various fixes in pdb2cif

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@179 a1961a4f-ab94-4bcc-80e8-33b5a54de466

include/cif++/BondMap.h

 // copyright
 
+#pragma once
+
 #include <unordered_map>
 
 #include "cif++/Structure.h"

include/cif++/CifValidator.h

@@ -18,7 +18,9 @@ struct ValidateCategory;
 class ValidationError : public std::exception
 {
   public:
-	ValidationError(const std::string& msg) : mMsg(msg) {}
+	ValidationError(const std::string& msg);
+	ValidationError(const std::string& cat, const std::string& item,
+		const std::string& msg);
 	const char* what() const noexcept		{ return mMsg.c_str(); }
 	std::string mMsg;
 };

src/CifValidator.cpp

@@ -17,6 +17,18 @@ extern int VERBOSE;
 namespace cif
 {
 
+ValidationError::ValidationError(const string& msg)
+	: mMsg(msg)
+{
+}
+
+ValidationError::ValidationError(const string& cat, const string& item, const string& msg)
+	: mMsg("When validating _" + cat + '.' + item + ": " + msg)
+{
+}
+
+// --------------------------------------------------------------------
+
 DDL_PrimitiveType mapToPrimitiveType(const string& s)
 {
 	DDL_PrimitiveType result;
@@ -137,18 +149,15 @@ void ValidateItem::setParent(ValidateItem* parent)
 
 void ValidateItem::operator()(string value) const
 {
-	if (VERBOSE >= 4)
-		cout << "validating '" << value << "' for '" << mTag << "'" << endl;
-
 	if (not value.empty() and value != "?" and value != ".")
 	{
 		if (mType != nullptr and not boost::regex_match(value, mType->mRx))
-			throw ValidationError("Value '" + value + "' does not match type expression for type " + mType->mName + " in item " + mTag);
+			throw ValidationError(mCategory->mName, mTag, "Value '" + value + "' does not match type expression for type " + mType->mName);
 
 		if (not mEnums.empty())
 		{
 			if (mEnums.count(value) == 0)
-				throw ValidationError("Value '" + value + "' is not in the list of allowed values for item " + mTag);
+				throw ValidationError(mCategory->mName, mTag, "Value '" + value + "' is not in the list of allowed values");
 		}
 	}
 }

src/Compound.cpp

@@ -260,7 +260,7 @@ const Compound* CompoundFactory::create(std::string id)
 				if (type == "single")		value = 1;
 				else if (type == "double")	value = 2;
 				else if (type == "triple")	value = 3;
-				else if (type == "deloc" or type == "aromat")
+				else if (type == "deloc" or type == "aromat" or type == "aromatic")
 											value = 1.5;
 				else
 				{

src/Edia.cpp

@@ -283,4 +283,42 @@ float CalculateEDIA(const Atom& atom, const clipper::Xmap<float>& xmap,
 	return result;
 }
 
+//
+//// --------------------------------------------------------------------
+//// test function
+//
+//double shellIntegration(float start, float end)
+//{
+//	double r = 1.35;
+//	
+//	PointWeightFunction w(Point(), r);
+//
+//	double volume = 0, positief = 0, negatief = 0;
+//	const size_t N = 10000;
+//	
+//	double h = 1.0 / N;
+//	
+//	for (size_t i = 0; i < N; ++i)
+//	{
+//		double x = start + i * h;
+//		auto y = w(Point(x * r, 0, 0));
+//		
+//		volume += x * y;
+//		if (y > 0)
+//			positief += x * y;
+//		if (y < 0)
+//			negatief += x * y;
+//	}
+//	
+//	volume *= 2 * kPI * h;
+//	positief *= 2 * kPI * h;
+//	negatief *= 2 * kPI * h;
+//	
+//	cout << "Volume: " << volume << endl
+//		 << "Positief: " << positief << endl
+//		 << "Negatief: " << negatief << endl;
+//
+//	return volume;
+//}
+
 }

src/PDB2Cif.cpp

@@ -387,9 +387,9 @@ class PDBFileParser
 		string	PDBIDCode;
 		char	chainID;
 		int		seqBegin;
-		char	insertBegin;
+		char	insertBegin = ' ';
 		int		seqEnd;
-		char	insertEnd;
+		char	insertEnd = ' ';
 		string	database;
 		string	dbAccession;
 		string	dbIdCode;
@@ -820,6 +820,7 @@ class PDBFileParser
 	cif::Datablock*	mDatablock = nullptr;
 
 	string		mStructureId;
+	string		mModelTypeDetails;
 	string		mOriginalDate;
 	string		mExpMethod = "X-RAY DIFFRACTION";
 	int			mCitationAuthorNr = 1, mCitationEditorNr = 1;
@@ -1232,7 +1233,8 @@ void PDBFileParser::ParseTitle()
 	if (mRec->is("CAVEAT"))							//	  1 - 6       Record name   "CAVEAT"
 	{													//	 9 - 10       Continuation  continuation   Allows concatenation of multiple records.
 		getCategory("database_PDB_caveat")->emplace({
-			{ "id", vS(12, 15) },						//	12 - 15       IDcode        idCode         PDB ID code of this datablock.                  
+//			{ "id", vS(12, 15) },						//	12 - 15       IDcode        idCode         PDB ID code of this datablock.                  
+			{ "id", 1 },								//	12 - 15       IDcode        idCode         PDB ID code of this datablock.                  
 			{ "text", string{mRec->vS(20) } }    		//	20 - 79       String        comment        Free text giving the reason for the  CAVEAT.
 		});
 		
@@ -1400,8 +1402,7 @@ void PDBFileParser::ParseTitle()
 	// MDLTYP
 	if (mRec->is("MDLTYP"))
 	{
-		if (VERBOSE)	
-			Error("skipping unimplemented MDLTYP record");
+		mModelTypeDetails = vS(11);
 		GetNextRecord();
 	}
 
@@ -1519,7 +1520,8 @@ void PDBFileParser::ParseCitation(const string& id)
 	
 	string auth, titl, edit, publ, refn, pmid, doi;
 	string pubname, volume, astm, country, issn, csd;
-	int pageFirst = 0, pageLast = 0, year = 0;
+	string pageFirst;
+	int year = 0;
 
 	auto extend = [](string& s, const string& p)
 	{
@@ -1541,7 +1543,7 @@ void PDBFileParser::ParseCitation(const string& id)
 				extend(pubname, vS(20, 47));
 				if (vS(50, 51) == "V.")
 					volume = ba::trim_copy(vS(52, 55));
-				pageFirst = vI(57, 61);
+				pageFirst = vS(57, 61);
 				year = vI(63, 66);
 			}
 			else
@@ -1568,8 +1570,7 @@ void PDBFileParser::ParseCitation(const string& id)
 		{ "title", titl },
 		{ "journal_abbrev", pubname },
 		{ "journal_volume", volume },
-		{ "page_first", pageFirst > 0 ? to_string(pageFirst) : "" },
-		{ "page_last", pageLast > 0 ? to_string(pageLast) : "" },
+		{ "page_first", pageFirst },
 		{ "year", year > 0 ? to_string(year) : "" },
 		{ "journal_id_ASTM", astm },
 		{ "country", country },
@@ -1889,8 +1890,8 @@ void PDBFileParser::ParseRemarks()
 					
 					string res = vS(16, 18);
 					char chain = vC(20);
-					int seq = vI(21, 25);
-					char iCode = vC(26);
+					int seq = vI(21, 24);
+					char iCode = vC(25);
 					
 					vector<string> atoms;
 					string atomStr = mRec->vS(29);
@@ -2052,8 +2053,8 @@ void PDBFileParser::ParseRemarks()
 								int model = vI(11, 13);
 								string resNam1 = vS(15, 17);
 								string chainID1 { vC(19) };
-								int seqNum1 = vI(20, 24);
-								string iCode1 { vC(25) };
+								int seqNum1 = vI(20, 23);
+								string iCode1 { vC(24) };
 								string alt1 = vS(30, 30);
 								string atm1 = vS(26, 29);
 
@@ -2106,8 +2107,8 @@ void PDBFileParser::ParseRemarks()
 								int model = vI(11, 13);
 								string resNam = vS(15, 17);
 								string chainID { vC(19) };
-								int seqNum = vI(20, 24);
-								string iCode { vC(25) };
+								int seqNum = vI(20, 23);
+								string iCode { vC(24) };
 								
 								if (iCode == " ")
 									iCode.clear();
@@ -2154,8 +2155,8 @@ void PDBFileParser::ParseRemarks()
 								int model = vI(11, 13);
 								string resNam = vS(15, 17);
 								string chainID { vC(19) };
-								int seqNum = vI(20, 24);
-								string iCode { vC(25) };
+								int seqNum = vI(20, 23);
+								string iCode { vC(24) };
 								
 								if (iCode == " ")
 									iCode.clear();
@@ -2229,8 +2230,8 @@ void PDBFileParser::ParseRemarks()
 								int model = vI(11, 13);
 								string resNam = vS(15, 17);
 								string chainID { vC(19) };
-								int seqNum = vI(20, 24);
-								string iCode { vC(25) };
+								int seqNum = vI(20, 23);
+								string iCode { vC(24) };
 								
 								if (iCode == " ")
 									iCode.clear();
@@ -3530,7 +3531,7 @@ void PDBFileParser::ConstructEntities()
 			
 			if (not dbref.database.empty())
 			{
-				auto insToStr = [](char i) -> string { return i == ' ' ? "" : string{ i }; };
+				auto insToStr = [](char i) -> string { return i == ' ' or not isprint(i) ? "" : string{ i }; };
 				
 				auto& pdbxPolySeqScheme = *getCategory("pdbx_poly_seq_scheme");
 				
@@ -3724,7 +3725,8 @@ void PDBFileParser::ConstructEntities()
 		getCategory("struct")->emplace({
 			{ "entry_id", mStructureId },
 			{ "title", ba::join(structTitle, ", ") },
-			{ "pdbx_descriptor", ba::join(structDescription, ", ") }
+			{ "pdbx_descriptor", ba::join(structDescription, ", ") },
+			{ "pdbx_model_type_details", mModelTypeDetails }
 		});
 	}
 	
@@ -4030,7 +4032,7 @@ void PDBFileParser::ConstructEntities()
 					{ "label_asym_id",	asymId },
 					{ "label_comp_id",	compId },		// TODO: change to correct comp_id
 					{ "label_seq_id",	seqNr > 0 ? to_string(seqNr) : "" },
-					{ "labelAtomId",	atom }
+					{ "label_atom_id",	atom }
 				});
 				
 			}
@@ -5246,7 +5248,15 @@ void ReadPDBFile(istream& pdbFile, cif::File& cifFile)
 
 	cifFile.loadDictionary("mmcif_pdbx");
 
-	p.Parse(pdbFile, cifFile);
+	try
+	{
+		p.Parse(pdbFile, cifFile);
+	}
+	catch (const exception& ex)
+	{
+		cerr << "Error parsing PDB file" << endl;
+		throw;
+	}
 	
 	cifFile.validate();
 }

src/PeptideDB.cpp

@@ -221,6 +221,7 @@ PeptideDB& PeptideDB::Instance()
 }
 
 PeptideDB::PeptideDB()
+	: mImpl(nullptr)
 {
 	const char* clibdMon = getenv("CLIBD_MON");
 	if (clibdMon == nullptr)

src/Structure.cpp

@@ -42,7 +42,7 @@ void FileImpl::load(fs::path p)
 		throw runtime_error("No such file: " + p.string());
 	
 	io::filtering_stream<io::input> in;
-	string ext;
+	string ext = p.extension().string();
 	
 	if (p.extension() == ".bz2")
 	{
@@ -57,43 +57,51 @@ void FileImpl::load(fs::path p)
 	
 	in.push(inFile);
 
-	// OK, we've got the file, now create a protein
-	if (ext == ".cif")
-		mData.load(in);
-	else if (ext == ".pdb" or ext == ".ent")
-		ReadPDBFile(in, mData);
-	else
+	try
 	{
-		try
-		{
-			if (VERBOSE)
-				cerr << "unrecognized file extension, trying cif" << endl;
-
+		// OK, we've got the file, now create a protein
+		if (ext == ".cif")
 			mData.load(in);
-		}
-		catch (const cif::CifParserError& e)
-		{
-			if (VERBOSE)
-				cerr << "Not cif, trying plain old PDB" << endl;
-
-			// pffft...
-			in.reset();
-
-			if (inFile.is_open())
-				inFile.seekg(0);
-			else
-				inFile.open(p, ios_base::in | ios::binary);
-
-			if (p.extension() == ".bz2")
-				in.push(io::bzip2_decompressor());
-			else if (p.extension() == ".gz")
-				in.push(io::gzip_decompressor());
-			
-			in.push(inFile);
-
+		else if (ext == ".pdb" or ext == ".ent")
 			ReadPDBFile(in, mData);
+		else
+		{
+			try
+			{
+				if (VERBOSE)
+					cerr << "unrecognized file extension, trying cif" << endl;
+	
+				mData.load(in);
+			}
+			catch (const cif::CifParserError& e)
+			{
+				if (VERBOSE)
+					cerr << "Not cif, trying plain old PDB" << endl;
+	
+				// pffft...
+				in.reset();
+	
+				if (inFile.is_open())
+					inFile.seekg(0);
+				else
+					inFile.open(p, ios_base::in | ios::binary);
+	
+				if (p.extension() == ".bz2")
+					in.push(io::bzip2_decompressor());
+				else if (p.extension() == ".gz")
+					in.push(io::gzip_decompressor());
+				
+				in.push(inFile);
+	
+				ReadPDBFile(in, mData);
+			}
 		}
 	}
+	catch (const exception& ex)
+	{
+		cerr << "Failed trying to load file " << p << endl;
+		throw;
+	}
 	
 	// Yes, we've parsed the data. Now locate the datablock.
 	mDb = &mData.firstDatablock();