changes from Debian included

GNUmakefile.in

@@ -161,7 +161,7 @@ else
 src/revision.hpp:
 src/revision.hpp:
 	@ echo 'const char kRevision[] = R"(' > $@
 	@ echo 'const char kRevision[] = R"(' > $@
 	@ echo libcifpp-version: $(VERSION) >> $@
 	@ echo libcifpp-version: $(VERSION) >> $@
-	@ echo Date:   $$(date --iso-8601) >> $@
+	@ echo Date:   $$(date --utc --date=@$(SOURCE_DATE_EPOCH) --iso-8601) >> $@
 	@ echo ')";' >> $@
 	@ echo ')";' >> $@
 
 
 endif
 endif

configure

@@ -640,6 +640,8 @@ BOOST_IOSTREAMS_LIB
 BOOST_LDFLAGS
 BOOST_LDFLAGS
 BOOST_CPPFLAGS
 BOOST_CPPFLAGS
 SET_MAKE
 SET_MAKE
+PKG_CONFIG_LIBDIR
+PKG_CONFIG_PATH
 PKG_CONFIG
 PKG_CONFIG
 CCP4
 CCP4
 UPDATE_REVISION
 UPDATE_REVISION
@@ -766,7 +768,10 @@ CC
 CFLAGS
 CFLAGS
 LT_SYS_LIBRARY_PATH
 LT_SYS_LIBRARY_PATH
 DEBUG
 DEBUG
-CCP4'
+CCP4
+PKG_CONFIG
+PKG_CONFIG_PATH
+PKG_CONFIG_LIBDIR'
 
 
 
 
 # Initialize some variables set by options.
 # Initialize some variables set by options.
@@ -1444,6 +1449,11 @@ Some influential environment variables:
               User-defined run-time library search path.
               User-defined run-time library search path.
   DEBUG       Build a debug version of the library
   DEBUG       Build a debug version of the library
   CCP4        The location where CCP4 is installed
   CCP4        The location where CCP4 is installed
+  PKG_CONFIG  path to pkg-config utility
+  PKG_CONFIG_PATH
+              directories to add to pkg-config's search path
+  PKG_CONFIG_LIBDIR
+              path overriding pkg-config's built-in search path
 
 
 Use these variables to override the choices made by `configure' or to help
 Use these variables to override the choices made by `configure' or to help
 it to find libraries and programs with nonstandard names/locations.
 it to find libraries and programs with nonstandard names/locations.
@@ -16101,8 +16111,17 @@ UPDATE_REVISION=$UPDATE_REVISION
 
 
 
 
 
 
-# Extract the first word of "pkg-config", so it can be a program name with args.
-set dummy pkg-config; ac_word=$2
+
+
+
+
+
+
+
+if test "x$ac_cv_env_PKG_CONFIG_set" != "xset"; then
+	if test -n "$ac_tool_prefix"; then
+  # Extract the first word of "${ac_tool_prefix}pkg-config", so it can be a program name with args.
+set dummy ${ac_tool_prefix}pkg-config; ac_word=$2
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
 $as_echo_n "checking for $ac_word... " >&6; }
 $as_echo_n "checking for $ac_word... " >&6; }
 if ${ac_cv_path_PKG_CONFIG+:} false; then :
 if ${ac_cv_path_PKG_CONFIG+:} false; then :
@@ -16141,6 +16160,77 @@ $as_echo "no" >&6; }
 fi
 fi
 
 
 
 
+fi
+if test -z "$ac_cv_path_PKG_CONFIG"; then
+  ac_pt_PKG_CONFIG=$PKG_CONFIG
+  # Extract the first word of "pkg-config", so it can be a program name with args.
+set dummy pkg-config; 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_path_ac_pt_PKG_CONFIG+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  case $ac_pt_PKG_CONFIG in
+  [\\/]* | ?:[\\/]*)
+  ac_cv_path_ac_pt_PKG_CONFIG="$ac_pt_PKG_CONFIG" # Let the user override the test with a path.
+  ;;
+  *)
+  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_path_ac_pt_PKG_CONFIG="$as_dir/$ac_word$ac_exec_ext"
+    $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+  done
+IFS=$as_save_IFS
+
+  ;;
+esac
+fi
+ac_pt_PKG_CONFIG=$ac_cv_path_ac_pt_PKG_CONFIG
+if test -n "$ac_pt_PKG_CONFIG"; then
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_pt_PKG_CONFIG" >&5
+$as_echo "$ac_pt_PKG_CONFIG" >&6; }
+else
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+  if test "x$ac_pt_PKG_CONFIG" = x; then
+    PKG_CONFIG=""
+  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
+    PKG_CONFIG=$ac_pt_PKG_CONFIG
+  fi
+else
+  PKG_CONFIG="$ac_cv_path_PKG_CONFIG"
+fi
+
+fi
+if test -n "$PKG_CONFIG"; then
+	_pkg_min_version=0.9.0
+	{ $as_echo "$as_me:${as_lineno-$LINENO}: checking pkg-config is at least version $_pkg_min_version" >&5
+$as_echo_n "checking pkg-config is at least version $_pkg_min_version... " >&6; }
+	if $PKG_CONFIG --atleast-pkgconfig-version $_pkg_min_version; then
+		{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+	else
+		{ $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+		PKG_CONFIG=""
+	fi
+fi
 
 
 for ac_func in floor pow rint sqrt strchr strerror
 for ac_func in floor pow rint sqrt strchr strerror
 do :
 do :

configure.ac

@@ -94,7 +94,7 @@ AC_SUBST([UPDATE_REVISION], [$UPDATE_REVISION])
 
 
 AC_ARG_VAR([CCP4], [The location where CCP4 is installed])
 AC_ARG_VAR([CCP4], [The location where CCP4 is installed])
 
 
-AC_PATH_PROG([PKG_CONFIG], [pkg-config])
+PKG_PROG_PKG_CONFIG
 
 
 AC_CHECK_FUNCS([floor pow rint sqrt strchr strerror])
 AC_CHECK_FUNCS([floor pow rint sqrt strchr strerror])
 AC_CHECK_HEADERS([sys/ioctl.h])
 AC_CHECK_HEADERS([sys/ioctl.h])

src/Cif2PDB.cpp

@@ -624,7 +624,10 @@ void WriteTitle(std::ostream& pdbFile, Datablock& db)
 				pdbFile << (boost::format(" %-6.6s") % (i < types.size() ? types[i] : std::string())).str();
 				pdbFile << (boost::format(" %-6.6s") % (i < types.size() ? types[i] : std::string())).str();
 			pdbFile << std::endl;
 			pdbFile << std::endl;
 			
 			
-			types.erase(types.begin(), types.begin() + std::min(types.size(), 4UL));
+			if (types.size() > 4)
+				types.erase(types.begin(), types.begin() + 4);
+			else
+				types.clear();
 		}
 		}
 		while (types.empty() == false);
 		while (types.empty() == false);
 	}
 	}

tools/update-dictionary-script

@@ -7,9 +7,18 @@ if [ "$EUID" -ne 0 ]
 	exit
 	exit
 fi
 fi
 
 
-# create cache directory if it doesn't exist
+if [ -f /etc/libcifpp.conf ] ; then
+	. /etc/libcifpp.conf
+fi
+
+# check to see if we're supposed to run at all
+if [ "$update" != "true" ] ; then
+	exit
+fi
+
+# if cache directory doesn't exist, exit. 
 if ! [ -d /var/cache/libcifpp ]; then
 if ! [ -d /var/cache/libcifpp ]; then
-	install -d -m755 /var/cache/libcifpp
+	exit
 fi
 fi
 
 
 # fetch the dictionary
 # fetch the dictionary