup="return searchResults.Nav(event,13)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_copy')">copy</a>
+  <div class="SRChildren">
+    <a id="Item13_c0" onkeydown="return searchResults.NavChild(event,13,0)" onkeypress="return searchResults.NavChild(event,13,0)" onkeyup="return searchResults.NavChild(event,13,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a085c530866442b6b3dfb8c969de2bfe8" target="_parent">ccp4srs::Angle::copy()</a>
+    <a id="Item13_c1" onkeydown="return searchResults.NavChild(event,13,1)" onkeypress="return searchResults.NavChild(event,13,1)" onkeyup="return searchResults.NavChild(event,13,1)" class="SRScope" href="../classccp4srs_1_1_atom.html#a5aa8172f59efa4ac90359b2be7424d92" target="_parent">ccp4srs::Atom::copy()</a>
+    <a id="Item13_c2" onkeydown="return searchResults.NavChild(event,13,2)" onkeypress="return searchResults.NavChild(event,13,2)" onkeyup="return searchResults.NavChild(event,13,2)" class="SRScope" href="../classccp4srs_1_1_bond.html#a4bb135bfcd9ee6078a2770fe9f15319c" target="_parent">ccp4srs::Bond::copy(Container&lt; Atom &gt; &amp;atoms, PBond bond, Container&lt; Atom &gt; &amp;bond_atoms)</a>
+    <a id="Item13_c3" onkeydown="return searchResults.NavChild(event,13,3)" onkeypress="return searchResults.NavChild(event,13,3)" onkeyup="return searchResults.NavChild(event,13,3)" class="SRScope" href="../classccp4srs_1_1_bond.html#a0c6c410020c5fad46d2987d9fc8de65e" target="_parent">ccp4srs::Bond::copy(PBond bond, mmdb::ivector anmatch=NULL)</a>
+    <a id="Item13_c4" onkeydown="return searchResults.NavChild(event,13,4)" onkeypress="return searchResults.NavChild(event,13,4)" onkeyup="return searchResults.NavChild(event,13,4)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#ab3dc0fe1813d51055e829586a27ddd15" target="_parent">ccp4srs::ChiCenter::copy()</a>
+    <a id="Item13_c5" onkeydown="return searchResults.NavChild(event,13,5)" onkeypress="return searchResults.NavChild(event,13,5)" onkeyup="return searchResults.NavChild(event,13,5)" class="SRScope" href="../classccp4srs_1_1_plane.html#a9db264baa4154922dfac882f4f437d34" target="_parent">ccp4srs::Plane::copy()</a>
+    <a id="Item13_c6" onkeydown="return searchResults.NavChild(event,13,6)" onkeypress="return searchResults.NavChild(event,13,6)" onkeyup="return searchResults.NavChild(event,13,6)" class="SRScope" href="../classccp4srs_1_1_torsion.html#a2a6ff05c37b9ce514fe557ab3817a072" target="_parent">ccp4srs::Torsion::copy()</a>
+    <a id="Item13_c7" onkeydown="return searchResults.NavChild(event,13,7)" onkeypress="return searchResults.NavChild(event,13,7)" onkeyup="return searchResults.NavChild(event,13,7)" class="SRScope" href="../classccp4srs_1_1_tree.html#acfc010d5d168bb288379e6b6721fb9fa" target="_parent">ccp4srs::Tree::copy()</a>
+    <a id="Item13_c8" onkeydown="return searchResults.NavChild(event,13,8)" onkeypress="return searchResults.NavChild(event,13,8)" onkeyup="return searchResults.NavChild(event,13,8)" class="SRScope" href="../structccp4srs_1_1_m_p_file_pos.html#a7f60e91b825a15d3def175dcdb71139d" target="_parent">ccp4srs::MPFilePos::Copy()</a>
+  </div>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_64.html ccp4srs/doc-html/html/search/functions_64.html
--- ccp4srs-old/doc-html/html/search/functions_64.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_64.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,58 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_defineclass">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_defineclass')">DefineClass</a>
+  <div class="SRChildren">
+    <a id="Item0_c0" onkeydown="return searchResults.NavChild(event,0,0)" onkeypress="return searchResults.NavChild(event,0,0)" onkeyup="return searchResults.NavChild(event,0,0)" class="SRScope" href="../namespaceccp4srs.html#afbb5df60616f08fcf36926a3585c185f" target="_parent">ccp4srs::DefineClass(Angle)</a>
+    <a id="Item0_c1" onkeydown="return searchResults.NavChild(event,0,1)" onkeypress="return searchResults.NavChild(event,0,1)" onkeyup="return searchResults.NavChild(event,0,1)" class="SRScope" href="../namespaceccp4srs.html#aaacc6a8b59c08ac1bbfd9305ee663a1b" target="_parent">ccp4srs::DefineClass(Atom)</a>
+    <a id="Item0_c2" onkeydown="return searchResults.NavChild(event,0,2)" onkeypress="return searchResults.NavChild(event,0,2)" onkeyup="return searchResults.NavChild(event,0,2)" class="SRScope" href="../namespaceccp4srs.html#a4c159612746fffa9c8740ead5f891bb4" target="_parent">ccp4srs::DefineClass(Base)</a>
+    <a id="Item0_c3" onkeydown="return searchResults.NavChild(event,0,3)" onkeypress="return searchResults.NavChild(event,0,3)" onkeyup="return searchResults.NavChild(event,0,3)" class="SRScope" href="../namespaceccp4srs.html#a156f31d96da750c94e75880a12fd5523" target="_parent">ccp4srs::DefineClass(Bond)</a>
+    <a id="Item0_c4" onkeydown="return searchResults.NavChild(event,0,4)" onkeypress="return searchResults.NavChild(event,0,4)" onkeyup="return searchResults.NavChild(event,0,4)" class="SRScope" href="../namespaceccp4srs.html#abe82012e7a8178ae1069f381769da72d" target="_parent">ccp4srs::DefineClass(Chem)</a>
+    <a id="Item0_c5" onkeydown="return searchResults.NavChild(event,0,5)" onkeypress="return searchResults.NavChild(event,0,5)" onkeyup="return searchResults.NavChild(event,0,5)" class="SRScope" href="../namespaceccp4srs.html#aed1b87fee568c115c3bbdb07ad9a5bd7" target="_parent">ccp4srs::DefineClass(ChiCenter)</a>
+    <a id="Item0_c6" onkeydown="return searchResults.NavChild(event,0,6)" onkeypress="return searchResults.NavChild(event,0,6)" onkeyup="return searchResults.NavChild(event,0,6)" class="SRScope" href="../namespaceccp4srs.html#aa72ee17a81ce821f1c37483a10153ae7" target="_parent">ccp4srs::DefineClass(Entry)</a>
+    <a id="Item0_c7" onkeydown="return searchResults.NavChild(event,0,7)" onkeypress="return searchResults.NavChild(event,0,7)" onkeyup="return searchResults.NavChild(event,0,7)" class="SRScope" href="../namespaceccp4srs.html#afeba477403b4f346ef1c74ab27c0a797" target="_parent">ccp4srs::DefineClass(Index)</a>
+    <a id="Item0_c8" onkeydown="return searchResults.NavChild(event,0,8)" onkeypress="return searchResults.NavChild(event,0,8)" onkeyup="return searchResults.NavChild(event,0,8)" class="SRScope" href="../namespaceccp4srs.html#a8c36728a6d09c1cb65fe3168735979cb" target="_parent">ccp4srs::DefineClass(Manager)</a>
+    <a id="Item0_c9" onkeydown="return searchResults.NavChild(event,0,9)" onkeypress="return searchResults.NavChild(event,0,9)" onkeyup="return searchResults.NavChild(event,0,9)" class="SRScope" href="../namespaceccp4srs.html#aea118bfa214275496e94e42beca05c35" target="_parent">ccp4srs::DefineClass(Monomer)</a>
+    <a id="Item0_c10" onkeydown="return searchResults.NavChild(event,0,10)" onkeypress="return searchResults.NavChild(event,0,10)" onkeyup="return searchResults.NavChild(event,0,10)" class="SRScope" href="../namespaceccp4srs.html#a299f5fc0ddc551524a80fe756cf2525d" target="_parent">ccp4srs::DefineClass(Plane)</a>
+    <a id="Item0_c11" onkeydown="return searchResults.NavChild(event,0,11)" onkeypress="return searchResults.NavChild(event,0,11)" onkeyup="return searchResults.NavChild(event,0,11)" class="SRScope" href="../namespaceccp4srs.html#a3e61bdd34189f80843c0e565ce68e628" target="_parent">ccp4srs::DefineClass(Torsion)</a>
+    <a id="Item0_c12" onkeydown="return searchResults.NavChild(event,0,12)" onkeypress="return searchResults.NavChild(event,0,12)" onkeyup="return searchResults.NavChild(event,0,12)" class="SRScope" href="../namespaceccp4srs.html#a6d1229e1b71f24fdb95a8700d402c6f8" target="_parent">ccp4srs::DefineClass(Tree)</a>
+    <a id="Item0_c13" onkeydown="return searchResults.NavChild(event,0,13)" onkeypress="return searchResults.NavChild(event,0,13)" onkeyup="return searchResults.NavChild(event,0,13)" class="SRScope" href="../namespaceccp4srs.html#a64bcbd2282ebaf1613021bf317bdf0cb" target="_parent">ccp4srs::DefineClass(MemIO)</a>
+    <a id="Item0_c14" onkeydown="return searchResults.NavChild(event,0,14)" onkeypress="return searchResults.NavChild(event,0,14)" onkeyup="return searchResults.NavChild(event,0,14)" class="SRScope" href="../namespaceccp4srs.html#aed1408df12f28bc4a3dd772230255597" target="_parent">ccp4srs::DefineClass(MPFile) class MPFile</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_definestructure">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_definestructure')">DefineStructure</a>
+  <div class="SRChildren">
+    <a id="Item1_c0" onkeydown="return searchResults.NavChild(event,1,0)" onkeypress="return searchResults.NavChild(event,1,0)" onkeyup="return searchResults.NavChild(event,1,0)" class="SRScope" href="../namespaceccp4srs.html#a38fd31a76e47d65dbd8f9343fdc2f001" target="_parent">ccp4srs::DefineStructure(AtomPair)</a>
+    <a id="Item1_c1" onkeydown="return searchResults.NavChild(event,1,1)" onkeypress="return searchResults.NavChild(event,1,1)" onkeyup="return searchResults.NavChild(event,1,1)" class="SRScope" href="../namespaceccp4srs.html#af0f84ef74e24251a016c6d27c196fe2e" target="_parent">ccp4srs::DefineStructure(DASelHnds)</a>
+    <a id="Item1_c2" onkeydown="return searchResults.NavChild(event,1,2)" onkeypress="return searchResults.NavChild(event,1,2)" onkeyup="return searchResults.NavChild(event,1,2)" class="SRScope" href="../namespaceccp4srs.html#aad79147ea920868ed625a8f693277d56" target="_parent">ccp4srs::DefineStructure(MPFilePos)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_deleteselections">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../structccp4srs_1_1_d_a_sel_hnds.html#a582873aa43d2c8708e99db1485013bef" target="_parent">deleteSelections</a>
+  <span class="SRScope">ccp4srs::DASelHnds</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_65.html ccp4srs/doc-html/html/search/functions_65.html
--- ccp4srs-old/doc-html/html/search/functions_65.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_65.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,70 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_element">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a78344a993072c3e8918a54c3259d55d8" target="_parent">element</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_element_5fpdb">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a8d78d445f18a9f9e83d82f66e715b274" target="_parent">element_pdb</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_empty">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_empty')">empty</a>
+  <div class="SRChildren">
+    <a id="Item2_c0" onkeydown="return searchResults.NavChild(event,2,0)" onkeypress="return searchResults.NavChild(event,2,0)" onkeyup="return searchResults.NavChild(event,2,0)" class="SRScope" href="../classccp4srs_1_1_container.html#aeed888e25348f83a53021beaa21a0b1e" target="_parent">ccp4srs::Container::empty()</a>
+    <a id="Item2_c1" onkeydown="return searchResults.NavChild(event,2,1)" onkeypress="return searchResults.NavChild(event,2,1)" onkeyup="return searchResults.NavChild(event,2,1)" class="SRScope" href="../classccp4srs_1_1_plane.html#a8da6c13ce79682d5f17e23f7c3e84849" target="_parent">ccp4srs::Plane::empty()</a>
+    <a id="Item2_c2" onkeydown="return searchResults.NavChild(event,2,2)" onkeypress="return searchResults.NavChild(event,2,2)" onkeyup="return searchResults.NavChild(event,2,2)" class="SRScope" href="../classccp4srs_1_1_tree.html#a5f5e595cfdb5623cc59c0651ff7a25d3" target="_parent">ccp4srs::Tree::empty()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_energy_5ftype">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#af9d89db887cdbfc5523a79ece1c1e117" target="_parent">energy_type</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_entry">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_entry.html#aa72cb70c4f1c115a2134e2da80b9bc34" target="_parent">Entry</a>
+  <span class="SRScope">ccp4srs::Entry</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_esd">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_esd')">esd</a>
+  <div class="SRChildren">
+    <a id="Item5_c0" onkeydown="return searchResults.NavChild(event,5,0)" onkeypress="return searchResults.NavChild(event,5,0)" onkeyup="return searchResults.NavChild(event,5,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a31b7030dec4dd77c0eefa3444c75901f" target="_parent">ccp4srs::Angle::esd()</a>
+    <a id="Item5_c1" onkeydown="return searchResults.NavChild(event,5,1)" onkeypress="return searchResults.NavChild(event,5,1)" onkeyup="return searchResults.NavChild(event,5,1)" class="SRScope" href="../classccp4srs_1_1_plane.html#ad9f1d004296b308a0955997695277ff4" target="_parent">ccp4srs::Plane::esd()</a>
+    <a id="Item5_c2" onkeydown="return searchResults.NavChild(event,5,2)" onkeypress="return searchResults.NavChild(event,5,2)" onkeyup="return searchResults.NavChild(event,5,2)" class="SRScope" href="../classccp4srs_1_1_torsion.html#a44095b8e5025c92a4b443a8715beceee" target="_parent">ccp4srs::Torsion::esd()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_esds">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_plane.html#a4fd16b46609257ebe87c7b7347597b2b" target="_parent">esds</a>
+  <span class="SRScope">ccp4srs::Plane</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_66.html ccp4srs/doc-html/html/search/functions_66.html
--- ccp4srs-old/doc-html/html/search/functions_66.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_66.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,38 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_forward">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_tree.html#ad52fadb719ce7ca269b9f6875a9ce8e6" target="_parent">forward</a>
+  <span class="SRScope">ccp4srs::Tree</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_free">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a4cda073662a49aa45b0c744ec88de39a" target="_parent">free</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_freememory">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_base.html#ab67f138edc7ae19791be69dde485c719" target="_parent">freeMemory</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_67.html ccp4srs/doc-html/html/search/functions_67.html
--- ccp4srs-old/doc-html/html/search/functions_67.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_67.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,318 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_get_5fangles">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a8d4b4084ca5c0e0fa42075f59eaf3e08" target="_parent">get_angles</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fatom_5ffrom_5fcif">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_get_5fatom_5ffrom_5fcif')">get_atom_from_cif</a>
+  <div class="SRChildren">
+    <a id="Item1_c0" onkeydown="return searchResults.NavChild(event,1,0)" onkeypress="return searchResults.NavChild(event,1,0)" onkeyup="return searchResults.NavChild(event,1,0)" class="SRScope" href="../namespaceccp4srs.html#adead0e638933d7d2949df9bb7b44f910" target="_parent">ccp4srs::get_atom_from_cif(int &amp;index, mmdb::mmcif::PLoop loop, mmdb::cpstr Tag, int row, Container&lt; Atom &gt; &amp;atoms, int &amp;rc)</a>
+    <a id="Item1_c1" onkeydown="return searchResults.NavChild(event,1,1)" onkeypress="return searchResults.NavChild(event,1,1)" onkeyup="return searchResults.NavChild(event,1,1)" class="SRScope" href="../namespaceccp4srs.html#a012e980439f3fcbb1844abf82ab2e95e" target="_parent">ccp4srs::get_atom_from_cif(int &amp;index, mmdb::mmcif::PStruct mmCIFStruct, mmdb::cpstr Tag, Container&lt; Atom &gt; &amp;atoms, int &amp;rc)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fatoms">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a1ca9838123fea51260be3c44abd6771f" target="_parent">get_atoms</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fbond_5ftype_5ffrom_5fcif">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../namespaceccp4srs.html#a66b5a7cbf87409e898be86c84505275a" target="_parent">get_bond_type_from_cif</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fbond_5ftype_5ffrom_5fcif_5fccp4">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../namespaceccp4srs.html#a134be7dad55bde913e9bbb02825064e0" target="_parent">get_bond_type_from_cif_ccp4</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fbond_5ftype_5ffrom_5fcif_5frcsb">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../namespaceccp4srs.html#a2fc315dbfb7012f8e39ff3a2f440a5d6" target="_parent">get_bond_type_from_cif_rcsb</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fbonds">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#af36aeb36b83f49d3b4fc28d4737b5efd" target="_parent">get_bonds</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fbool">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a0bbc28ba1593463385ae8f28b65225fa" target="_parent">get_bool</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fbound">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_get_5fbound')">get_bound</a>
+  <div class="SRChildren">
+    <a id="Item8_c0" onkeydown="return searchResults.NavChild(event,8,0)" onkeypress="return searchResults.NavChild(event,8,0)" onkeyup="return searchResults.NavChild(event,8,0)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a7b6acc92258007c15351989930e8672f" target="_parent">ccp4srs::Monomer::get_bound(int atomNo, mmdb::cpstr elem, int serNo)</a>
+    <a id="Item8_c1" onkeydown="return searchResults.NavChild(event,8,1)" onkeypress="return searchResults.NavChild(event,8,1)" onkeyup="return searchResults.NavChild(event,8,1)" class="SRScope" href="../classccp4srs_1_1_monomer.html#ae60200771fdf1a869023dacebfb98278" target="_parent">ccp4srs::Monomer::get_bound(int atomNo, int n)</a>
+    <a id="Item8_c2" onkeydown="return searchResults.NavChild(event,8,2)" onkeypress="return searchResults.NavChild(event,8,2)" onkeyup="return searchResults.NavChild(event,8,2)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a8ae0097e0e9950fc3f443f373a0a9359" target="_parent">ccp4srs::Monomer::get_bound(mmdb::cpstr aname, int n)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fbuffer">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_get_5fbuffer')">get_buffer</a>
+  <div class="SRChildren">
+    <a id="Item9_c0" onkeydown="return searchResults.NavChild(event,9,0)" onkeypress="return searchResults.NavChild(event,9,0)" onkeyup="return searchResults.NavChild(event,9,0)" class="SRScope" href="../classccp4srs_1_1_mem_i_o.html#aa1d1ea86d64ee50cab284d4a18f55ab8" target="_parent">ccp4srs::MemIO::get_buffer(const int length)</a>
+    <a id="Item9_c1" onkeydown="return searchResults.NavChild(event,9,1)" onkeypress="return searchResults.NavChild(event,9,1)" onkeyup="return searchResults.NavChild(event,9,1)" class="SRScope" href="../classccp4srs_1_1_mem_i_o.html#adad4a428c7530e61362f46d37b87d524" target="_parent">ccp4srs::MemIO::get_buffer(mmdb::pstr *buf, int *length)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fbyte">
+ <div class="SREntry">
+  <a id="Item10" onkeydown="return searchResults.Nav(event,10)" onkeypress="return searchResults.Nav(event,10)" onkeyup="return searchResults.Nav(event,10)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a296d38484504311f2773ff313298dda9" target="_parent">get_byte</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fchicenters">
+ <div class="SREntry">
+  <a id="Item11" onkeydown="return searchResults.Nav(event,11)" onkeypress="return searchResults.Nav(event,11)" onkeyup="return searchResults.Nav(event,11)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a591d5f8275f5b5756442d96221039ef3" target="_parent">get_chicenters</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fchirality">
+ <div class="SREntry">
+  <a id="Item12" onkeydown="return searchResults.Nav(event,12)" onkeypress="return searchResults.Nav(event,12)" onkeyup="return searchResults.Nav(event,12)" class="SRSymbol" href="../classccp4srs_1_1_chi_center.html#a1aa5ee605cdc3756abcb075279eeb8af" target="_parent">get_chirality</a>
+  <span class="SRScope">ccp4srs::ChiCenter</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5ffloat">
+ <div class="SREntry">
+  <a id="Item13" onkeydown="return searchResults.Nav(event,13)" onkeypress="return searchResults.Nav(event,13)" onkeyup="return searchResults.Nav(event,13)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#adf95c15823dd0fb1067002d2ee3d8095" target="_parent">get_float</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fibyte">
+ <div class="SREntry">
+  <a id="Item14" onkeydown="return searchResults.Nav(event,14)" onkeypress="return searchResults.Nav(event,14)" onkeyup="return searchResults.Nav(event,14)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a7bc9b6d871402f5b5601d05ad4012326" target="_parent">get_ibyte</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5finteger">
+ <div class="SREntry">
+  <a id="Item15" onkeydown="return searchResults.Nav(event,15)" onkeypress="return searchResults.Nav(event,15)" onkeyup="return searchResults.Nav(event,15)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a2d311d3bf0798e1c2bcb1cbe7f5d622f" target="_parent">get_integer</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fishort">
+ <div class="SREntry">
+  <a id="Item16" onkeydown="return searchResults.Nav(event,16)" onkeypress="return searchResults.Nav(event,16)" onkeyup="return searchResults.Nav(event,16)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a55e1b2e8f826ab2d6c0aef09f3beac9f" target="_parent">get_ishort</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fline">
+ <div class="SREntry">
+  <a id="Item17" onkeydown="return searchResults.Nav(event,17)" onkeypress="return searchResults.Nav(event,17)" onkeyup="return searchResults.Nav(event,17)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a6cab031cef522531846e3ced7984f276" target="_parent">get_line</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5flong">
+ <div class="SREntry">
+  <a id="Item18" onkeydown="return searchResults.Nav(event,18)" onkeypress="return searchResults.Nav(event,18)" onkeyup="return searchResults.Nav(event,18)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a950878f651e3bb037cf7ddc4a9c00201" target="_parent">get_long</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fplanes">
+ <div class="SREntry">
+  <a id="Item19" onkeydown="return searchResults.Nav(event,19)" onkeypress="return searchResults.Nav(event,19)" onkeyup="return searchResults.Nav(event,19)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#aa454ac38a87c19006580a42bc38958fc" target="_parent">get_planes</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5freal">
+ <div class="SREntry">
+  <a id="Item20" onkeydown="return searchResults.Nav(event,20)" onkeypress="return searchResults.Nav(event,20)" onkeyup="return searchResults.Nav(event,20)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#afcc2e5eede7a829347985f646f24dcb3" target="_parent">get_real</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fshort">
+ <div class="SREntry">
+  <a id="Item21" onkeydown="return searchResults.Nav(event,21)" onkeypress="return searchResults.Nav(event,21)" onkeyup="return searchResults.Nav(event,21)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#af2d1b382de42e06ce1dc5ae4ad6bb20f" target="_parent">get_short</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fshortreal">
+ <div class="SREntry">
+  <a id="Item22" onkeydown="return searchResults.Nav(event,22)" onkeypress="return searchResults.Nav(event,22)" onkeyup="return searchResults.Nav(event,22)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a039402bc82d9d0de0bd3664769355573" target="_parent">get_shortreal</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fstring">
+ <div class="SREntry">
+  <a id="Item23" onkeydown="return searchResults.Nav(event,23)" onkeypress="return searchResults.Nav(event,23)" onkeyup="return searchResults.Nav(event,23)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a22abd9cc96e80e4d3e71f0d1acbf1c4d" target="_parent">get_string</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5ftorsions">
+ <div class="SREntry">
+  <a id="Item24" onkeydown="return searchResults.Nav(event,24)" onkeypress="return searchResults.Nav(event,24)" onkeyup="return searchResults.Nav(event,24)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a7b31b6675690c2edc0baa0e070d349ad" target="_parent">get_torsions</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5ftree">
+ <div class="SREntry">
+  <a id="Item25" onkeydown="return searchResults.Nav(event,25)" onkeypress="return searchResults.Nav(event,25)" onkeyup="return searchResults.Nav(event,25)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a351a18b323af41b74d1b415fcd1df640" target="_parent">get_tree</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_get_5fword">
+ <div class="SREntry">
+  <a id="Item26" onkeydown="return searchResults.Nav(event,26)" onkeypress="return searchResults.Nav(event,26)" onkeyup="return searchResults.Nav(event,26)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#ab932bc5aa0e98c9e681a3f3a9cc532c8" target="_parent">get_word</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_getatnames">
+ <div class="SREntry">
+  <a id="Item27" onkeydown="return searchResults.Nav(event,27)" onkeypress="return searchResults.Nav(event,27)" onkeyup="return searchResults.Nav(event,27)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_getatnames')">getAtNames</a>
+  <div class="SRChildren">
+    <a id="Item27_c0" onkeydown="return searchResults.NavChild(event,27,0)" onkeypress="return searchResults.NavChild(event,27,0)" onkeyup="return searchResults.NavChild(event,27,0)" class="SRScope" href="../classccp4srs_1_1_base.html#af9a1789b20b43e97a8eb6a56b4ef32c4" target="_parent">ccp4srs::Base::getAtNames(int entryNo, mmdb::PAtomName AtName, int &amp;nAtoms, int &amp;nH)</a>
+    <a id="Item27_c1" onkeydown="return searchResults.NavChild(event,27,1)" onkeypress="return searchResults.NavChild(event,27,1)" onkeyup="return searchResults.NavChild(event,27,1)" class="SRScope" href="../classccp4srs_1_1_base.html#afbe234eef9c84fde630b72fbcfe27946" target="_parent">ccp4srs::Base::getAtNames(mmdb::io::PFile structFile, int entryNo, mmdb::PAtomName AtName, int &amp;nAtoms, int &amp;nH)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_getatomnamematch">
+ <div class="SREntry">
+  <a id="Item28" onkeydown="return searchResults.Nav(event,28)" onkeypress="return searchResults.Nav(event,28)" onkeyup="return searchResults.Nav(event,28)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_getatomnamematch')">getAtomNameMatch</a>
+  <div class="SRChildren">
+    <a id="Item28_c0" onkeydown="return searchResults.NavChild(event,28,0)" onkeypress="return searchResults.NavChild(event,28,0)" onkeyup="return searchResults.NavChild(event,28,0)" class="SRScope" href="../classccp4srs_1_1_monomer.html#abb514ab63af7e9dbb68f59bc13551618" target="_parent">ccp4srs::Monomer::getAtomNameMatch(mmdb::PPAtom A, int nat, mmdb::pstr altLoc, mmdb::ivector anmatch)</a>
+    <a id="Item28_c1" onkeydown="return searchResults.NavChild(event,28,1)" onkeypress="return searchResults.NavChild(event,28,1)" onkeyup="return searchResults.NavChild(event,28,1)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a17d26aa3a5b3b637cf6148499013c345" target="_parent">ccp4srs::Monomer::getAtomNameMatch(Container&lt; Atom &gt; *A, mmdb::ivector anmatch)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_getatoms">
+ <div class="SREntry">
+  <a id="Item29" onkeydown="return searchResults.Nav(event,29)" onkeypress="return searchResults.Nav(event,29)" onkeyup="return searchResults.Nav(event,29)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a7e47408dacc9bd80de046504e235cc06" target="_parent">getAtoms</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_getbonds">
+ <div class="SREntry">
+  <a id="Item30" onkeydown="return searchResults.Nav(event,30)" onkeypress="return searchResults.Nav(event,30)" onkeyup="return searchResults.Nav(event,30)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a8bb61486d7dd2df0566b8e3a1c7f1c89" target="_parent">getBonds</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_getenergytypes">
+ <div class="SREntry">
+  <a id="Item31" onkeydown="return searchResults.Nav(event,31)" onkeypress="return searchResults.Nav(event,31)" onkeyup="return searchResults.Nav(event,31)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_getenergytypes')">getEnergyTypes</a>
+  <div class="SRChildren">
+    <a id="Item31_c0" onkeydown="return searchResults.NavChild(event,31,0)" onkeypress="return searchResults.NavChild(event,31,0)" onkeyup="return searchResults.NavChild(event,31,0)" class="SRScope" href="../classccp4srs_1_1_chem.html#a301341ad4a91bf6cc4e7641efeb56309" target="_parent">ccp4srs::Chem::getEnergyTypes(mmdb::PResidue R, mmdb::io::PFile structFile)</a>
+    <a id="Item31_c1" onkeydown="return searchResults.NavChild(event,31,1)" onkeypress="return searchResults.NavChild(event,31,1)" onkeyup="return searchResults.NavChild(event,31,1)" class="SRScope" href="../classccp4srs_1_1_chem.html#acb540af5e9036d7765dfdaa762fb6b2f" target="_parent">ccp4srs::Chem::getEnergyTypes(mmdb::PPResidue R, int nRes, mmdb::io::PFile structFile)</a>
+    <a id="Item31_c2" onkeydown="return searchResults.NavChild(event,31,2)" onkeypress="return searchResults.NavChild(event,31,2)" onkeyup="return searchResults.NavChild(event,31,2)" class="SRScope" href="../classccp4srs_1_1_chem.html#a6993968f40984c210ffad03588321d70" target="_parent">ccp4srs::Chem::getEnergyTypes(mmdb::PChain chain, mmdb::io::PFile structFile)</a>
+    <a id="Item31_c3" onkeydown="return searchResults.NavChild(event,31,3)" onkeypress="return searchResults.NavChild(event,31,3)" onkeyup="return searchResults.NavChild(event,31,3)" class="SRScope" href="../classccp4srs_1_1_chem.html#a6a9f477d2484e2e2d71328934432e1f8" target="_parent">ccp4srs::Chem::getEnergyTypes(mmdb::PModel model, mmdb::io::PFile structFile)</a>
+    <a id="Item31_c4" onkeydown="return searchResults.NavChild(event,31,4)" onkeypress="return searchResults.NavChild(event,31,4)" onkeyup="return searchResults.NavChild(event,31,4)" class="SRScope" href="../classccp4srs_1_1_chem.html#a227201ea4eedc8464c764dd015b7b190" target="_parent">ccp4srs::Chem::getEnergyTypes(mmdb::PManager MMDB, mmdb::io::PFile structFile)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_getentryno">
+ <div class="SREntry">
+  <a id="Item32" onkeydown="return searchResults.Nav(event,32)" onkeypress="return searchResults.Nav(event,32)" onkeyup="return searchResults.Nav(event,32)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a57b706684f3e84c741099ff904e01152" target="_parent">getEntryNo</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_getgraph">
+ <div class="SREntry">
+  <a id="Item33" onkeydown="return searchResults.Nav(event,33)" onkeypress="return searchResults.Nav(event,33)" onkeyup="return searchResults.Nav(event,33)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_getgraph')">getGraph</a>
+  <div class="SRChildren">
+    <a id="Item33_c0" onkeydown="return searchResults.NavChild(event,33,0)" onkeypress="return searchResults.NavChild(event,33,0)" onkeyup="return searchResults.NavChild(event,33,0)" class="SRScope" href="../classccp4srs_1_1_base.html#a17b78139832b00d7025236171ab31b7e" target="_parent">ccp4srs::Base::getGraph(mmdb::io::PFile graphFile, mmdb::math::RPGraph G)</a>
+    <a id="Item33_c1" onkeydown="return searchResults.NavChild(event,33,1)" onkeypress="return searchResults.NavChild(event,33,1)" onkeyup="return searchResults.NavChild(event,33,1)" class="SRScope" href="../classccp4srs_1_1_base.html#a8421066e4a9117cd380ff4362c355986" target="_parent">ccp4srs::Base::getGraph(mmdb::io::PFile graphFile, int entryNo, mmdb::math::RPGraph G, int Hflag)</a>
+    <a id="Item33_c2" onkeydown="return searchResults.NavChild(event,33,2)" onkeypress="return searchResults.NavChild(event,33,2)" onkeyup="return searchResults.NavChild(event,33,2)" class="SRScope" href="../classccp4srs_1_1_base.html#af00d1ee772d045c048aa292457755b50" target="_parent">ccp4srs::Base::getGraph(mmdb::io::PFile graphFile, mmdb::math::RPGraph G, int Hflag)</a>
+    <a id="Item33_c3" onkeydown="return searchResults.NavChild(event,33,3)" onkeypress="return searchResults.NavChild(event,33,3)" onkeyup="return searchResults.NavChild(event,33,3)" class="SRScope" href="../classccp4srs_1_1_base.html#a418f3d4d079e0c4b93ebc6fff1fd0639" target="_parent">ccp4srs::Base::getGraph(int entryNo, mmdb::math::RPGraph G, int Hflag)</a>
+    <a id="Item33_c4" onkeydown="return searchResults.NavChild(event,33,4)" onkeypress="return searchResults.NavChild(event,33,4)" onkeyup="return searchResults.NavChild(event,33,4)" class="SRScope" href="../classccp4srs_1_1_base.html#a1f9dd08ea6c39fc0bb0a3885e6b3efac" target="_parent">ccp4srs::Base::getGraph(mmdb::cpstr entryID, mmdb::math::RPGraph G, int Hflag)</a>
+    <a id="Item33_c5" onkeydown="return searchResults.NavChild(event,33,5)" onkeypress="return searchResults.NavChild(event,33,5)" onkeyup="return searchResults.NavChild(event,33,5)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a9d1a2b0facb208344413158d74446755" target="_parent">ccp4srs::Monomer::getGraph()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_getgraphfile">
+ <div class="SREntry">
+  <a id="Item34" onkeydown="return searchResults.Nav(event,34)" onkeypress="return searchResults.Nav(event,34)" onkeyup="return searchResults.Nav(event,34)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a656b776b70ead2f8346b352b3bd1311e" target="_parent">getGraphFile</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_gethetinfo">
+ <div class="SREntry">
+  <a id="Item35" onkeydown="return searchResults.Nav(event,35)" onkeypress="return searchResults.Nav(event,35)" onkeyup="return searchResults.Nav(event,35)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a88c88924e247250d08cc4795b345c66a" target="_parent">getHetInfo</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_getindex">
+ <div class="SREntry">
+  <a id="Item36" onkeydown="return searchResults.Nav(event,36)" onkeypress="return searchResults.Nav(event,36)" onkeyup="return searchResults.Nav(event,36)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_getindex')">getIndex</a>
+  <div class="SRChildren">
+    <a id="Item36_c0" onkeydown="return searchResults.NavChild(event,36,0)" onkeypress="return searchResults.NavChild(event,36,0)" onkeyup="return searchResults.NavChild(event,36,0)" class="SRScope" href="../classccp4srs_1_1_base.html#affa058db2078bc7835e9c78ca3bdde81" target="_parent">ccp4srs::Base::getIndex(mmdb::cpstr entryID)</a>
+    <a id="Item36_c1" onkeydown="return searchResults.NavChild(event,36,1)" onkeypress="return searchResults.NavChild(event,36,1)" onkeyup="return searchResults.NavChild(event,36,1)" class="SRScope" href="../classccp4srs_1_1_base.html#a399ff3d49a14dd3bb8250058f6452f4f" target="_parent">ccp4srs::Base::getIndex(int n)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_getleavingatoms">
+ <div class="SREntry">
+  <a id="Item37" onkeydown="return searchResults.Nav(event,37)" onkeypress="return searchResults.Nav(event,37)" onkeyup="return searchResults.Nav(event,37)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a6c3ad68f13fb779921605d0e696add1c" target="_parent">getLeavingAtoms</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_getmonomer">
+ <div class="SREntry">
+  <a id="Item38" onkeydown="return searchResults.Nav(event,38)" onkeypress="return searchResults.Nav(event,38)" onkeyup="return searchResults.Nav(event,38)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_getmonomer')">getMonomer</a>
+  <div class="SRChildren">
+    <a id="Item38_c0" onkeydown="return searchResults.NavChild(event,38,0)" onkeypress="return searchResults.NavChild(event,38,0)" onkeyup="return searchResults.NavChild(event,38,0)" class="SRScope" href="../classccp4srs_1_1_base.html#a339033984c68dd221cd6db184b734694" target="_parent">ccp4srs::Base::getMonomer(mmdb::cpstr entryID)</a>
+    <a id="Item38_c1" onkeydown="return searchResults.NavChild(event,38,1)" onkeypress="return searchResults.NavChild(event,38,1)" onkeyup="return searchResults.NavChild(event,38,1)" class="SRScope" href="../classccp4srs_1_1_base.html#a6f3f6564a30198bfe82215bceb6806e2" target="_parent">ccp4srs::Base::getMonomer(int entryNo, mmdb::io::PFile structFile)</a>
+    <a id="Item38_c2" onkeydown="return searchResults.NavChild(event,38,2)" onkeypress="return searchResults.NavChild(event,38,2)" onkeyup="return searchResults.NavChild(event,38,2)" class="SRScope" href="../classccp4srs_1_1_base.html#ad25bf7474ec0574a39081ec5eeaefc5b" target="_parent">ccp4srs::Base::getMonomer(mmdb::cpstr entryID, mmdb::io::PFile structFile)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_getnewhandles">
+ <div class="SREntry">
+  <a id="Item39" onkeydown="return searchResults.Nav(event,39)" onkeypress="return searchResults.Nav(event,39)" onkeyup="return searchResults.Nav(event,39)" class="SRSymbol" href="../structccp4srs_1_1_d_a_sel_hnds.html#a3e8624665274bf47da9408f3b21f35d8" target="_parent">getNewHandles</a>
+  <span class="SRScope">ccp4srs::DASelHnds</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_getnofatoms">
+ <div class="SREntry">
+  <a id="Item40" onkeydown="return searchResults.Nav(event,40)" onkeypress="return searchResults.Nav(event,40)" onkeyup="return searchResults.Nav(event,40)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_getnofatoms')">getNofAtoms</a>
+  <div class="SRChildren">
+    <a id="Item40_c0" onkeydown="return searchResults.NavChild(event,40,0)" onkeypress="return searchResults.NavChild(event,40,0)" onkeyup="return searchResults.NavChild(event,40,0)" class="SRScope" href="../classccp4srs_1_1_base.html#a646d2c4349be4a740f2121dfd2091150" target="_parent">ccp4srs::Base::getNofAtoms(mmdb::cpstr entryID)</a>
+    <a id="Item40_c1" onkeydown="return searchResults.NavChild(event,40,1)" onkeypress="return searchResults.NavChild(event,40,1)" onkeyup="return searchResults.NavChild(event,40,1)" class="SRScope" href="../classccp4srs_1_1_base.html#a025a5622f0bfb83808cdad7cbf7af974" target="_parent">ccp4srs::Base::getNofAtoms(int entryNo)</a>
+    <a id="Item40_c2" onkeydown="return searchResults.NavChild(event,40,2)" onkeypress="return searchResults.NavChild(event,40,2)" onkeyup="return searchResults.NavChild(event,40,2)" class="SRScope" href="../classccp4srs_1_1_base.html#af0653379d9db757dcc64c44c0e9ce070" target="_parent">ccp4srs::Base::getNofAtoms(int entryNo, int &amp;nNonHAtoms, int &amp;nHAtoms)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_getpath">
+ <div class="SREntry">
+  <a id="Item41" onkeydown="return searchResults.Nav(event,41)" onkeypress="return searchResults.Nav(event,41)" onkeyup="return searchResults.Nav(event,41)" class="SRSymbol" href="../classccp4srs_1_1_base.html#ac5481a8eeeb26ead06d7df61f605dac9" target="_parent">getPath</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_getstructfile">
+ <div class="SREntry">
+  <a id="Item42" onkeydown="return searchResults.Nav(event,42)" onkeypress="return searchResults.Nav(event,42)" onkeyup="return searchResults.Nav(event,42)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a03eac100b52d1f2d2d13981799f928bb" target="_parent">getStructFile</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_68.html ccp4srs/doc-html/html/search/functions_68.html
--- ccp4srs-old/doc-html/html/search/functions_68.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_68.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,26 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_hb_5ftype">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#ab45d65bdba2966ce382687548921cd56" target="_parent">hb_type</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_69.html ccp4srs/doc-html/html/search/functions_69.html
--- ccp4srs-old/doc-html/html/search/functions_69.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_69.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,80 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_id">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_id')">id</a>
+  <div class="SRChildren">
+    <a id="Item0_c0" onkeydown="return searchResults.NavChild(event,0,0)" onkeypress="return searchResults.NavChild(event,0,0)" onkeyup="return searchResults.NavChild(event,0,0)" class="SRScope" href="../classccp4srs_1_1_atom.html#a276b8b3e31130e6f0116af498e3a7766" target="_parent">ccp4srs::Atom::id()</a>
+    <a id="Item0_c1" onkeydown="return searchResults.NavChild(event,0,1)" onkeypress="return searchResults.NavChild(event,0,1)" onkeyup="return searchResults.NavChild(event,0,1)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#a9bd5958f4cb3519a6a745d1db16b135b" target="_parent">ccp4srs::ChiCenter::id()</a>
+    <a id="Item0_c2" onkeydown="return searchResults.NavChild(event,0,2)" onkeypress="return searchResults.NavChild(event,0,2)" onkeyup="return searchResults.NavChild(event,0,2)" class="SRScope" href="../classccp4srs_1_1_plane.html#ac47f99cd6bf3190767da8fc85d01dc18" target="_parent">ccp4srs::Plane::id()</a>
+    <a id="Item0_c3" onkeydown="return searchResults.NavChild(event,0,3)" onkeypress="return searchResults.NavChild(event,0,3)" onkeyup="return searchResults.NavChild(event,0,3)" class="SRScope" href="../classccp4srs_1_1_torsion.html#a63cbef738a4be2da8a46367802f83e3d" target="_parent">ccp4srs::Torsion::id()</a>
+    <a id="Item0_c4" onkeydown="return searchResults.NavChild(event,0,4)" onkeypress="return searchResults.NavChild(event,0,4)" onkeyup="return searchResults.NavChild(event,0,4)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a1eca7f4a9537bddf81de26df20984183" target="_parent">ccp4srs::Monomer::ID()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_index">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_index')">index</a>
+  <div class="SRChildren">
+    <a id="Item1_c0" onkeydown="return searchResults.NavChild(event,1,0)" onkeypress="return searchResults.NavChild(event,1,0)" onkeyup="return searchResults.NavChild(event,1,0)" class="SRScope" href="../classccp4srs_1_1_container.html#a6afe8d51f68e07697d7362464e433cac" target="_parent">ccp4srs::Container::index()</a>
+    <a id="Item1_c1" onkeydown="return searchResults.NavChild(event,1,1)" onkeypress="return searchResults.NavChild(event,1,1)" onkeyup="return searchResults.NavChild(event,1,1)" class="SRScope" href="../classccp4srs_1_1_index.html#aaff51df26ae81aff0425bda97d6f7030" target="_parent">ccp4srs::Index::Index()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_indexinit">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_index.html#aedec88e9928356d4f7c913d449ca0d3e" target="_parent">IndexInit</a>
+  <span class="SRScope">ccp4srs::Index</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_init">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_init')">Init</a>
+  <div class="SRChildren">
+    <a id="Item3_c0" onkeydown="return searchResults.NavChild(event,3,0)" onkeypress="return searchResults.NavChild(event,3,0)" onkeyup="return searchResults.NavChild(event,3,0)" class="SRScope" href="../classccp4srs_1_1_atom.html#ab6a22850541822e026c9d6a241079fd6" target="_parent">ccp4srs::Atom::Init()</a>
+    <a id="Item3_c1" onkeydown="return searchResults.NavChild(event,3,1)" onkeypress="return searchResults.NavChild(event,3,1)" onkeyup="return searchResults.NavChild(event,3,1)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a6a50cfb8d8e87162309106c66f5fc155" target="_parent">ccp4srs::Monomer::Init()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_init_5fbase">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a9fb463b8df4034fefb6e136ab56d135b" target="_parent">init_base</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_init_5fchem">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_chem.html#a7ed4ac373981270bc1af2b8cc99b461d" target="_parent">init_chem</a>
+  <span class="SRScope">ccp4srs::Chem</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_ion_5fradius">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a4cbbb8a7a4d9f69eca5caadfffa6c956" target="_parent">ion_radius</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_isleaving">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a7da89fae287dcf0c0838108fd442ec53" target="_parent">isLeaving</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_6c.html ccp4srs/doc-html/html/search/functions_6c.html
--- ccp4srs-old/doc-html/html/search/functions_6c.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_6c.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,53 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_leaving">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#ac7f1f1f474b56199e70bb0dcd364bb4b" target="_parent">leaving</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_length">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_length')">length</a>
+  <div class="SRChildren">
+    <a id="Item1_c0" onkeydown="return searchResults.NavChild(event,1,0)" onkeypress="return searchResults.NavChild(event,1,0)" onkeyup="return searchResults.NavChild(event,1,0)" class="SRScope" href="../classccp4srs_1_1_bond.html#a3ebb971fa0af7886f076da460b4875e9" target="_parent">ccp4srs::Bond::length()</a>
+    <a id="Item1_c1" onkeydown="return searchResults.NavChild(event,1,1)" onkeypress="return searchResults.NavChild(event,1,1)" onkeyup="return searchResults.NavChild(event,1,1)" class="SRScope" href="../classccp4srs_1_1_mem_i_o.html#a5e4ae24f25179a720de85f185f8074ff" target="_parent">ccp4srs::MemIO::length()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_length_5fesd">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#a28f3638c15b007dddaab637362635009" target="_parent">length_esd</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_loadindex">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_base.html#ae95af9ff2fb5c9d0edb437be3bcbe016" target="_parent">loadIndex</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_loadstructure">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a663ef26d53b80f6c8b1f9c9cdeb70d2c" target="_parent">loadStructure</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_6d.html ccp4srs/doc-html/html/search/functions_6d.html
--- ccp4srs-old/doc-html/html/search/functions_6d.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_6d.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,99 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_makeatom">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_makeatom')">makeAtom</a>
+  <div class="SRChildren">
+    <a id="Item0_c0" onkeydown="return searchResults.NavChild(event,0,0)" onkeypress="return searchResults.NavChild(event,0,0)" onkeyup="return searchResults.NavChild(event,0,0)" class="SRScope" href="../classccp4srs_1_1_atom.html#a40ec4d3c3ea0384ab4d2c56b3ee5389b" target="_parent">ccp4srs::Atom::makeAtom(mmdb::RPAtom a)</a>
+    <a id="Item0_c1" onkeydown="return searchResults.NavChild(event,0,1)" onkeypress="return searchResults.NavChild(event,0,1)" onkeyup="return searchResults.NavChild(event,0,1)" class="SRScope" href="../classccp4srs_1_1_atom.html#a2528b66c2480aa6e3db8d6cfba0c4586" target="_parent">ccp4srs::Atom::makeAtom()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_makebonds">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_chem.html#ad60a617bc151e054eb306e8c6bf592f4" target="_parent">makeBonds</a>
+  <span class="SRScope">ccp4srs::Chem</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_makecif">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a5e3fb1e64eab3e764cc83ff1e6c61fa3" target="_parent">makeCIF</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_makeciftags">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_makeciftags')">makeCIFTags</a>
+  <div class="SRChildren">
+    <a id="Item3_c0" onkeydown="return searchResults.NavChild(event,3,0)" onkeypress="return searchResults.NavChild(event,3,0)" onkeyup="return searchResults.NavChild(event,3,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a257cefe6949d4371175d4c1573a1d40e" target="_parent">ccp4srs::Angle::makeCIFTags()</a>
+    <a id="Item3_c1" onkeydown="return searchResults.NavChild(event,3,1)" onkeypress="return searchResults.NavChild(event,3,1)" onkeyup="return searchResults.NavChild(event,3,1)" class="SRScope" href="../classccp4srs_1_1_atom.html#ac1bcbe4ebfbf35c7d0369d41afa07714" target="_parent">ccp4srs::Atom::makeCIFTags()</a>
+    <a id="Item3_c2" onkeydown="return searchResults.NavChild(event,3,2)" onkeypress="return searchResults.NavChild(event,3,2)" onkeyup="return searchResults.NavChild(event,3,2)" class="SRScope" href="../classccp4srs_1_1_bond.html#a781542dae98140ea687a5d83a3e02e8e" target="_parent">ccp4srs::Bond::makeCIFTags()</a>
+    <a id="Item3_c3" onkeydown="return searchResults.NavChild(event,3,3)" onkeypress="return searchResults.NavChild(event,3,3)" onkeyup="return searchResults.NavChild(event,3,3)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#a93d09528c86718358137aaf48c1a8ce1" target="_parent">ccp4srs::ChiCenter::makeCIFTags()</a>
+    <a id="Item3_c4" onkeydown="return searchResults.NavChild(event,3,4)" onkeypress="return searchResults.NavChild(event,3,4)" onkeyup="return searchResults.NavChild(event,3,4)" class="SRScope" href="../classccp4srs_1_1_plane.html#a1ac0cfa095deac2bd97e99ce2b30de96" target="_parent">ccp4srs::Plane::makeCIFTags()</a>
+    <a id="Item3_c5" onkeydown="return searchResults.NavChild(event,3,5)" onkeypress="return searchResults.NavChild(event,3,5)" onkeyup="return searchResults.NavChild(event,3,5)" class="SRScope" href="../classccp4srs_1_1_torsion.html#ae33b6fc8d12fdbd48a299cf488e16f0e" target="_parent">ccp4srs::Torsion::makeCIFTags()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_makecompositions">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_index.html#afda5436941f171c791be43b9d28f43a5" target="_parent">MakeCompositions</a>
+  <span class="SRScope">ccp4srs::Index</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_makeelementtype">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../namespaceccp4srs.html#a8b4dcaee4f20949271ceaadfb7b5a96f" target="_parent">makeElementType</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_makeselindexes">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../structccp4srs_1_1_d_a_sel_hnds.html#aaca5f89914d27b9869b6f082931c53d5" target="_parent">makeSelIndexes</a>
+  <span class="SRScope">ccp4srs::DASelHnds</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_manager">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_manager.html#a7b1bcc6f68308560b402c5b3f8533158" target="_parent">Manager</a>
+  <span class="SRScope">ccp4srs::Manager</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_memio">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#af2490447442255fa19b2a1c05c011f96" target="_parent">MemIO</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_merge">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_merge')">merge</a>
+  <div class="SRChildren">
+    <a id="Item9_c0" onkeydown="return searchResults.NavChild(event,9,0)" onkeypress="return searchResults.NavChild(event,9,0)" onkeyup="return searchResults.NavChild(event,9,0)" class="SRScope" href="../classccp4srs_1_1_atom.html#af28439c95edf554364f29e988b47acd1" target="_parent">ccp4srs::Atom::merge()</a>
+    <a id="Item9_c1" onkeydown="return searchResults.NavChild(event,9,1)" onkeypress="return searchResults.NavChild(event,9,1)" onkeyup="return searchResults.NavChild(event,9,1)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a6453406b0256cf9fbf74177a7db8770b" target="_parent">ccp4srs::Monomer::merge()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_monomer">
+ <div class="SREntry">
+  <a id="Item10" onkeydown="return searchResults.Nav(event,10)" onkeypress="return searchResults.Nav(event,10)" onkeyup="return searchResults.Nav(event,10)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#abd3a6efc83918f121e3e83165681ccd5" target="_parent">Monomer</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_6e.html ccp4srs/doc-html/html/search/functions_6e.html
--- ccp4srs-old/doc-html/html/search/functions_6e.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_6e.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,80 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_n_5fangles">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a832521f11b1adb4a0deb9fd92b4bc725" target="_parent">n_angles</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_n_5fatoms">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a3e3e771e2d60581384b1169648b4d751" target="_parent">n_atoms</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_n_5fbonds">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a6a6e470c174fd570667bf43f95757c0d" target="_parent">n_bonds</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_n_5fchicenters">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a047ec20b44f73aa0027fdd071aa265d6" target="_parent">n_chicenters</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_n_5fentries">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_base.html#aeb551e05e822e5eb3673aba1fa85bda6" target="_parent">n_entries</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_n_5fplanes">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a123cf02246e052730361055de3f0d477" target="_parent">n_planes</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_n_5ftorsions">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a0bf10d776d5d992424b99d88d884f101" target="_parent">n_torsions</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_name">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#ad8288e82eeab398bf90da3f35ebe15c5" target="_parent">name</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_name_5fpdb">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a357cfea9384684a64bb3220d02b3afa7" target="_parent">name_pdb</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_numberof">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="../classccp4srs_1_1_container.html#abbc5e6eeb9ea4d37b8d2025892ebd9ff" target="_parent">numberOf</a>
+  <span class="SRScope">ccp4srs::Container</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_6f.html ccp4srs/doc-html/html/search/functions_6f.html
--- ccp4srs-old/doc-html/html/search/functions_6f.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_6f.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,44 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_old_5fname">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#acda740ae967221e50f1d383ce70d58d9" target="_parent">old_name</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_old_5fname_5fpdb">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#abd73ea1b813b1321048f850b88914982" target="_parent">old_name_pdb</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_oldid">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a271e6aaeed7ace67e36f2c5fea626d70" target="_parent">oldID</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_order">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#ae18a9e08399e96910028f01a376d41f0" target="_parent">order</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_70.html ccp4srs/doc-html/html/search/functions_70.html
--- ccp4srs-old/doc-html/html/search/functions_70.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_70.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,113 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_period">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_torsion.html#a8fd30d637a8002a46ff4c50cadc8d34f" target="_parent">period</a>
+  <span class="SRScope">ccp4srs::Torsion</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_plane">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_plane')">plane</a>
+  <div class="SRChildren">
+    <a id="Item1_c0" onkeydown="return searchResults.NavChild(event,1,0)" onkeypress="return searchResults.NavChild(event,1,0)" onkeyup="return searchResults.NavChild(event,1,0)" class="SRScope" href="../classccp4srs_1_1_monomer.html#afdebf230f6aa9bf2692a82b919d59918" target="_parent">ccp4srs::Monomer::plane()</a>
+    <a id="Item1_c1" onkeydown="return searchResults.NavChild(event,1,1)" onkeypress="return searchResults.NavChild(event,1,1)" onkeyup="return searchResults.NavChild(event,1,1)" class="SRScope" href="../classccp4srs_1_1_plane.html#ab45260579cf6dd22ecdaa93ad3b5c183" target="_parent">ccp4srs::Plane::Plane()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5fbool">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#ac3420c8a37ce57f324cf66eb4ccb9b13" target="_parent">put_bool</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5fbyte">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a3c30e4f73927173a9ce5731fab39d170" target="_parent">put_byte</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5ffloat">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#ad82c1eca930cc9d5535f2da1ab3cde1a" target="_parent">put_float</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5fibyte">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a55ccb2d1a276365eadb422c75e982de3" target="_parent">put_ibyte</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5finteger">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a6c563469a6978a9c1c62a33457c90661" target="_parent">put_integer</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5fishort">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a1a5cd9341de994fa17ae8efae3d61732" target="_parent">put_ishort</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5fline">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a98548fca1e008178fef523b271db5423" target="_parent">put_line</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5flong">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#af300f12e3fe4b3d878f80caf19b66341" target="_parent">put_long</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5freal">
+ <div class="SREntry">
+  <a id="Item10" onkeydown="return searchResults.Nav(event,10)" onkeypress="return searchResults.Nav(event,10)" onkeyup="return searchResults.Nav(event,10)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a1d8e03e12f2420c9650f4a8956a1c0a7" target="_parent">put_real</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5fshort">
+ <div class="SREntry">
+  <a id="Item11" onkeydown="return searchResults.Nav(event,11)" onkeypress="return searchResults.Nav(event,11)" onkeyup="return searchResults.Nav(event,11)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a7117ff86d20006f7a693ea3a36035674" target="_parent">put_short</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5fshortreal">
+ <div class="SREntry">
+  <a id="Item12" onkeydown="return searchResults.Nav(event,12)" onkeypress="return searchResults.Nav(event,12)" onkeyup="return searchResults.Nav(event,12)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a4eb6ba2e97922bf9509d828ee075aa8e" target="_parent">put_shortreal</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5fstring">
+ <div class="SREntry">
+  <a id="Item13" onkeydown="return searchResults.Nav(event,13)" onkeypress="return searchResults.Nav(event,13)" onkeyup="return searchResults.Nav(event,13)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#aa35e6bbff841d942f793e50ee813fc97" target="_parent">put_string</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_put_5fword">
+ <div class="SREntry">
+  <a id="Item14" onkeydown="return searchResults.Nav(event,14)" onkeypress="return searchResults.Nav(event,14)" onkeyup="return searchResults.Nav(event,14)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#abf6e925edc35b60fe7816223ceb7a15f" target="_parent">put_word</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_72.html ccp4srs/doc-html/html/search/functions_72.html
--- ccp4srs-old/doc-html/html/search/functions_72.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_72.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,127 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_rcsb_5fchirality">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a1dc09ecc6dee155b93e5c3431d4c548e" target="_parent">rcsb_chirality</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_rcsb_5fname">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#af0bbf72624e0f7de9900ec931b673410" target="_parent">rcsb_name</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_rcsb_5fname_5fpdb">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#ace51a15043535b0fef9b2816dba48cdb" target="_parent">rcsb_name_pdb</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_read">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_read')">read</a>
+  <div class="SRChildren">
+    <a id="Item3_c0" onkeydown="return searchResults.NavChild(event,3,0)" onkeypress="return searchResults.NavChild(event,3,0)" onkeyup="return searchResults.NavChild(event,3,0)" class="SRScope" href="../classccp4srs_1_1_entry.html#a262e2814d9a1bc35fbbfd75e46397343" target="_parent">ccp4srs::Entry::read()</a>
+    <a id="Item3_c1" onkeydown="return searchResults.NavChild(event,3,1)" onkeypress="return searchResults.NavChild(event,3,1)" onkeyup="return searchResults.NavChild(event,3,1)" class="SRScope" href="../classccp4srs_1_1_index.html#a17c3250780def030676fef212a19731c" target="_parent">ccp4srs::Index::read()</a>
+    <a id="Item3_c2" onkeydown="return searchResults.NavChild(event,3,2)" onkeypress="return searchResults.NavChild(event,3,2)" onkeyup="return searchResults.NavChild(event,3,2)" class="SRScope" href="../classccp4srs_1_1_mem_i_o.html#ad8c19ab9e2bd98b40caf95cc6d7e071e" target="_parent">ccp4srs::MemIO::read(mmdb::cpstr fileName, mmdb::io::GZ_MODE gzMode=mmdb::io::GZM_NONE)</a>
+    <a id="Item3_c3" onkeydown="return searchResults.NavChild(event,3,3)" onkeypress="return searchResults.NavChild(event,3,3)" onkeyup="return searchResults.NavChild(event,3,3)" class="SRScope" href="../classccp4srs_1_1_mem_i_o.html#aebd3a0d6614c77b533433bc75de6d069" target="_parent">ccp4srs::MemIO::read(mmdb::io::RFile f)</a>
+    <a id="Item3_c4" onkeydown="return searchResults.NavChild(event,3,4)" onkeypress="return searchResults.NavChild(event,3,4)" onkeyup="return searchResults.NavChild(event,3,4)" class="SRScope" href="../structccp4srs_1_1_m_p_file_pos.html#a8351d37471b7cdab264a91bb1a92db1c" target="_parent">ccp4srs::MPFilePos::read()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_read_5fbuffer">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a7df5365c01565a15ac3bca748e46146b" target="_parent">read_buffer</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_read_5fmem">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_read_5fmem')">read_mem</a>
+  <div class="SRChildren">
+    <a id="Item5_c0" onkeydown="return searchResults.NavChild(event,5,0)" onkeypress="return searchResults.NavChild(event,5,0)" onkeyup="return searchResults.NavChild(event,5,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a2f34c77527204676236a28c863f5adee" target="_parent">ccp4srs::Angle::read_mem()</a>
+    <a id="Item5_c1" onkeydown="return searchResults.NavChild(event,5,1)" onkeypress="return searchResults.NavChild(event,5,1)" onkeyup="return searchResults.NavChild(event,5,1)" class="SRScope" href="../classccp4srs_1_1_atom.html#a150503215d6820dda3726b107e8e1bc7" target="_parent">ccp4srs::Atom::read_mem()</a>
+    <a id="Item5_c2" onkeydown="return searchResults.NavChild(event,5,2)" onkeypress="return searchResults.NavChild(event,5,2)" onkeyup="return searchResults.NavChild(event,5,2)" class="SRScope" href="../classccp4srs_1_1_bond.html#a47ad8a18d4c0363dc1f04f3cfbc670ec" target="_parent">ccp4srs::Bond::read_mem()</a>
+    <a id="Item5_c3" onkeydown="return searchResults.NavChild(event,5,3)" onkeypress="return searchResults.NavChild(event,5,3)" onkeyup="return searchResults.NavChild(event,5,3)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#a64588b20c5010e22ad5d571343a7e6d0" target="_parent">ccp4srs::ChiCenter::read_mem()</a>
+    <a id="Item5_c4" onkeydown="return searchResults.NavChild(event,5,4)" onkeypress="return searchResults.NavChild(event,5,4)" onkeyup="return searchResults.NavChild(event,5,4)" class="SRScope" href="../classccp4srs_1_1_container.html#a9f42bc8ec160490ba2dd8d7a8eeae15e" target="_parent">ccp4srs::Container::read_mem()</a>
+    <a id="Item5_c5" onkeydown="return searchResults.NavChild(event,5,5)" onkeypress="return searchResults.NavChild(event,5,5)" onkeyup="return searchResults.NavChild(event,5,5)" class="SRScope" href="../classccp4srs_1_1_entry.html#a2d3193b4e34c21b286526931e2e5b62d" target="_parent">ccp4srs::Entry::read_mem()</a>
+    <a id="Item5_c6" onkeydown="return searchResults.NavChild(event,5,6)" onkeypress="return searchResults.NavChild(event,5,6)" onkeyup="return searchResults.NavChild(event,5,6)" class="SRScope" href="../classccp4srs_1_1_index.html#a06b50353c15a21a56688b3e00aad2e2d" target="_parent">ccp4srs::Index::read_mem()</a>
+    <a id="Item5_c7" onkeydown="return searchResults.NavChild(event,5,7)" onkeypress="return searchResults.NavChild(event,5,7)" onkeyup="return searchResults.NavChild(event,5,7)" class="SRScope" href="../classccp4srs_1_1_monomer.html#ac12b93e766cfbcfd4288512df739a56e" target="_parent">ccp4srs::Monomer::read_mem()</a>
+    <a id="Item5_c8" onkeydown="return searchResults.NavChild(event,5,8)" onkeypress="return searchResults.NavChild(event,5,8)" onkeyup="return searchResults.NavChild(event,5,8)" class="SRScope" href="../classccp4srs_1_1_plane.html#a148162145438f6f97414eee0aa72275a" target="_parent">ccp4srs::Plane::read_mem()</a>
+    <a id="Item5_c9" onkeydown="return searchResults.NavChild(event,5,9)" onkeypress="return searchResults.NavChild(event,5,9)" onkeyup="return searchResults.NavChild(event,5,9)" class="SRScope" href="../classccp4srs_1_1_torsion.html#af65ef2e18a3b6494070300afec0099e1" target="_parent">ccp4srs::Torsion::read_mem()</a>
+    <a id="Item5_c10" onkeydown="return searchResults.NavChild(event,5,10)" onkeypress="return searchResults.NavChild(event,5,10)" onkeyup="return searchResults.NavChild(event,5,10)" class="SRScope" href="../classccp4srs_1_1_tree.html#a7e39da9840cb8815e8854cd11552c3a9" target="_parent">ccp4srs::Tree::read_mem()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_readfromcif">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_readfromcif')">readFromCIF</a>
+  <div class="SRChildren">
+    <a id="Item6_c0" onkeydown="return searchResults.NavChild(event,6,0)" onkeypress="return searchResults.NavChild(event,6,0)" onkeyup="return searchResults.NavChild(event,6,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a9a366216e8c07f33829fd26db9df4f00" target="_parent">ccp4srs::Angle::readFromCIF()</a>
+    <a id="Item6_c1" onkeydown="return searchResults.NavChild(event,6,1)" onkeypress="return searchResults.NavChild(event,6,1)" onkeyup="return searchResults.NavChild(event,6,1)" class="SRScope" href="../classccp4srs_1_1_atom.html#a94f5f81532b98126f3383f29c077473c" target="_parent">ccp4srs::Atom::readFromCIF()</a>
+    <a id="Item6_c2" onkeydown="return searchResults.NavChild(event,6,2)" onkeypress="return searchResults.NavChild(event,6,2)" onkeyup="return searchResults.NavChild(event,6,2)" class="SRScope" href="../classccp4srs_1_1_bond.html#a24976c4962050d858ca00fa6f72684e2" target="_parent">ccp4srs::Bond::readFromCIF()</a>
+    <a id="Item6_c3" onkeydown="return searchResults.NavChild(event,6,3)" onkeypress="return searchResults.NavChild(event,6,3)" onkeyup="return searchResults.NavChild(event,6,3)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#a8c038c3d35ef4effbe5e02db4cdf9f88" target="_parent">ccp4srs::ChiCenter::readFromCIF()</a>
+    <a id="Item6_c4" onkeydown="return searchResults.NavChild(event,6,4)" onkeypress="return searchResults.NavChild(event,6,4)" onkeyup="return searchResults.NavChild(event,6,4)" class="SRScope" href="../classccp4srs_1_1_monomer.html#aa9b0a99023e890070aec088182f8a65b" target="_parent">ccp4srs::Monomer::readFromCIF()</a>
+    <a id="Item6_c5" onkeydown="return searchResults.NavChild(event,6,5)" onkeypress="return searchResults.NavChild(event,6,5)" onkeyup="return searchResults.NavChild(event,6,5)" class="SRScope" href="../classccp4srs_1_1_plane.html#a656a93b833de401dcac75db47b5bcf57" target="_parent">ccp4srs::Plane::readFromCIF()</a>
+    <a id="Item6_c6" onkeydown="return searchResults.NavChild(event,6,6)" onkeypress="return searchResults.NavChild(event,6,6)" onkeyup="return searchResults.NavChild(event,6,6)" class="SRScope" href="../classccp4srs_1_1_torsion.html#aaf9375ff9aeb22a2a148763276ec80d1" target="_parent">ccp4srs::Torsion::readFromCIF()</a>
+    <a id="Item6_c7" onkeydown="return searchResults.NavChild(event,6,7)" onkeypress="return searchResults.NavChild(event,6,7)" onkeyup="return searchResults.NavChild(event,6,7)" class="SRScope" href="../classccp4srs_1_1_tree.html#af50e009eb63e2bdf8da129afa193d637" target="_parent">ccp4srs::Tree::readFromCIF()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_readfromcif_5fccp4">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_readfromcif_5fccp4')">readFromCIF_ccp4</a>
+  <div class="SRChildren">
+    <a id="Item7_c0" onkeydown="return searchResults.NavChild(event,7,0)" onkeypress="return searchResults.NavChild(event,7,0)" onkeyup="return searchResults.NavChild(event,7,0)" class="SRScope" href="../classccp4srs_1_1_atom.html#a0e4f39d4293b8e1907b0295e215c4230" target="_parent">ccp4srs::Atom::readFromCIF_ccp4()</a>
+    <a id="Item7_c1" onkeydown="return searchResults.NavChild(event,7,1)" onkeypress="return searchResults.NavChild(event,7,1)" onkeyup="return searchResults.NavChild(event,7,1)" class="SRScope" href="../classccp4srs_1_1_bond.html#ac6a267f1cb4e7553d746537cf36e5ea3" target="_parent">ccp4srs::Bond::readFromCIF_ccp4()</a>
+    <a id="Item7_c2" onkeydown="return searchResults.NavChild(event,7,2)" onkeypress="return searchResults.NavChild(event,7,2)" onkeyup="return searchResults.NavChild(event,7,2)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a9e457d3f7633b79b598b66f382fa5c5c" target="_parent">ccp4srs::Monomer::readFromCIF_ccp4()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_readfromcif_5frcsb">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_readfromcif_5frcsb')">readFromCIF_rcsb</a>
+  <div class="SRChildren">
+    <a id="Item8_c0" onkeydown="return searchResults.NavChild(event,8,0)" onkeypress="return searchResults.NavChild(event,8,0)" onkeyup="return searchResults.NavChild(event,8,0)" class="SRScope" href="../classccp4srs_1_1_atom.html#a12b7ff09ff7aa0cc7581a55e89ac9e0e" target="_parent">ccp4srs::Atom::readFromCIF_rcsb()</a>
+    <a id="Item8_c1" onkeydown="return searchResults.NavChild(event,8,1)" onkeypress="return searchResults.NavChild(event,8,1)" onkeyup="return searchResults.NavChild(event,8,1)" class="SRScope" href="../classccp4srs_1_1_bond.html#a54c6291defa953cc5f5750b0f116719c" target="_parent">ccp4srs::Bond::readFromCIF_rcsb()</a>
+    <a id="Item8_c2" onkeydown="return searchResults.NavChild(event,8,2)" onkeypress="return searchResults.NavChild(event,8,2)" onkeyup="return searchResults.NavChild(event,8,2)" class="SRScope" href="../classccp4srs_1_1_monomer.html#aaaec1b93dd1dcfe0e20484fd4bbc2a72" target="_parent">ccp4srs::Monomer::readFromCIF_rcsb()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_readmonidfromcif">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_readmonidfromcif')">readMonIDFromCIF</a>
+  <div class="SRChildren">
+    <a id="Item9_c0" onkeydown="return searchResults.NavChild(event,9,0)" onkeypress="return searchResults.NavChild(event,9,0)" onkeyup="return searchResults.NavChild(event,9,0)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a4e12236b18de645dabd1afe57b46ebc0" target="_parent">ccp4srs::Monomer::readMonIDFromCIF(mmdb::mmcif::PLoop loop)</a>
+    <a id="Item9_c1" onkeydown="return searchResults.NavChild(event,9,1)" onkeypress="return searchResults.NavChild(event,9,1)" onkeyup="return searchResults.NavChild(event,9,1)" class="SRScope" href="../classccp4srs_1_1_monomer.html#acbe4714fc7593d649b5e8901668d5c5c" target="_parent">ccp4srs::Monomer::readMonIDFromCIF(mmdb::mmcif::PStruct mmCIFStruct)</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_reset">
+ <div class="SREntry">
+  <a id="Item10" onkeydown="return searchResults.Nav(event,10)" onkeypress="return searchResults.Nav(event,10)" onkeyup="return searchResults.Nav(event,10)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_reset')">reset</a>
+  <div class="SRChildren">
+    <a id="Item10_c0" onkeydown="return searchResults.NavChild(event,10,0)" onkeypress="return searchResults.NavChild(event,10,0)" onkeyup="return searchResults.NavChild(event,10,0)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a42598d1f669c5e539cb024bb023e0551" target="_parent">ccp4srs::Monomer::reset()</a>
+    <a id="Item10_c1" onkeydown="return searchResults.NavChild(event,10,1)" onkeypress="return searchResults.NavChild(event,10,1)" onkeyup="return searchResults.NavChild(event,10,1)" class="SRScope" href="../classccp4srs_1_1_mem_i_o.html#a855507e19582e7ab9b7236fb9d453da3" target="_parent">ccp4srs::MemIO::reset()</a>
+  </div>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_73.html ccp4srs/doc-html/html/search/functions_73.html
--- ccp4srs-old/doc-html/html/search/functions_73.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_73.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,125 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_set_5fbuffer_5flength">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#ac84f72f62362171b812f386ef786a677" target="_parent">set_buffer_length</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_set_5fchirality">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a4839e285360f50dbe4dbfff765ece82c" target="_parent">set_chirality</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_set_5fenergy_5ftype">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#abab85177d8d15e5dfc51e12ed9af4d69" target="_parent">set_energy_type</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_set_5fhb_5ftype">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a983a276a7821c272f3952f4edfb826c6" target="_parent">set_hb_type</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_set_5fion_5fradius">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a132fd6895be46a1afa96bb0529c0a6ba" target="_parent">set_ion_radius</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_set_5fold_5fname">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a67142fe2e03f768fea4dc3334826ef2e" target="_parent">set_old_name</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_set_5frcsb_5fchirality">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#af46102bc6356f36610eda68ced6e9202" target="_parent">set_rcsb_chirality</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_set_5fsp">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#aa9fe3297f6d6de92f1520a6631361861" target="_parent">set_sp</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_set_5fvalency">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#af50fcb98ad0f4a42768079e985adec5b" target="_parent">set_valency</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_set_5fvdw_5fradius">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#aa2c293fa289d7a24bc8858578dd3357e" target="_parent">set_vdw_radius</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_set_5fvdwh_5fradius">
+ <div class="SREntry">
+  <a id="Item10" onkeydown="return searchResults.Nav(event,10)" onkeypress="return searchResults.Nav(event,10)" onkeyup="return searchResults.Nav(event,10)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a8912626b88300dcb9e736cf1b4369f82" target="_parent">set_vdwh_radius</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_setcompressionlevel">
+ <div class="SREntry">
+  <a id="Item11" onkeydown="return searchResults.Nav(event,11)" onkeypress="return searchResults.Nav(event,11)" onkeyup="return searchResults.Nav(event,11)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#abfd614fba0e035434e9c7f1c4a58ad89" target="_parent">setCompressionLevel</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_setoldid">
+ <div class="SREntry">
+  <a id="Item12" onkeydown="return searchResults.Nav(event,12)" onkeypress="return searchResults.Nav(event,12)" onkeyup="return searchResults.Nav(event,12)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a3d9cd816f0e032e64e0d47ed7673ec63" target="_parent">setOldID</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_sign">
+ <div class="SREntry">
+  <a id="Item13" onkeydown="return searchResults.Nav(event,13)" onkeypress="return searchResults.Nav(event,13)" onkeyup="return searchResults.Nav(event,13)" class="SRSymbol" href="../classccp4srs_1_1_chi_center.html#a17574c6830e27efde72575acdf154d80" target="_parent">sign</a>
+  <span class="SRScope">ccp4srs::ChiCenter</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_size">
+ <div class="SREntry">
+  <a id="Item14" onkeydown="return searchResults.Nav(event,14)" onkeypress="return searchResults.Nav(event,14)" onkeyup="return searchResults.Nav(event,14)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_size')">size</a>
+  <div class="SRChildren">
+    <a id="Item14_c0" onkeydown="return searchResults.NavChild(event,14,0)" onkeypress="return searchResults.NavChild(event,14,0)" onkeyup="return searchResults.NavChild(event,14,0)" class="SRScope" href="../classccp4srs_1_1_plane.html#a61ab65ef97a61c79d1190673a5a1b8e3" target="_parent">ccp4srs::Plane::size()</a>
+    <a id="Item14_c1" onkeydown="return searchResults.NavChild(event,14,1)" onkeypress="return searchResults.NavChild(event,14,1)" onkeyup="return searchResults.NavChild(event,14,1)" class="SRScope" href="../classccp4srs_1_1_tree.html#a308ddfce7a902729218e39356db92cc0" target="_parent">ccp4srs::Tree::size()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_sp">
+ <div class="SREntry">
+  <a id="Item15" onkeydown="return searchResults.Nav(event,15)" onkeypress="return searchResults.Nav(event,15)" onkeyup="return searchResults.Nav(event,15)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a9ae7f9281596f659071394247d484ffb" target="_parent">sp</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_superpose_5fatoms">
+ <div class="SREntry">
+  <a id="Item16" onkeydown="return searchResults.Nav(event,16)" onkeypress="return searchResults.Nav(event,16)" onkeyup="return searchResults.Nav(event,16)" class="SRSymbol" href="../namespaceccp4srs.html#ab9a709bd669d7de2cf530774f80905c7" target="_parent">superpose_atoms</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_74.html ccp4srs/doc-html/html/search/functions_74.html
--- ccp4srs-old/doc-html/html/search/functions_74.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_74.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,47 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_torsion">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_torsion')">Torsion</a>
+  <div class="SRChildren">
+    <a id="Item0_c0" onkeydown="return searchResults.NavChild(event,0,0)" onkeypress="return searchResults.NavChild(event,0,0)" onkeyup="return searchResults.NavChild(event,0,0)" class="SRScope" href="../classccp4srs_1_1_torsion.html#a1939dda0f4d9e56c3762acade101e938" target="_parent">ccp4srs::Torsion::Torsion()</a>
+    <a id="Item0_c1" onkeydown="return searchResults.NavChild(event,0,1)" onkeypress="return searchResults.NavChild(event,0,1)" onkeyup="return searchResults.NavChild(event,0,1)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a1fdc6bd34cea4b7ea59d5399a8367f70" target="_parent">ccp4srs::Monomer::torsion()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_tree">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_tree')">Tree</a>
+  <div class="SRChildren">
+    <a id="Item1_c0" onkeydown="return searchResults.NavChild(event,1,0)" onkeypress="return searchResults.NavChild(event,1,0)" onkeyup="return searchResults.NavChild(event,1,0)" class="SRScope" href="../classccp4srs_1_1_tree.html#a342a1de215612310580d0cd6a06262cb" target="_parent">ccp4srs::Tree::Tree()</a>
+    <a id="Item1_c1" onkeydown="return searchResults.NavChild(event,1,1)" onkeypress="return searchResults.NavChild(event,1,1)" onkeyup="return searchResults.NavChild(event,1,1)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a79a4445aa7279951aa8426dc79114ebf" target="_parent">ccp4srs::Monomer::tree()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_type">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_type')">type</a>
+  <div class="SRChildren">
+    <a id="Item2_c0" onkeydown="return searchResults.NavChild(event,2,0)" onkeypress="return searchResults.NavChild(event,2,0)" onkeyup="return searchResults.NavChild(event,2,0)" class="SRScope" href="../classccp4srs_1_1_entry.html#a401d0e96699c34bef6b408e054f14540" target="_parent">ccp4srs::Entry::type()</a>
+    <a id="Item2_c1" onkeydown="return searchResults.NavChild(event,2,1)" onkeypress="return searchResults.NavChild(event,2,1)" onkeyup="return searchResults.NavChild(event,2,1)" class="SRScope" href="../classccp4srs_1_1_monomer.html#a01201fb01a7ed370e593563b129c74af" target="_parent">ccp4srs::Monomer::type()</a>
+  </div>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_75.html ccp4srs/doc-html/html/search/functions_75.html
--- ccp4srs-old/doc-html/html/search/functions_75.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_75.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,26 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_unloadstructure">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a6d15803597f5a515c19848a5e8dbe164" target="_parent">unloadStructure</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_76.html ccp4srs/doc-html/html/search/functions_76.html
--- ccp4srs-old/doc-html/html/search/functions_76.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_76.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,47 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_valency">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a86606a9614641a62a9b477c0b90c3a87" target="_parent">valency</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_value">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_value')">value</a>
+  <div class="SRChildren">
+    <a id="Item1_c0" onkeydown="return searchResults.NavChild(event,1,0)" onkeypress="return searchResults.NavChild(event,1,0)" onkeyup="return searchResults.NavChild(event,1,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a6ec0de44c0f607bcb5634a907fe9018a" target="_parent">ccp4srs::Angle::value()</a>
+    <a id="Item1_c1" onkeydown="return searchResults.NavChild(event,1,1)" onkeypress="return searchResults.NavChild(event,1,1)" onkeyup="return searchResults.NavChild(event,1,1)" class="SRScope" href="../classccp4srs_1_1_torsion.html#a001451fd28649a8df65416d7e551b7a9" target="_parent">ccp4srs::Torsion::value()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_vdw_5fradius">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a2c283b644afb507ec45667611a685827" target="_parent">vdw_radius</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_vdwh_5fradius">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a2a2e411586e9a0be619a5ab5c634169d" target="_parent">vdwh_radius</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_77.html ccp4srs/doc-html/html/search/functions_77.html
--- ccp4srs-old/doc-html/html/search/functions_77.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_77.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,76 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_weight">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a4c6e0a23b45563f10657d839d4479961" target="_parent">weight</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_write">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_write')">write</a>
+  <div class="SRChildren">
+    <a id="Item1_c0" onkeydown="return searchResults.NavChild(event,1,0)" onkeypress="return searchResults.NavChild(event,1,0)" onkeyup="return searchResults.NavChild(event,1,0)" class="SRScope" href="../classccp4srs_1_1_entry.html#a46d1eaa50c45f6e40ff054b30b93790d" target="_parent">ccp4srs::Entry::write()</a>
+    <a id="Item1_c1" onkeydown="return searchResults.NavChild(event,1,1)" onkeypress="return searchResults.NavChild(event,1,1)" onkeyup="return searchResults.NavChild(event,1,1)" class="SRScope" href="../classccp4srs_1_1_index.html#a2d6f487a5a3e945f92b90fc6f034f08b" target="_parent">ccp4srs::Index::write()</a>
+    <a id="Item1_c2" onkeydown="return searchResults.NavChild(event,1,2)" onkeypress="return searchResults.NavChild(event,1,2)" onkeyup="return searchResults.NavChild(event,1,2)" class="SRScope" href="../classccp4srs_1_1_mem_i_o.html#ae2fd4e637343f3f9ac5ccfc3af085293" target="_parent">ccp4srs::MemIO::write(mmdb::cpstr fileName, mmdb::io::GZ_MODE gzMode=mmdb::io::GZM_NONE)</a>
+    <a id="Item1_c3" onkeydown="return searchResults.NavChild(event,1,3)" onkeypress="return searchResults.NavChild(event,1,3)" onkeyup="return searchResults.NavChild(event,1,3)" class="SRScope" href="../classccp4srs_1_1_mem_i_o.html#a501f0773dd4ebb8f8f9b369cf59f07e0" target="_parent">ccp4srs::MemIO::write(mmdb::io::RFile f)</a>
+    <a id="Item1_c4" onkeydown="return searchResults.NavChild(event,1,4)" onkeypress="return searchResults.NavChild(event,1,4)" onkeyup="return searchResults.NavChild(event,1,4)" class="SRScope" href="../structccp4srs_1_1_m_p_file_pos.html#a6e1a52091171d7462c6b8334f1483998" target="_parent">ccp4srs::MPFilePos::write()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_write_5fbuffer">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#a98b3d03fd613c62e0d16bfda509aa630" target="_parent">write_buffer</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_write_5fmem">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_write_5fmem')">write_mem</a>
+  <div class="SRChildren">
+    <a id="Item3_c0" onkeydown="return searchResults.NavChild(event,3,0)" onkeypress="return searchResults.NavChild(event,3,0)" onkeyup="return searchResults.NavChild(event,3,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a5fcc085237045429dd4a946595c1488f" target="_parent">ccp4srs::Angle::write_mem()</a>
+    <a id="Item3_c1" onkeydown="return searchResults.NavChild(event,3,1)" onkeypress="return searchResults.NavChild(event,3,1)" onkeyup="return searchResults.NavChild(event,3,1)" class="SRScope" href="../classccp4srs_1_1_atom.html#adaebb2b3897e6758befc7c76d77c0420" target="_parent">ccp4srs::Atom::write_mem()</a>
+    <a id="Item3_c2" onkeydown="return searchResults.NavChild(event,3,2)" onkeypress="return searchResults.NavChild(event,3,2)" onkeyup="return searchResults.NavChild(event,3,2)" class="SRScope" href="../classccp4srs_1_1_bond.html#aa44d448aa0181e6d51048beda35052f4" target="_parent">ccp4srs::Bond::write_mem()</a>
+    <a id="Item3_c3" onkeydown="return searchResults.NavChild(event,3,3)" onkeypress="return searchResults.NavChild(event,3,3)" onkeyup="return searchResults.NavChild(event,3,3)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#ac36306727683e319c2282b936bd11d37" target="_parent">ccp4srs::ChiCenter::write_mem()</a>
+    <a id="Item3_c4" onkeydown="return searchResults.NavChild(event,3,4)" onkeypress="return searchResults.NavChild(event,3,4)" onkeyup="return searchResults.NavChild(event,3,4)" class="SRScope" href="../classccp4srs_1_1_container.html#ae3d1a80023e670f0828814b887af5dc8" target="_parent">ccp4srs::Container::write_mem()</a>
+    <a id="Item3_c5" onkeydown="return searchResults.NavChild(event,3,5)" onkeypress="return searchResults.NavChild(event,3,5)" onkeyup="return searchResults.NavChild(event,3,5)" class="SRScope" href="../classccp4srs_1_1_entry.html#a817f6f566baf41280c5cee0fc3507871" target="_parent">ccp4srs::Entry::write_mem()</a>
+    <a id="Item3_c6" onkeydown="return searchResults.NavChild(event,3,6)" onkeypress="return searchResults.NavChild(event,3,6)" onkeyup="return searchResults.NavChild(event,3,6)" class="SRScope" href="../classccp4srs_1_1_index.html#a5591c13f7296928d053492322b8bd02b" target="_parent">ccp4srs::Index::write_mem()</a>
+    <a id="Item3_c7" onkeydown="return searchResults.NavChild(event,3,7)" onkeypress="return searchResults.NavChild(event,3,7)" onkeyup="return searchResults.NavChild(event,3,7)" class="SRScope" href="../classccp4srs_1_1_monomer.html#ac0eb44f5d4ec3da57994cd741c8d6b0b" target="_parent">ccp4srs::Monomer::write_mem()</a>
+    <a id="Item3_c8" onkeydown="return searchResults.NavChild(event,3,8)" onkeypress="return searchResults.NavChild(event,3,8)" onkeyup="return searchResults.NavChild(event,3,8)" class="SRScope" href="../classccp4srs_1_1_plane.html#a759255f2b21b770caa535f129e5f60bb" target="_parent">ccp4srs::Plane::write_mem()</a>
+    <a id="Item3_c9" onkeydown="return searchResults.NavChild(event,3,9)" onkeypress="return searchResults.NavChild(event,3,9)" onkeyup="return searchResults.NavChild(event,3,9)" class="SRScope" href="../classccp4srs_1_1_torsion.html#a9b4f1d2c543776a8e0412eae4c7db651" target="_parent">ccp4srs::Torsion::write_mem()</a>
+    <a id="Item3_c10" onkeydown="return searchResults.NavChild(event,3,10)" onkeypress="return searchResults.NavChild(event,3,10)" onkeyup="return searchResults.NavChild(event,3,10)" class="SRScope" href="../classccp4srs_1_1_tree.html#a357b27f65ab5b653fc17a387e9653c4f" target="_parent">ccp4srs::Tree::write_mem()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_writetocif">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_writetocif')">writeToCIF</a>
+  <div class="SRChildren">
+    <a id="Item4_c0" onkeydown="return searchResults.NavChild(event,4,0)" onkeypress="return searchResults.NavChild(event,4,0)" onkeyup="return searchResults.NavChild(event,4,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a8a293c96f55ee3b13cc9b9db86d265cd" target="_parent">ccp4srs::Angle::writeToCIF()</a>
+    <a id="Item4_c1" onkeydown="return searchResults.NavChild(event,4,1)" onkeypress="return searchResults.NavChild(event,4,1)" onkeyup="return searchResults.NavChild(event,4,1)" class="SRScope" href="../classccp4srs_1_1_atom.html#ac83667146ec86aeab8fdcce133c2fea0" target="_parent">ccp4srs::Atom::writeToCIF()</a>
+    <a id="Item4_c2" onkeydown="return searchResults.NavChild(event,4,2)" onkeypress="return searchResults.NavChild(event,4,2)" onkeyup="return searchResults.NavChild(event,4,2)" class="SRScope" href="../classccp4srs_1_1_bond.html#a89214f5f730f603bdd8dacea6317428f" target="_parent">ccp4srs::Bond::writeToCIF()</a>
+    <a id="Item4_c3" onkeydown="return searchResults.NavChild(event,4,3)" onkeypress="return searchResults.NavChild(event,4,3)" onkeyup="return searchResults.NavChild(event,4,3)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#a04b85d396a4ebc8d5163d3184206329d" target="_parent">ccp4srs::ChiCenter::writeToCIF()</a>
+    <a id="Item4_c4" onkeydown="return searchResults.NavChild(event,4,4)" onkeypress="return searchResults.NavChild(event,4,4)" onkeyup="return searchResults.NavChild(event,4,4)" class="SRScope" href="../classccp4srs_1_1_plane.html#abd5b6df5e6d2bdafdd064a04974cf82a" target="_parent">ccp4srs::Plane::writeToCIF()</a>
+    <a id="Item4_c5" onkeydown="return searchResults.NavChild(event,4,5)" onkeypress="return searchResults.NavChild(event,4,5)" onkeyup="return searchResults.NavChild(event,4,5)" class="SRScope" href="../classccp4srs_1_1_torsion.html#ae53494ec218062be243d5e7b36f43dd0" target="_parent">ccp4srs::Torsion::writeToCIF()</a>
+    <a id="Item4_c6" onkeydown="return searchResults.NavChild(event,4,6)" onkeypress="return searchResults.NavChild(event,4,6)" onkeyup="return searchResults.NavChild(event,4,6)" class="SRScope" href="../classccp4srs_1_1_tree.html#ade370b24c17b2d47a4cb8f89c096e5c1" target="_parent">ccp4srs::Tree::writeToCIF()</a>
+  </div>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_78.html ccp4srs/doc-html/html/search/functions_78.html
--- ccp4srs-old/doc-html/html/search/functions_78.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_78.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,38 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_x">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a9af114ebe576f3a0af965579100da463" target="_parent">x</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_x_5fmlib">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a7f9331955d7f98b1d2e869f8741a2188" target="_parent">x_mlib</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_x_5fpdbx">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#ac0fc0e47750a53f2be7ab60efc604d3b" target="_parent">x_pdbx</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_79.html ccp4srs/doc-html/html/search/functions_79.html
--- ccp4srs-old/doc-html/html/search/functions_79.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_79.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,38 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_y">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a10fc0f0f21af2cd5311c7d957b59f52b" target="_parent">y</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_y_5fmlib">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#acc50ad679a297a2626a6662cd0b61d3e" target="_parent">y_mlib</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_y_5fpdbx">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a65cdadf3090a0fa712b6c47040adb578" target="_parent">y_pdbx</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_7a.html ccp4srs/doc-html/html/search/functions_7a.html
--- ccp4srs-old/doc-html/html/search/functions_7a.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_7a.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,38 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_z">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a9d07e03f19613858142105d9f287466e" target="_parent">z</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_z_5fmlib">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a73c4871fccf3ce91502449de659f835a" target="_parent">z_mlib</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_z_5fpdbx">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#aed837e19a61e89ce1e1eda0c35f10b2e" target="_parent">z_pdbx</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/functions_7e.html ccp4srs/doc-html/html/search/functions_7e.html
--- ccp4srs-old/doc-html/html/search/functions_7e.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/functions_7e.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,110 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR__7eangle">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_angle.html#a8b6036ed3908589a9cee50f60f5e3806" target="_parent">~Angle</a>
+  <span class="SRScope">ccp4srs::Angle</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7eatom">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a27de39105bac03d49c949780edda55fd" target="_parent">~Atom</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7ebase">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a2c46b036cb9701ac6a2d22fcec3fbdcf" target="_parent">~Base</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7ebond">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#a695a8236689b60df2ad108c7cc55eb1a" target="_parent">~Bond</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7echem">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_chem.html#a939cae4367e5e32664e60c725fabafbe" target="_parent">~Chem</a>
+  <span class="SRScope">ccp4srs::Chem</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7echicenter">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_chi_center.html#a051ae00e2cdb590a2dd7f4899c264cb9" target="_parent">~ChiCenter</a>
+  <span class="SRScope">ccp4srs::ChiCenter</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7econtainer">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_container.html#a831fc7371918ff96de32b96c35fe31a2" target="_parent">~Container</a>
+  <span class="SRScope">ccp4srs::Container</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7eentry">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_entry.html#a191661efae468b8e2a62b69a247bcd3a" target="_parent">~Entry</a>
+  <span class="SRScope">ccp4srs::Entry</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7eindex">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="../classccp4srs_1_1_index.html#a5a0d5db83db471eae5aa87dcfa6a151c" target="_parent">~Index</a>
+  <span class="SRScope">ccp4srs::Index</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7emanager">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="../classccp4srs_1_1_manager.html#ac6d91d47cb19b9f6ea6c7b64a7f69bb5" target="_parent">~Manager</a>
+  <span class="SRScope">ccp4srs::Manager</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7ememio">
+ <div class="SREntry">
+  <a id="Item10" onkeydown="return searchResults.Nav(event,10)" onkeypress="return searchResults.Nav(event,10)" onkeyup="return searchResults.Nav(event,10)" class="SRSymbol" href="../classccp4srs_1_1_mem_i_o.html#abb2d68b86867b62480e6f036a2f8bcbb" target="_parent">~MemIO</a>
+  <span class="SRScope">ccp4srs::MemIO</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7emonomer">
+ <div class="SREntry">
+  <a id="Item11" onkeydown="return searchResults.Nav(event,11)" onkeypress="return searchResults.Nav(event,11)" onkeyup="return searchResults.Nav(event,11)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a33207c3c799fe120851007002464e2e2" target="_parent">~Monomer</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7eplane">
+ <div class="SREntry">
+  <a id="Item12" onkeydown="return searchResults.Nav(event,12)" onkeypress="return searchResults.Nav(event,12)" onkeyup="return searchResults.Nav(event,12)" class="SRSymbol" href="../classccp4srs_1_1_plane.html#a521911d044ea2aa8ca4e769b9d8d4e58" target="_parent">~Plane</a>
+  <span class="SRScope">ccp4srs::Plane</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7etorsion">
+ <div class="SREntry">
+  <a id="Item13" onkeydown="return searchResults.Nav(event,13)" onkeypress="return searchResults.Nav(event,13)" onkeyup="return searchResults.Nav(event,13)" class="SRSymbol" href="../classccp4srs_1_1_torsion.html#a45434048948cdf6fc5f01a6e3ca149a8" target="_parent">~Torsion</a>
+  <span class="SRScope">ccp4srs::Torsion</span>
+ </div>
+</div>
+<div class="SRResult" id="SR__7etree">
+ <div class="SREntry">
+  <a id="Item14" onkeydown="return searchResults.Nav(event,14)" onkeypress="return searchResults.Nav(event,14)" onkeyup="return searchResults.Nav(event,14)" class="SRSymbol" href="../classccp4srs_1_1_tree.html#ab5a113a9574397dbb5e7679211ee3c24" target="_parent">~Tree</a>
+  <span class="SRScope">ccp4srs::Tree</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
Binary files ccp4srs-old/doc-html/html/search/mag_sel.png and ccp4srs/doc-html/html/search/mag_sel.png differ
diff -ruN ccp4srs-old/doc-html/html/search/namespaces_63.html ccp4srs/doc-html/html/search/namespaces_63.html
--- ccp4srs-old/doc-html/html/search/namespaces_63.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/namespaces_63.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,25 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_ccp4srs">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../namespaceccp4srs.html" target="_parent">ccp4srs</a>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/nomatches.html ccp4srs/doc-html/html/search/nomatches.html
--- ccp4srs-old/doc-html/html/search/nomatches.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/nomatches.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,12 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="NoMatches">No Matches</div>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/search.css ccp4srs/doc-html/html/search/search.css
--- ccp4srs-old/doc-html/html/search/search.css	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/search.css	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,240 @@
+/*---------------- Search Box */
+
+#FSearchBox {
+    float: left;
+}
+
+#searchli {
+    float: right;
+    display: block;
+    width: 170px;
+    height: 36px;
+}
+
+#MSearchBox {
+    white-space : nowrap;
+    position: absolute;
+    float: none;
+    display: inline;
+    margin-top: 8px;
+    right: 0px;
+    width: 170px;
+    z-index: 102;
+}
+
+#MSearchBox .left
+{
+    display:block;
+    position:absolute;
+    left:10px;
+    width:20px;
+    height:19px;
+    background:url('search_l.png') no-repeat;
+    background-position:right;
+}
+
+#MSearchSelect {
+    display:block;
+    position:absolute;
+    width:20px;
+    height:19px;
+}
+
+.left #MSearchSelect {
+    left:4px;
+}
+
+.right #MSearchSelect {
+    right:5px;
+}
+
+#MSearchField {
+    display:block;
+    position:absolute;
+    height:19px;
+    background:url('search_m.png') repeat-x;
+    border:none;
+    width:116px;
+    margin-left:20px;
+    padding-left:4px;
+    color: #909090;
+    outline: none;
+    font: 9pt Arial, Verdana, sans-serif;
+}
+
+#FSearchBox #MSearchField {
+    margin-left:15px;
+}
+
+#MSearchBox .right {
+    display:block;
+    position:absolute;
+    right:10px;
+    top:0px;
+    width:20px;
+    height:19px;
+    background:url('search_r.png') no-repeat;
+    background-position:left;
+}
+
+#MSearchClose {
+    display: none;
+    position: absolute;
+    top: 4px;
+    background : none;
+    border: none;
+    margin: 0px 4px 0px 0px;
+    padding: 0px 0px;
+    outline: none;
+}
+
+.left #MSearchClose {
+    left: 6px;
+}
+
+.right #MSearchClose {
+    right: 2px;
+}
+
+.MSearchBoxActive #MSearchField {
+    color: #000000;
+}
+
+/*---------------- Search filter selection */
+
+#MSearchSelectWindow {
+    display: none;
+    position: absolute;
+    left: 0; top: 0;
+    border: 1px solid #90A5CE;
+    background-color: #F9FAFC;
+    z-index: 1;
+    padding-top: 4px;
+    padding-bottom: 4px;
+    -moz-border-radius: 4px;
+    -webkit-border-top-left-radius: 4px;
+    -webkit-border-top-right-radius: 4px;
+    -webkit-border-bottom-left-radius: 4px;
+    -webkit-border-bottom-right-radius: 4px;
+    -webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+}
+
+.SelectItem {
+    font: 8pt Arial, Verdana, sans-serif;
+    padding-left:  2px;
+    padding-right: 12px;
+    border: 0px;
+}
+
+span.SelectionMark {
+    margin-right: 4px;
+    font-family: monospace;
+    outline-style: none;
+    text-decoration: none;
+}
+
+a.SelectItem {
+    display: block;
+    outline-style: none;
+    color: #000000; 
+    text-decoration: none;
+    padding-left:   6px;
+    padding-right: 12px;
+}
+
+a.SelectItem:focus,
+a.SelectItem:active {
+    color: #000000; 
+    outline-style: none;
+    text-decoration: none;
+}
+
+a.SelectItem:hover {
+    color: #FFFFFF;
+    background-color: #3D578C;
+    outline-style: none;
+    text-decoration: none;
+    cursor: pointer;
+    display: block;
+}
+
+/*---------------- Search results window */
+
+iframe#MSearchResults {
+    width: 60ex;
+    height: 15em;
+}
+
+#MSearchResultsWindow {
+    display: none;
+    position: absolute;
+    left: 0; top: 0;
+    border: 1px solid #000;
+    background-color: #EEF1F7;
+}
+
+/* ----------------------------------- */
+
+
+#SRIndex {
+    clear:both; 
+    padding-bottom: 15px;
+}
+
+.SREntry {
+    font-size: 10pt;
+    padding-left: 1ex;
+}
+
+.SRPage .SREntry {
+    font-size: 8pt;
+    padding: 1px 5px;
+}
+
+body.SRPage {
+    margin: 5px 2px;
+}
+
+.SRChildren {
+    padding-left: 3ex; padding-bottom: .5em 
+}
+
+.SRPage .SRChildren {
+    display: none;
+}
+
+.SRSymbol {
+    font-weight: bold; 
+    color: #425E97;
+    font-family: Arial, Verdana, sans-serif;
+    text-decoration: none;
+    outline: none;
+}
+
+a.SRScope {
+    display: block;
+    color: #425E97; 
+    font-family: Arial, Verdana, sans-serif;
+    text-decoration: none;
+    outline: none;
+}
+
+a.SRSymbol:focus, a.SRSymbol:active,
+a.SRScope:focus, a.SRScope:active {
+    text-decoration: underline;
+}
+
+.SRPage .SRStatus {
+    padding: 2px 5px;
+    font-size: 8pt;
+    font-style: italic;
+}
+
+.SRResult {
+    display: none;
+}
+
+DIV.searchresults {
+    margin-left: 10px;
+    margin-right: 10px;
+}
diff -ruN ccp4srs-old/doc-html/html/search/search.js ccp4srs/doc-html/html/search/search.js
--- ccp4srs-old/doc-html/html/search/search.js	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/search.js	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,744 @@
+// Search script generated by doxygen
+// Copyright (C) 2009 by Dimitri van Heesch.
+
+// The code in this file is loosly based on main.js, part of Natural Docs,
+// which is Copyright (C) 2003-2008 Greg Valure
+// Natural Docs is licensed under the GPL.
+
+var indexSectionsWithContent =
+{
+  0: "0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000010111111111001111101111111110001000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000",
+  1: "0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111110001000100100010000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000",
+  2: "0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000",
+  3: "0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001000000000100000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000",
+  4: "0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000010111111111001111101111111110001000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000",
+  5: "0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111001000111101110100000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000",
+  6: "0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001000000000000100010000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000",
+  7: "0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000",
+  8: "0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000101110000001111001111010000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000",
+  9: "0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000100000000100000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000"
+};
+
+var indexSectionNames =
+{
+  0: "all",
+  1: "classes",
+  2: "namespaces",
+  3: "files",
+  4: "functions",
+  5: "variables",
+  6: "typedefs",
+  7: "enums",
+  8: "enumvalues",
+  9: "defines"
+};
+
+function convertToId(search)
+{
+  var result = '';
+  for (i=0;i<search.length;i++)
+  {
+    var c = search.charAt(i);
+    var cn = c.charCodeAt(0);
+    if (c.match(/[a-z0-9]/))
+    {
+      result+=c;
+    }
+    else if (cn<16) 
+    {
+      result+="_0"+cn.toString(16);
+    }
+    else 
+    {
+      result+="_"+cn.toString(16);
+    }
+  }
+  return result;
+}
+
+function getXPos(item)
+{
+  var x = 0;
+  if (item.offsetWidth)
+  {
+    while (item && item!=document.body)
+    {
+      x   += item.offsetLeft;
+      item = item.offsetParent;
+    }
+  }
+  return x;
+}
+
+function getYPos(item)
+{
+  var y = 0;
+  if (item.offsetWidth)
+  {
+     while (item && item!=document.body)
+     {
+       y   += item.offsetTop;
+       item = item.offsetParent;
+     }
+  }
+  return y;
+}
+
+/* A class handling everything associated with the search panel.
+
+   Parameters:
+   name - The name of the global variable that will be 
+          storing this instance.  Is needed to be able to set timeouts.
+   resultPath - path to use for external files
+*/
+function SearchBox(name, resultsPath, inFrame, label)
+{
+  if (!name || !resultsPath) {  alert("Missing parameters to SearchBox."); }
+   
+  // ---------- Instance variables
+  this.name                  = name;
+  this.resultsPath           = resultsPath;
+  this.keyTimeout            = 0;
+  this.keyTimeoutLength      = 500;
+  this.closeSelectionTimeout = 300;
+  this.lastSearchValue       = "";
+  this.lastResultsPage       = "";
+  this.hideTimeout           = 0;
+  this.searchIndex           = 0;
+  this.searchActive          = false;
+  this.insideFrame           = inFrame;
+  this.searchLabel           = label;
+
+  // ----------- DOM Elements
+
+  this.DOMSearchField = function()
+  {  return document.getElementById("MSearchField");  }
+
+  this.DOMSearchSelect = function()
+  {  return document.getElementById("MSearchSelect");  }
+
+  this.DOMSearchSelectWindow = function()
+  {  return document.getElementById("MSearchSelectWindow");  }
+
+  this.DOMPopupSearchResults = function()
+  {  return document.getElementById("MSearchResults");  }
+
+  this.DOMPopupSearchResultsWindow = function()
+  {  return document.getElementById("MSearchResultsWindow");  }
+
+  this.DOMSearchClose = function()
+  {  return document.getElementById("MSearchClose"); }
+
+  this.DOMSearchBox = function()
+  {  return document.getElementById("MSearchBox");  }
+
+  // ------------ Event Handlers
+
+  // Called when focus is added or removed from the search field.
+  this.OnSearchFieldFocus = function(isActive)
+  {
+    this.Activate(isActive);
+  }
+
+  this.OnSearchSelectShow = function()
+  {
+    var searchSelectWindow = this.DOMSearchSelectWindow();
+    var searchField        = this.DOMSearchSelect();
+
+    if (this.insideFrame)
+    {
+      var left = getXPos(searchField);
+      var top  = getYPos(searchField);
+      left += searchField.offsetWidth + 6;
+      top += searchField.offsetHeight;
+
+      // show search selection popup
+      searchSelectWindow.style.display='block';
+      left -= searchSelectWindow.offsetWidth;
+      searchSelectWindow.style.left =  left + 'px';
+      searchSelectWindow.style.top  =  top  + 'px';
+    }
+    else
+    {
+      var left = getXPos(searchField);
+      var top  = getYPos(searchField);
+      top += searchField.offsetHeight;
+
+      // show search selection popup
+      searchSelectWindow.style.display='block';
+      searchSelectWindow.style.left =  left + 'px';
+      searchSelectWindow.style.top  =  top  + 'px';
+    }
+
+    // stop selection hide timer
+    if (this.hideTimeout) 
+    {
+      clearTimeout(this.hideTimeout);
+      this.hideTimeout=0;
+    }
+    return false; // to avoid "image drag" default event
+  }
+
+  this.OnSearchSelectHide = function()
+  {
+    this.hideTimeout = setTimeout(this.name +".CloseSelectionWindow()",
+                                  this.closeSelectionTimeout);
+  }
+
+  // Called when the content of the search field is changed.
+  this.OnSearchFieldChange = function(evt)
+  {
+    if (this.keyTimeout) // kill running timer
+    {
+      clearTimeout(this.keyTimeout);
+      this.keyTimeout = 0;
+    }
+
+    var e  = (evt) ? evt : window.event; // for IE
+    if (e.keyCode==40 || e.keyCode==13)
+    {
+      if (e.shiftKey==1)
+      {
+        this.OnSearchSelectShow();
+        var win=this.DOMSearchSelectWindow(); 
+        for (i=0;i<win.childNodes.length;i++)
+        {
+          var child = win.childNodes[i]; // get span within a
+          if (child.className=='SelectItem')
+          {
+            child.focus();
+            return;
+          }
+        }
+        return;
+      }
+      else if (window.frames.MSearchResults.searchResults)
+      {
+        var elem = window.frames.MSearchResults.searchResults.NavNext(0);
+        if (elem) elem.focus();
+      }
+    }
+    else if (e.keyCode==27) // Escape out of the search field
+    {
+      this.DOMSearchField().blur();
+      this.DOMPopupSearchResultsWindow().style.display = 'none';
+      this.DOMSearchClose().style.display = 'none';
+      this.lastSearchValue = '';
+      this.Activate(false);
+      return;
+    }
+
+    // strip whitespaces
+    var searchValue = this.DOMSearchField().value.replace(/ +/g, "");
+
+    if (searchValue != this.lastSearchValue) // search value has changed
+    {
+      if (searchValue != "") // non-empty search
+      {
+        // set timer for search update
+        this.keyTimeout = setTimeout(this.name + '.Search()',
+                                     this.keyTimeoutLength);
+      }
+      else // empty search field
+      {
+        this.DOMPopupSearchResultsWindow().style.display = 'none';
+        this.DOMSearchClose().style.display = 'none';
+        this.lastSearchValue = '';
+      }
+    }
+  }
+
+  this.SelectItemCount = function(id)
+  {
+    var count=0;
+    var win=this.DOMSearchSelectWindow(); 
+    for (i=0;i<win.childNodes.length;i++)
+    {
+      var child = win.childNodes[i]; // get span within a
+      if (child.className=='SelectItem')
+      {
+        count++;
+      }
+    }
+    return count;
+  }
+
+  this.SelectItemSet = function(id)
+  {
+    var i,j=0;
+    var win=this.DOMSearchSelectWindow(); 
+    for (i=0;i<win.childNodes.length;i++)
+    {
+      var child = win.childNodes[i]; // get span within a
+      if (child.className=='SelectItem')
+      {
+        var node = child.firstChild;
+        if (j==id)
+        {
+          node.innerHTML='&bull;';
+        }
+        else
+        {
+          node.innerHTML='&#160;';
+        }
+        j++;
+      }
+    }
+  }
+
+  // Called when an search filter selection is made.
+  // set item with index id as the active item
+  this.OnSelectItem = function(id)
+  {
+    this.searchIndex = id;
+    this.SelectItemSet(id);
+    var searchValue = this.DOMSearchField().value.replace(/ +/g, "");
+    if (searchValue!="" && this.searchActive) // something was found -> do a search
+    {
+      this.Search();
+    }
+  }
+
+  this.OnSearchSelectKey = function(evt)
+  {
+    var e = (evt) ? evt : window.event; // for IE
+    if (e.keyCode==40 && this.searchIndex<this.SelectItemCount()) // Down
+    {
+      this.searchIndex++;
+      this.OnSelectItem(this.searchIndex);
+    }
+    else if (e.keyCode==38 && this.searchIndex>0) // Up
+    {
+      this.searchIndex--;
+      this.OnSelectItem(this.searchIndex);
+    }
+    else if (e.keyCode==13 || e.keyCode==27)
+    {
+      this.OnSelectItem(this.searchIndex);
+      this.CloseSelectionWindow();
+      this.DOMSearchField().focus();
+    }
+    return false;
+  }
+
+  // --------- Actions
+
+  // Closes the results window.
+  this.CloseResultsWindow = function()
+  {
+    this.DOMPopupSearchResultsWindow().style.display = 'none';
+    this.DOMSearchClose().style.display = 'none';
+    this.Activate(false);
+  }
+
+  this.CloseSelectionWindow = function()
+  {
+    this.DOMSearchSelectWindow().style.display = 'none';
+  }
+
+  // Performs a search.
+  this.Search = function()
+  {
+    this.keyTimeout = 0;
+
+    // strip leading whitespace
+    var searchValue = this.DOMSearchField().value.replace(/^ +/, "");
+
+    var code = searchValue.toLowerCase().charCodeAt(0);
+    var hexCode;
+    if (code<16) 
+    {
+      hexCode="0"+code.toString(16);
+    }
+    else 
+    {
+      hexCode=code.toString(16);
+    }
+
+    var resultsPage;
+    var resultsPageWithSearch;
+    var hasResultsPage;
+
+    if (indexSectionsWithContent[this.searchIndex].charAt(code) == '1')
+    {
+       resultsPage = this.resultsPath + '/' + indexSectionNames[this.searchIndex] + '_' + hexCode + '.html';
+       resultsPageWithSearch = resultsPage+'?'+escape(searchValue);
+       hasResultsPage = true;
+    }
+    else // nothing available for this search term
+    {
+       resultsPage = this.resultsPath + '/nomatches.html';
+       resultsPageWithSearch = resultsPage;
+       hasResultsPage = false;
+    }
+
+    window.frames.MSearchResults.location.href = resultsPageWithSearch;  
+    var domPopupSearchResultsWindow = this.DOMPopupSearchResultsWindow();
+
+    if (domPopupSearchResultsWindow.style.display!='block')
+    {
+       var domSearchBox = this.DOMSearchBox();
+       this.DOMSearchClose().style.display = 'inline';
+       if (this.insideFrame)
+       {
+         var domPopupSearchResults = this.DOMPopupSearchResults();
+         domPopupSearchResultsWindow.style.position = 'relative';
+         domPopupSearchResultsWindow.style.display  = 'block';
+         var width = document.body.clientWidth - 8; // the -8 is for IE :-(
+         domPopupSearchResultsWindow.style.width    = width + 'px';
+         domPopupSearchResults.style.width          = width + 'px';
+       }
+       else
+       {
+         var domPopupSearchResults = this.DOMPopupSearchResults();
+         var left = getXPos(domSearchBox) + 150; // domSearchBox.offsetWidth;
+         var top  = getYPos(domSearchBox) + 20;  // domSearchBox.offsetHeight + 1;
+         domPopupSearchResultsWindow.style.display = 'block';
+         left -= domPopupSearchResults.offsetWidth;
+         domPopupSearchResultsWindow.style.top     = top  + 'px';
+         domPopupSearchResultsWindow.style.left    = left + 'px';
+       }
+    }
+
+    this.lastSearchValue = searchValue;
+    this.lastResultsPage = resultsPage;
+  }
+
+  // -------- Activation Functions
+
+  // Activates or deactivates the search panel, resetting things to 
+  // their default values if necessary. 
+  this.Activate = function(isActive)
+  {
+    if (isActive || // open it
+        this.DOMPopupSearchResultsWindow().style.display == 'block' 
+       )
+    {
+      this.DOMSearchBox().className = 'MSearchBoxActive';
+
+      var searchField = this.DOMSearchField();
+
+      if (searchField.value == this.searchLabel) // clear "Search" term upon entry
+      {  
+        searchField.value = '';  
+        this.searchActive = true;
+      }
+    }
+    else if (!isActive) // directly remove the panel
+    {
+      this.DOMSearchBox().className = 'MSearchBoxInactive';
+      this.DOMSearchField().value   = this.searchLabel;
+      this.searchActive             = false;
+      this.lastSearchValue          = ''
+      this.lastResultsPage          = '';
+    }
+  }
+}
+
+// -----------------------------------------------------------------------
+
+// The class that handles everything on the search results page.
+function SearchResults(name)
+{
+    // The number of matches from the last run of <Search()>.
+    this.lastMatchCount = 0;
+    this.lastKey = 0;
+    this.repeatOn = false;
+
+    // Toggles the visibility of the passed element ID.
+    this.FindChildElement = function(id)
+    {
+      var parentElement = document.getElementById(id);
+      var element = parentElement.firstChild;
+
+      while (element && element!=parentElement)
+      {
+        if (element.nodeName == 'DIV' && element.className == 'SRChildren')
+        {
+          return element;
+        }
+
+        if (element.nodeName == 'DIV' && element.hasChildNodes())
+        {  
+           element = element.firstChild;  
+        }
+        else if (element.nextSibling)
+        {  
+           element = element.nextSibling;  
+        }
+        else
+        {
+          do
+          {
+            element = element.parentNode;
+          }
+          while (element && element!=parentElement && !element.nextSibling);
+
+          if (element && element!=parentElement)
+          {  
+            element = element.nextSibling;  
+          }
+        }
+      }
+    }
+
+    this.Toggle = function(id)
+    {
+      var element = this.FindChildElement(id);
+      if (element)
+      {
+        if (element.style.display == 'block')
+        {
+          element.style.display = 'none';
+        }
+        else
+        {
+          element.style.display = 'block';
+        }
+      }
+    }
+
+    // Searches for the passed string.  If there is no parameter,
+    // it takes it from the URL query.
+    //
+    // Always returns true, since other documents may try to call it
+    // and that may or may not be possible.
+    this.Search = function(search)
+    {
+      if (!search) // get search word from URL
+      {
+        search = window.location.search;
+        search = search.substring(1);  // Remove the leading '?'
+        search = unescape(search);
+      }
+
+      search = search.replace(/^ +/, ""); // strip leading spaces
+      search = search.replace(/ +$/, ""); // strip trailing spaces
+      search = search.toLowerCase();
+      search = convertToId(search);
+
+      var resultRows = document.getElementsByTagName("div");
+      var matches = 0;
+
+      var i = 0;
+      while (i < resultRows.length)
+      {
+        var row = resultRows.item(i);
+        if (row.className == "SRResult")
+        {
+          var rowMatchName = row.id.toLowerCase();
+          rowMatchName = rowMatchName.replace(/^sr\d*_/, ''); // strip 'sr123_'
+
+          if (search.length<=rowMatchName.length && 
+             rowMatchName.substr(0, search.length)==search)
+          {
+            row.style.display = 'block';
+            matches++;
+          }
+          else
+          {
+            row.style.display = 'none';
+          }
+        }
+        i++;
+      }
+      document.getElementById("Searching").style.display='none';
+      if (matches == 0) // no results
+      {
+        document.getElementById("NoMatches").style.display='block';
+      }
+      else // at least one result
+      {
+        document.getElementById("NoMatches").style.display='none';
+      }
+      this.lastMatchCount = matches;
+      return true;
+    }
+
+    // return the first item with index index or higher that is visible
+    this.NavNext = function(index)
+    {
+      var focusItem;
+      while (1)
+      {
+        var focusName = 'Item'+index;
+        focusItem = document.getElementById(focusName);
+        if (focusItem && focusItem.parentNode.parentNode.style.display=='block')
+        {
+          break;
+        }
+        else if (!focusItem) // last element
+        {
+          break;
+        }
+        focusItem=null;
+        index++;
+      }
+      return focusItem;
+    }
+
+    this.NavPrev = function(index)
+    {
+      var focusItem;
+      while (1)
+      {
+        var focusName = 'Item'+index;
+        focusItem = document.getElementById(focusName);
+        if (focusItem && focusItem.parentNode.parentNode.style.display=='block')
+        {
+          break;
+        }
+        else if (!focusItem) // last element
+        {
+          break;
+        }
+        focusItem=null;
+        index--;
+      }
+      return focusItem;
+    }
+
+    this.ProcessKeys = function(e)
+    {
+      if (e.type == "keydown") 
+      {
+        this.repeatOn = false;
+        this.lastKey = e.keyCode;
+      }
+      else if (e.type == "keypress")
+      {
+        if (!this.repeatOn)
+        {
+          if (this.lastKey) this.repeatOn = true;
+          return false; // ignore first keypress after keydown
+        }
+      }
+      else if (e.type == "keyup")
+      {
+        this.lastKey = 0;
+        this.repeatOn = false;
+      }
+      return this.lastKey!=0;
+    }
+
+    this.Nav = function(evt,itemIndex) 
+    {
+      var e  = (evt) ? evt : window.event; // for IE
+      if (e.keyCode==13) return true;
+      if (!this.ProcessKeys(e)) return false;
+
+      if (this.lastKey==38) // Up
+      {
+        var newIndex = itemIndex-1;
+        var focusItem = this.NavPrev(newIndex);
+        if (focusItem)
+        {
+          var child = this.FindChildElement(focusItem.parentNode.parentNode.id);
+          if (child && child.style.display == 'block') // children visible
+          { 
+            var n=0;
+            var tmpElem;
+            while (1) // search for last child
+            {
+              tmpElem = document.getElementById('Item'+newIndex+'_c'+n);
+              if (tmpElem)
+              {
+                focusItem = tmpElem;
+              }
+              else // found it!
+              {
+                break;
+              }
+              n++;
+            }
+          }
+        }
+        if (focusItem)
+        {
+          focusItem.focus();
+        }
+        else // return focus to search field
+        {
+           parent.document.getElementById("MSearchField").focus();
+        }
+      }
+      else if (this.lastKey==40) // Down
+      {
+        var newIndex = itemIndex+1;
+        var focusItem;
+        var item = document.getElementById('Item'+itemIndex);
+        var elem = this.FindChildElement(item.parentNode.parentNode.id);
+        if (elem && elem.style.display == 'block') // children visible
+        {
+          focusItem = document.getElementById('Item'+itemIndex+'_c0');
+        }
+        if (!focusItem) focusItem = this.NavNext(newIndex);
+        if (focusItem)  focusItem.focus();
+      }
+      else if (this.lastKey==39) // Right
+      {
+        var item = document.getElementById('Item'+itemIndex);
+        var elem = this.FindChildElement(item.parentNode.parentNode.id);
+        if (elem) elem.style.display = 'block';
+      }
+      else if (this.lastKey==37) // Left
+      {
+        var item = document.getElementById('Item'+itemIndex);
+        var elem = this.FindChildElement(item.parentNode.parentNode.id);
+        if (elem) elem.style.display = 'none';
+      }
+      else if (this.lastKey==27) // Escape
+      {
+        parent.searchBox.CloseResultsWindow();
+        parent.document.getElementById("MSearchField").focus();
+      }
+      else if (this.lastKey==13) // Enter
+      {
+        return true;
+      }
+      return false;
+    }
+
+    this.NavChild = function(evt,itemIndex,childIndex)
+    {
+      var e  = (evt) ? evt : window.event; // for IE
+      if (e.keyCode==13) return true;
+      if (!this.ProcessKeys(e)) return false;
+
+      if (this.lastKey==38) // Up
+      {
+        if (childIndex>0)
+        {
+          var newIndex = childIndex-1;
+          document.getElementById('Item'+itemIndex+'_c'+newIndex).focus();
+        }
+        else // already at first child, jump to parent
+        {
+          document.getElementById('Item'+itemIndex).focus();
+        }
+      }
+      else if (this.lastKey==40) // Down
+      {
+        var newIndex = childIndex+1;
+        var elem = document.getElementById('Item'+itemIndex+'_c'+newIndex);
+        if (!elem) // last child, jump to parent next parent
+        {
+          elem = this.NavNext(itemIndex+1);
+        }
+        if (elem)
+        {
+          elem.focus();
+        } 
+      }
+      else if (this.lastKey==27) // Escape
+      {
+        parent.searchBox.CloseResultsWindow();
+        parent.document.getElementById("MSearchField").focus();
+      }
+      else if (this.lastKey==13) // Enter
+      {
+        return true;
+      }
+      return false;
+    }
+}
Binary files ccp4srs-old/doc-html/html/search/search_l.png and ccp4srs/doc-html/html/search/search_l.png differ
Binary files ccp4srs-old/doc-html/html/search/search_m.png and ccp4srs/doc-html/html/search/search_m.png differ
Binary files ccp4srs-old/doc-html/html/search/search_r.png and ccp4srs/doc-html/html/search/search_r.png differ
diff -ruN ccp4srs-old/doc-html/html/search/typedefs_63.html ccp4srs/doc-html/html/search/typedefs_63.html
--- ccp4srs-old/doc-html/html/search/typedefs_63.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/typedefs_63.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,26 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_chicenterid">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../namespaceccp4srs.html#ae91f970060d687d02ccfb78cbd6222bb" target="_parent">ChiCenterID</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/typedefs_70.html ccp4srs/doc-html/html/search/typedefs_70.html
--- ccp4srs-old/doc-html/html/search/typedefs_70.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/typedefs_70.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,26 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_planeid">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../namespaceccp4srs.html#ac768cc62149be89b81a30d88a09f0166" target="_parent">PlaneID</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
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+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/typedefs_74.html ccp4srs/doc-html/html/search/typedefs_74.html
--- ccp4srs-old/doc-html/html/search/typedefs_74.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/typedefs_74.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,26 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_torsionid">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../namespaceccp4srs.html#a192f47d1deb71790866bce922f50bba1" target="_parent">TorsionID</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
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+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/variables_61.html ccp4srs/doc-html/html/search/variables_61.html
--- ccp4srs-old/doc-html/html/search/variables_61.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/variables_61.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,154 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_a1">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../structccp4srs_1_1_atom_pair.html#a0277f099acfa557ac20bf6fd3320bcaa" target="_parent">a1</a>
+  <span class="SRScope">ccp4srs::AtomPair</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_a2">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../structccp4srs_1_1_atom_pair.html#a1f8f7df44905ac32088ccfcf1b80dda2" target="_parent">a2</a>
+  <span class="SRScope">ccp4srs::AtomPair</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_angle">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_angle.html#abf55314566cb2fa1d3764d0485284113" target="_parent">angle</a>
+  <span class="SRScope">ccp4srs::Angle</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_angle_5fesd">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_angle.html#a39e05de948ddbf9c944bf0b14123caf8" target="_parent">angle_esd</a>
+  <span class="SRScope">ccp4srs::Angle</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_angles">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a9177ec12ea5aeaa59228831d4127e592" target="_parent">angles</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom_5f1">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_atom_5f1')">atom_1</a>
+  <div class="SRChildren">
+    <a id="Item5_c0" onkeydown="return searchResults.NavChild(event,5,0)" onkeypress="return searchResults.NavChild(event,5,0)" onkeyup="return searchResults.NavChild(event,5,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#ab59c639612d7dcae2b34213a647cdb45" target="_parent">ccp4srs::Angle::atom_1()</a>
+    <a id="Item5_c1" onkeydown="return searchResults.NavChild(event,5,1)" onkeypress="return searchResults.NavChild(event,5,1)" onkeyup="return searchResults.NavChild(event,5,1)" class="SRScope" href="../classccp4srs_1_1_bond.html#ad359689c475101246c6c3061d31c2541" target="_parent">ccp4srs::Bond::atom_1()</a>
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+    <a id="Item5_c3" onkeydown="return searchResults.NavChild(event,5,3)" onkeypress="return searchResults.NavChild(event,5,3)" onkeyup="return searchResults.NavChild(event,5,3)" class="SRScope" href="../classccp4srs_1_1_torsion.html#ae6bb750e2ebd67defafc5bd38515e923" target="_parent">ccp4srs::Torsion::atom_1()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom_5f2">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_atom_5f2')">atom_2</a>
+  <div class="SRChildren">
+    <a id="Item6_c0" onkeydown="return searchResults.NavChild(event,6,0)" onkeypress="return searchResults.NavChild(event,6,0)" onkeyup="return searchResults.NavChild(event,6,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a8a4fd7f9e6196f259b6ec0989b5cb64c" target="_parent">ccp4srs::Angle::atom_2()</a>
+    <a id="Item6_c1" onkeydown="return searchResults.NavChild(event,6,1)" onkeypress="return searchResults.NavChild(event,6,1)" onkeyup="return searchResults.NavChild(event,6,1)" class="SRScope" href="../classccp4srs_1_1_bond.html#a277aee984c745dcdfd338f19e7df1e48" target="_parent">ccp4srs::Bond::atom_2()</a>
+    <a id="Item6_c2" onkeydown="return searchResults.NavChild(event,6,2)" onkeypress="return searchResults.NavChild(event,6,2)" onkeyup="return searchResults.NavChild(event,6,2)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#aa80d6d7fbec0a8497b62af13b16e2a12" target="_parent">ccp4srs::ChiCenter::atom_2()</a>
+    <a id="Item6_c3" onkeydown="return searchResults.NavChild(event,6,3)" onkeypress="return searchResults.NavChild(event,6,3)" onkeyup="return searchResults.NavChild(event,6,3)" class="SRScope" href="../classccp4srs_1_1_torsion.html#aae803284861c24535f6ea3cab02f00b8" target="_parent">ccp4srs::Torsion::atom_2()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom_5f3">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_atom_5f3')">atom_3</a>
+  <div class="SRChildren">
+    <a id="Item7_c0" onkeydown="return searchResults.NavChild(event,7,0)" onkeypress="return searchResults.NavChild(event,7,0)" onkeyup="return searchResults.NavChild(event,7,0)" class="SRScope" href="../classccp4srs_1_1_angle.html#a545fb1039055e640aa938964b64c7d0a" target="_parent">ccp4srs::Angle::atom_3()</a>
+    <a id="Item7_c1" onkeydown="return searchResults.NavChild(event,7,1)" onkeypress="return searchResults.NavChild(event,7,1)" onkeyup="return searchResults.NavChild(event,7,1)" class="SRScope" href="../classccp4srs_1_1_chi_center.html#a2b249cab1cc7c2ea80ea9259914fcd34" target="_parent">ccp4srs::ChiCenter::atom_3()</a>
+    <a id="Item7_c2" onkeydown="return searchResults.NavChild(event,7,2)" onkeypress="return searchResults.NavChild(event,7,2)" onkeyup="return searchResults.NavChild(event,7,2)" class="SRScope" href="../classccp4srs_1_1_torsion.html#a16456310c79412ef19e6b3dd22baf3b3" target="_parent">ccp4srs::Torsion::atom_3()</a>
+  </div>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom_5f4">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="../classccp4srs_1_1_torsion.html#a73c5cc1a3f37ac0998b1316beb35c579" target="_parent">atom_4</a>
+  <span class="SRScope">ccp4srs::Torsion</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom_5fbackward">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="../classccp4srs_1_1_tree.html#a612df27ef2431bf2ac087f7190e0f9d1" target="_parent">atom_backward</a>
+  <span class="SRScope">ccp4srs::Tree</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom_5fcenter">
+ <div class="SREntry">
+  <a id="Item10" onkeydown="return searchResults.Nav(event,10)" onkeypress="return searchResults.Nav(event,10)" onkeyup="return searchResults.Nav(event,10)" class="SRSymbol" href="../classccp4srs_1_1_chi_center.html#a5fe75db982419a5d7f3c3ff8b2e41f46" target="_parent">atom_center</a>
+  <span class="SRScope">ccp4srs::ChiCenter</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom_5fforward">
+ <div class="SREntry">
+  <a id="Item11" onkeydown="return searchResults.Nav(event,11)" onkeypress="return searchResults.Nav(event,11)" onkeyup="return searchResults.Nav(event,11)" class="SRSymbol" href="../classccp4srs_1_1_tree.html#a3c63a71c2935da20a0feccad01d5ceaf" target="_parent">atom_forward</a>
+  <span class="SRScope">ccp4srs::Tree</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atom_5ftree">
+ <div class="SREntry">
+  <a id="Item12" onkeydown="return searchResults.Nav(event,12)" onkeypress="return searchResults.Nav(event,12)" onkeyup="return searchResults.Nav(event,12)" class="SRSymbol" href="../classccp4srs_1_1_tree.html#a27d256081e9d371ff22a6644d9ee8a91" target="_parent">atom_tree</a>
+  <span class="SRScope">ccp4srs::Tree</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atomcharge">
+ <div class="SREntry">
+  <a id="Item13" onkeydown="return searchResults.Nav(event,13)" onkeypress="return searchResults.Nav(event,13)" onkeyup="return searchResults.Nav(event,13)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a0e7a7e76f9fba1a8277dae436f900821" target="_parent">atomCharge</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atomid_5fna">
+ <div class="SREntry">
+  <a id="Item14" onkeydown="return searchResults.Nav(event,14)" onkeypress="return searchResults.Nav(event,14)" onkeyup="return searchResults.Nav(event,14)" class="SRSymbol" href="../namespaceccp4srs.html#aa44a92ce883cd1c525381111cd1a4ab3" target="_parent">AtomID_NA</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atomname">
+ <div class="SREntry">
+  <a id="Item15" onkeydown="return searchResults.Nav(event,15)" onkeypress="return searchResults.Nav(event,15)" onkeyup="return searchResults.Nav(event,15)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a75168bfe9aa3e0e24ba5f81854323039" target="_parent">atomName</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atoms">
+ <div class="SREntry">
+  <a id="Item16" onkeydown="return searchResults.Nav(event,16)" onkeypress="return searchResults.Nav(event,16)" onkeyup="return searchResults.Nav(event,16)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#abd7decc2129038a1416f324fee53afa1" target="_parent">atoms</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atomsp">
+ <div class="SREntry">
+  <a id="Item17" onkeydown="return searchResults.Nav(event,17)" onkeypress="return searchResults.Nav(event,17)" onkeyup="return searchResults.Nav(event,17)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#acb4d50d536b22d4dd3f971072354f784" target="_parent">atomSP</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atomvalency">
+ <div class="SREntry">
+  <a id="Item18" onkeydown="return searchResults.Nav(event,18)" onkeypress="return searchResults.Nav(event,18)" onkeyup="return searchResults.Nav(event,18)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#aeaa06e2eac23c671be3f49c0caaa7d12" target="_parent">atomValency</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_atomweight">
+ <div class="SREntry">
+  <a id="Item19" onkeydown="return searchResults.Nav(event,19)" onkeypress="return searchResults.Nav(event,19)" onkeyup="return searchResults.Nav(event,19)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#ac470c0fd96b775b2b1d979c353449ee4" target="_parent">atomWeight</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/variables_62.html ccp4srs/doc-html/html/search/variables_62.html
--- ccp4srs-old/doc-html/html/search/variables_62.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/variables_62.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,44 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_bond_5flength">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#a43513fb523b43f7f5f407a0bae151a95" target="_parent">bond_length</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_bond_5flength_5fesd">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#af438937a89d3cb3c7f2342ca6f38301c" target="_parent">bond_length_esd</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_bond_5forder">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_bond.html#ac6365bacbc07dd7cf914b6c7ad6cd5d7" target="_parent">bond_order</a>
+  <span class="SRScope">ccp4srs::Bond</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_bonds">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a19495bb3c7e8d1c27f12f06729979d9e" target="_parent">bonds</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/variables_63.html ccp4srs/doc-html/html/search/variables_63.html
--- ccp4srs-old/doc-html/html/search/variables_63.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/variables_63.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,68 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_ccp4srs_5ffile_5fversion">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../namespaceccp4srs.html#a4938160ce6172269adc59b8077014f7c" target="_parent">CCP4SRS_file_version</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_chemelement">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a621e19772fdb901353b6f60288afdb70" target="_parent">chemElement</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_chicenter_5fid">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_chi_center.html#ac2387dc7a46c0c4451bcd08e23b25ae5" target="_parent">chicenter_id</a>
+  <span class="SRScope">ccp4srs::ChiCenter</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_chicenters">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a96a126d39760ce281f8bf04186e29c13" target="_parent">chicenters</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_chunkno">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../structccp4srs_1_1_m_p_file_pos.html#ab84443c24cd9b322d81f2e165af4bd8a" target="_parent">chunkNo</a>
+  <span class="SRScope">ccp4srs::MPFilePos</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_comp1">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_index.html#af2a41a666517311e8877a3ec9e288916" target="_parent">Comp1</a>
+  <span class="SRScope">ccp4srs::Index</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_comp2">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_index.html#af4ce5b42fe2cf6364f9916d0a42f08b2" target="_parent">Comp2</a>
+  <span class="SRScope">ccp4srs::Index</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_connect_5ftype">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_tree.html#a97ee818b7a1b1724cfb712453be05743" target="_parent">connect_type</a>
+  <span class="SRScope">ccp4srs::Tree</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/variables_64.html ccp4srs/doc-html/html/search/variables_64.html
--- ccp4srs-old/doc-html/html/search/variables_64.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/variables_64.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,26 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_dist_5fesd">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_plane.html#a5837e387b59c8d350271fd11a644ee8d" target="_parent">dist_esd</a>
+  <span class="SRScope">ccp4srs::Plane</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/variables_65.html ccp4srs/doc-html/html/search/variables_65.html
--- ccp4srs-old/doc-html/html/search/variables_65.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/variables_65.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,32 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_energytype">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#ac429b2d0c02fe21432c4b651ad181fdb" target="_parent">energyType</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_entryid">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_index.html#a0bd1aedcf3b32bdd48d0de5cd2cc563e" target="_parent">entryID</a>
+  <span class="SRScope">ccp4srs::Index</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/variables_66.html ccp4srs/doc-html/html/search/variables_66.html
--- ccp4srs-old/doc-html/html/search/variables_66.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/variables_66.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,32 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_fgraphpos">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_index.html#a3be74bae1c6afc52ea36690b45ec5b96" target="_parent">fGraphPos</a>
+  <span class="SRScope">ccp4srs::Index</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_fstructpos">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_index.html#a21a1eddc77e99baf8df0b7450dee548b" target="_parent">fStructPos</a>
+  <span class="SRScope">ccp4srs::Index</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/variables_69.html ccp4srs/doc-html/html/search/variables_69.html
--- ccp4srs-old/doc-html/html/search/variables_69.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/variables_69.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,32 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_index">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_base.html#ada41928311fa3ba94bcb48a1ebf4b4df" target="_parent">index</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_ionradius">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#aeb773fbdd5b04c0311969ad498622185" target="_parent">ionRadius</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/variables_6d.html ccp4srs/doc-html/html/search/variables_6d.html
--- ccp4srs-old/doc-html/html/search/variables_6d.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/variables_6d.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,116 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_maxdaacos">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_chem.html#aa32277562470e13dfe292f01bc269c17" target="_parent">maxDAAcos</a>
+  <span class="SRScope">ccp4srs::Chem</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_maxdadist">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_chem.html#a6655092e23b55ff3d6465a60101c135d" target="_parent">maxDAdist</a>
+  <span class="SRScope">ccp4srs::Chem</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_maxddacos">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_chem.html#aa5d2547bfa92f55c755aa57fce717a65" target="_parent">maxDDAcos</a>
+  <span class="SRScope">ccp4srs::Chem</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_maxdhacos">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_chem.html#a7408580f10d8868ae368f3faa1253577" target="_parent">maxDHAcos</a>
+  <span class="SRScope">ccp4srs::Chem</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_maxhaacos">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_chem.html#a71cea07257deb2795443e04e07ee4bed" target="_parent">maxHAAcos</a>
+  <span class="SRScope">ccp4srs::Chem</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_maxhadist2">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_chem.html#ada14781ad5390841304d35f262705c57" target="_parent">maxHAdist2</a>
+  <span class="SRScope">ccp4srs::Chem</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_maxsbdist">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_chem.html#aeeb0e6bc6cc2e1a3f5ce78d59d8b496d" target="_parent">maxSBdist</a>
+  <span class="SRScope">ccp4srs::Chem</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_memio">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_base.html#adf128b2adae954f6b25463c70ede5a58" target="_parent">memIO</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_mindadist">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="../classccp4srs_1_1_chem.html#a2e63b74dcf71dbf8583a64342de3848c" target="_parent">minDAdist</a>
+  <span class="SRScope">ccp4srs::Chem</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_mlib_5fx">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a641d281e9661ff8ca51bc768b2db5628" target="_parent">mlib_x</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_mlib_5fy">
+ <div class="SREntry">
+  <a id="Item10" onkeydown="return searchResults.Nav(event,10)" onkeypress="return searchResults.Nav(event,10)" onkeyup="return searchResults.Nav(event,10)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a92043cd1d43d17069c0c8f96020218b9" target="_parent">mlib_y</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_mlib_5fz">
+ <div class="SREntry">
+  <a id="Item11" onkeydown="return searchResults.Nav(event,11)" onkeypress="return searchResults.Nav(event,11)" onkeyup="return searchResults.Nav(event,11)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a0b6c2ba6990da454ea672a64e285653f" target="_parent">mlib_z</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_monformula">
+ <div class="SREntry">
+  <a id="Item12" onkeydown="return searchResults.Nav(event,12)" onkeypress="return searchResults.Nav(event,12)" onkeyup="return searchResults.Nav(event,12)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#aeb6bee62372a765e8aca0c1496689b3a" target="_parent">monFormula</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_monid">
+ <div class="SREntry">
+  <a id="Item13" onkeydown="return searchResults.Nav(event,13)" onkeypress="return searchResults.Nav(event,13)" onkeyup="return searchResults.Nav(event,13)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a34240535a6e703495662936dba863026" target="_parent">monID</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_monname">
+ <div class="SREntry">
+  <a id="Item14" onkeydown="return searchResults.Nav(event,14)" onkeypress="return searchResults.Nav(event,14)" onkeyup="return searchResults.Nav(event,14)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a53b8d5232f3b2085d531eca33fb7c55a" target="_parent">monName</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_montype">
+ <div class="SREntry">
+  <a id="Item15" onkeydown="return searchResults.Nav(event,15)" onkeypress="return searchResults.Nav(event,15)" onkeyup="return searchResults.Nav(event,15)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#af0a573429afbbea61647c9851f0deba7" target="_parent">monType</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/variables_6e.html ccp4srs/doc-html/html/search/variables_6e.html
--- ccp4srs-old/doc-html/html/search/variables_6e.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/variables_6e.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,62 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_n_5fatoms">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_plane.html#aa76a845ff6abce3d2c8f40db13717842" target="_parent">n_atoms</a>
+  <span class="SRScope">ccp4srs::Plane</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_n_5fobjects">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_container.html#abf366ff76d063e04beddf484e4993748" target="_parent">n_objects</a>
+  <span class="SRScope">ccp4srs::Container</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_n_5fsections">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_tree.html#a4056f0bb5ef8add5a55133eb8166c639" target="_parent">n_sections</a>
+  <span class="SRScope">ccp4srs::Tree</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_natoms">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_index.html#abba65d2d400f004fa3815a06101ac478" target="_parent">nAtoms</a>
+  <span class="SRScope">ccp4srs::Index</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_nbonds">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_index.html#a5906658999e6e4e095589e0cdffabf11" target="_parent">nBonds</a>
+  <span class="SRScope">ccp4srs::Index</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_nentries">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_base.html#a863fd5090d78f3bada7f351dd2f33859" target="_parent">nEntries</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_nnonhatoms">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_index.html#aa97eb5251314eeb77e5acd2af72ce1aa" target="_parent">nNonHAtoms</a>
+  <span class="SRScope">ccp4srs::Index</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/variables_6f.html ccp4srs/doc-html/html/search/variables_6f.html
--- ccp4srs-old/doc-html/html/search/variables_6f.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/variables_6f.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,44 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_object">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_container.html#a25a4ad3660f2ef6760c949be2c1372a8" target="_parent">object</a>
+  <span class="SRScope">ccp4srs::Container</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_offset">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../structccp4srs_1_1_m_p_file_pos.html#afb6853252f03dbbc698dea44b425d2d9" target="_parent">offset</a>
+  <span class="SRScope">ccp4srs::MPFilePos</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_oldatomname">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a45682b942f2f9262bc8fa1b5316a702b" target="_parent">oldAtomName</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_oldmonid">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a896cc0c3979b65913de25be2c2f75ec9" target="_parent">oldMonID</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/variables_70.html ccp4srs/doc-html/html/search/variables_70.html
--- ccp4srs-old/doc-html/html/search/variables_70.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/variables_70.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,80 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_pdb_5fx">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a49ff7aadab557a536541009606a2db12" target="_parent">pdb_x</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_pdb_5fy">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a901c15656be6fa36e191df297d25521d" target="_parent">pdb_y</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_pdb_5fz">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#ae33b2033023270f96202151aed27a710" target="_parent">pdb_z</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_pdbx_5fx">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#aec57c2566b6a42361a8215d7b15a7e29" target="_parent">pdbx_x</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_pdbx_5fy">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a1d138de5fa3e222554a95b796c246d40" target="_parent">pdbx_y</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_pdbx_5fz">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a424a6001bc93ea1c8256f9f1fb48a585" target="_parent">pdbx_z</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_plane_5fatoms">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classccp4srs_1_1_plane.html#a4c8155332953ddb6cf79acf018c98c85" target="_parent">plane_atoms</a>
+  <span class="SRScope">ccp4srs::Plane</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_plane_5fid">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classccp4srs_1_1_plane.html#afdfdff5528e19537d834061022c2b2bf" target="_parent">plane_id</a>
+  <span class="SRScope">ccp4srs::Plane</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_planes">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#a2f927ab2a3e517f9fe6cba6e89954cfe" target="_parent">planes</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_property">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#aa363093b5746f782b8c4e60a73ec6438" target="_parent">property</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/variables_72.html ccp4srs/doc-html/html/search/variables_72.html
--- ccp4srs-old/doc-html/html/search/variables_72.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/variables_72.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,26 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_rcsbatomname">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a198154f097c4f42a4ae1dd73d5394734" target="_parent">rcsbAtomName</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/variables_73.html ccp4srs/doc-html/html/search/variables_73.html
--- ccp4srs-old/doc-html/html/search/variables_73.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/variables_73.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,80 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_selhndacceptor">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../structccp4srs_1_1_d_a_sel_hnds.html#a6df62532c19c06870cb386b3e1d4cc3c" target="_parent">selHndAcceptor</a>
+  <span class="SRScope">ccp4srs::DASelHnds</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_selhnddonor">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../structccp4srs_1_1_d_a_sel_hnds.html#a0291cf6e8fc47959f00d5dfa536d4d3c" target="_parent">selHndDonor</a>
+  <span class="SRScope">ccp4srs::DASelHnds</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_selhndhydrogen">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../structccp4srs_1_1_d_a_sel_hnds.html#a0dd02cde05c05d8d5f1c99c55aa6e251" target="_parent">selHndHydrogen</a>
+  <span class="SRScope">ccp4srs::DASelHnds</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_selkey">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../structccp4srs_1_1_d_a_sel_hnds.html#ab9e53854d32fb72fb9003efc870354df" target="_parent">selKey</a>
+  <span class="SRScope">ccp4srs::DASelHnds</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_srsdir">
+ <div class="SREntry">
+  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classccp4srs_1_1_base.html#af3caa0403ce8a1c4489948fa4fc62b0c" target="_parent">srsDir</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_srsgraphfile">
+ <div class="SREntry">
+  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../namespaceccp4srs.html#a4132afa4ce21fdcd2ff268bf6e980cfc" target="_parent">srsGraphFile</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_srsindexfile">
+ <div class="SREntry">
+  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../namespaceccp4srs.html#a3f27798432992515be969c17425412d3" target="_parent">srsIndexFile</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_srsstructfile">
+ <div class="SREntry">
+  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../namespaceccp4srs.html#af51e5a096118e643d5fcf5490d44c6db" target="_parent">srsStructFile</a>
+  <span class="SRScope">ccp4srs</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_srsversion">
+ <div class="SREntry">
+  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="../classccp4srs_1_1_base.html#ad18087156761086530c1f01f3078f869" target="_parent">srsVersion</a>
+  <span class="SRScope">ccp4srs::Base</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_struct_5ftree">
+ <div class="SREntry">
+  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="../classccp4srs_1_1_monomer.html#aef8794097a333f1e4e20dd3d876f1432" target="_parent">struct_tree</a>
+  <span class="SRScope">ccp4srs::Monomer</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
+document.getElementById("Loading").style.display="none";
+document.getElementById("NoMatches").style.display="none";
+var searchResults = new SearchResults("searchResults");
+searchResults.Search();
+--></script>
+</div>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/search/variables_74.html ccp4srs/doc-html/html/search/variables_74.html
--- ccp4srs-old/doc-html/html/search/variables_74.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/variables_74.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,50 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html><head><title></title>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<link rel="stylesheet" type="text/css" href="search.css"/>
+<script type="text/javascript" src="search.js"></script>
+</head>
+<body class="SRPage">
+<div id="SRIndex">
+<div class="SRStatus" id="Loading">Loading...</div>
+<div class="SRResult" id="SR_torsion">
+ <div class="SREntry">
+  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="../classccp4srs_1_1_torsion.html#a68b1d2a3529f1b153db01830a6cde818" target="_parent">torsion</a>
+  <span class="SRScope">ccp4srs::Torsion</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_torsion_5fesd">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_torsion.html#a34011e29f9c0faa8bc15a31274dd27c3" target="_parent">torsion_esd</a>
+  <span class="SRScope">ccp4srs::Torsion</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_torsion_5fid">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_torsion.html#ab82fe72dc4fb966139befa1636f0c4bd" target="_parent">torsion_id</a>
+  <span class="SRScope">ccp4srs::Torsion</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_torsion_5fperiod">
+ <div class="SREntry">
+  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="../classccp4srs_1_1_torsion.html#a681cd0d538d13fa8d30dee2eb0c7df20" target="_parent">torsion_period</a>
+  <span class="SRScope">ccp4srs::Torsion</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_torsions">
+ <div class="SREntry">
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+  <span class="SRScope">ccp4srs::Monomer</span>
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--- ccp4srs-old/doc-html/html/search/variables_76.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/search/variables_76.html	2014-09-09 21:34:12.000000000 -0700
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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
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+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_vdwradius">
+ <div class="SREntry">
+  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classccp4srs_1_1_atom.html#a74216b4c442b716656e5a55e908cea11" target="_parent">vdwRadius</a>
+  <span class="SRScope">ccp4srs::Atom</span>
+ </div>
+</div>
+<div class="SRResult" id="SR_volume_5fsign">
+ <div class="SREntry">
+  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classccp4srs_1_1_chi_center.html#a6fc568ab5bcd12bc56b58d6b9f2933a1" target="_parent">volume_sign</a>
+  <span class="SRScope">ccp4srs::ChiCenter</span>
+ </div>
+</div>
+<div class="SRStatus" id="Searching">Searching...</div>
+<div class="SRStatus" id="NoMatches">No Matches</div>
+<script type="text/javascript"><!--
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diff -ruN ccp4srs-old/doc-html/html/structccp4srs_1_1_atom_pair-members.html ccp4srs/doc-html/html/structccp4srs_1_1_atom_pair-members.html
--- ccp4srs-old/doc-html/html/structccp4srs_1_1_atom_pair-members.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/structccp4srs_1_1_atom_pair-members.html	2014-09-09 21:34:12.000000000 -0700
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+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
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+<body onload='searchBox.OnSelectItem(0);'>
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+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
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+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
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+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>ccp4srs::AtomPair Member List</h1>  </div>
+</div>
+<div class="contents">
+This is the complete list of members for <a class="el" href="structccp4srs_1_1_atom_pair.html">ccp4srs::AtomPair</a>, including all inherited members.<table>
+  <tr class="memlist"><td><a class="el" href="structccp4srs_1_1_atom_pair.html#a0277f099acfa557ac20bf6fd3320bcaa">a1</a></td><td><a class="el" href="structccp4srs_1_1_atom_pair.html">ccp4srs::AtomPair</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="structccp4srs_1_1_atom_pair.html#a1f8f7df44905ac32088ccfcf1b80dda2">a2</a></td><td><a class="el" href="structccp4srs_1_1_atom_pair.html">ccp4srs::AtomPair</a></td><td></td></tr>
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+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
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diff -ruN ccp4srs-old/doc-html/html/structccp4srs_1_1_atom_pair.html ccp4srs/doc-html/html/structccp4srs_1_1_atom_pair.html
--- ccp4srs-old/doc-html/html/structccp4srs_1_1_atom_pair.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/structccp4srs_1_1_atom_pair.html	2014-09-09 21:34:12.000000000 -0700
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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: ccp4srs::AtomPair Struct Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
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+<!-- Generated by Doxygen 1.7.2 -->
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+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
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+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
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+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
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+    <ul>
+      <li><a class="el" href="namespaceccp4srs.html">ccp4srs</a>      </li>
+      <li><a class="el" href="structccp4srs_1_1_atom_pair.html">AtomPair</a>      </li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="summary">
+<a href="#pub-attribs">Public Attributes</a>  </div>
+  <div class="headertitle">
+<h1>ccp4srs::AtomPair Struct Reference</h1>  </div>
+</div>
+<div class="contents">
+<!-- doxytag: class="ccp4srs::AtomPair" -->
+<p><code>#include &lt;<a class="el" href="ccp4srs__types_8h_source.html">ccp4srs_types.h</a>&gt;</code></p>
+
+<p><a href="structccp4srs_1_1_atom_pair-members.html">List of all members.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="pub-attribs"></a>
+Public Attributes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::PAtom&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structccp4srs_1_1_atom_pair.html#a0277f099acfa557ac20bf6fd3320bcaa">a1</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::PAtom&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structccp4srs_1_1_atom_pair.html#a1f8f7df44905ac32088ccfcf1b80dda2">a2</a></td></tr>
+</table>
+<hr/><h2>Member Data Documentation</h2>
+<a class="anchor" id="a0277f099acfa557ac20bf6fd3320bcaa"></a><!-- doxytag: member="ccp4srs::AtomPair::a1" ref="a0277f099acfa557ac20bf6fd3320bcaa" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::PAtom <a class="el" href="structccp4srs_1_1_atom_pair.html#a0277f099acfa557ac20bf6fd3320bcaa">ccp4srs::AtomPair::a1</a></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a1f8f7df44905ac32088ccfcf1b80dda2"></a><!-- doxytag: member="ccp4srs::AtomPair::a2" ref="a1f8f7df44905ac32088ccfcf1b80dda2" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::PAtom <a class="el" href="structccp4srs_1_1_atom_pair.html#a1f8f7df44905ac32088ccfcf1b80dda2">ccp4srs::AtomPair::a2</a></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/>The documentation for this struct was generated from the following file:<ul>
+<li>src/<a class="el" href="ccp4srs__types_8h_source.html">ccp4srs_types.h</a></li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
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+
+<!-- iframe showing the search results (closed by default) -->
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+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
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+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
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diff -ruN ccp4srs-old/doc-html/html/structccp4srs_1_1_d_a_sel_hnds-members.html ccp4srs/doc-html/html/structccp4srs_1_1_d_a_sel_hnds-members.html
--- ccp4srs-old/doc-html/html/structccp4srs_1_1_d_a_sel_hnds-members.html	1969-12-31 16:00:00.000000000 -0800
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@@ -0,0 +1,82 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
+<script type="text/javascript"><!--
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
+               onblur="searchBox.OnSearchFieldFocus(false)" 
+               onkeyup="searchBox.OnSearchFieldChange(event)"/>
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+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>ccp4srs::DASelHnds Member List</h1>  </div>
+</div>
+<div class="contents">
+This is the complete list of members for <a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html">ccp4srs::DASelHnds</a>, including all inherited members.<table>
+  <tr class="memlist"><td><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a582873aa43d2c8708e99db1485013bef">deleteSelections</a>(mmdb::PManager MMDB)</td><td><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html">ccp4srs::DASelHnds</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a3e8624665274bf47da9408f3b21f35d8">getNewHandles</a>(mmdb::PManager MMDB)</td><td><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html">ccp4srs::DASelHnds</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#aaca5f89914d27b9869b6f082931c53d5">makeSelIndexes</a>(mmdb::PManager MMDB)</td><td><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html">ccp4srs::DASelHnds</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a6df62532c19c06870cb386b3e1d4cc3c">selHndAcceptor</a></td><td><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html">ccp4srs::DASelHnds</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a0291cf6e8fc47959f00d5dfa536d4d3c">selHndDonor</a></td><td><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html">ccp4srs::DASelHnds</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a0dd02cde05c05d8d5f1c99c55aa6e251">selHndHydrogen</a></td><td><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html">ccp4srs::DASelHnds</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#ab9e53854d32fb72fb9003efc870354df">selKey</a></td><td><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html">ccp4srs::DASelHnds</a></td><td></td></tr>
+</table></div>
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+
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+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/structccp4srs_1_1_d_a_sel_hnds.html ccp4srs/doc-html/html/structccp4srs_1_1_d_a_sel_hnds.html
--- ccp4srs-old/doc-html/html/structccp4srs_1_1_d_a_sel_hnds.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/structccp4srs_1_1_d_a_sel_hnds.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,209 @@
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: ccp4srs::DASelHnds Struct Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
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+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
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+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="navpath">
+    <ul>
+      <li><a class="el" href="namespaceccp4srs.html">ccp4srs</a>      </li>
+      <li><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html">DASelHnds</a>      </li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pub-attribs">Public Attributes</a>  </div>
+  <div class="headertitle">
+<h1>ccp4srs::DASelHnds Struct Reference</h1>  </div>
+</div>
+<div class="contents">
+<!-- doxytag: class="ccp4srs::DASelHnds" -->
+<p><code>#include &lt;<a class="el" href="ccp4srs__types_8h_source.html">ccp4srs_types.h</a>&gt;</code></p>
+
+<p><a href="structccp4srs_1_1_d_a_sel_hnds-members.html">List of all members.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a3e8624665274bf47da9408f3b21f35d8">getNewHandles</a> (mmdb::PManager MMDB)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#aaca5f89914d27b9869b6f082931c53d5">makeSelIndexes</a> (mmdb::PManager MMDB)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a582873aa43d2c8708e99db1485013bef">deleteSelections</a> (mmdb::PManager MMDB)</td></tr>
+<tr><td colspan="2"><h2><a name="pub-attribs"></a>
+Public Attributes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a0291cf6e8fc47959f00d5dfa536d4d3c">selHndDonor</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a6df62532c19c06870cb386b3e1d4cc3c">selHndAcceptor</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a0dd02cde05c05d8d5f1c99c55aa6e251">selHndHydrogen</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::SELECTION_KEY&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#ab9e53854d32fb72fb9003efc870354df">selKey</a></td></tr>
+</table>
+<hr/><h2>Member Function Documentation</h2>
+<a class="anchor" id="a582873aa43d2c8708e99db1485013bef"></a><!-- doxytag: member="ccp4srs::DASelHnds::deleteSelections" ref="a582873aa43d2c8708e99db1485013bef" args="(mmdb::PManager MMDB)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::DASelHnds::deleteSelections </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::PManager&#160;</td>
+          <td class="paramname"> <em>MMDB</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a3e8624665274bf47da9408f3b21f35d8"></a><!-- doxytag: member="ccp4srs::DASelHnds::getNewHandles" ref="a3e8624665274bf47da9408f3b21f35d8" args="(mmdb::PManager MMDB)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::DASelHnds::getNewHandles </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::PManager&#160;</td>
+          <td class="paramname"> <em>MMDB</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="aaca5f89914d27b9869b6f082931c53d5"></a><!-- doxytag: member="ccp4srs::DASelHnds::makeSelIndexes" ref="aaca5f89914d27b9869b6f082931c53d5" args="(mmdb::PManager MMDB)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::DASelHnds::makeSelIndexes </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::PManager&#160;</td>
+          <td class="paramname"> <em>MMDB</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Data Documentation</h2>
+<a class="anchor" id="a6df62532c19c06870cb386b3e1d4cc3c"></a><!-- doxytag: member="ccp4srs::DASelHnds::selHndAcceptor" ref="a6df62532c19c06870cb386b3e1d4cc3c" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a6df62532c19c06870cb386b3e1d4cc3c">ccp4srs::DASelHnds::selHndAcceptor</a></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a0291cf6e8fc47959f00d5dfa536d4d3c"></a><!-- doxytag: member="ccp4srs::DASelHnds::selHndDonor" ref="a0291cf6e8fc47959f00d5dfa536d4d3c" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a0291cf6e8fc47959f00d5dfa536d4d3c">ccp4srs::DASelHnds::selHndDonor</a></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a0dd02cde05c05d8d5f1c99c55aa6e251"></a><!-- doxytag: member="ccp4srs::DASelHnds::selHndHydrogen" ref="a0dd02cde05c05d8d5f1c99c55aa6e251" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">int <a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#a0dd02cde05c05d8d5f1c99c55aa6e251">ccp4srs::DASelHnds::selHndHydrogen</a></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ab9e53854d32fb72fb9003efc870354df"></a><!-- doxytag: member="ccp4srs::DASelHnds::selKey" ref="ab9e53854d32fb72fb9003efc870354df" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::SELECTION_KEY <a class="el" href="structccp4srs_1_1_d_a_sel_hnds.html#ab9e53854d32fb72fb9003efc870354df">ccp4srs::DASelHnds::selKey</a></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/>The documentation for this struct was generated from the following files:<ul>
+<li>src/<a class="el" href="ccp4srs__types_8h_source.html">ccp4srs_types.h</a></li>
+<li>src/<a class="el" href="ccp4srs__types_8cpp.html">ccp4srs_types.cpp</a></li>
+</ul>
+</div>
+<!--- window showing the filter options -->
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+
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+<a href="http://www.doxygen.org/index.html">
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diff -ruN ccp4srs-old/doc-html/html/structccp4srs_1_1_m_p_file_pos-members.html ccp4srs/doc-html/html/structccp4srs_1_1_m_p_file_pos-members.html
--- ccp4srs-old/doc-html/html/structccp4srs_1_1_m_p_file_pos-members.html	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/structccp4srs_1_1_m_p_file_pos-members.html	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,80 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javaScript" src="search/search.js"></script>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
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+<body onload='searchBox.OnSelectItem(0);'>
+<!-- Generated by Doxygen 1.7.2 -->
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+--></script>
+<div class="navigation" id="top">
+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+      <li><a href="files.html"><span>Files</span></a></li>
+      <li id="searchli">
+        <div id="MSearchBox" class="MSearchBoxInactive">
+        <span class="left">
+          <img id="MSearchSelect" src="search/mag_sel.png"
+               onmouseover="return searchBox.OnSearchSelectShow()"
+               onmouseout="return searchBox.OnSearchSelectHide()"
+               alt=""/>
+          <input type="text" id="MSearchField" value="Search" accesskey="S"
+               onfocus="searchBox.OnSearchFieldFocus(true)" 
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+            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+          </span>
+        </div>
+      </li>
+    </ul>
+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="headertitle">
+<h1>ccp4srs::MPFilePos Member List</h1>  </div>
+</div>
+<div class="contents">
+This is the complete list of members for <a class="el" href="structccp4srs_1_1_m_p_file_pos.html">ccp4srs::MPFilePos</a>, including all inherited members.<table>
+  <tr class="memlist"><td><a class="el" href="structccp4srs_1_1_m_p_file_pos.html#ab84443c24cd9b322d81f2e165af4bd8a">chunkNo</a></td><td><a class="el" href="structccp4srs_1_1_m_p_file_pos.html">ccp4srs::MPFilePos</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="structccp4srs_1_1_m_p_file_pos.html#a7f60e91b825a15d3def175dcdb71139d">Copy</a>(RMPFilePos dbf_pos)</td><td><a class="el" href="structccp4srs_1_1_m_p_file_pos.html">ccp4srs::MPFilePos</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="structccp4srs_1_1_m_p_file_pos.html#afb6853252f03dbbc698dea44b425d2d9">offset</a></td><td><a class="el" href="structccp4srs_1_1_m_p_file_pos.html">ccp4srs::MPFilePos</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="structccp4srs_1_1_m_p_file_pos.html#a8351d37471b7cdab264a91bb1a92db1c">read</a>(mmdb::io::RFile f)</td><td><a class="el" href="structccp4srs_1_1_m_p_file_pos.html">ccp4srs::MPFilePos</a></td><td></td></tr>
+  <tr class="memlist"><td><a class="el" href="structccp4srs_1_1_m_p_file_pos.html#a6e1a52091171d7462c6b8334f1483998">write</a>(mmdb::io::RFile f)</td><td><a class="el" href="structccp4srs_1_1_m_p_file_pos.html">ccp4srs::MPFilePos</a></td><td></td></tr>
+</table></div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
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+
+<!-- iframe showing the search results (closed by default) -->
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+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
diff -ruN ccp4srs-old/doc-html/html/structccp4srs_1_1_m_p_file_pos.html ccp4srs/doc-html/html/structccp4srs_1_1_m_p_file_pos.html
--- ccp4srs-old/doc-html/html/structccp4srs_1_1_m_p_file_pos.html	1969-12-31 16:00:00.000000000 -0800
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<title>ccp4srs: ccp4srs::MPFilePos Struct Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
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+  <div class="tabs">
+    <ul class="tablist">
+      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
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+  </div>
+  <div class="tabs2">
+    <ul class="tablist">
+      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
+      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
+      <li><a href="hierarchy.html"><span>Class&#160;Hierarchy</span></a></li>
+      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
+    </ul>
+  </div>
+  <div class="navpath">
+    <ul>
+      <li><a class="el" href="namespaceccp4srs.html">ccp4srs</a>      </li>
+      <li><a class="el" href="structccp4srs_1_1_m_p_file_pos.html">MPFilePos</a>      </li>
+    </ul>
+  </div>
+</div>
+<div class="header">
+  <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#pub-attribs">Public Attributes</a>  </div>
+  <div class="headertitle">
+<h1>ccp4srs::MPFilePos Struct Reference</h1>  </div>
+</div>
+<div class="contents">
+<!-- doxytag: class="ccp4srs::MPFilePos" -->
+<p><code>#include &lt;<a class="el" href="mpfile___8h_source.html">mpfile_.h</a>&gt;</code></p>
+
+<p><a href="structccp4srs_1_1_m_p_file_pos-members.html">List of all members.</a></p>
+<table class="memberdecls">
+<tr><td colspan="2"><h2><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structccp4srs_1_1_m_p_file_pos.html#a7f60e91b825a15d3def175dcdb71139d">Copy</a> (RMPFilePos dbf_pos)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structccp4srs_1_1_m_p_file_pos.html#a6e1a52091171d7462c6b8334f1483998">write</a> (mmdb::io::RFile f)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structccp4srs_1_1_m_p_file_pos.html#a8351d37471b7cdab264a91bb1a92db1c">read</a> (mmdb::io::RFile f)</td></tr>
+<tr><td colspan="2"><h2><a name="pub-attribs"></a>
+Public Attributes</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">mmdb::byte&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structccp4srs_1_1_m_p_file_pos.html#ab84443c24cd9b322d81f2e165af4bd8a">chunkNo</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">long&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structccp4srs_1_1_m_p_file_pos.html#afb6853252f03dbbc698dea44b425d2d9">offset</a></td></tr>
+</table>
+<hr/><h2>Member Function Documentation</h2>
+<a class="anchor" id="a7f60e91b825a15d3def175dcdb71139d"></a><!-- doxytag: member="ccp4srs::MPFilePos::Copy" ref="a7f60e91b825a15d3def175dcdb71139d" args="(RMPFilePos dbf_pos)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::MPFilePos::Copy </td>
+          <td>(</td>
+          <td class="paramtype">RMPFilePos&#160;</td>
+          <td class="paramname"> <em>dbf_pos</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a8351d37471b7cdab264a91bb1a92db1c"></a><!-- doxytag: member="ccp4srs::MPFilePos::read" ref="a8351d37471b7cdab264a91bb1a92db1c" args="(mmdb::io::RFile f)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::MPFilePos::read </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::io::RFile&#160;</td>
+          <td class="paramname"> <em>f</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="a6e1a52091171d7462c6b8334f1483998"></a><!-- doxytag: member="ccp4srs::MPFilePos::write" ref="a6e1a52091171d7462c6b8334f1483998" args="(mmdb::io::RFile f)" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void ccp4srs::MPFilePos::write </td>
+          <td>(</td>
+          <td class="paramtype">mmdb::io::RFile&#160;</td>
+          <td class="paramname"> <em>f</em>&#160;)</td>
+          <td></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/><h2>Member Data Documentation</h2>
+<a class="anchor" id="ab84443c24cd9b322d81f2e165af4bd8a"></a><!-- doxytag: member="ccp4srs::MPFilePos::chunkNo" ref="ab84443c24cd9b322d81f2e165af4bd8a" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">mmdb::byte <a class="el" href="structccp4srs_1_1_m_p_file_pos.html#ab84443c24cd9b322d81f2e165af4bd8a">ccp4srs::MPFilePos::chunkNo</a></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="afb6853252f03dbbc698dea44b425d2d9"></a><!-- doxytag: member="ccp4srs::MPFilePos::offset" ref="afb6853252f03dbbc698dea44b425d2d9" args="" -->
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">long <a class="el" href="structccp4srs_1_1_m_p_file_pos.html#afb6853252f03dbbc698dea44b425d2d9">ccp4srs::MPFilePos::offset</a></td>
+        </tr>
+      </table>
+</div>
+<div class="memdoc">
+
+</div>
+</div>
+<hr/>The documentation for this struct was generated from the following files:<ul>
+<li>src/<a class="el" href="mpfile___8h_source.html">mpfile_.h</a></li>
+<li>src/<a class="el" href="mpfile___8cpp.html">mpfile_.cpp</a></li>
+</ul>
+</div>
+<!--- window showing the filter options -->
+<div id="MSearchSelectWindow"
+     onmouseover="return searchBox.OnSearchSelectShow()"
+     onmouseout="return searchBox.OnSearchSelectHide()"
+     onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Defines</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
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+        name="MSearchResults" id="MSearchResults">
+</iframe>
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+
+<hr class="footer"/><address class="footer"><small>Generated on Wed Sep 25 2013 15:32:21 for ccp4srs by&#160;
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.7.2 </small></address>
+</body>
+</html>
Binary files ccp4srs-old/doc-html/html/tab_a.png and ccp4srs/doc-html/html/tab_a.png differ
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diff -ruN ccp4srs-old/doc-html/html/tabs.css ccp4srs/doc-html/html/tabs.css
--- ccp4srs-old/doc-html/html/tabs.css	1969-12-31 16:00:00.000000000 -0800
+++ ccp4srs/doc-html/html/tabs.css	2014-09-09 21:34:12.000000000 -0700
@@ -0,0 +1,59 @@
+.tabs, .tabs2, .tabs3 {
+    background-image: url('tab_b.png');
+    width: 100%;
+    z-index: 101;
+    font-size: 13px;
+}
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+    font-size: 9px;
+}
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+    margin: 0;
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+}
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+    float: left;
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+    background-image: url('tab_b.png');
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+}
diff -ruN ccp4srs-old/m4/libtool.m4 ccp4srs/m4/libtool.m4
--- ccp4srs-old/m4/libtool.m4	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/m4/libtool.m4	2014-09-09 21:34:12.000000000 -0700
@@ -1,8 +1,8 @@
 # libtool.m4 - Configure libtool for the host system. -*-Autoconf-*-
 #
 #   Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005,
-#                 2006, 2007, 2008, 2009, 2010 Free Software Foundation,
-#                 Inc.
+#                 2006, 2007, 2008, 2009, 2010, 2011 Free Software
+#                 Foundation, Inc.
 #   Written by Gordon Matzigkeit, 1996
 #
 # This file is free software; the Free Software Foundation gives
@@ -11,8 +11,8 @@
 
 m4_define([_LT_COPYING], [dnl
 #   Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005,
-#                 2006, 2007, 2008, 2009, 2010 Free Software Foundation,
-#                 Inc.
+#                 2006, 2007, 2008, 2009, 2010, 2011 Free Software
+#                 Foundation, Inc.
 #   Written by Gordon Matzigkeit, 1996
 #
 #   This file is part of GNU Libtool.
@@ -146,6 +146,8 @@
 AC_REQUIRE([_LT_PREPARE_SED_QUOTE_VARS])dnl
 AC_REQUIRE([_LT_PROG_ECHO_BACKSLASH])dnl
 
+_LT_DECL([], [PATH_SEPARATOR], [1], [The PATH separator for the build system])dnl
+dnl
 _LT_DECL([], [host_alias], [0], [The host system])dnl
 _LT_DECL([], [host], [0])dnl
 _LT_DECL([], [host_os], [0])dnl
@@ -637,7 +639,7 @@
 m4_ifset([AC_PACKAGE_VERSION], [ AC_PACKAGE_VERSION])
 configured by $[0], generated by m4_PACKAGE_STRING.
 
-Copyright (C) 2010 Free Software Foundation, Inc.
+Copyright (C) 2011 Free Software Foundation, Inc.
 This config.lt script is free software; the Free Software Foundation
 gives unlimited permision to copy, distribute and modify it."
 
@@ -801,6 +803,7 @@
 m4_case([$1],
   [C],			[_LT_LANG(C)],
   [C++],		[_LT_LANG(CXX)],
+  [Go],			[_LT_LANG(GO)],
   [Java],		[_LT_LANG(GCJ)],
   [Fortran 77],		[_LT_LANG(F77)],
   [Fortran],		[_LT_LANG(FC)],
@@ -822,6 +825,31 @@
 ])# _LT_LANG
 
 
+m4_ifndef([AC_PROG_GO], [
+############################################################
+# NOTE: This macro has been submitted for inclusion into   #
+#  GNU Autoconf as AC_PROG_GO.  When it is available in    #
+#  a released version of Autoconf we should remove this    #
+#  macro and use it instead.                               #
+############################################################
+m4_defun([AC_PROG_GO],
+[AC_LANG_PUSH(Go)dnl
+AC_ARG_VAR([GOC],     [Go compiler command])dnl
+AC_ARG_VAR([GOFLAGS], [Go compiler flags])dnl
+_AC_ARG_VAR_LDFLAGS()dnl
+AC_CHECK_TOOL(GOC, gccgo)
+if test -z "$GOC"; then
+  if test -n "$ac_tool_prefix"; then
+    AC_CHECK_PROG(GOC, [${ac_tool_prefix}gccgo], [${ac_tool_prefix}gccgo])
+  fi
+fi
+if test -z "$GOC"; then
+  AC_CHECK_PROG(GOC, gccgo, gccgo, false)
+fi
+])#m4_defun
+])#m4_ifndef
+
+
 # _LT_LANG_DEFAULT_CONFIG
 # -----------------------
 m4_defun([_LT_LANG_DEFAULT_CONFIG],
@@ -852,6 +880,10 @@
        m4_ifdef([LT_PROG_GCJ],
 	[m4_define([LT_PROG_GCJ], defn([LT_PROG_GCJ])[LT_LANG(GCJ)])])])])])
 
+AC_PROVIDE_IFELSE([AC_PROG_GO],
+  [LT_LANG(GO)],
+  [m4_define([AC_PROG_GO], defn([AC_PROG_GO])[LT_LANG(GO)])])
+
 AC_PROVIDE_IFELSE([LT_PROG_RC],
   [LT_LANG(RC)],
   [m4_define([LT_PROG_RC], defn([LT_PROG_RC])[LT_LANG(RC)])])
@@ -954,7 +986,13 @@
 	$LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \
 	  -dynamiclib -Wl,-single_module conftest.c 2>conftest.err
         _lt_result=$?
-	if test -f libconftest.dylib && test ! -s conftest.err && test $_lt_result = 0; then
+	# If there is a non-empty error log, and "single_module"
+	# appears in it, assume the flag caused a linker warning
+        if test -s conftest.err && $GREP single_module conftest.err; then
+	  cat conftest.err >&AS_MESSAGE_LOG_FD
+	# Otherwise, if the output was created with a 0 exit code from
+	# the compiler, it worked.
+	elif test -f libconftest.dylib && test $_lt_result -eq 0; then
 	  lt_cv_apple_cc_single_mod=yes
 	else
 	  cat conftest.err >&AS_MESSAGE_LOG_FD
@@ -962,6 +1000,7 @@
 	rm -rf libconftest.dylib*
 	rm -f conftest.*
       fi])
+
     AC_CACHE_CHECK([for -exported_symbols_list linker flag],
       [lt_cv_ld_exported_symbols_list],
       [lt_cv_ld_exported_symbols_list=no
@@ -973,6 +1012,7 @@
 	[lt_cv_ld_exported_symbols_list=no])
 	LDFLAGS="$save_LDFLAGS"
     ])
+
     AC_CACHE_CHECK([for -force_load linker flag],[lt_cv_ld_force_load],
       [lt_cv_ld_force_load=no
       cat > conftest.c << _LT_EOF
@@ -990,7 +1030,9 @@
       echo "$LTCC $LTCFLAGS $LDFLAGS -o conftest conftest.c -Wl,-force_load,./libconftest.a" >&AS_MESSAGE_LOG_FD
       $LTCC $LTCFLAGS $LDFLAGS -o conftest conftest.c -Wl,-force_load,./libconftest.a 2>conftest.err
       _lt_result=$?
-      if test -f conftest && test ! -s conftest.err && test $_lt_result = 0 && $GREP forced_load conftest 2>&1 >/dev/null; then
+      if test -s conftest.err && $GREP force_load conftest.err; then
+	cat conftest.err >&AS_MESSAGE_LOG_FD
+      elif test -f conftest && test $_lt_result -eq 0 && $GREP forced_load conftest >/dev/null 2>&1 ; then
 	lt_cv_ld_force_load=yes
       else
 	cat conftest.err >&AS_MESSAGE_LOG_FD
@@ -1035,8 +1077,8 @@
 ])
 
 
-# _LT_DARWIN_LINKER_FEATURES
-# --------------------------
+# _LT_DARWIN_LINKER_FEATURES([TAG])
+# ---------------------------------
 # Checks for linker and compiler features on darwin
 m4_defun([_LT_DARWIN_LINKER_FEATURES],
 [
@@ -1047,6 +1089,8 @@
   _LT_TAGVAR(hardcode_shlibpath_var, $1)=unsupported
   if test "$lt_cv_ld_force_load" = "yes"; then
     _LT_TAGVAR(whole_archive_flag_spec, $1)='`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience ${wl}-force_load,$conv\"; done; func_echo_all \"$new_convenience\"`'
+    m4_case([$1], [F77], [_LT_TAGVAR(compiler_needs_object, $1)=yes],
+                  [FC],  [_LT_TAGVAR(compiler_needs_object, $1)=yes])
   else
     _LT_TAGVAR(whole_archive_flag_spec, $1)=''
   fi
@@ -1330,14 +1374,27 @@
     CFLAGS="$SAVE_CFLAGS"
   fi
   ;;
-sparc*-*solaris*)
+*-*solaris*)
   # Find out which ABI we are using.
   echo 'int i;' > conftest.$ac_ext
   if AC_TRY_EVAL(ac_compile); then
     case `/usr/bin/file conftest.o` in
     *64-bit*)
       case $lt_cv_prog_gnu_ld in
-      yes*) LD="${LD-ld} -m elf64_sparc" ;;
+      yes*)
+        case $host in
+        i?86-*-solaris*)
+          LD="${LD-ld} -m elf_x86_64"
+          ;;
+        sparc*-*-solaris*)
+          LD="${LD-ld} -m elf64_sparc"
+          ;;
+        esac
+        # GNU ld 2.21 introduced _sol2 emulations.  Use them if available.
+        if ${LD-ld} -V | grep _sol2 >/dev/null 2>&1; then
+          LD="${LD-ld}_sol2"
+        fi
+        ;;
       *)
 	if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then
 	  LD="${LD-ld} -64"
@@ -1414,13 +1471,13 @@
 if test -n "$RANLIB"; then
   case $host_os in
   openbsd*)
-    old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib"
+    old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$tool_oldlib"
     ;;
   *)
-    old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib"
+    old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$tool_oldlib"
     ;;
   esac
-  old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib"
+  old_archive_cmds="$old_archive_cmds~\$RANLIB \$tool_oldlib"
 fi
 
 case $host_os in
@@ -1600,6 +1657,11 @@
     lt_cv_sys_max_cmd_len=196608
     ;;
 
+  os2*)
+    # The test takes a long time on OS/2.
+    lt_cv_sys_max_cmd_len=8192
+    ;;
+
   osf*)
     # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure
     # due to this test when exec_disable_arg_limit is 1 on Tru64. It is not
@@ -1639,7 +1701,7 @@
       # If test is not a shell built-in, we'll probably end up computing a
       # maximum length that is only half of the actual maximum length, but
       # we can't tell.
-      while { test "X"`func_fallback_echo "$teststring$teststring" 2>/dev/null` \
+      while { test "X"`env echo "$teststring$teststring" 2>/dev/null` \
 	         = "X$teststring$teststring"; } >/dev/null 2>&1 &&
 	      test $i != 17 # 1/2 MB should be enough
       do
@@ -2185,7 +2247,7 @@
 
 case $host_os in
 aix3*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
   shlibpath_var=LIBPATH
 
@@ -2194,7 +2256,7 @@
   ;;
 
 aix[[4-9]]*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   hardcode_into_libs=yes
@@ -2259,7 +2321,7 @@
   ;;
 
 bsdi[[45]]*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_version=no
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
   soname_spec='${libname}${release}${shared_ext}$major'
@@ -2398,7 +2460,7 @@
   ;;
 
 dgux*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
@@ -2406,10 +2468,6 @@
   shlibpath_var=LD_LIBRARY_PATH
   ;;
 
-freebsd1*)
-  dynamic_linker=no
-  ;;
-
 freebsd* | dragonfly*)
   # DragonFly does not have aout.  When/if they implement a new
   # versioning mechanism, adjust this.
@@ -2417,7 +2475,7 @@
     objformat=`/usr/bin/objformat`
   else
     case $host_os in
-    freebsd[[123]]*) objformat=aout ;;
+    freebsd[[23]].*) objformat=aout ;;
     *) objformat=elf ;;
     esac
   fi
@@ -2435,7 +2493,7 @@
   esac
   shlibpath_var=LD_LIBRARY_PATH
   case $host_os in
-  freebsd2*)
+  freebsd2.*)
     shlibpath_overrides_runpath=yes
     ;;
   freebsd3.[[01]]* | freebsdelf3.[[01]]*)
@@ -2455,17 +2513,18 @@
   ;;
 
 gnu*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
   soname_spec='${libname}${release}${shared_ext}$major'
   shlibpath_var=LD_LIBRARY_PATH
+  shlibpath_overrides_runpath=no
   hardcode_into_libs=yes
   ;;
 
 haiku*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   dynamic_linker="$host_os runtime_loader"
@@ -2526,7 +2585,7 @@
   ;;
 
 interix[[3-9]]*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
@@ -2542,7 +2601,7 @@
     nonstopux*) version_type=nonstopux ;;
     *)
 	if test "$lt_cv_prog_gnu_ld" = yes; then
-		version_type=linux
+		version_type=linux # correct to gnu/linux during the next big refactor
 	else
 		version_type=irix
 	fi ;;
@@ -2579,9 +2638,9 @@
   dynamic_linker=no
   ;;
 
-# This must be Linux ELF.
+# This must be glibc/ELF.
 linux* | k*bsd*-gnu | kopensolaris*-gnu)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
@@ -2610,14 +2669,10 @@
   # before this can be enabled.
   hardcode_into_libs=yes
 
-  # Add ABI-specific directories to the system library path.
-  sys_lib_dlsearch_path_spec="/lib64 /usr/lib64 /lib /usr/lib"
-
   # Append ld.so.conf contents to the search path
   if test -f /etc/ld.so.conf; then
     lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \[$]2)); skip = 1; } { if (!skip) print \[$]0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[	 ]*hwcap[	 ]/d;s/[:,	]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;s/"//g;/^$/d' | tr '\n' ' '`
-    sys_lib_dlsearch_path_spec="$sys_lib_dlsearch_path_spec $lt_ld_extra"
-
+    sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
   fi
 
   # We used to test for /lib/ld.so.1 and disable shared libraries on
@@ -2648,7 +2703,7 @@
   ;;
 
 newsos6)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
   shlibpath_var=LD_LIBRARY_PATH
   shlibpath_overrides_runpath=yes
@@ -2717,7 +2772,7 @@
   ;;
 
 solaris*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
@@ -2742,7 +2797,7 @@
   ;;
 
 sysv4 | sysv4.3*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
   soname_spec='${libname}${release}${shared_ext}$major'
   shlibpath_var=LD_LIBRARY_PATH
@@ -2766,7 +2821,7 @@
 
 sysv4*MP*)
   if test -d /usr/nec ;then
-    version_type=linux
+    version_type=linux # correct to gnu/linux during the next big refactor
     library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
     soname_spec='$libname${shared_ext}.$major'
     shlibpath_var=LD_LIBRARY_PATH
@@ -2797,7 +2852,7 @@
 
 tpf*)
   # TPF is a cross-target only.  Preferred cross-host = GNU/Linux.
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   need_lib_prefix=no
   need_version=no
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
@@ -2807,7 +2862,7 @@
   ;;
 
 uts4*)
-  version_type=linux
+  version_type=linux # correct to gnu/linux during the next big refactor
   library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
   soname_spec='${libname}${release}${shared_ext}$major'
   shlibpath_var=LD_LIBRARY_PATH
@@ -3229,7 +3284,7 @@
   lt_cv_deplibs_check_method=pass_all
   ;;
 
-# This must be Linux ELF.
+# This must be glibc/ELF.
 linux* | k*bsd*-gnu | kopensolaris*-gnu)
   lt_cv_deplibs_check_method=pass_all
   ;;
@@ -3649,6 +3704,7 @@
     # which start with @ or ?.
     lt_cv_sys_global_symbol_pipe="$AWK ['"\
 "     {last_section=section; section=\$ 3};"\
+"     /^COFF SYMBOL TABLE/{for(i in hide) delete hide[i]};"\
 "     /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\
 "     \$ 0!~/External *\|/{next};"\
 "     / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\
@@ -4233,7 +4289,9 @@
     case $cc_basename in
     nvcc*) # Cuda Compiler Driver 2.2
       _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Xlinker '
-      _LT_TAGVAR(lt_prog_compiler_pic, $1)='-Xcompiler -fPIC'
+      if test -n "$_LT_TAGVAR(lt_prog_compiler_pic, $1)"; then
+        _LT_TAGVAR(lt_prog_compiler_pic, $1)="-Xcompiler $_LT_TAGVAR(lt_prog_compiler_pic, $1)"
+      fi
       ;;
     esac
   else
@@ -4325,18 +4383,33 @@
 	;;
       *)
 	case `$CC -V 2>&1 | sed 5q` in
-	*Sun\ F* | *Sun*Fortran*)
+	*Sun\ Ceres\ Fortran* | *Sun*Fortran*\ [[1-7]].* | *Sun*Fortran*\ 8.[[0-3]]*)
 	  # Sun Fortran 8.3 passes all unrecognized flags to the linker
 	  _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
 	  _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
 	  _LT_TAGVAR(lt_prog_compiler_wl, $1)=''
 	  ;;
+	*Sun\ F* | *Sun*Fortran*)
+	  _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+	  _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+	  _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld '
+	  ;;
 	*Sun\ C*)
 	  # Sun C 5.9
 	  _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
 	  _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
 	  _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
 	  ;;
+        *Intel*\ [[CF]]*Compiler*)
+	  _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+	  _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+	  _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+	  ;;
+	*Portland\ Group*)
+	  _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+	  _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fpic'
+	  _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+	  ;;
 	esac
 	;;
       esac
@@ -4496,7 +4569,9 @@
     ;;
   cygwin* | mingw* | cegcc*)
     case $cc_basename in
-    cl*) ;;
+    cl*)
+      _LT_TAGVAR(exclude_expsyms, $1)='_NULL_IMPORT_DESCRIPTOR|_IMPORT_DESCRIPTOR_.*'
+      ;;
     *)
       _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[[BCDGRS]][[ ]]/s/.*[[ ]]\([[^ ]]*\)/\1 DATA/;s/^.*[[ ]]__nm__\([[^ ]]*\)[[ ]][[^ ]]*/\1 DATA/;/^I[[ ]]/d;/^[[AITW]][[ ]]/s/.* //'\'' | sort | uniq > $export_symbols'
       _LT_TAGVAR(exclude_expsyms, $1)=['[_]+GLOBAL_OFFSET_TABLE_|[_]+GLOBAL__[FID]_.*|[_]+head_[A-Za-z0-9_]+_dll|[A-Za-z0-9_]+_dll_iname']
@@ -4521,7 +4596,6 @@
   _LT_TAGVAR(hardcode_direct, $1)=no
   _LT_TAGVAR(hardcode_direct_absolute, $1)=no
   _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
-  _LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
   _LT_TAGVAR(hardcode_libdir_separator, $1)=
   _LT_TAGVAR(hardcode_minus_L, $1)=no
   _LT_TAGVAR(hardcode_shlibpath_var, $1)=unsupported
@@ -4772,8 +4846,7 @@
 	xlf* | bgf* | bgxlf* | mpixlf*)
 	  # IBM XL Fortran 10.1 on PPC cannot create shared libs itself
 	  _LT_TAGVAR(whole_archive_flag_spec, $1)='--whole-archive$convenience --no-whole-archive'
-	  _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
-	  _LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)='-rpath $libdir'
+	  _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
 	  _LT_TAGVAR(archive_cmds, $1)='$LD -shared $libobjs $deplibs $linker_flags -soname $soname -o $lib'
 	  if test "x$supports_anon_versioning" = xyes; then
 	    _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~
@@ -5068,6 +5141,7 @@
 	# The linker will not automatically build a static lib if we build a DLL.
 	# _LT_TAGVAR(old_archive_from_new_cmds, $1)='true'
 	_LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes
+	_LT_TAGVAR(exclude_expsyms, $1)='_NULL_IMPORT_DESCRIPTOR|_IMPORT_DESCRIPTOR_.*'
 	_LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[[BCDGRS]][[ ]]/s/.*[[ ]]\([[^ ]]*\)/\1,DATA/'\'' | $SED -e '\''/^[[AITW]][[ ]]/s/.*[[ ]]//'\'' | sort | uniq > $export_symbols'
 	# Don't use ranlib
 	_LT_TAGVAR(old_postinstall_cmds, $1)='chmod 644 $oldlib'
@@ -5114,10 +5188,6 @@
       _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
       ;;
 
-    freebsd1*)
-      _LT_TAGVAR(ld_shlibs, $1)=no
-      ;;
-
     # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor
     # support.  Future versions do this automatically, but an explicit c++rt0.o
     # does not break anything, and helps significantly (at the cost of a little
@@ -5130,7 +5200,7 @@
       ;;
 
     # Unfortunately, older versions of FreeBSD 2 do not have this feature.
-    freebsd2*)
+    freebsd2.*)
       _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
       _LT_TAGVAR(hardcode_direct, $1)=yes
       _LT_TAGVAR(hardcode_minus_L, $1)=yes
@@ -5169,7 +5239,6 @@
       fi
       if test "$with_gnu_ld" = no; then
 	_LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
-	_LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)='+b $libdir'
 	_LT_TAGVAR(hardcode_libdir_separator, $1)=:
 	_LT_TAGVAR(hardcode_direct, $1)=yes
 	_LT_TAGVAR(hardcode_direct_absolute, $1)=yes
@@ -5611,9 +5680,6 @@
 _LT_TAGDECL([], [hardcode_libdir_flag_spec], [1],
     [Flag to hardcode $libdir into a binary during linking.
     This must work even if $libdir does not exist])
-_LT_TAGDECL([], [hardcode_libdir_flag_spec_ld], [1],
-    [[If ld is used when linking, flag to hardcode $libdir into a binary
-    during linking.  This must work even if $libdir does not exist]])
 _LT_TAGDECL([], [hardcode_libdir_separator], [1],
     [Whether we need a single "-rpath" flag with a separated argument])
 _LT_TAGDECL([], [hardcode_direct], [0],
@@ -5771,7 +5837,6 @@
 _LT_TAGVAR(hardcode_direct, $1)=no
 _LT_TAGVAR(hardcode_direct_absolute, $1)=no
 _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
-_LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
 _LT_TAGVAR(hardcode_libdir_separator, $1)=
 _LT_TAGVAR(hardcode_minus_L, $1)=no
 _LT_TAGVAR(hardcode_shlibpath_var, $1)=unsupported
@@ -6141,7 +6206,7 @@
         esac
         ;;
 
-      freebsd[[12]]*)
+      freebsd2.*)
         # C++ shared libraries reported to be fairly broken before
 	# switch to ELF
         _LT_TAGVAR(ld_shlibs, $1)=no
@@ -6902,12 +6967,18 @@
   }
 };
 _LT_EOF
+], [$1], [GO], [cat > conftest.$ac_ext <<_LT_EOF
+package foo
+func foo() {
+}
+_LT_EOF
 ])
 
 _lt_libdeps_save_CFLAGS=$CFLAGS
 case "$CC $CFLAGS " in #(
 *\ -flto*\ *) CFLAGS="$CFLAGS -fno-lto" ;;
 *\ -fwhopr*\ *) CFLAGS="$CFLAGS -fno-whopr" ;;
+*\ -fuse-linker-plugin*\ *) CFLAGS="$CFLAGS -fno-use-linker-plugin" ;;
 esac
 
 dnl Parse the compiler output and extract the necessary
@@ -7104,7 +7175,6 @@
 _LT_TAGVAR(hardcode_direct, $1)=no
 _LT_TAGVAR(hardcode_direct_absolute, $1)=no
 _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
-_LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
 _LT_TAGVAR(hardcode_libdir_separator, $1)=
 _LT_TAGVAR(hardcode_minus_L, $1)=no
 _LT_TAGVAR(hardcode_automatic, $1)=no
@@ -7237,7 +7307,6 @@
 _LT_TAGVAR(hardcode_direct, $1)=no
 _LT_TAGVAR(hardcode_direct_absolute, $1)=no
 _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
-_LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
 _LT_TAGVAR(hardcode_libdir_separator, $1)=
 _LT_TAGVAR(hardcode_minus_L, $1)=no
 _LT_TAGVAR(hardcode_automatic, $1)=no
@@ -7424,6 +7493,77 @@
 ])# _LT_LANG_GCJ_CONFIG
 
 
+# _LT_LANG_GO_CONFIG([TAG])
+# --------------------------
+# Ensure that the configuration variables for the GNU Go compiler
+# are suitably defined.  These variables are subsequently used by _LT_CONFIG
+# to write the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_GO_CONFIG],
+[AC_REQUIRE([LT_PROG_GO])dnl
+AC_LANG_SAVE
+
+# Source file extension for Go test sources.
+ac_ext=go
+
+# Object file extension for compiled Go test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code="package main; func main() { }"
+
+# Code to be used in simple link tests
+lt_simple_link_test_code='package main; func main() { }'
+
+# ltmain only uses $CC for tagged configurations so make sure $CC is set.
+_LT_TAG_COMPILER
+
+# save warnings/boilerplate of simple test code
+_LT_COMPILER_BOILERPLATE
+_LT_LINKER_BOILERPLATE
+
+# Allow CC to be a program name with arguments.
+lt_save_CC=$CC
+lt_save_CFLAGS=$CFLAGS
+lt_save_GCC=$GCC
+GCC=yes
+CC=${GOC-"gccgo"}
+CFLAGS=$GOFLAGS
+compiler=$CC
+_LT_TAGVAR(compiler, $1)=$CC
+_LT_TAGVAR(LD, $1)="$LD"
+_LT_CC_BASENAME([$compiler])
+
+# Go did not exist at the time GCC didn't implicitly link libc in.
+_LT_TAGVAR(archive_cmds_need_lc, $1)=no
+
+_LT_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds
+_LT_TAGVAR(reload_flag, $1)=$reload_flag
+_LT_TAGVAR(reload_cmds, $1)=$reload_cmds
+
+## CAVEAT EMPTOR:
+## There is no encapsulation within the following macros, do not change
+## the running order or otherwise move them around unless you know exactly
+## what you are doing...
+if test -n "$compiler"; then
+  _LT_COMPILER_NO_RTTI($1)
+  _LT_COMPILER_PIC($1)
+  _LT_COMPILER_C_O($1)
+  _LT_COMPILER_FILE_LOCKS($1)
+  _LT_LINKER_SHLIBS($1)
+  _LT_LINKER_HARDCODE_LIBPATH($1)
+
+  _LT_CONFIG($1)
+fi
+
+AC_LANG_RESTORE
+
+GCC=$lt_save_GCC
+CC=$lt_save_CC
+CFLAGS=$lt_save_CFLAGS
+])# _LT_LANG_GO_CONFIG
+
+
 # _LT_LANG_RC_CONFIG([TAG])
 # -------------------------
 # Ensure that the configuration variables for the Windows resource compiler
@@ -7493,6 +7633,13 @@
 dnl AC_DEFUN([LT_AC_PROG_GCJ], [])
 
 
+# LT_PROG_GO
+# ----------
+AC_DEFUN([LT_PROG_GO],
+[AC_CHECK_TOOL(GOC, gccgo,)
+])
+
+
 # LT_PROG_RC
 # ----------
 AC_DEFUN([LT_PROG_RC],
diff -ruN ccp4srs-old/m4/ltoptions.m4 ccp4srs/m4/ltoptions.m4
--- ccp4srs-old/m4/ltoptions.m4	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/m4/ltoptions.m4	2014-09-09 21:34:12.000000000 -0700
@@ -326,9 +326,24 @@
 # MODE is either `yes' or `no'.  If omitted, it defaults to `both'.
 m4_define([_LT_WITH_PIC],
 [AC_ARG_WITH([pic],
-    [AS_HELP_STRING([--with-pic],
+    [AS_HELP_STRING([--with-pic@<:@=PKGS@:>@],
 	[try to use only PIC/non-PIC objects @<:@default=use both@:>@])],
-    [pic_mode="$withval"],
+    [lt_p=${PACKAGE-default}
+    case $withval in
+    yes|no) pic_mode=$withval ;;
+    *)
+      pic_mode=default
+      # Look at the argument we got.  We use all the common list separators.
+      lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+      for lt_pkg in $withval; do
+	IFS="$lt_save_ifs"
+	if test "X$lt_pkg" = "X$lt_p"; then
+	  pic_mode=yes
+	fi
+      done
+      IFS="$lt_save_ifs"
+      ;;
+    esac],
     [pic_mode=default])
 
 test -z "$pic_mode" && pic_mode=m4_default([$1], [default])
diff -ruN ccp4srs-old/srsgen.cpp ccp4srs/srsgen.cpp
--- ccp4srs-old/srsgen.cpp	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/srsgen.cpp	2014-09-09 21:34:12.000000000 -0700
@@ -65,9 +65,9 @@
 #endif
 
 
-#include "mmdb/mmdb_tables.h"
-#include "mmdb/mmdb_mmcif.h"
-#include "mmdb/mmdb_graph.h"
+#include "mmdb2/mmdb_tables.h"
+#include "mmdb2/mmdb_mmcif_.h"
+#include "mmdb2/mmdb_math_graph.h"
 
 
 #ifdef  _WIN32
@@ -926,7 +926,7 @@
 }
 */
 
-void printInstructions ( pstr argv0 )  {
+void printInstructions ( mmdb::pstr argv0 )  {
 
   printf (
     "\n"
@@ -959,33 +959,33 @@
 
 DefineClass(CSortSRSIndex)
 
-class CSortSRSIndex : public CQuickSort  {
+class CSortSRSIndex : public mmdb::QuickSort  {
   public :
-    CSortSRSIndex() : CQuickSort() {}
+    CSortSRSIndex() : mmdb::QuickSort() {}
     int  Compare ( int i, int j );
     void Swap    ( int i, int j );
-    void Sort    ( PPCCP4SRSIndex   index,
-                   PPCCP4SRSMonomer monomer,
-                   PPCGraph         graph,
+    void Sort    ( ccp4srs::PPIndex    index,
+                   ccp4srs::PPMonomer  monomer,
+                   mmdb::math::PPGraph graph,
                    int nEntries );
   protected:
-    PPCCP4SRSMonomer m_array;
-    PPCGraph         g_array;
+    ccp4srs::PPMonomer  m_array;
+    mmdb::math::PPGraph g_array;
 };
 
 int CSortSRSIndex::Compare ( int i, int j )  {
-  return strcmp ( ((PPCCP4SRSIndex)data)[i]->entryID,
-                  ((PPCCP4SRSIndex)data)[j]->entryID );
+  return strcmp ( ((ccp4srs::PPIndex)data)[i]->entryID,
+                  ((ccp4srs::PPIndex)data)[j]->entryID );
 }
 
 void CSortSRSIndex::Swap ( int i, int j )  {
-PCCP4SRSIndex   I;
-PCCP4SRSMonomer M;
-PCGraph         G;
-
-  I = ((PPCCP4SRSIndex)data)[i];
-  ((PPCCP4SRSIndex)data)[i] = ((PPCCP4SRSIndex)data)[j];
-  ((PPCCP4SRSIndex)data)[j] = I;
+ccp4srs::PIndex    I;
+ccp4srs::PMonomer  M;
+mmdb::math::PGraph G;
+
+  I = ((ccp4srs::PPIndex)data)[i];
+  ((ccp4srs::PPIndex)data)[i] = ((ccp4srs::PPIndex)data)[j];
+  ((ccp4srs::PPIndex)data)[j] = I;
 
   M = m_array[i];
   m_array[i] = m_array[j];
@@ -998,13 +998,13 @@
 }
 
 
-void CSortSRSIndex::Sort ( PPCCP4SRSIndex   index,
-                           PPCCP4SRSMonomer monomer,
-                           PPCGraph         graph,
+void CSortSRSIndex::Sort ( ccp4srs::PPIndex    index,
+                           ccp4srs::PPMonomer  monomer,
+                           mmdb::math::PPGraph graph,
                            int nEntries )  {
   m_array = monomer;
   g_array = graph;
-  CQuickSort::Sort ( &(index[0]),nEntries );
+  mmdb::QuickSort::Sort ( &(index[0]),nEntries );
 }
 
 
@@ -1016,29 +1016,29 @@
 
     void FreeMemory();
 
-    int  openLogs ( cpstr dir );
-    void prints   ( cpstr S, int key );
+    int  openLogs ( mmdb::cpstr dir );
+    void prints   ( mmdb::cpstr S, int key );
     void closeLogs();
 
-    int readEnergyLib      ( cpstr monLib  );
-    int scanRCSBLibrary    ( cpstr rcsbLib );
-    int scanMonomerLibrary ( cpstr monLib, bool match_only );
+    int readEnergyLib      ( mmdb::cpstr monLib  );
+    int scanRCSBLibrary    ( mmdb::cpstr rcsbLib );
+    int scanMonomerLibrary ( mmdb::cpstr monLib, bool match_only );
 
     void sortIndex         ();
-    int  writeSRS          ( cpstr srsDir );
+    int  writeSRS          ( mmdb::cpstr srsDir );
 
   protected:
-    CMMCIFData       energyLib;
-    CGraphMatch      graphMatch;
-    CFile            fout;
-    CFile            ferr;
-    PPCCP4SRSIndex   srsIndex;
-    PPCCP4SRSMonomer srsMonomer;
-    PPCGraph         srsGraph;
-    CMemIO           memIO;
-    int              srsVersion;
-    int              nEntries,nEntries0;
-    bool             matchOnly;
+    mmdb::mmcif::Data      energyLib;
+    mmdb::math::GraphMatch graphMatch;
+    mmdb::io::File         fout;
+    mmdb::io::File         ferr;
+    ccp4srs::PPIndex       srsIndex;
+    ccp4srs::PPMonomer     srsMonomer;
+    mmdb::math::PPGraph    srsGraph;
+    ccp4srs::MemIO         memIO;
+    int                    srsVersion;
+    int                    nEntries,nEntries0;
+    bool                   matchOnly;
 
     // error counters
     int              n_rcsb_read_err;
@@ -1050,14 +1050,14 @@
     int              n_oldml_not_found;
     int              n_oldml_no_matches;
 
-    int  scanMonLibDirectory ( cpstr dirPath  );
-    int  processMonLibFile   ( cpstr filePath );
-    int  processRCSBFile     ( cpstr filePath );
-    void FillETLibData       ( PCCP4SRSMonomer monomer );
-    int  matchAtomNames      ( PCCP4SRSMonomer mon,
-                               PCCP4SRSMonomer mon_old );
-    int  processMonomer      ( PCCP4SRSMonomer monomer );
-    int  getMonomerNo        ( cpstr monID );
+    int  scanMonLibDirectory ( mmdb::cpstr dirPath  );
+    int  processMonLibFile   ( mmdb::cpstr filePath );
+    int  processRCSBFile     ( mmdb::cpstr filePath );
+    void FillETLibData       ( ccp4srs::PMonomer monomer );
+    int  matchAtomNames      ( ccp4srs::PMonomer mon,
+                               ccp4srs::PMonomer mon_old );
+    int  processMonomer      ( ccp4srs::PMonomer monomer );
+    int  getMonomerNo        ( mmdb::cpstr monID );
 
   private:
     int index_alloc;
@@ -1068,7 +1068,7 @@
 
 CMakeSRS::CMakeSRS()  {
 
-  srsVersion  = CCP4SRS_file_version;
+  srsVersion  = ccp4srs::CCP4SRS_file_version;
   srsIndex    = NULL;
   srsMonomer  = NULL;
   srsGraph    = NULL;
@@ -1117,19 +1117,19 @@
 
 }
 
-int CMakeSRS::openLogs ( cpstr dir )  {
-pstr fname;
-int  rc;
+int CMakeSRS::openLogs ( mmdb::cpstr dir )  {
+mmdb::pstr fname;
+int        rc;
 
   fname = NULL;
   rc    = 0;
 
-  CreateCopCat ( fname,dir,"srsgen_out.txt" );
-  fout.assign ( fname,True );
+  mmdb::CreateCopCat ( fname,dir,"srsgen_out.txt" );
+  fout.assign ( fname,true );
   if (!fout.rewrite())  rc = -1;
 
-  CreateCopCat ( fname,dir,"srsgen_err.txt" );
-  ferr.assign ( fname,True );
+  mmdb::CreateCopCat ( fname,dir,"srsgen_err.txt" );
+  ferr.assign ( fname,true );
   if (!ferr.rewrite())  rc = -2;
 
   delete[] fname;
@@ -1172,17 +1172,17 @@
 
 }
 
-void CMakeSRS::prints ( cpstr S, int key )  {
+void CMakeSRS::prints ( mmdb::cpstr S, int key )  {
   printf ( "%s",S );
   if (key & 0x00000001)  fout.Write ( S );
   if (key & 0x00000002)  ferr.Write ( S );
 }
 
-int CMakeSRS::getMonomerNo ( cpstr monID )  {
-int     l1,l2,l,k;
-ResName id;
+int CMakeSRS::getMonomerNo ( mmdb::cpstr monID )  {
+mmdb::ResName id;
+int           l1,l2,l,k;
 
-  strcpy_css ( id,monID );
+  mmdb::strcpy_css ( id,monID );
 
   k = -1;
 
@@ -1191,7 +1191,7 @@
       if (!strcmp(srsIndex[l]->entryID,id))
         k = l;
     if (k>=0)  return k;
-    return CCP4SRS_EntryNotFound;
+    return ccp4srs::CCP4SRS_EntryNotFound;
   }
 
   l  = 0;
@@ -1215,23 +1215,18 @@
     if (!strcmp(srsIndex[l1]->entryID,id))  return l1;
   }
 
-  return CCP4SRS_EntryNotFound;
+  return ccp4srs::CCP4SRS_EntryNotFound;
 
 }
 
 
-void CMakeSRS::FillETLibData ( PCCP4SRSMonomer monomer )  {
-PCMMCIFLoop  Loop;
-PCCP4SRSAtom Atom;
-//PCSBBond     Bond,Bond2;
-//PCSBAngle    angle;
-realtype     vdwRadius,vdwhRadius,ionRadius;
-//realtype     blength,blength_esd;
-cpstr         at1,et1,bt; //,at2, bt, et1,et2;
-//pstr         at21,at22;
-int          valency,sp;
-int          i,j,l,a1, rc;//,a2,order,btype, rc,found,nb,nb_esd;
-//int          a21,a22;
+void CMakeSRS::FillETLibData ( ccp4srs::PMonomer monomer )  {
+mmdb::mmcif::PLoop  Loop;
+ccp4srs::PAtom      Atom;
+mmdb::realtype      vdwRadius,vdwhRadius,ionRadius;
+mmdb::cpstr         at1,et1,bt;
+int                 valency,sp;
+int                 i,j,l,a1, rc;
 
   // 1. Set atom properties depending on energy type
 
@@ -1260,26 +1255,26 @@
         valency    = Atom->valency    ();
         sp         = Atom->sp         ();
         if (vdwRadius<=0.01)  {
-          if (Loop->GetReal(vdwRadius,"vdw_radius",a1,False))
-            vdwRadius = getVdWaalsRadius  ( Atom->element() );
+          if (Loop->GetReal(vdwRadius,"vdw_radius",a1,false))
+            vdwRadius = mmdb::getVdWaalsRadius  ( Atom->element() );
           Atom->set_vdw_radius ( vdwRadius );
         }
         if (vdwhRadius<=0.01)  {
-          if (Loop->GetReal(vdwhRadius,"vdwh_radius",a1,False))
-            vdwhRadius = vdwRadius + getVdWaalsRadius  ( "H" );
+          if (Loop->GetReal(vdwhRadius,"vdwh_radius",a1,false))
+            vdwhRadius = vdwRadius + mmdb::getVdWaalsRadius  ( "H" );
           Atom->set_vdwh_radius ( vdwhRadius );
         }
         if (ionRadius<=0.01)  {
-          if (Loop->GetReal(ionRadius,"ion_radius",a1,False))
-            ionRadius = getCovalentRadius ( Atom->element() );
+          if (Loop->GetReal(ionRadius,"ion_radius",a1,false))
+            ionRadius = mmdb::getCovalentRadius ( Atom->element() );
           Atom->set_ion_radius ( ionRadius );
         }
         if (valency<=0)  {
-          Loop->GetInteger ( valency,"valency",a1,False );
+          Loop->GetInteger ( valency,"valency",a1,false );
           Atom->set_valency ( valency );
         }
         if (sp<=0)  {
-          Loop->GetInteger ( sp,"sp",a1,False );
+          Loop->GetInteger ( sp,"sp",a1,false );
           if (sp<0)  sp = 0;
           Atom->set_sp ( sp );
         }
@@ -1296,10 +1291,10 @@
     }
     if (a1<0)  {
       // take whatever is possible from MMDB tables
-      Atom->set_vdw_radius  ( getVdWaalsRadius(Atom->element()) );
+      Atom->set_vdw_radius  ( mmdb::getVdWaalsRadius(Atom->element()) );
       Atom->set_vdwh_radius ( Atom->vdw_radius() +
-                              getVdWaalsRadius("H") );
-      Atom->set_ion_radius ( getCovalentRadius(Atom->element()) );
+                              mmdb::getVdWaalsRadius("H") );
+      Atom->set_ion_radius  ( mmdb::getCovalentRadius(Atom->element()) );
       Atom->set_valency ( 0 );    // valency is unknown
       Atom->set_sp      ( 0 );    // sp is unknown
       Atom->set_hb_type ( 'N' );  // no hydrogen bonding
@@ -1450,31 +1445,19 @@
 
 }
 
-/*
-int MakeElementType ( int ElType, char chirality, Boolean Cflag )  {
-  if (Cflag)  {
-    if (chirality=='S')  return ElType | CHIRAL_LEFT;
-    if (chirality=='R')  return ElType | CHIRAL_RIGHT;
-  }
-  return ElType;
-}
-*/
 
-int CMakeSRS::processMonomer ( PCCP4SRSMonomer monomer )  {
-PCCP4SRSIndex    index;
-//PCCP4SRSAtom     atom;
-//PCVertex         vertex;
-//PCEdge           edge;
-PPCCP4SRSIndex   kndex;
-PPCCP4SRSMonomer marray;
-PPCGraph         garray;
-PCGraph          graph;
-char             S[500];
-int              rc,i;//,vtype,vx1,vx2;
+int CMakeSRS::processMonomer ( ccp4srs::PMonomer monomer )  {
+ccp4srs::PIndex     index;
+ccp4srs::PPIndex    kndex;
+ccp4srs::PPMonomer  marray;
+mmdb::math::PPGraph garray;
+mmdb::math::PGraph  graph;
+char                S[500];
+int                 rc,i;
 
   rc    = 0;
 
-  index = new CCP4SRSIndex();
+  index = new ccp4srs::Index();
 
   strcpy ( index->entryID,monomer->ID() );
   index->nAtoms = monomer->n_atoms();
@@ -1573,9 +1556,9 @@
 
   if (nEntries>=index_alloc)  {
     index_alloc = nEntries + 5000;
-    kndex  = new PCCP4SRSIndex  [index_alloc];
-    marray = new PCCP4SRSMonomer[index_alloc];
-    garray = new PCGraph        [index_alloc];
+    kndex  = new ccp4srs::PIndex   [index_alloc];
+    marray = new ccp4srs::PMonomer [index_alloc];
+    garray = new mmdb::math::PGraph[index_alloc];
     for (i=0;i<nEntries;i++)  {
       kndex [i] = srsIndex  [i];
       marray[i] = srsMonomer[i];
@@ -1603,17 +1586,18 @@
 
 }
 
-int CMakeSRS::matchAtomNames ( PCCP4SRSMonomer mon,
-                               PCCP4SRSMonomer mon_old )  {
-PCGraph  graph;
-PCGraph  graph_old;
-AtomName aname1,aname2;
-ivector  FV1,FV2;
-ivector  amap;
-ivector  hcnt;
-realtype p1,p2;
-char     S[500];
-int      htype,nv,i,n1,n2, atm_old,atm_new,atm_h;
+
+int CMakeSRS::matchAtomNames ( ccp4srs::PMonomer mon,
+                               ccp4srs::PMonomer mon_old )  {
+mmdb::math::PGraph  graph;
+mmdb::math::PGraph  graph_old;
+mmdb::AtomName      aname1,aname2;
+mmdb::ivector       FV1,FV2;
+mmdb::ivector       amap;
+mmdb::ivector       hcnt;
+mmdb::realtype      p1,p2;
+char                S[500];
+int                 htype,nv,i,n1,n2, atm_old,atm_new,atm_h;
 
   if (mon->n_bonds()<=0)  {
     sprintf ( S," +++++ compound '%s' does not have a structure\n",
@@ -1649,23 +1633,23 @@
     return -2;
   }
 
-  htype = getElementNo(pstr("H"));
+  htype = mmdb::getElementNo(mmdb::pstr("H"));
 
   graph->ExcludeType ( htype );
   graph->MakeVertexIDs();
-  graph->MakeSymmetryRelief ( False );
-  graph->Build ( False );
+  graph->MakeSymmetryRelief ( false );
+  graph->Build ( false );
 
   graph_old->ExcludeType ( htype );
   graph_old->MakeVertexIDs();
-  graph_old->MakeSymmetryRelief ( False );
-  graph_old->Build ( False );
+  graph_old->MakeSymmetryRelief ( false );
+  graph_old->Build ( false );
 
-  graphMatch.SetMaxNofMatches ( 2,True );
+  graphMatch.SetMaxNofMatches ( 2,true );
   graphMatch.MatchGraphs ( graph,graph_old,
-                           IMin(graph->GetNofVertices(),
-                                graph_old->GetNofVertices()),
-                           True,EXTTYPE_Ignore );
+                           mmdb::IMin(graph->GetNofVertices(),
+                                      graph_old->GetNofVertices()),
+                           true,mmdb::math::EXTTYPE_Ignore );
 
   if (graphMatch.GetNofMatches()<=0)  {
 
@@ -1692,9 +1676,9 @@
     FV2 = NULL;
     graphMatch.GetMatch ( 0,FV1,FV2,nv,p1,p2 );
 
-    n1 = IMax(mon_old->n_atoms(),mon->n_atoms());
-    GetVectorMemory ( amap,n1,0 );
-    GetVectorMemory ( hcnt,n1,0 );
+    n1 = mmdb::IMax(mon_old->n_atoms(),mon->n_atoms());
+    mmdb::GetVectorMemory ( amap,n1,0 );
+    mmdb::GetVectorMemory ( hcnt,n1,0 );
     for (i=0;i<n1;i++)  {
       amap[i] = -1;
       hcnt[i] = 0;
@@ -1746,8 +1730,8 @@
         }
       }
 
-    FreeVectorMemory ( hcnt,0 );
-    FreeVectorMemory ( amap,0 );
+    mmdb::FreeVectorMemory ( hcnt,0 );
+    mmdb::FreeVectorMemory ( amap,0 );
 
   }
 
@@ -1760,19 +1744,19 @@
 }
 
 
-int CMakeSRS::processMonLibFile ( cpstr filePath )  {
+int CMakeSRS::processMonLibFile ( mmdb::cpstr filePath )  {
 // processing an entry from Monomer Library
-CMMCIFFile      mmCIFFile;
-PCMMCIFData     mmCIFData;
-PCCP4SRSMonomer monomer;
-PCCP4SRSAtom    atom;
-char            ErrLog[1000];
-ResName         rname;
-pstr            p;
-char            S[500];
-int             rc, nData,i,j, nMon;
+mmdb::mmcif::File  mmCIFFile;
+mmdb::mmcif::PData mmCIFData;
+ccp4srs::PMonomer  monomer;
+ccp4srs::PAtom     atom;
+char               ErrLog[1000];
+mmdb::ResName      rname;
+mmdb::pstr         p;
+char               S[500];
+int                rc, nData,i,j, nMon;
 
-  rc = mmCIFFile.ReadMMCIFFile ( filePath,GZM_CHECK );
+  rc = mmCIFFile.ReadMMCIFFile ( filePath,mmdb::io::GZM_CHECK );
 
   if (rc)  {
     sprintf ( S," +++ file %s read with return code %i\n",
@@ -1789,7 +1773,7 @@
     mmCIFData = mmCIFFile.GetCIFData ( i );
     if (strcmp(mmCIFData->GetDataName(),"comp_list"))  {
 
-      monomer = new CCP4SRSMonomer();
+      monomer = new ccp4srs::Monomer();
       rc      = monomer->readFromCIF ( mmCIFData,ErrLog );
       if (rc)  {
         sprintf ( S," +++ error reading monomer %s:\n"
@@ -1804,12 +1788,12 @@
       if (monomer)  {
 
         strcpy ( rname,mmCIFData->GetDataName() );
-        p = strchr ( rname,'_' );
+        p = mmdb::FirstOccurence ( rname,'_' );
         if (!p)  p  = rname;
            else  p++;
 
         nMon = getMonomerNo ( p );
-        if (nMon==CCP4SRS_EntryNotFound)  {
+        if (nMon==ccp4srs::CCP4SRS_EntryNotFound)  {
 
           if (matchOnly)  {
             sprintf ( S," +++ [%4i] compound '%s' from old ML is not "
@@ -1877,16 +1861,16 @@
 }
 
 
-int CMakeSRS::scanMonLibDirectory ( cpstr dirPath )  {
+int CMakeSRS::scanMonLibDirectory ( mmdb::cpstr dirPath )  {
 DIR    *dir;
 #if USE_DIRENT_H
 dirent *dp;
 #else
 direct *dp;
 #endif
-pstr  p;
-pstr  filePath;
-int   rc;
+mmdb::pstr p;
+mmdb::pstr filePath;
+int        rc;
 
   filePath = NULL;
   rc       = 0;
@@ -1897,10 +1881,10 @@
 
   dp = readdir ( dir );
   while (dp)  {
-    p = strrchr ( dp->d_name,'.' );
+    p = mmdb::LastOccurence ( dp->d_name,'.' );
     if (p)  {
       if (!strcmp(p,".cif"))  {
-        CreateCopCat ( filePath,dirPath,dp->d_name );
+        mmdb::CreateCopCat ( filePath,dirPath,dp->d_name );
         rc = processMonLibFile ( filePath );
       }
     }
@@ -1913,17 +1897,17 @@
 
 }
 
-int CMakeSRS::processRCSBFile ( cpstr filePath )  {
-CFile           compFile;
-CMMCIFData      mmCIFData;
-PCCP4SRSMonomer monomer;
-char            S[1000];
-char            L[1000];
-char            ErrLog[1000];
-int             lcount,rc;
+int CMakeSRS::processRCSBFile ( mmdb::cpstr filePath )  {
+mmdb::io::File    compFile;
+mmdb::mmcif::Data mmCIFData;
+ccp4srs::PMonomer monomer;
+char              S[1000];
+char              L[1000];
+char              ErrLog[1000];
+int               lcount,rc;
 
-  compFile.assign ( filePath,True,False );
-  if (!compFile.reset(True))  {
+  compFile.assign ( filePath,true,false );
+  if (!compFile.reset(true))  {
     sprintf ( S," *** cannot open components file %s\n",filePath );
     prints  ( S,3 );
     n_rcsb_read_err++;
@@ -1934,28 +1918,28 @@
 
     lcount     = 0;
     rc         = 0;
+    S[0] = char(0);
 
     while (!compFile.FileEnd())  {
 
-      S[0] = char(0);
       rc = mmCIFData.ReadMMCIFData ( compFile,S,lcount );
 
-      if (rc!=CIFRC_Ok)  {
+      if (rc!=mmdb::mmcif::CIFRC_Ok)  {
 
         if (rc<0)  {
-          sprintf ( S," *** error reading file:\n"
-                      "     %s\n",GetCIFMessage(L,rc) );
+          sprintf ( S," *** error reading file (%i):\n"
+                      "     %s\n",rc,mmdb::mmcif::GetCIFMessage(L,rc) );
           prints  ( S,3 );
           n_rcsb_read_err++;
         } else  {
           sprintf ( S," ... warning on reading file:\n"
-                      "     %s\n",GetCIFMessage(L,rc) );
+                      "     %s\n",mmdb::mmcif::GetCIFMessage(L,rc) );
           prints  ( S,3 );
         }
 
       } else  {
 
-        monomer = new CCP4SRSMonomer();
+        monomer = new ccp4srs::Monomer();
         rc = monomer->readFromCIF ( &mmCIFData,ErrLog );
         if (rc)  {
           sprintf ( S," +++ error reading monomer %s:\n"
@@ -1976,17 +1960,17 @@
 
 }
 
-int CMakeSRS::readEnergyLib ( cpstr monLib )  {
-pstr S;
-char L[1000];
-int  rc;
+int CMakeSRS::readEnergyLib ( mmdb::cpstr monLib )  {
+mmdb::pstr S;
+char       L[1000];
+int        rc;
 
   S  = NULL;
   rc = 0;
 
   S = NULL;
-  CreateCopCat ( S,monLib,"ener_lib.cif" );
-  energyLib.SetFlag ( CIFFL_PrintWarnings );
+  mmdb::CreateCopCat ( S,monLib,"ener_lib.cif" );
+  energyLib.SetFlag  ( mmdb::mmcif::CIFFL_PrintWarnings );
   rc = energyLib.ReadMMCIFData ( S );
   if (rc)  {
     sprintf ( L," *** cannot read energy type library:\n"
@@ -1994,7 +1978,7 @@
     prints  ( L,3 );
     delete[] S;
     S = new char[2000];
-    sprintf ( L," %s\n",GetCIFMessage(S,rc) );
+    sprintf ( L," %s\n",mmdb::mmcif::GetCIFMessage(S,rc) );
     prints  ( L,3 );
     delete S;
     n_elib_err++;
@@ -2011,16 +1995,16 @@
 
 }
 
-int CMakeSRS::scanRCSBLibrary ( cpstr rcsbLib )  {
+int CMakeSRS::scanRCSBLibrary ( mmdb::cpstr rcsbLib )  {
 DIR    *dir;
 #if USE_DIRENT_H
 dirent *dp;
 #else
 direct *dp;
 #endif
-pstr    S;
-char    L[1000];
-int     rc;
+mmdb::pstr S;
+char       L[1000];
+int        rc;
 
   S  = NULL;
   rc = 0;
@@ -2036,7 +2020,7 @@
   dp = readdir ( dir );
   while (dp)  {
     if (dp->d_name[0]!='.')  {
-      CreateCopCat ( S,rcsbLib,dp->d_name );
+      mmdb::CreateCopCat ( S,rcsbLib,dp->d_name );
       rc = processRCSBFile ( S );
     }
     dp = readdir ( dir );
@@ -2051,16 +2035,17 @@
 }
 
 
-int CMakeSRS::scanMonomerLibrary ( cpstr monLib, bool match_only )  {
+int CMakeSRS::scanMonomerLibrary ( mmdb::cpstr monLib,
+                                   bool match_only )  {
 DIR    *dir;
 #if USE_DIRENT_H
 dirent *dp;
 #else
 direct *dp;
 #endif
-pstr    S;
-char    L[1000];
-int     rc;
+mmdb::pstr S;
+char       L[1000];
+int        rc;
 
   matchOnly = match_only;
 
@@ -2078,7 +2063,7 @@
   dp = readdir ( dir );
   while (dp)  {
     if ((dp->d_name[0]!='.') && (!dp->d_name[1]))  {
-      CreateCopCat ( S,monLib,dp->d_name,_dir_sep );
+      mmdb::CreateCopCat ( S,monLib,dp->d_name,_dir_sep );
       rc = scanMonLibDirectory ( S );
     }
     dp = readdir ( dir );
@@ -2095,35 +2080,35 @@
   sortSRSIndex.Sort ( srsIndex,srsMonomer,srsGraph,nEntries );
 }
 
-int  CMakeSRS::writeSRS ( cpstr srsDir )  {
-CFile graphFile;
-CFile structFile;
-CFile indexFile;
-pstr  S;
-pstr  buffer;
-char  L[1000];
-int   i,n,k, buffer_length;
+int  CMakeSRS::writeSRS ( mmdb::cpstr srsDir )  {
+mmdb::io::File graphFile;
+mmdb::io::File structFile;
+mmdb::io::File indexFile;
+mmdb::pstr     S;
+mmdb::pstr     buffer;
+char           L[1000];
+int            i,n,k, buffer_length;
 
   S = NULL;
 
-  CreateCopCat ( S,srsDir,srsGraphFile );
-  graphFile.assign ( S,False,True );
+  mmdb::CreateCopCat ( S,srsDir,ccp4srs::srsGraphFile );
+  graphFile.assign ( S,false,true );
   if (!graphFile.rewrite())  {
     sprintf ( L," *** can't open srs file '%s' file.\n",S );
     prints  ( L,3 );
     return -111113;
   }
 
-  CreateCopCat ( S,srsDir,srsStructFile );
-  structFile.assign ( S,False,True );
+  mmdb::CreateCopCat ( S,srsDir,ccp4srs::srsStructFile );
+  structFile.assign ( S,false,true );
   if (!structFile.rewrite())  {
     sprintf ( L," *** can't open srs file '%s' file.\n",S );
     prints  ( L,3 );
     return -111114;
   }
 
-  CreateCopCat ( S,srsDir,srsIndexFile );
-  indexFile.assign ( S,False,True );
+  mmdb::CreateCopCat ( S,srsDir,ccp4srs::srsIndexFile );
+  indexFile.assign ( S,false,true );
   if (!indexFile.rewrite())  {
     sprintf ( L," *** can't open srs file '%s' file.\n",S );
     prints  ( L,3 );
@@ -2131,7 +2116,7 @@
   }
 
   prints ( "\n ... writing SRS files: ",1 );
-  k = 50;
+  k = mmdb::IMin(50,nEntries);
   for (i=0;i<k;i++)
     prints ( ".",1 );
   printf ( "\r ... writing SRS files: " );
@@ -2189,19 +2174,19 @@
 int main ( int argc, char ** argv, char ** env )  {
 UNUSED_ARGUMENT(env);
 CMakeSRS makeSRS;
-pstr     rcsbLib;
-pstr     monLib;
-pstr     oldMonLib;
-pstr     srsDir;
-char     S[1000];
-int      argNo,rc;
+mmdb::pstr rcsbLib;
+mmdb::pstr monLib;
+mmdb::pstr oldMonLib;
+mmdb::pstr srsDir;
+char       S[1000];
+int        argNo,rc;
 
   if (argc<2)  {
     printInstructions ( argv[0] );
     return 1;
   }
 
-  InitMatType();
+  mmdb::InitMatType();
   makeSRS.openLogs ( NULL );
 
   rcsbLib   = NULL;
@@ -2212,36 +2197,36 @@
   rc    = 0;
   argNo = 1;
 
-  CreateCopy ( rcsbLib,argv[argNo++] );
+  mmdb::CreateCopy ( rcsbLib,argv[argNo++] );
   if (rcsbLib[strlen(rcsbLib)-1]!=_dir_sep_c)
-    CreateConcat ( rcsbLib,_dir_sep );
+    mmdb::CreateConcat ( rcsbLib,_dir_sep );
 
   if (argNo<argc)  {
-    CreateCopy ( monLib,argv[argNo++] );
+    mmdb::CreateCopy ( monLib,argv[argNo++] );
     if (monLib[strlen(monLib)-1]!=_dir_sep_c)
-      CreateConcat ( monLib,_dir_sep );
+      mmdb::CreateConcat ( monLib,_dir_sep );
   }
 
   if (argNo<argc)  {
     if (!strcmp(argv[argNo],"-d"))  {
       argNo++;
-      CreateCopy ( srsDir,argv[argNo] );
+      mmdb::CreateCopy ( srsDir,argv[argNo] );
     } else {
-      CreateCopy ( oldMonLib,argv[argNo++] );
+      mmdb::CreateCopy ( oldMonLib,argv[argNo++] );
       if (oldMonLib[strlen(oldMonLib)-1]!=_dir_sep_c)
-        CreateConcat ( oldMonLib,_dir_sep );
+        mmdb::CreateConcat ( oldMonLib,_dir_sep );
       if (argNo<argc)  {
         if (!strcmp(argv[argNo++],"-d"))
-          CreateCopy ( srsDir,argv[argNo] );
+          mmdb::CreateCopy ( srsDir,argv[argNo] );
       }
     }
   }
 
   if (srsDir)  {
     if (srsDir[strlen(srsDir)-1]!=_dir_sep_c)
-      CreateConcat ( srsDir,_dir_sep );
+      mmdb::CreateConcat ( srsDir,_dir_sep );
   } else
-    CreateCopy ( srsDir,"" );
+    mmdb::CreateCopy ( srsDir,"" );
 
   sprintf ( S," \n"
               " ... RCSB library            : %s\n",rcsbLib );
@@ -2252,6 +2237,8 @@
     sprintf ( S," ... old CCP4 monomer library: %s\n",oldMonLib );
     makeSRS.prints ( S,1 );
   }
+  rc = makeSRS.readEnergyLib ( monLib );
+  if (rc)  return rc;
 
   sprintf ( S," ... SRS directory           : %s\n"
               "\n ... machine properties:\n"
@@ -2259,7 +2246,7 @@
               "      sizeof(short)  = %lu\n"
               "      sizeof(int)    = %lu\n"
               "      sizeof(long)   = %lu\n\n",
-              srsDir,MaxShortReal,
+              srsDir,mmdb::MaxShortReal,
               sizeof(short),sizeof(int),sizeof(long)  );
   makeSRS.prints ( S,1 );
 
diff -ruN ccp4srs-old/srsrem.cpp ccp4srs/srsrem.cpp
--- ccp4srs-old/srsrem.cpp	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/srsrem.cpp	2014-09-09 21:34:12.000000000 -0700
@@ -17,10 +17,10 @@
 #include "ccp4srs/ccp4srs_manager.h"
 #include "ccp4srs/ccp4srs_defs.h"
 
-#include "mmdb/mmdb_tables.h"
+#include "mmdb2/mmdb_tables.h"
 
 
-void printInstructions ( cpstr argv0 )  {
+void printInstructions ( mmdb::cpstr argv0 )  {
 
   printf (
     "\n"
@@ -37,20 +37,23 @@
 }
 
 
-PCMMDBManager getPDB ( cpstr fileName )  {
-PCMMDBManager mmdb;
-char          S[1000];
-int           rc,lcount;
+mmdb::PManager getPDB ( mmdb::cpstr fileName )  {
+mmdb::PManager mmdb;
+char           S[1000];
+int            lcount;
+mmdb::ERROR_CODE rc;
 
   //  1.  Create an instance of MMDB
-  mmdb = new CMMDBManager();
+  mmdb = new mmdb::Manager();
 
   //  2.  Read coordinate file.
   //  2.1 Set all necessary read flags -- check with the top of
   //      file  mmdb_file.h  as needed
-  mmdb->SetFlag ( MMDBF_PrintCIFWarnings | MMDBF_FixSpaceGroup |
-                  MMDBF_IgnoreDuplSeqNum | MMDBF_IgnoreHash    |
-                  MMDBF_IgnoreNonCoorPDBErrors );
+  mmdb->SetFlag ( mmdb::MMDBF_PrintCIFWarnings |
+                  mmdb::MMDBF_FixSpaceGroup    |
+                  mmdb::MMDBF_IgnoreDuplSeqNum |
+                  mmdb::MMDBF_IgnoreHash       |
+                  mmdb::MMDBF_IgnoreNonCoorPDBErrors );
 
   //  3. Read file
   rc = mmdb->ReadCoorFile ( fileName );
@@ -61,7 +64,7 @@
     //  function for easy error message printing.
     printf ( " ***** error #%i on reading file %s:\n\n %s\n\n",
              rc,fileName,
-             GetErrorDescription(rc) );
+             mmdb::GetErrorDescription(rc) );
     //  Location of the error may be identified as precise as line
     //  number and the line itself (PDB only. Errors in mmCIF are
     //  located by category/item name). This information is now
@@ -78,9 +81,9 @@
     //  MMDB allows to identify the type of file that has been just
     //  read:
     switch (mmdb->GetFileType())  {
-      case MMDB_FILE_PDB    : printf ( " PDB"         );  break;
-      case MMDB_FILE_CIF    : printf ( " mmCIF"       );  break;
-      case MMDB_FILE_Binary : printf ( " MMDB binary" );  break;
+      case mmdb::MMDB_FILE_PDB    : printf ( " PDB"         );  break;
+      case mmdb::MMDB_FILE_CIF    : printf ( " mmCIF"       );  break;
+      case mmdb::MMDB_FILE_Binary : printf ( " MMDB binary" );  break;
       default : printf ( " Unknown (report as a bug!)" );
     }
     printf ( " ... file %s has been read in.\n",fileName );
@@ -90,20 +93,21 @@
 
 }
 
-int translateHydrogens ( PCCP4SRSMonomer monomer,
-                         PPCAtom atom, AtomName aname[],
-                         ivector elem, ivector amap, int nAtoms )  {
-AtomName      a;
-realtype      dx,dy,dz,d0;
-ivector       amapm;
-int           i,j,k, mon_atom, rc;
-Boolean       done;
+int translateHydrogens ( ccp4srs::PMonomer monomer,
+                         mmdb::PPAtom atom, mmdb::AtomName aname[],
+                         mmdb::ivector elem, mmdb::ivector amap,
+                         int nAtoms )  {
+mmdb::AtomName a;
+mmdb::realtype dx,dy,dz,d0;
+mmdb::ivector  amapm;
+int            i,j,k, mon_atom, rc;
+bool           done;
 
   // calculate nearest neighbours for hydrogens
 
   for (i=0;i<nAtoms;i++)
     if (elem[i]==1)  {  // check only hydrogens
-      d0 = MaxReal;
+      d0 = mmdb::MaxReal;
       k  = -1;
       for (j=0;j<nAtoms;j++)
         if (elem[j]>1)  {
@@ -128,11 +132,11 @@
   // make all possible name-based renamings
 
   amapm = NULL;
-  GetVectorMemory ( amapm,monomer->n_atoms(),0 );
+  mmdb::GetVectorMemory ( amapm,monomer->n_atoms(),0 );
   for (j=0;j<monomer->n_atoms();j++)
     amapm[j] = 0;
 
-  done = True;
+  done = true;
   for (i=0;i<nAtoms;i++)
     if (elem[i]==1)  {  // check only hydrogens
       k = -1;
@@ -149,7 +153,7 @@
         amap [i] = -1; // mapped
         amapm[k] = -1; // used
       } else  {
-        done = False;
+        done = false;
       }
     }
 
@@ -159,7 +163,7 @@
 
     for (i=0;i<nAtoms;i++)
       if ((elem[i]==1) && (amap[i]>=0))  {
-        strcpy_css ( a,atom[amap[i]]->name );
+        mmdb::strcpy_css ( a,atom[amap[i]]->name );
         mon_atom = monomer->atom_no ( a );
         if (mon_atom>=0)  {
           k = 0;
@@ -188,20 +192,21 @@
 
   }
 
-  FreeVectorMemory ( amapm,0 );
+  mmdb::FreeVectorMemory ( amapm,0 );
 
   return rc;
 
 }
 
-int processMonomer ( PCCP4SRSMonomer monomer,
-                     PPCAtom atom, AtomName aname[],
-                     ivector elem, ivector amap, int nAtoms )  {
-AtomName a;
-int      i,j,k;
-Boolean  areHydrogens;
+int processMonomer ( ccp4srs::PMonomer monomer,
+                     mmdb::PPAtom atom, mmdb::AtomName aname[],
+                     mmdb::ivector elem, mmdb::ivector amap,
+                     int nAtoms )  {
+mmdb::AtomName a;
+int            i,j,k;
+bool           areHydrogens;
 
-  areHydrogens = False;
+  areHydrogens = false;
 
   // named as in current Monomer Library?
   k = 1;
@@ -212,7 +217,7 @@
         if (!strcmp(aname[i],monomer->atom(j)->name()))
           k = j;
     } else
-      areHydrogens = True;
+      areHydrogens = true;
 
   if (k>=0)  {
     if (areHydrogens)
@@ -265,7 +270,7 @@
 
 
 
-cpstr special_name[] = {
+mmdb::cpstr special_name[] = {
     "Ar", "A",
     "Cr", "C",
     "Tr", "T",
@@ -311,29 +316,29 @@
 };
 
 
-void translateResidue ( PCResidue res, PCCP4SRSManager srs,
-                        PCFile structFile )  {
-PCCP4SRSMonomer monomer;
-PPCAtom         atom;
-AtomName       *aname;
-ivector         elem,amap;
-char            S[1000];
-cpstr           p;
-int             nAtoms,nAtoms0,nNonHAtoms0, i,rc;
+void translateResidue ( mmdb::PResidue res, ccp4srs::PManager srs,
+                        mmdb::io::PFile structFile )  {
+ccp4srs::PMonomer monomer;
+mmdb::PPAtom      atom;
+mmdb::AtomName   *aname;
+mmdb::ivector     elem,amap;
+char              S[1000];
+mmdb::cpstr       p;
+int               nAtoms,nAtoms0,nNonHAtoms0, i,rc;
 
   atom   = NULL;
   elem   = NULL;
   nAtoms = 0;
   res->GetAtomTable1 ( atom,nAtoms );
-  aname       = new AtomName[nAtoms];
-  GetVectorMemory ( elem,nAtoms,0 );
-  GetVectorMemory ( amap,nAtoms,0 );
+  aname       = new mmdb::AtomName[nAtoms];
+  mmdb::GetVectorMemory ( elem,nAtoms,0 );
+  mmdb::GetVectorMemory ( amap,nAtoms,0 );
 
   nAtoms0     = 0; // number of atoms in main location
   nNonHAtoms0 = 0;
   for (i=0;i<nAtoms;i++)  {
-    strcpy_css ( aname[i],atom[i]->name );
-    elem[i] = getElementNo ( atom[i]->element );
+    mmdb::strcpy_css ( aname[i],atom[i]->name );
+    elem[i] = mmdb::getElementNo ( atom[i]->element );
     if ((!atom[i]->altLoc[0]) || (!atom[i]->altLoc==' '))  {
       nAtoms0++;
       if (elem[i]>1)
@@ -411,8 +416,8 @@
     printf ( " *** residue %s could not be identified\n",
              res->GetResidueID(S) );
 
-  FreeVectorMemory ( amap,0 );
-  FreeVectorMemory ( elem,0 );
+  mmdb::FreeVectorMemory ( amap,0 );
+  mmdb::FreeVectorMemory ( elem,0 );
 
   delete[] aname;
   if (atom)  delete[] atom;
@@ -422,13 +427,13 @@
 
 int main ( int argc, char ** argv, char ** env )  {
 UNUSED_ARGUMENT(env);
-PCCP4SRSManager srs;
-PCMMDBManager   mmdb;
-PPCResidue      res;
-PCFile          structFile;
-char            S[1000];
-int             selHnd,nResidues;
-int             argNo,rc, i;
+ccp4srs::PManager srs;
+mmdb::PManager    mmdb;
+mmdb::PPResidue   res;
+mmdb::io::PFile   structFile;
+char              S[1000];
+int               selHnd,nResidues;
+int               argNo,rc, i;
 
   if (argc<3)  {
     printInstructions ( argv[0] );
@@ -437,7 +442,7 @@
 
   //  1.  Make routine initializations, which must always be done
   //      before working with MMDB
-  InitMatType();
+  mmdb::InitMatType();
 
   // $CLIB/ccp4srs/srsdata
 
@@ -457,9 +462,9 @@
     argNo = 1;
   }
 
-  srs = new CCP4SRSManager();
+  srs = new ccp4srs::Manager();
   rc = srs->loadIndex ( S );
-  if (rc!=CCP4SRS_Ok)  {
+  if (rc!=ccp4srs::CCP4SRS_Ok)  {
     printf ( " *** *.srs files not found at '%s'.\n",S );
     delete srs;
     return 1;
@@ -472,7 +477,7 @@
 
   // 4. Select all residues
   selHnd = mmdb->NewSelection();
-  mmdb->Select ( selHnd,STYPE_RESIDUE,"*",SKEY_NEW );
+  mmdb->Select ( selHnd,mmdb::STYPE_RESIDUE,"*",mmdb::SKEY_NEW );
 
   // 5. Obtain selected residues
   mmdb->GetSelIndex ( selHnd,res,nResidues );
diff -ruN ccp4srs-old/srsview.cpp ccp4srs/srsview.cpp
--- ccp4srs-old/srsview.cpp	2014-03-24 10:40:19.000000000 -0700
+++ ccp4srs/srsview.cpp	2014-09-09 21:34:12.000000000 -0700
@@ -12,16 +12,14 @@
 // =================================================================
 //
 
-#ifndef  __STRING_H
 #include <string.h>
-#endif
 
 #include "ccp4srs/ccp4srs_manager.h"
 #include "ccp4srs/ccp4srs_defs.h"
 
 
 
-void printInstructions ( cpstr argv0 )  {
+void printInstructions ( mmdb::cpstr argv0 )  {
 
   printf (
     "\n"
@@ -47,20 +45,48 @@
 
 }
 
+void printSmiles ( mmdb::cpstr title, ccp4srs::PSmiles smiles )  {
+mmdb::cpstr  ver,plain,canonical;
+  if (!smiles->isEmpty())  {
+    ver       = smiles->getVersion();
+    plain     = smiles->getSmiles();
+    canonical = smiles->getCanonical();
+    printf ( " Smiles from %s version %s\n",title,ver );
+    if (plain)
+      printf ( "      plain: %s\n",plain );
+    if (canonical)
+      printf ( "  canonical: %s\n",canonical );
+  }
+}
+
+void printInChiI ( ccp4srs::PSmiles smiles )  {
+mmdb::cpstr  ver,plain,canonical;
+  if (!smiles->isEmpty())  {
+    ver       = smiles->getVersion();
+    plain     = smiles->getInChI();
+    canonical = smiles->getInChIKey();
+    printf ( " InChI version %s\n",ver );
+    if (plain)
+      printf ( "      InChI: %s\n",plain );
+    if (canonical)
+      printf ( "  InChI Key: %s\n",canonical );
+  }
+}
+
 
 int main ( int argc, char ** argv, char ** env )  {
 UNUSED_ARGUMENT(env);
-PCCP4SRSManager srs;
-PCCP4SRSMonomer Monomer;
-PCCP4SRSAtom    Atom;
-PCCP4SRSBond    Bond;
-PCCP4SRSAngle   Angle;
-PCGraph         Graph;
-AtomName        aname;
-Element         elem;
-char            S[1000];
-realtype        total_charge;
-int             rc,i,l, argNo;
+ccp4srs::PManager  srs;
+ccp4srs::PMonomer  Monomer;
+ccp4srs::PAtom     Atom;
+ccp4srs::PBond     Bond;
+ccp4srs::PAngle    Angle;
+mmdb::math::PGraph Graph;
+mmdb::AtomName     aname;
+mmdb::Element      elem;
+char               S[1000];
+mmdb::realtype     total_charge;
+int                rc,i,l, argNo;
 
   if (argc<2)  {
     printInstructions ( argv[0] );
@@ -69,7 +95,7 @@
 
   //  1.  Make routine initializations, which must always be done
   //      before working with MMDB
-  InitMatType();
+  mmdb::InitMatType();
 
   //  2.  Load SRS index
   if (!strcmp(argv[1],"-f"))  {
@@ -87,9 +113,9 @@
     argNo = 1;
   }
 
-  srs = new CCP4SRSManager();
+  srs = new ccp4srs::Manager();
   rc = srs->loadIndex ( S );
-  if (rc!=CCP4SRS_Ok)  {
+  if (rc!=ccp4srs::CCP4SRS_Ok)  {
     printf ( " *** *.srs files not found at '%s'.\n",S );
     delete srs;
     return 1;
@@ -163,7 +189,7 @@
                  Atom->energy_type(),
                  Atom->chirality  (),
                  Atom->leaving    () );
-        if (Atom->x()>-MaxShortReal/2.1)
+        if (Atom->x()>-mmdb::MaxShortReal/2.1)
               printf ( "|%10.3f|%10.3f|%10.3f\n",
                        Atom->x(),Atom->y(),Atom->z() );
         else  printf ( "|   ****   |   ****   |   ****   \n" );
@@ -211,15 +237,15 @@
       for (i=0;i<Monomer->n_bonds();i++)  {
         Bond = Monomer->bond(i);
         switch (Bond->order())  {
-          case CCP4SRSBond::noOrder : strcpy ( S,"nord" );  break;
-          case CCP4SRSBond::Single  : strcpy ( S,"sing" );  break;
-          case CCP4SRSBond::Aromatic: strcpy ( S,"arom" );  break;
-          case CCP4SRSBond::Double  : strcpy ( S,"doub" );  break;
-          case CCP4SRSBond::Triple  : strcpy ( S,"trip" );  break;
-          case CCP4SRSBond::Deloc   : strcpy ( S,"delc" );  break;
-          case CCP4SRSBond::Covalent: strcpy ( S,"covl" );  break;
-          case CCP4SRSBond::Metal   : strcpy ( S,"metl" );  break;
-          default                   : strcpy ( S,"unkn" );
+          case ccp4srs::Bond::noOrder : strcpy ( S,"nord" );  break;
+          case ccp4srs::Bond::Single  : strcpy ( S,"sing" );  break;
+          case ccp4srs::Bond::Aromatic: strcpy ( S,"arom" );  break;
+          case ccp4srs::Bond::Double  : strcpy ( S,"doub" );  break;
+          case ccp4srs::Bond::Triple  : strcpy ( S,"trip" );  break;
+          case ccp4srs::Bond::Deloc   : strcpy ( S,"delc" );  break;
+          case ccp4srs::Bond::Covalent: strcpy ( S,"covl" );  break;
+          case ccp4srs::Bond::Metal   : strcpy ( S,"metl" );  break;
+          default                     : strcpy ( S,"unkn" );
         }
         printf ( "%4i| %3i  %3i|%5s|%10.3f|%10.3f\n",
                  i+1,Bond->atom1()+1,Bond->atom2()+1,S,
@@ -240,6 +266,12 @@
         }
       }
 
+
+      printSmiles ( "ACDLabs",Monomer->getACDLabs() );
+      printSmiles ( "CACTVS" ,Monomer->getCACTVS () );
+      printSmiles ( "OpenEye",Monomer->getOpenEye() );
+      printInChiI ( Monomer->getInChI() );
+
       /*
       if (Monomer->nSBS->nLeavingAtoms>0)  {
         printf ( "\n Leaving atoms:\n" );
@@ -255,9 +287,9 @@
     Graph = NULL;  // must!
     i     = srs->getGraph ( argv[argNo+1],Graph,0 );
 
-    if (i==CCP4SRS_EntryNotFound)
+    if (i==ccp4srs::CCP4SRS_EntryNotFound)
       printf ( " --- compound %s not found in SRS.\n",argv[argNo+1]);
-    else if (i==CCP4SRS_FileNotFound)
+    else if (i==ccp4srs::CCP4SRS_FileNotFound)
       printf ( " --- graph descriptions are not found in SRS.\n" );
     else  {
 
