loading compound info, finished with error checking and verbose mode

src/Cif2PDB.cpp

@@ -3922,8 +3922,7 @@ std::string GetPDBSOURCELine(cif::File& cifFile, std::string::size_type truncate
 			{ "pdbx_host_org_vector_type",		"EXPRESSION_SYSTEM_VECTOR_TYPE" },
 			{ "pdbx_host_org_vector",			"EXPRESSION_SYSTEM_VECTOR" },
 			{ "pdbx_host_org_gene",				"EXPRESSION_SYSTEM_GENE" },
-			{ "plasmid_name",					"EXPRESSION_SYSTEM_PLASMID" },
-			{ "details",						"OTHER_DETAILS" }
+			{ "plasmid_name",					"EXPRESSION_SYSTEM_PLASMID" }
 		};
 
 		for (auto gr: gen.find(cif::Key("entity_id") == entityID))

src/Compound.cpp

@@ -621,8 +621,14 @@ CompoundFactory::CompoundFactory()
 	const char *clibd_mon = getenv("CLIBD_MON");
 	if (clibd_mon != nullptr and fs::is_directory(clibd_mon))
 		mImpl = new CCP4CompoundFactoryImpl(clibd_mon);
+	else if (cif::VERBOSE)
+		std::cerr << "CCP4 monomers library not found, CLIBD_MON is not defined" << std::endl;
 
-	mImpl = new CCDCompoundFactoryImpl(mImpl);
+	auto ccd = cif::loadResource("components.cif");
+	if (ccd)
+		mImpl = new CCDCompoundFactoryImpl(mImpl);
+	else if (cif::VERBOSE)
+		std::cerr << "CCD components.cif file was not found" << std::endl;
 }
 
 CompoundFactory::~CompoundFactory()
@@ -685,17 +691,25 @@ void CompoundFactory::popDictionary()
 
 const Compound *CompoundFactory::create(std::string id)
 {
-	return mImpl->get(id);
+	static bool warned = false;
+
+	if (mImpl == nullptr and warned == false)
+	{
+		std::cerr << "Warning: no compound information library was found, resulting data may be incorrect or incomplete" << std::endl;
+		warned = true;
+	}
+
+	return mImpl ? mImpl->get(id) : nullptr;
 }
 
 bool CompoundFactory::isKnownPeptide(const std::string &resName) const
 {
-	return mImpl->isKnownPeptide(resName);
+	return mImpl ? mImpl->isKnownPeptide(resName) : kAAMap.count(resName) > 0;
 }
 
 bool CompoundFactory::isKnownBase(const std::string &resName) const
 {
-	return mImpl->isKnownBase(resName);
+	return mImpl ? mImpl->isKnownBase(resName) : kBaseMap.count(resName) > 0;
 }
 
 } // namespace mmcif

src/Secondary.cpp

@@ -512,11 +512,7 @@ double Res::CalculateSurface(const std::vector<Res>& inResidues)
 
 void CalculateAccessibilities(std::vector<Res>& inResidues, DSSP_Statistics& stats)
 {
-	if (cif::VERBOSE)
-		std::cerr << "Calculate accessibilities" << std::endl;
-
 	stats.accessibleSurface = 0;
-
 	for (auto& residue: inResidues)
 		stats.accessibleSurface += residue.CalculateSurface(inResidues);
 }
@@ -1186,9 +1182,6 @@ DSSPImpl::DSSPImpl(const Structure& s, int min_poly_proline_stretch_length)
 	, mPolymers(mStructure.polymers())
 	, m_min_poly_proline_stretch_length(min_poly_proline_stretch_length)
 {
-	if (cif::VERBOSE)
-		std::cerr << "Calculating DSSP ";
-
 	size_t nRes = accumulate(mPolymers.begin(), mPolymers.end(),
 		0.0, [](double s, auto& p) { return s + p.size(); });
 
@@ -1266,20 +1259,11 @@ void DSSPImpl::calculateSecondaryStructure()
 		mSSBonds.emplace_back(&*r1, &*r2);
 	}
 
-	if (cif::VERBOSE) std::cerr << ".";
 	CalculateHBondEnergies(mResidues);
-
-	if (cif::VERBOSE) std::cerr << ".";
 	CalculateBetaSheets(mResidues, mStats);
-
-	if (cif::VERBOSE) std::cerr << ".";
 	CalculateAlphaHelices(mResidues, mStats);
-
-	if (cif::VERBOSE) std::cerr << ".";
 	CalculatePPHelices(mResidues, mStats, m_min_poly_proline_stretch_length);
 
-	if (cif::VERBOSE) std::cerr << std::endl;
-
 	if (cif::VERBOSE > 1)
 	{
 		for (auto& r: mResidues)