Renaming internal use of mmcif_pdbx dictionary. It was wrong to use the name mmcif_pdbx_v50

CMakeLists.txt

@@ -362,7 +362,7 @@ install(
 
 install(FILES
 	${PROJECT_SOURCE_DIR}/rsrc/mmcif_ddl.dic
-	${PROJECT_SOURCE_DIR}/rsrc/mmcif_pdbx_v50.dic
+	${PROJECT_SOURCE_DIR}/rsrc/mmcif_pdbx.dic
 	${COMPONENTS_CIF}
 	DESTINATION ${SHARE_INSTALL_DIR}
 )
@@ -435,7 +435,7 @@ if(CIFPP_BUILD_TESTS)
 		target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp::cifpp Boost::boost)
 
 		if(CIFPP_USE_RSRC)
-			mrc_target_resources(${CIFPP_TEST} ${CMAKE_SOURCE_DIR}/rsrc/mmcif_pdbx_v50.dic)
+			mrc_target_resources(${CIFPP_TEST} ${CMAKE_SOURCE_DIR}/rsrc/mmcif_pdbx.dic)
 		endif()
 
 		if(MSVC)

examples/example.cpp

@@ -8,7 +8,6 @@ namespace fs = std::filesystem;
 int main()
 {
 	cif::file file;
-	file.load_dictionary("mmcif_pdbx_v50");
 	file.load("1cbs.cif.gz");
 
 	auto& db = file.front();

include/cif++/structure/Compound.hpp

@@ -46,7 +46,7 @@ class Compound;
 struct CompoundAtom;
 class CompoundFactoryImpl;
 
-/// \brief The bond type as defined in the CCD, possible values taken from the mmcif_pdbx_v50 file
+/// \brief The bond type as defined in the CCD, possible values taken from the mmcif_pdbx file
 enum class BondType
 {
 	sing, // 'single bond'

src/Cif++.cpp

@@ -1798,7 +1798,7 @@ auto Category::erase(iterator pos) -> iterator
 	}
 
 	// links are created based on the _pdbx_item_linked_group_list entries
-	// in mmcif_pdbx_v50.dic dictionary.
+	// in mmcif_pdbx.dic dictionary.
 	//
 	// For each link group in _pdbx_item_linked_group_list
 	// a std::set of keys from one category is mapped to another.

src/cif/file.cpp

@@ -61,7 +61,8 @@ bool file::is_valid()
 		load_dictionary();
 	}
 
-	bool result = true;
+	bool result = not empty();
+
 	for (auto &d : *this)
 		result = d.is_valid() and result;
 
@@ -76,9 +77,10 @@ void file::load_dictionary()
 		if (audit_conform and not audit_conform->empty())
 		{
 			std::string name;
-			cif::tie(name) = audit_conform->front().get("name");
+			cif::tie(name) = audit_conform->front().get("dict_name");
 
-			load_dictionary(name);
+			if (not name.empty())
+				load_dictionary(name);
 		}
 	}
 
@@ -158,10 +160,9 @@ void file::load(std::istream &is)
 	p.parse_file();
 
 	if (saved != nullptr)
-	{
 		set_validator(saved);
-		(void)is_valid();
-	}
+	else
+		load_dictionary();
 }
 
 void file::save(const std::filesystem::path &p) const

src/pdb/PDB2Cif.cpp

@@ -6055,10 +6055,11 @@ void ReadPDBFile(std::istream &pdbFile, cif::File &cifFile)
 {
 	PDBFileParser p;
 
-	cifFile.loadDictionary("mmcif_pdbx_v50");
-
 	p.Parse(pdbFile, cifFile);
 
+	cifFile.loadDictionary("mmcif_pdbx");
+
+
 	if (not cifFile.isValid() and cif::VERBOSE >= 0)
 		std::cerr << "Resulting mmCIF file is not valid!" << std::endl;
 }

src/structure/Compound.cpp

@@ -416,7 +416,7 @@ CompoundFactoryImpl::CompoundFactoryImpl(const fs::path &file, std::shared_ptr<C
 	else
 	{
 		// A CCD components file, validate it first
-		cifFile.load_dictionary("mmcif_pdbx_v50");
+		cifFile.load_dictionary("mmcif_pdbx");
 
 		if (not cifFile.is_valid())
 			throw std::runtime_error("Invalid compound file");

src/structure/Structure.cpp

@@ -1297,7 +1297,7 @@ void File::load(const std::filesystem::path &path)
 		cif::File::load(in);
 
 	// validate, otherwise lots of functionality won't work
-	loadDictionary("mmcif_pdbx_v50");
+	loadDictionary("mmcif_pdbx");
 	if (not isValid() and cif::VERBOSE >= 0)
 		std::cerr << "Invalid mmCIF file" << (cif::VERBOSE > 0 ? "." : " use --verbose option to see errors") << std::endl;
 }

test/dssp-test.cpp

@@ -64,7 +64,7 @@ bool init_unit_test()
 		gTestDir = boost::unit_test::framework::master_test_suite().argv[1];
 
 	// do this now, avoids the need for installing
-	cif::add_file_resource("mmcif_pdbx_v50.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx_v50.dic");
+	cif::add_file_resource("mmcif_pdbx.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic");
 
 	// initialize CCD location
 	cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
@@ -76,12 +76,9 @@ bool init_unit_test()
 
 BOOST_AUTO_TEST_CASE(dssp_1)
 {
-	// using namespace mmcif;
-
 	cif::file f(gTestDir / "1cbs.cif");
-	f.load_dictionary("mmcif_pdbx_v50");
 
-	BOOST_CHECK(f.is_valid());
+	BOOST_ASSERT(f.is_valid());
 
 	std::ifstream t(gTestDir / "1cbs-dssp-test.tsv");
 

test/rename-compound-test.cpp

@@ -19,8 +19,8 @@ int main(int argc, char* argv[])
 		if (std::filesystem::exists(testdir / ".." / "data" / "ccd-subset.cif"))
 			cif::add_file_resource("components.cif", testdir / ".." / "data" / "ccd-subset.cif");
 
-		if (std::filesystem::exists(testdir / ".." / "rsrc" / "mmcif_pdbx_v50.dic"))
-			cif::add_file_resource("mmcif_pdbx_v50.dic", testdir / ".." / "rsrc" / "mmcif_pdbx_v50.dic");
+		if (std::filesystem::exists(testdir / ".." / "rsrc" / "mmcif_pdbx.dic"))
+			cif::add_file_resource("mmcif_pdbx.dic", testdir / ".." / "rsrc" / "mmcif_pdbx.dic");
 
 		mmcif::CompoundFactory::instance().pushDictionary(testdir / "REA.cif");
 		mmcif::CompoundFactory::instance().pushDictionary(testdir / "RXA.cif");

test/structure-test.cpp

@@ -61,7 +61,7 @@ bool init_unit_test()
 		gTestDir = boost::unit_test::framework::master_test_suite().argv[1];
 
 	// do this now, avoids the need for installing
-	cif::add_file_resource("mmcif_pdbx_v50.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx_v50.dic");
+	cif::add_file_resource("mmcif_pdbx.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic");
 
 	// initialize CCD location
 	cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
@@ -78,7 +78,7 @@ BOOST_AUTO_TEST_CASE(create_nonpoly_1)
     cif::VERBOSE = 1;
 
 	mmcif::File file;
-	file.loadDictionary("mmcif_pdbx_v50.dic");
+	file.loadDictionary("mmcif_pdbx.dic");
 	file.emplace("TEST");	// create a datablock
 	
 	mmcif::Structure structure(file);
@@ -180,7 +180,7 @@ _struct_asym.details                       ?
 #
 )"_cf;
 
-	expected.loadDictionary("mmcif_pdbx_v50.dic");
+	expected.loadDictionary("mmcif_pdbx.dic");
 
 	if (not (expected.firstDatablock() == structure.datablock()))
 	{
@@ -280,7 +280,7 @@ _struct_asym.details                       ?
 #
 )"_cf;
 
-	data.loadDictionary("mmcif_pdbx_v50.dic");
+	data.loadDictionary("mmcif_pdbx.dic");
 
 	mmcif::Structure s(data);
 

test/sugar-test.cpp

@@ -61,7 +61,7 @@ bool init_unit_test()
 		gTestDir = boost::unit_test::framework::master_test_suite().argv[1];
 
 	// do this now, avoids the need for installing
-	cif::add_file_resource("mmcif_pdbx_v50.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx_v50.dic");
+	cif::add_file_resource("mmcif_pdbx.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic");
 
 	// initialize CCD location
 	cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");

test/unit-test.cpp

@@ -67,7 +67,7 @@ bool init_unit_test()
 		gTestDir = boost::unit_test::framework::master_test_suite().argv[1];
 
 	// do this now, avoids the need for installing
-	cif::add_file_resource("mmcif_pdbx_v50.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx_v50.dic");
+	cif::add_file_resource("mmcif_pdbx.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic");
 
 	// initialize CCD location
 	cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");
@@ -295,7 +295,6 @@ save__cat_2.desc
 	cif::Validator validator("test", is_dict);
 
 	cif::File f;
-	f.setValidator(&validator);
 
 	// --------------------------------------------------------------------
 
@@ -327,6 +326,7 @@ _cat_2.desc
 
 	std::istream is_data(&data_buffer);
 	f.load(is_data);
+	f.setValidator(&validator);
 
 	auto &cat1 = f.firstDatablock()["cat_1"];
 	auto &cat2 = f.firstDatablock()["cat_2"];

test/unit-v2-test.cpp

@@ -69,7 +69,7 @@ bool init_unit_test()
 	// 	gTestDir = boost::unit_test::framework::master_test_suite().argv[1];
 
 	// // do this now, avoids the need for installing
-	// cif::add_file_resource("mmcif_pdbx_v50.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx_v50.dic");
+	// cif::add_file_resource("mmcif_pdbx.dic", gTestDir / ".." / "rsrc" / "mmcif_pdbx.dic");
 
 	// // initialize CCD location
 	// cif::add_file_resource("components.cif", gTestDir / ".." / "data" / "ccd-subset.cif");

tools/update-dictionary-script

@@ -43,7 +43,7 @@ fetch_dictionary () {
 
 # fetch the dictionaries
 
-fetch_dictionary "/var/cache/libcifpp/mmcif_pdbx_v50.dic" "https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic.gz"
+fetch_dictionary "/var/cache/libcifpp/mmcif_pdbx.dic" "https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic.gz"
 fetch_dictionary "/var/cache/libcifpp/components.cif" "ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz"
 
 # this one is not compressed

tools/update-libcifpp-data.in

@@ -43,7 +43,7 @@ fetch_dictionary () {
 
 # fetch the dictionaries
 
-fetch_dictionary "@CIFPP_CACHE_DIR@/mmcif_pdbx_v50.dic" "https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic.gz"
+fetch_dictionary "@CIFPP_CACHE_DIR@/mmcif_pdbx.dic" "https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic.gz"
 fetch_dictionary "@CIFPP_CACHE_DIR@/components.cif" "ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz"
 
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