start

GNUmakefile.in

@@ -62,6 +62,14 @@ CXXFLAGS			+= -O2
 DEFINES				+= NDEBUG
 endif
 
+MRC					= @MRC@
+CIFPP_RSRC			= @CIFPP_RSRC@
+
+ifneq "$(MRC)" ""
+
+DEFINES += USE_RSRC
+endif
+
 # targets
 
 VPATH += src:test
@@ -79,7 +87,14 @@ $(OBJDIR):
 APPLICATION = @PACKAGE_NAME@
 
 OBJECTS = $(APPLICATION:%=$(OBJDIR)/%.o)
-	
+
+ifneq "$(MRC)" ""
+OBJECTS += $(APPLICATION:%=$(OBJDIR)/%_rsrc.o)
+
+$(OBJDIR)/$(APPLICATION)_rsrc.o: $(CIFPP_RSRC)/dictionaries
+	$(MRC) -o $@ $^
+endif
+
 -include $(OBJECTS:%.o=%.d)
 
 $(OBJECTS:.o=.d):

configure

@@ -625,6 +625,7 @@ ac_includes_default="\
 
 ac_subst_vars='LTLIBOBJS
 LIBOBJS
+HAVE_DLADDR
 LIBBZ2_LDFLAGS
 LIBBZ2_CPPFLAGS
 LIBZ_LDFLAGS
@@ -635,6 +636,7 @@ CCP4
 CXXCPP
 LIBCIFPP_LDFLAGS
 LIBCIFPP_CPPFLAGS
+CIFPP_RSRC
 BOOST_PROGRAM_OPTIONS_LIB
 BOOST_REGEX_LIB
 BOOST_THREAD_LIB
@@ -660,6 +662,7 @@ build_os
 build_vendor
 build_cpu
 build
+MRC
 PKG_CONFIG
 DEBUG
 INSTALL_DATA
@@ -735,6 +738,7 @@ LIBS
 CPPFLAGS
 CCC
 DEBUG
+MRC
 CC
 CFLAGS
 CPP
@@ -1414,6 +1418,7 @@ Some influential environment variables:
   CPPFLAGS    (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
               you have headers in a nonstandard directory <include dir>
   DEBUG       Build a debug version of the application
+  MRC         Specify a location for the mrc executable
   CC          C compiler command
   CFLAGS      C compiler flags
   CPP         C preprocessor
@@ -3437,6 +3442,55 @@ fi
 
 
 
+
+
+if test "x$MRC" = "x"; then
+	# Extract the first word of "mrc", so it can be a program name with args.
+set dummy mrc; 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_MRC+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  case $MRC in
+  [\\/]* | ?:[\\/]*)
+  ac_cv_path_MRC="$MRC" # 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_MRC="$as_dir/$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
+MRC=$ac_cv_path_MRC
+if test -n "$MRC"; then
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MRC" >&5
+$as_echo "$MRC" >&6; }
+else
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+
+if test "x$MRC" = "x"; then
+	as_fn_error $? "mrc not found, the application will be built without resources" "$LINENO" 5
+fi
+
 # 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
@@ -6334,6 +6388,8 @@ if test "${with_cif__+set}" = set; then :
 			CXXFLAGS="$CXXFLAGS -I ${withval}/include"
 			LDFLAGS="$LDFLAGS -L${withval}/.libs"
 			LIBS="$LIBS -lcif++"
+			CIFPP_RSRC=${withval}/rsrc
+
 
 fi
 
@@ -6990,6 +7046,69 @@ else
 fi
 
 
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing dladdr1" >&5
+$as_echo_n "checking for library containing dladdr1... " >&6; }
+if ${ac_cv_search_dladdr1+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  ac_func_search_save_LIBS=$LIBS
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dladdr1 ();
+int
+main ()
+{
+return dladdr1 ();
+  ;
+  return 0;
+}
+_ACEOF
+for ac_lib in '' dl; do
+  if test -z "$ac_lib"; then
+    ac_res="none required"
+  else
+    ac_res=-l$ac_lib
+    LIBS="-l$ac_lib  $ac_func_search_save_LIBS"
+  fi
+  if ac_fn_cxx_try_link "$LINENO"; then :
+  ac_cv_search_dladdr1=$ac_res
+fi
+rm -f core conftest.err conftest.$ac_objext \
+    conftest$ac_exeext
+  if ${ac_cv_search_dladdr1+:} false; then :
+  break
+fi
+done
+if ${ac_cv_search_dladdr1+:} false; then :
+
+else
+  ac_cv_search_dladdr1=no
+fi
+rm conftest.$ac_ext
+LIBS=$ac_func_search_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_dladdr1" >&5
+$as_echo "$ac_cv_search_dladdr1" >&6; }
+ac_res=$ac_cv_search_dladdr1
+if test "$ac_res" != no; then :
+  test "$ac_res" = "none required" || LIBS="$ac_res $LIBS"
+
+
+$as_echo "#define HAVE_DLADDR 1" >>confdefs.h
+
+
+fi
+
+
+
+
 
 ac_config_files="$ac_config_files GNUmakefile"
 

configure.ac

@@ -16,6 +16,17 @@ AC_ARG_VAR([DEBUG], [Build a debug version of the application])
 
 AC_PATH_PROG([PKG_CONFIG], [pkg-config])
 
+AC_ARG_VAR([MRC], [Specify a location for the mrc executable])
+
+dnl We really want to use mrc
+if test "x$MRC" = "x"; then
+	AC_PATH_PROG([MRC], [mrc])
+fi
+
+if test "x$MRC" = "x"; then
+	AC_MSG_ERROR([mrc not found, the application will be built without resources])
+fi
+
 AX_PTHREAD
 
 AX_BOOST_BASE([1.65.1], [], [AC_MSG_ERROR([Could not find a recent version of boost])])
@@ -32,6 +43,7 @@ AC_ARG_WITH([cif++],
 			CXXFLAGS="$CXXFLAGS -I ${withval}/include"
 			LDFLAGS="$LDFLAGS -L${withval}/.libs"
 			LIBS="$LIBS -lcif++"
+			AC_SUBST([CIFPP_RSRC], [${withval}/rsrc]) 
 		])
 
 
@@ -99,6 +111,13 @@ AX_CHECK_LIBRARY([LIBBZ2], [bzlib.h], [bz2],
 				 [ LIBS="$LIBS -lbz2"],
                  [AC_MSG_ERROR([libbz2 not found - compressed files not supported])])
 
+AC_SEARCH_LIBS([dladdr1], [dl],
+	[
+		AC_DEFINE([HAVE_DLADDR], 1, [Define if the system has dladdr])
+	], [], [])
+
+AC_SUBST([HAVE_DLADDR])
+
 dnl AC_MSG_CHECKING([clipper version])
 dnl AC_COMPILE_IFELSE(
 dnl 	[read_test(clipper-test.cpp)],

src/dssp.cpp

@@ -9,6 +9,8 @@
 
 #include <cif++/Config.h>
 #include <cif++/Structure.h>
+#include <cif++/Secondary.h>
+#include <cif++/CifUtils.h>
 
 #include <boost/program_options.hpp>
 
@@ -33,6 +35,19 @@ void print_what (const std::exception& e)
 
 // --------------------------------------------------------------------
 
+void writeDSSP(const mmcif::Structure& structure, std::ostream& os)
+{
+	mmcif::DSSP dssp(structure);
+
+}
+
+void annotateDSSP(const mmcif::Structure& structure, std::ostream& os)
+{
+
+}
+
+// --------------------------------------------------------------------
+
 int main(int argc, char* argv[])
 {
 	using namespace std::literals;
@@ -47,7 +62,13 @@ int main(int argc, char* argv[])
 
 		("help,h",											"Display help message")
 		("version",											"Print version")
-		
+
+		("output-format",		po::value<std::string>(),	"Output format, can be either 'dssp' for classic DSSP or 'mmcif' for annotated mmCIF. The default is chosen based on the extension of the output file, if any.")
+
+#if not USE_RSRC
+		("rsrc-dir",			po::value<std::string>(),	"Directory containing the 'resources' used by this application")
+#endif
+
 		("verbose,v",										"verbose output")
 		;
 	
@@ -88,10 +109,27 @@ int main(int argc, char* argv[])
 		exit(1);
 	}
 
+	if (vm.count("output-format") and vm["output-format"].as<std::string>() != "dsps" and vm["output-format"].as<std::string>() != "mmcif")
+	{
+		std::cerr << "Output format should be one of 'dssp' or 'mmcif'" << std::endl;
+		exit(1);
+	}
+
 	cif::VERBOSE = vm.count("verbose") != 0;
 	if (vm.count("debug"))
 		cif::VERBOSE = vm["debug"].as<int>();
 
+	// --------------------------------------------------------------------
+	
+#if USE_RSRC
+	cif::rsrc_loader::init();
+#else
+	std::string rsrc_dir = ".";
+	cif::rsrc_loader::init({ { cif::rsrc_loader_type::file, rsrc_dir }});
+#endif
+
+	// --------------------------------------------------------------------
+	
 	if (vm.count("dict"))
 	{
 		for (auto dict: vm["dict"].as<std::vector<std::string>>())
@@ -102,6 +140,8 @@ int main(int argc, char* argv[])
 	mmcif::Structure structure(f);
 	
 	// --------------------------------------------------------------------
+
+	auto fmt = vm["output-format"].as<std::string>();
 	
 	if (vm.count("output"))
 	{
@@ -111,10 +151,19 @@ int main(int argc, char* argv[])
 			std::cerr << "Could not open output file" << std::endl;
 			exit(1);
 		}
-		// of << calculateZScores(structure, nShuffles);
+		
+		if (fmt == "dssp")
+			writeDSSP(structure, of);
+		else
+			annotateDSSP(structure, of);
+	}
+	else
+	{
+		if (fmt == "dssp")
+			writeDSSP(structure, std::cout);
+		else
+			annotateDSSP(structure, std::cout);
 	}
-	// else
-	// 	cout << calculateZScores(structure, nShuffles) << endl;
 	
 	return 0;
 }