Update for new libcifpp

.gitignore

@@ -4,3 +4,5 @@ version-info*.txt
 mkdssp
 .vs/
 build
+.gdb_history
+**/*.dssp

CMakeLists.txt

@@ -25,7 +25,7 @@
 cmake_minimum_required(VERSION 3.15)
 
 # set the project name
-project(mkdssp VERSION 4.0.4 LANGUAGES CXX)
+project(mkdssp VERSION 4.0.5 LANGUAGES CXX)
 
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 
@@ -120,7 +120,7 @@ find_package(Threads)
 
 # Note: use -DBoost_USE_STATIC_LIBS=ON to use boost static libraries
 
-find_package(cifpp 2.0.0 REQUIRED)
+find_package(cifpp 4.0.1 REQUIRED)
 find_package(Boost COMPONENTS date_time program_options)
 
 add_executable(mkdssp

changelog

+Version 4.0.5
+- The options for loading custom dictionary files and the like are now
+  visible in the help again.
+
 Version 4.0.4
 - New version string logic
 - Improved makefile

doc/mkdssp.1

-.TH mkdssp 1 "2021-08-31" "version 4.0.2" "User Commands"
+.TH mkdssp 1 "2021-08-31" "version 4.0.5" "User Commands"
 .if n .ad l
 .nh
 .SH NAME
@@ -40,6 +40,20 @@ angles within the range required to assing a PP helix.
 \fB--write-other\fR
 By default the new format does not write the structure information for OTHER.
 Use this flag to change that.
+.TP
+\fB--components\fR
+The knowledge of compounds is loaded from the CCD file \fIcomponents.cif\fR
+that should have been installed by \fIlibcifpp\fR. You can override that file
+by using this option.
+.TP
+\fB--extra-compounds\fR
+As an addition to the standard \fIcomponents.cif\fR file, you can add more
+files using this option. Files should be either in CCD format or should be
+CCP4 restraints files.
+.TP
+\fB--mmcif-dictionary\fR
+The default mmCIF dictionary file is installed by the \fIlibcifpp\fR library
+but you can override it using this option.
 .SH DETAILS
 The DSSP algorithm assings secondary structure based on the energy calculated
 for H-bonds.

src/dssp.cpp

@@ -154,6 +154,8 @@ std::string ResidueToDSSPLine(const mmcif::DSSP::ResidueInfo& info)
 
 void writeDSSP(const mmcif::Structure& structure, const mmcif::DSSP& dssp, std::ostream& os)
 {
+	auto &db = structure.datablock();
+
 	const std::string kFirstLine("==== Secondary Structure Definition by the program DSSP, NKI version 4.0                           ==== ");
 	boost::format kHeaderLine("%1% %|127t|%2%");
 
@@ -163,14 +165,14 @@ void writeDSSP(const mmcif::Structure& structure, const mmcif::DSSP& dssp, std::
 
 	date today = day_clock::local_day();
 
-	auto& cf = structure.getFile().file();
+	// auto& cf = structure.file();
 
 	os << kHeaderLine % (kFirstLine + "DATE=" + to_iso_extended_string(today)) % '.' << std::endl
 	   << kHeaderLine % "REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637" % '.' << std::endl
-	   << GetPDBHEADERLine(cf, 127) << '.' << std::endl
-	   << GetPDBCOMPNDLine(cf, 127) << '.' << std::endl
-	   << GetPDBSOURCELine(cf, 127) << '.' << std::endl
-	   << GetPDBAUTHORLine(cf, 127) << '.' << std::endl;
+	   << GetPDBHEADERLine(db, 127) << '.' << std::endl
+	   << GetPDBCOMPNDLine(db, 127) << '.' << std::endl
+	   << GetPDBSOURCELine(db, 127) << '.' << std::endl
+	   << GetPDBAUTHORLine(db, 127) << '.' << std::endl;
 
 	os << boost::format("%5.5d%3.3d%3.3d%3.3d%3.3d TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN) %|127t|%c") %
 			 stats.nrOfResidues % stats.nrOfChains % stats.nrOfSSBridges % stats.nrOfIntraChainSSBridges % (stats.nrOfSSBridges - stats.nrOfIntraChainSSBridges) % '.' << std::endl;
@@ -235,7 +237,7 @@ void writeDSSP(const mmcif::Structure& structure, const mmcif::DSSP& dssp, std::
 
 void annotateDSSP(mmcif::Structure& structure, const mmcif::DSSP& dssp, bool writeOther, std::ostream& os)
 {
-	auto& db = structure.getFile().data();
+	auto& db = structure.datablock();
 
 	if (dssp.empty())
 	{

src/mkdssp.cpp

@@ -83,6 +83,10 @@ int d_main(int argc, const char* argv[])
 		("min-pp-stretch",		po::value<short>(),			"Minimal number of residues having PSI/PHI in range for a PP helix, default is 3")
 		("write-other",										"If set, write the type OTHER for loops, default is to leave this out")
 
+		("components",			po::value<std::string>(),	"Location of the components.cif file from CCD")
+		("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")
+		("mmcif-dictionary",	po::value<std::string>(),	"Path to the mmcif_pdbx.dic file to use instead of default")
+
 		("help,h",											"Display help message")
 		("version",											"Print version")
 		("verbose,v",										"verbose output")
@@ -94,10 +98,7 @@ int d_main(int argc, const char* argv[])
 		("output,o",            po::value<std::string>(),	"Output to this file")
 		("debug,d",				po::value<int>(),			"Debug level (for even more verbose output)")
 
-		("compounds",			po::value<std::string>(),	"Location of the components.cif file from CCD")
-		("components",			po::value<std::string>(),	"Location of the components.cif file from CCD, alias")
-		("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")
-		("mmcif-dictionary",	po::value<std::string>(),	"Path to the mmcif_pdbx.dic file to use instead of default")
+		("compounds",			po::value<std::string>(),	"Location of the components.cif file from CCD, alias")
 		;
 
 	po::options_description cmdline_options;

test/1cbs-dssp.cif

@@ -2,6 +2,10 @@ data_1CBS
 # 
 _entry.id   1CBS
 #
+_audit_conform.dict_name       mmcif_pdbx.dic
+_audit_conform.dict_version    5.279
+_audit_conform.dict_location   http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
+# 
 loop_
 _database_2.database_id 
 _database_2.database_code 

test/unit-test.cpp

@@ -92,7 +92,7 @@ BOOST_AUTO_TEST_CASE(ut_mmcif_2)
 	using namespace cif::literals;
 
 	mmcif::File f("1cbs.cif.gz");
-	f.file().loadDictionary("mmcif_pdbx_v50");
+	f.loadDictionary("mmcif_pdbx_v50");
 
 	mmcif::Structure structure(f, 1, mmcif::StructureOpenOptions::SkipHydrogen);