update configure to configure data directories

.gitignore

@@ -18,3 +18,4 @@ src/Config.hpp.in~
 src/Config.hpp
 aclocal.m4
 version-info-*.txt
+tools/update-dictionary-script

GNUmakefile.in

@@ -47,8 +47,8 @@ pkgconfigdir		= $(libdir)/pkgconfig
 CCP4DIR				= @CCP4@
 CLIBD				= $(CCP4DIR:%=%/lib/data)
 
-CACHE_DIR			= $(DESTDIR)/var/cache/libcifpp
-DATA_DIR			= $(datadir)/libcifpp
+CACHE_DIR			= $(DESTDIR)@DATA_CACHE_DIR@
+DATA_DIR			= @DATA_LIB_DIR@
 CRON_DIR			= $(DESTDIR)/etc/cron.weekly
 
 DEFINES				+= CACHE_DIR='"$(CACHE_DIR)"' DATA_DIR='"$(DATA_DIR)"'

configure

@@ -635,6 +635,8 @@ ac_includes_default="\
 
 ac_subst_vars='LTLIBOBJS
 LIBOBJS
+DATA_CACHE_DIR
+DATA_LIB_DIR
 BOOST_REGEX_LIB
 BOOST_DATE_TIME_LIB
 BOOST_IOSTREAMS_LIB
@@ -779,7 +781,9 @@ DEBUG
 CCP4
 PKG_CONFIG
 PKG_CONFIG_PATH
-PKG_CONFIG_LIBDIR'
+PKG_CONFIG_LIBDIR
+DATA_LIB_DIR
+DATA_CACHE_DIR'
 
 
 # Initialize some variables set by options.
@@ -1467,6 +1471,10 @@ Some influential environment variables:
               directories to add to pkg-config's search path
   PKG_CONFIG_LIBDIR
               path overriding pkg-config's built-in search path
+  DATA_LIB_DIR
+              The location where to store packaged dictionary files
+  DATA_CACHE_DIR
+              The location where to store cached dictionary files
 
 Use these variables to override the choices made by `configure' or to help
 it to find libraries and programs with nonstandard names/locations.
@@ -18364,7 +18372,15 @@ _ACEOF
 fi
 
 
-ac_config_files="$ac_config_files GNUmakefile libcifpp.pc"
+
+
+DATA_LIB_DIR=$datadir/libcifpp
+
+
+
+DATA_CACHE_DIR=/var/cache/libcifpp
+
+ac_config_files="$ac_config_files GNUmakefile libcifpp.pc tools/update-dictionary-script"
 
 cat >confcache <<\_ACEOF
 # This file is a shell script that caches the results of configure
@@ -19450,6 +19466,7 @@ do
     "libtool") CONFIG_COMMANDS="$CONFIG_COMMANDS libtool" ;;
     "GNUmakefile") CONFIG_FILES="$CONFIG_FILES GNUmakefile" ;;
     "libcifpp.pc") CONFIG_FILES="$CONFIG_FILES libcifpp.pc" ;;
+    "tools/update-dictionary-script") CONFIG_FILES="$CONFIG_FILES tools/update-dictionary-script" ;;
 
   *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
   esac

configure.ac

@@ -114,5 +114,15 @@ AX_BOOST_REGEX
 
 AC_CHECK_LIB([atomic], [atomic_flag_clear])
 
+dnl Set output variables for the various directories
+AC_ARG_VAR([DATA_LIB_DIR], [The location where to store packaged dictionary files])
+AC_SUBST([DATA_LIB_DIR])
+DATA_LIB_DIR=$datadir/libcifpp
+
+AC_ARG_VAR([DATA_CACHE_DIR], [The location where to store cached dictionary files])
+AC_SUBST([DATA_CACHE_DIR])
+DATA_CACHE_DIR=/var/cache/libcifpp
+
 AC_OUTPUT([GNUmakefile
-		   libcifpp.pc])
+		   libcifpp.pc
+		   tools/update-dictionary-script])

libcifpp.pc.in

@@ -2,6 +2,7 @@ prefix=@prefix@
 exec_prefix=@exec_prefix@
 libdir=@libdir@
 includedir=@includedir@
+datalibdir=@datarootdir@/libcifpp
 
 Name: libcifpp
 Description: C++ library for the manipulation of mmCIF files.

src/PDB2Cif.cpp

@@ -5778,24 +5778,6 @@ void PDBFileParser::Parse(std::istream& is, cif::File& result)
 
 		auto& atom_site = *getCategory("atom_site");
 
-		// for (const auto& [asym1, seq1, atom1, asym2, seq2, atom2]: getCategory("struct_conn")
-		// 	->find<std::string,std::string,std::string,std::string,std::string,std::string>(
-		// 		"pdbx_dist_value"_key == 0 or "pdbx_dist_value"_key == Null,
-		// 		{ "ptnr1_label_asym_id", "ptnr1_label_seq_id", "ptnr1_label_atom_id",
-		// 		"ptnr2_label_asym_id", "ptnr2_label_seq_id", "ptnr2_label_atom_id" }))
-		// {
-		// 	auto a1 = atom_site.find1("label_asym_id"_key == asym1 and "label_seq_id"_key == seq1 and "label_atom_id"_key == atom1);
-		// 	auto a2 = atom_site.find1("label_asym_id"_key == asym2 and "label_seq_id"_key == seq2 and "label_atom_id"_key == atom2);
-
-		// 	const auto& [x1, y1, z1] = a1.get<float,float,float>({"cartn_x", "cartn_y", "cartn_z"});
-		// 	const auto& [x2, y2, z2] = a2.get<float,float,float>({"cartn_x", "cartn_y", "cartn_z"});
-
-		// 	float distance = mmcif::Distance(mmcif::Point{x1, y1, z1}, mmcif::Point{x2, y2, z2});
-
-		// 	std::cerr << "Distance for link: " << distance << std::endl;
-
-		// }
-
 		for (auto r: getCategory("struct_conn")->find("pdbx_dist_value"_key == 0 or "pdbx_dist_value"_key == Null))
 		{
 			const auto& [asym1, seq1, atom1, symm1, asym2, seq2, atom2, symm2] = r.get<std::string,std::string,std::string,std::string,std::string,std::string,std::string,std::string>(

tools/update-dictionary-script.in

@@ -17,13 +17,13 @@ if [ "$update" != "true" ] ; then
 fi
 
 # if cache directory doesn't exist, exit. 
-if ! [ -d /var/cache/libcifpp ]; then
+if ! [ -d @DATA_CACHE_DIR@ ]; then
 	exit
 fi
 
 # fetch the dictionary
 
-dict=/var/cache/libcifpp/mmcif_pdbx_v50.dic
+dict=@DATA_CACHE_DIR@/mmcif_pdbx_v50.dic
 source=https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic.gz
 
 wget -O${dict}.gz ${source}