Merge branch 'develop' of github.com:PDB-REDO/libcifpp into develop

changelog

@@ -3,6 +3,10 @@ Version 3.0.0
   performance reasons.
   performance reasons.
 - Upgraded mmcif::Structure
 - Upgraded mmcif::Structure
 
 
+Version 2.0.3
+- Fixed reading mmCIF files where model numbers are used and
+  model number 1 is missing.
+
 Version 2.0.2
 Version 2.0.2
 - Added configuration flag to disable downloading CCD data during build
 - Added configuration flag to disable downloading CCD data during build
   Note that there are now two flags for CCD data:
   Note that there are now two flags for CCD data:

include/cif++/Structure.hpp

@@ -543,6 +543,8 @@ class Structure
 	void loadData();
 	void loadData();
 	void updateAtomIndex();
 	void updateAtomIndex();
 
 
+	void loadAtomsForModel(StructureOpenOptions options);
+
 	File &mFile;
 	File &mFile;
 	size_t mModelNr;
 	size_t mModelNr;
 	AtomView mAtoms;
 	AtomView mAtoms;

src/Compound.cpp

@@ -636,17 +636,18 @@ void CompoundFactory::init(bool useThreadLocalInstanceOnly)
 CompoundFactory::CompoundFactory()
 CompoundFactory::CompoundFactory()
 	: mImpl(nullptr)
 	: mImpl(nullptr)
 {
 {
+	auto ccd = cif::loadResource("components.cif");
+	if (ccd)
+		mImpl.reset(new CCDCompoundFactoryImpl(mImpl));
+	else if (cif::VERBOSE)
+		std::cerr << "CCD components.cif file was not found" << std::endl;
+
 	const char *clibd_mon = getenv("CLIBD_MON");
 	const char *clibd_mon = getenv("CLIBD_MON");
 	if (clibd_mon != nullptr and fs::is_directory(clibd_mon))
 	if (clibd_mon != nullptr and fs::is_directory(clibd_mon))
 		mImpl.reset(new CCP4CompoundFactoryImpl(clibd_mon));
 		mImpl.reset(new CCP4CompoundFactoryImpl(clibd_mon));
 	else if (cif::VERBOSE)
 	else if (cif::VERBOSE)
 		std::cerr << "CCP4 monomers library not found, CLIBD_MON is not defined" << std::endl;
 		std::cerr << "CCP4 monomers library not found, CLIBD_MON is not defined" << std::endl;
 
 
-	auto ccd = cif::loadResource("components.cif");
-	if (ccd)
-		mImpl.reset(new CCDCompoundFactoryImpl(mImpl));
-	else if (cif::VERBOSE)
-		std::cerr << "CCD components.cif file was not found" << std::endl;
 }
 }
 
 
 CompoundFactory::~CompoundFactory()
 CompoundFactory::~CompoundFactory()

src/Structure.cpp

@@ -1790,6 +1790,33 @@ Structure::Structure(File &f, size_t modelNr, StructureOpenOptions options)
 
 
 	auto &atomCat = (*db)["atom_site"];
 	auto &atomCat = (*db)["atom_site"];
 
 
+	loadAtomsForModel(options);
+
+	// Check to see if we should actually load another model?
+	if (mAtoms.empty() and mModelNr == 1)
+	{
+		std::optional<size_t> model_nr;
+		cif::tie(model_nr) = atomCat.front().get("pdbx_PDB_model_num");
+		if (model_nr and *model_nr != mModelNr)
+		{
+			if (cif::VERBOSE)
+				std::cerr << "No atoms loaded for model 1, trying model " << *model_nr << std::endl;
+			mModelNr = *model_nr;
+			loadAtomsForModel(options);
+		}
+	}
+
+	if (mAtoms.empty())
+		throw std::runtime_error("No atoms loaded, refuse to continue");
+
+	loadData();
+}
+
+void Structure::loadAtomsForModel(StructureOpenOptions options)
+{
+	auto db = mFile.impl().mDb;
+	auto &atomCat = (*db)["atom_site"];
+
 	for (auto &a : atomCat)
 	for (auto &a : atomCat)
 	{
 	{
 		std::string id, type_symbol;
 		std::string id, type_symbol;
@@ -1805,10 +1832,9 @@ Structure::Structure(File &f, size_t modelNr, StructureOpenOptions options)
 
 
 		mAtoms.emplace_back(new AtomImpl(*db, id, a));
 		mAtoms.emplace_back(new AtomImpl(*db, id, a));
 	}
 	}
-
-	loadData();
 }
 }
 
 
+
 Structure::Structure(const Structure &s)
 Structure::Structure(const Structure &s)
 	: mFile(s.mFile)
 	: mFile(s.mFile)
 	, mModelNr(s.mModelNr)
 	, mModelNr(s.mModelNr)