Version update, changelog, options

CMakeLists.txt

@@ -25,7 +25,7 @@
 cmake_minimum_required(VERSION 3.15)
 cmake_minimum_required(VERSION 3.15)
 
 
 # set the project name
 # set the project name
-project(mkdssp VERSION 4.2.3 LANGUAGES CXX)
+project(mkdssp VERSION 4.3 LANGUAGES CXX)
 
 
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 
 

changelog

+Version 4.3
+- Write new output by default
+- Fix some issues with this new output, typo e.g.
+- Added web service implementation
+- Added mmcif_pdbx dictionary extension
+
 Version 4.2.2.1
 Version 4.2.2.1
 - Fixed dependency on libcifpp
 - Fixed dependency on libcifpp
 
 

src/mkdssp.cpp

@@ -72,10 +72,8 @@ int d_main(int argc, const char *argv[])
 		mcfp::make_option<std::string>("output-format", "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."),
 		mcfp::make_option<std::string>("output-format", "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."),
 		mcfp::make_option<short>("min-pp-stretch", 3, "Minimal number of residues having PSI/PHI in range for a PP helix, default is 3"),
 		mcfp::make_option<short>("min-pp-stretch", 3, "Minimal number of residues having PSI/PHI in range for a PP helix, default is 3"),
 		mcfp::make_option("write-other", "If set, write the type OTHER for loops, default is to leave this out"),
 		mcfp::make_option("write-other", "If set, write the type OTHER for loops, default is to leave this out"),
-		mcfp::make_option("write-experimental", "If set, write the new, experimental DSSP output in mmCIF format, default is to leave this out"),
+		mcfp::make_option("no-dssp-categories", "If set, will suppress output of new DSSP output in mmCIF format"),
 
 
-		// mcfp::make_option("components",			po::value<std::string,	"Location of the components.cif file from CCD")
-	    // mcfp::make_option("extra-compounds",		po::value<std::string,	"File containing residue information for extra compounds in this specific target, should be either in CCD format or a CCP4 restraints file")
 		mcfp::make_option<std::string>("mmcif-dictionary", "Path to the mmcif_pdbx.dic file to use instead of default"),
 		mcfp::make_option<std::string>("mmcif-dictionary", "Path to the mmcif_pdbx.dic file to use instead of default"),
 
 
 		mcfp::make_option("help,h", "Display help message"),
 		mcfp::make_option("help,h", "Display help message"),
@@ -120,17 +118,7 @@ int d_main(int argc, const char *argv[])
 
 
 	// --------------------------------------------------------------------
 	// --------------------------------------------------------------------
 
 
-	// Load extra CCD definitions, if any
-
-	// if (config.has("compounds"))
-	// 	cif::add_file_resource("components.cif", config.get<std::string>("compounds"));
-	// else if (config.has("components"))
-	// 	cif::add_file_resource("components.cif", config.get<std::string>("components"));
-
-	// if (config.has("extra-compounds"))
-	// 	mmcif::CompoundFactory::instance().pushDictionary(config.get<std::string>("extra-compounds"));
-
-	// And perhaps a private mmcif_pdbx dictionary
+	// private mmcif_pdbx dictionary?
 	if (config.has("mmcif-dictionary"))
 	if (config.has("mmcif-dictionary"))
 		cif::add_file_resource("mmcif_pdbx.dic", config.get<std::string>("mmcif-dictionary"));
 		cif::add_file_resource("mmcif_pdbx.dic", config.get<std::string>("mmcif-dictionary"));
 
 
@@ -191,14 +179,14 @@ int d_main(int argc, const char *argv[])
 		if (fmt == "dssp")
 		if (fmt == "dssp")
 			writeDSSP(dssp, out);
 			writeDSSP(dssp, out);
 		else
 		else
-			annotateDSSP(f.front(), dssp, writeOther, config.has("write-experimental"), out);
+			annotateDSSP(f.front(), dssp, writeOther, not config.has("no-dssp-categories"), out);
 	}
 	}
 	else
 	else
 	{
 	{
 		if (fmt == "dssp")
 		if (fmt == "dssp")
 			writeDSSP(dssp, std::cout);
 			writeDSSP(dssp, std::cout);
 		else
 		else
-			annotateDSSP(f.front(), dssp, writeOther, config.has("write-experimental"), std::cout);
+			annotateDSSP(f.front(), dssp, writeOther, not config.has("no-dssp-categories"), std::cout);
 	}
 	}
 
 
 	return 0;
 	return 0;