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libcifpp
Commit c3930428 by Maarten L. Hekkelman
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sugar tree work in pdb2cif

parent 5e5e5c21
Showing with 230 additions and 140 deletions
GNUmakefile.in
......@@ -196,7 +196,7 @@ $(1)_OBJECTS = $$(OBJDIR)/$(1)-test.o
test/$(1)-test: $(LIB_TARGET) $$($(1)_OBJECTS)
@ echo ">>> building $(1)-test"
$(LIBTOOL) --silent --tag=CXX --mode=link $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $$@ $$($(1)_OBJECTS) -L.libs -lcif++ $(LIBS)
$(LIBTOOL) --silent --tag=CXX --mode=link $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $$@ $$($(1)_OBJECTS) -L.libs -lcif++ -lboost_date_time $(LIBS)
.PHONY: $(1)-test
$(1)-test: test/$(1)-test
......@@ -204,7 +204,7 @@ $(1)-test: test/$(1)-test
endef
TESTS = unit
TESTS = unit pdb2cif
$(foreach part,$(TESTS),$(eval $(call TEST_template,$(part))))
......
src/PDB2Cif.cpp
......@@ -448,23 +448,24 @@ class PDBFileParser
struct HET
{
std::string hetID;
char chainID;
int seqNum;
char iCode;
int numHetAtoms;
std::string text;
std::string asymID;
std::set<int> atoms;
std::string hetID;
char chainID;
int seqNum;
char iCode;
int numHetAtoms;
std::string text;
std::string asymID;
std::vector<PDBRecord*> atoms;
bool processedSugar = false;
};
struct UNOBS
{
int modelNr;
std::string res;
char chain;
int seq;
char iCode;
int modelNr;
std::string res;
char chain;
int seq;
char iCode;
std::vector<std::string> atoms;
};
......@@ -487,12 +488,12 @@ class PDBFileParser
struct PDBCompound
{
int mMolID;
std::string mTitle;
std::set<char> mChains;
std::map<std::string,std::string> mInfo;
std::map<std::string,std::string> mSource;
int mCount = 0;
int mMolID;
std::string mTitle;
std::set<char> mChains;
std::map<std::string,std::string> mInfo;
std::map<std::string,std::string> mSource;
int mCount = 0;
};
struct PDBSeqRes
......@@ -867,28 +868,28 @@ class PDBFileParser
// ----------------------------------------------------------------
PDBRecord* mData;
PDBRecord* mRec;
PDBRecord* mData;
PDBRecord* mRec;
cif::Datablock* mDatablock = nullptr;
std::string mStructureID;
std::string mModelTypeDetails;
std::string mOriginalDate;
std::string mExpMethod = "X-RAY DIFFRACTION";
int mCitationAuthorNr = 1, mCitationEditorNr = 1;
int mNextMolID = 1, mNextEntityNr = 1;
int mNextSoftwareOrd = 1;
int mCitationAuthorNr = 1, mCitationEditorNr = 1;
int mNextMolID = 1, mNextEntityNr = 1;
int mNextSoftwareOrd = 1;
struct SEQADV
{
std::string resName;
char chainID;
int seqNum;
char iCode;
char chainID;
int seqNum;
char iCode;
std::string database;
std::string dbAccession;
std::string dbRes;
int dbSeq;
int dbSeq;
std::string conflict;
};
......@@ -897,26 +898,26 @@ class PDBFileParser
std::list<PDBCompound> mCompounds;
std::list<PDBChain> mChains;
std::vector<HET> mHets;
std::map<std::string,std::string> mHetnams;
std::map<std::string,std::string> mHetsyns;
std::map<std::string,std::string> mFormuls;
std::map<std::string,std::string> mHetnams;
std::map<std::string,std::string> mHetsyns;
std::map<std::string,std::string> mFormuls;
std::string mWaterHetID;
std::vector<std::string> mChemComp, mAtomTypes;
std::vector<std::string> mChemComp, mAtomTypes;
std::map<std::string,std::string> mRemark200;
std::map<std::string,std::string> mRemark200;
std::string mRefinementSoftware;
int mAtomID = 0;
int mPdbxDifOrdinal = 0;
int mAtomID = 0;
int mPdbxDifOrdinal = 0;
std::vector<UNOBS> mUnobs;
// various maps between numbering schemes
std::map<std::tuple<char,int,char>,std::tuple<std::string,int,bool>> mChainSeq2AsymSeq;
std::map<int,std::string> mMolID2EntityID;
std::map<std::string,std::string> mHet2EntityID;
std::map<std::string,std::string> mAsymID2EntityID;
std::map<std::string,std::string> mMod2parent;
std::map<int,std::string> mMolID2EntityID;
std::map<std::string,std::string> mHet2EntityID;
std::map<std::string,std::string> mAsymID2EntityID;
std::map<std::string,std::string> mMod2parent;
};
// --------------------------------------------------------------------
......@@ -930,7 +931,7 @@ std::vector<char> PDBFileParser::altLocsForAtom(char inChainID, int inResSeq, ch
{
if (r->is("ATOM ") or r->is("HETATM")) // 1 - 6 Record name "ATOM "
{ // ...
std::string name = r->vS(13, 16); // 13 - 16 Atom name Atom name.
std::string name = r->vS(13, 16); // 13 - 16 Atom name Atom name.
char altLoc = r->vC(17); // 17 Character altLoc Alternate location indicator.
char chainID = r->vC(22); // 22 Character chainID Chain identifier.
int resSeq = r->vI(23, 26); // 23 - 26 Integer resSeq Residue sequence number.
......@@ -1275,7 +1276,7 @@ void PDBFileParser::ParseTitle()
// HEADER
// 1 - 6 Record name "HEADER"
// 11 - 50 std::String(40) classification Classifies the molecule(s).
// 11 - 50 String(40) classification Classifies the molecule(s).
// 51 - 59 Date depDate Deposition date. This is the date the
// coordinates were received at the PDB.
// 63 - 66 IDcode idCode This identifier is unique within the PDB.
......@@ -1339,7 +1340,7 @@ void PDBFileParser::ParseTitle()
std::string title;
if (mRec->is("TITLE ")) // 1 - 6 Record name "TITLE "
{ // 9 - 10 Continuation continuation Allows concatenation of multiple records.
title = vS(11); // 11 - 80 std::String title Title of the experiment.
title = vS(11); // 11 - 80 String title Title of the experiment.
GetNextRecord();
}
......@@ -1359,7 +1360,7 @@ void PDBFileParser::ParseTitle()
{
getCategory("database_PDB_caveat")->emplace({
{ "id", caveatID++ },
{ "text", std::string{mRec->vS(20) } } // 20 - 79 std::String comment Free text giving the reason for the CAVEAT.
{ "text", std::string{mRec->vS(20) } } // 20 - 79 String comment Free text giving the reason for the CAVEAT.
});
GetNextRecord();
......@@ -1586,15 +1587,15 @@ void PDBFileParser::ParseTitle()
// 1 - 6 Record name "REVDAT"
int revNum = vI(8, 10); // 8 - 10 Integer modNum Modification number.
// 11 - 12 Continuation continuation Allows concatenation of multiple records.
std::string date = pdb2cifDate(vS(14, 22)); // 14 - 22 Date modDate Date of modification (or release for
std::string date = pdb2cifDate(vS(14, 22)); // 14 - 22 Date modDate Date of modification (or release for
// new entries) in DD-MMM-YY format. This is
// not repeated on continued lines.
std::string modID = vS(24, 27); // 24 - 27 IDCode modID ID code of this datablock. This is not repeated on
std::string modID = vS(24, 27); // 24 - 27 IDCode modID ID code of this datablock. This is not repeated on
// continuation lines.
int modType = vI(32, 32); // 32 Integer modType An integer identifying the type of
// modification. For all revisions, the
// modification type is listed as 1
std::string value = vS(40); // 40 - 45 LString(6) record Modification detail.
std::string value = vS(40); // 40 - 45 LString(6) record Modification detail.
// 47 - 52 LString(6) record Modification detail.
// 54 - 59 LString(6) record Modification detail.
// 61 - 66 LString(6) record Modification detail.
......@@ -3140,25 +3141,25 @@ void PDBFileParser::ParsePrimaryStructure()
if (mRec->is("DBREF ")) // 1 - 6 Record name "DBREF "
{
cur.PDBIDCode = vS(8, 11); // 8 - 11 IDcode idCode ID code of this datablock.
cur.chainID = vC(13); // 13 Character chainID Chain identifier.
cur.seqBegin = vI(15, 18); // 15 - 18 Integer seqBegin Initial sequence number of the
cur.chainID = vC(13); // 13 Character chainID Chain identifier.
cur.seqBegin = vI(15, 18); // 15 - 18 Integer seqBegin Initial sequence number of the
// PDB sequence segment.
cur.insertBegin = vC(19); // 19 AChar insertBegin Initial insertion code of the
cur.insertBegin = vC(19); // 19 AChar insertBegin Initial insertion code of the
// PDB sequence segment.
cur.seqEnd = vI(21, 24); // 21 - 24 Integer seqEnd Ending sequence number of the
cur.seqEnd = vI(21, 24); // 21 - 24 Integer seqEnd Ending sequence number of the
// PDB sequence segment.
cur.insertEnd = vC(25); // 25 AChar insertEnd Ending insertion code of the
cur.insertEnd = vC(25); // 25 AChar insertEnd Ending insertion code of the
// PDB sequence segment.
cur.database = vS(27, 32); // 27 - 32 LString database Sequence database name.
cur.dbAccession = vS(34, 41); // 34 - 41 LString dbAccession Sequence database accession code.
cur.dbIdCode = vS(43, 54); // 43 - 54 LString dbIdCode Sequence database identification code.
cur.dbSeqBegin = vI(56, 60); // 56 - 60 Integer dbseqBegin Initial sequence number of the
cur.database = vS(27, 32); // 27 - 32 LString database Sequence database name.
cur.dbAccession = vS(34, 41); // 34 - 41 LString dbAccession Sequence database accession code.
cur.dbIdCode = vS(43, 54); // 43 - 54 LString dbIdCode Sequence database identification code.
cur.dbSeqBegin = vI(56, 60); // 56 - 60 Integer dbseqBegin Initial sequence number of the
// database seqment.
cur.dbinsBeg = vC(61); // 61 AChar idbnsBeg Insertion code of initial residue of the
cur.dbinsBeg = vC(61); // 61 AChar idbnsBeg Insertion code of initial residue of the
// segment, if PDB is the reference.
cur.dbSeqEnd = vI(63, 67); // 63 - 67 Integer dbseqEnd Ending sequence number of the
cur.dbSeqEnd = vI(63, 67); // 63 - 67 Integer dbseqEnd Ending sequence number of the
// database segment.
cur.dbinsEnd = vC(68); // 68 AChar dbinsEnd Insertion code of the ending residue of
cur.dbinsEnd = vC(68); // 68 AChar dbinsEnd Insertion code of the ending residue of
// the segment, if PDB is the reference.
auto& chain = GetChainForID(cur.chainID);
chain.mDbref = cur;
......@@ -3219,17 +3220,17 @@ void PDBFileParser::ParsePrimaryStructure()
GetNextRecord();
}
while (mRec->is("SEQRES")) // 1 - 6 Record name "SEQRES"
{ // 8 - 10 Integer serNum Serial number of the SEQRES record for the
// current chain. Starts at 1 and increments
// by one each line. Reset to 1 for each chain.
char chainID = vC(12); // 12 Character chainID Chain identifier. This may be any single
// legal character, including a blank which is
// is used if there is only one chain.
int numRes = vI(14, 17); // 14 - 17 Integer numRes Number of residues in the chain.
// This value is repeated on every record.
while (mRec->is("SEQRES")) // 1 - 6 Record name "SEQRES"
{ // 8 - 10 Integer serNum Serial number of the SEQRES record for the
// current chain. Starts at 1 and increments
// by one each line. Reset to 1 for each chain.
char chainID = vC(12); // 12 Character chainID Chain identifier. This may be any single
// legal character, including a blank which is
// is used if there is only one chain.
int numRes = vI(14, 17); // 14 - 17 Integer numRes Number of residues in the chain.
// This value is repeated on every record.
std::string monomers = vS(20, 70); // 20 - 22 Residue name resName Residue name.
// ...
// ...
auto& chain = GetChainForID(chainID, numRes);
......@@ -3248,14 +3249,14 @@ void PDBFileParser::ParsePrimaryStructure()
}
// First pass over MODRES, only store relevant information required in ConstructEntities
while (mRec->is("MODRES")) // 1 - 6 Record name "MODRES"
{ // 8 - 11 IDcode idCode ID code of this datablock.
while (mRec->is("MODRES")) // 1 - 6 Record name "MODRES"
{ // 8 - 11 IDcode idCode ID code of this datablock.
std::string resName = vS(13, 15); // 13 - 15 Residue name resName Residue name used in this datablock.
// char chainID = vC(17); // 17 Character chainID Chain identifier.
// int seqNum = vI(19, 22); // 19 - 22 Integer seqNum Sequence number.
// char iCode = vC(23); // 23 AChar iCode Insertion code.
// char chainID = vC(17); // 17 Character chainID Chain identifier.
// int seqNum = vI(19, 22); // 19 - 22 Integer seqNum Sequence number.
// char iCode = vC(23); // 23 AChar iCode Insertion code.
std::string stdRes = vS(25, 27); // 25 - 27 Residue name stdRes Standard residue name.
// std::string comment = vS(30, 70); // 30 - 70 std::String comment Description of the residue modification.
// std::string comment = vS(30, 70); // 30 - 70 String comment Description of the residue modification.
mMod2parent[resName] = stdRes;
......@@ -3267,13 +3268,13 @@ void PDBFileParser::ParseHeterogen()
{
while (mRec->is("HET "))
{ // 1 - 6 Record name "HET "
std::string hetID = vS(8, 10); // 8 - 10 LString(3) hetID Het identifier, right-justified.
std::string hetID = vS(8, 10); // 8 - 10 LString(3) hetID Het identifier, right-justified.
char chainID = vC(13); // 13 Character ChainID Chain identifier.
int seqNum = vI(14, 17); // 14 - 17 Integer seqNum Sequence number.
char iCode = vC(18); // 18 AChar iCode Insertion code.
int numHetAtoms = vI(21, 25); // 21 - 25 Integer numHetAtoms Number of HETATM records for the group
// present in the datablock.
std::string text = vS(31, 70); // 31 - 70 std::String text Text describing Het group.
std::string text = vS(31, 70); // 31 - 70 String text Text describing Het group.
mHets.push_back({ hetID, chainID, seqNum, iCode, numHetAtoms, text });
......@@ -3282,10 +3283,10 @@ void PDBFileParser::ParseHeterogen()
for (;;)
{
if (mRec->is("HETNAM")) // 1 - 6 Record name "HETNAM"
{ // 9 - 10 Continuation continuation Allows concatenation of multiple records.
if (mRec->is("HETNAM")) // 1 - 6 Record name "HETNAM"
{ // 9 - 10 Continuation continuation Allows concatenation of multiple records.
std::string hetID = vS(12, 14); // 12 - 14 LString(3) hetID Het identifier, right-justified.
std::string text = vS(16); // 16 - 70 std::String text Chemical name.
std::string text = vS(16); // 16 - 70 String text Chemical name.
mHetnams[hetID] = text;
InsertChemComp(hetID);
......@@ -3294,8 +3295,8 @@ void PDBFileParser::ParseHeterogen()
continue;
}
if (mRec->is("HETSYN")) // 1 - 6 Record name "HETSYN"
{ // 9 - 10 Continuation continuation Allows concatenation of multiple records.
if (mRec->is("HETSYN")) // 1 - 6 Record name "HETSYN"
{ // 9 - 10 Continuation continuation Allows concatenation of multiple records.
std::string hetID = vS(12, 14); // 12 - 14 LString(3) hetID Het identifier, right-justified.
std::string syn = vS(16); // 16 - 70 SList hetSynonyms List of synonyms.
......@@ -3310,10 +3311,10 @@ void PDBFileParser::ParseHeterogen()
while (mRec->is("FORMUL")) // 1 - 6 Record name "FORMUL"
{ // 9 - 10 Integer compNum Component number.
std::string hetID = vS(13, 15); // 13 - 15 LString(3) hetID Het identifier.
std::string hetID = vS(13, 15); // 13 - 15 LString(3) hetID Het identifier.
// 17 - 18 Integer continuation Continuation number.
char waterMark = vC(19); // 19 Character asterisk "*" for water.
std::string formula = vS(20); // 20 - 70 std::String text Chemical formula.
std::string formula = vS(20); // 20 - 70 String text Chemical formula.
mFormuls[hetID] = formula;
......@@ -3347,9 +3348,9 @@ void PDBFileParser::ConstructEntities()
if (r->is("ATOM ") or r->is("HETATM")) // 1 - 6 Record name "ATOM "
{ // ...
std::string name = r->vS(13, 16); // 13 - 16 Atom name Atom name.
std::string name = r->vS(13, 16); // 13 - 16 Atom name Atom name.
char altLoc = r->vC(17); // 17 Character altLoc Alternate location indicator.
std::string resName = r->vS(18, 20); // 18 - 20 Residue name resName Residue name.
std::string resName = r->vS(18, 20); // 18 - 20 Residue name resName Residue name.
char chainID = r->vC(22); // 22 Character chainID Chain identifier.
int resSeq = r->vI(23, 26); // 23 - 26 Integer resSeq Residue sequence number.
char iCode = r->vC(27); // 27 AChar iCode Code for insertion of residues.
......@@ -3488,7 +3489,7 @@ void PDBFileParser::ConstructEntities()
int serial = r->vI(7, 11); // 7 - 11 Integer serial Atom serial number.
// ...
char altLoc = vC(17); // 17 Character altLoc Alternate location indicator.
std::string resName = r->vS(18, 20); // 18 - 20 Residue name resName Residue name.
std::string resName = r->vS(18, 20); // 18 - 20 Residue name resName Residue name.
char chainID = r->vC(22); // 22 Character chainID Chain identifier.
int resSeq = r->vI(23, 26); // 23 - 26 Integer resSeq Residue sequence number.
char iCode = r->vC(27); // 27 AChar iCode Code for insertion of residues.
......@@ -3553,7 +3554,7 @@ void PDBFileParser::ConstructEntities()
h = prev(mHets.end());
}
h->atoms.insert(serial);
h->atoms.push_back(r);
}
continue;
......@@ -3988,6 +3989,46 @@ void PDBFileParser::ConstructEntities()
});
}
// build sugar trees first
for (;;)
{
// find a first NAG/NDG
auto si = std::find_if(mHets.begin(), mHets.end(), [](const HET& h) { return (h.hetID == "NAG" or h.hetID == "NDG") and not h.processedSugar; });
if (si != mHets.end())
{
si->processedSugar = true;
// take the location of the C1 atom(s?)
std::vector<std::tuple<std::string,float,float,float>> ci;
for (auto a: si->atoms)
{
std::string name = a->vS(13, 16); // 13 - 16 Atom name Atom name.
if (name != "ND2")
continue;
ci.emplace_back(
std::string{ a->vC(17) }, // 17 Character altLoc Alternate location indicator.
std::stof(a->vF(31, 38)), // 31 - 38 Real(8.3) x Orthogonal coordinates for X in Angstroms.
std::stof(a->vF(39, 46)), // 39 - 46 Real(8.3) y Orthogonal coordinates for Y in Angstroms.
std::stof(a->vF(47, 54)) // 47 - 54 Real(8.3) z Orthogonal coordinates for Z in Angstroms.
);
}
// find a free ASN near by
}
}
// done with the sugar, resume operation as before
std::map<char,std::string> waterChains;
std::map<std::tuple<std::string,std::string>,int> ndbSeqNum; // for nonpoly scheme
......@@ -4149,12 +4190,12 @@ void PDBFileParser::ConstructEntities()
for (auto rec = FindRecord("MODRES"); rec != nullptr and rec->is("MODRES");
rec = rec->mNext) // 1 - 6 Record name "MODRES"
{ // 8 - 11 IDcode idCode ID code of this datablock.
std::string resName = rec->vS(13, 15); // 13 - 15 Residue name resName Residue name used in this datablock.
std::string resName = rec->vS(13, 15); // 13 - 15 Residue name resName Residue name used in this datablock.
char chainID = rec->vC(17); // 17 Character chainID Chain identifier.
int seqNum = rec->vI(19, 22); // 19 - 22 Integer seqNum Sequence number.
char iCode = rec->vC(23); // 23 AChar iCode Insertion code.
std::string stdRes = rec->vS(25, 27); // 25 - 27 Residue name stdRes Standard residue name.
std::string comment = rec->vS(30, 70); // 30 - 70 std::String comment Description of the residue modification.
std::string stdRes = rec->vS(25, 27); // 25 - 27 Residue name stdRes Standard residue name.
std::string comment = rec->vS(30, 70); // 30 - 70 String comment Description of the residue modification.
std::string asymID;
int seq;
......@@ -4324,7 +4365,7 @@ void PDBFileParser::ParseSecondaryStructure()
// 34 - 37 Integer endSeqNum Sequence number of the terminal residue.
// 38 AChar endICode Insertion code of the terminal residue.
// 39 - 40 Integer helixClass Helix class (see below).
// 41 - 70 std::String comment Comment about this helix.
// 41 - 70 String comment Comment about this helix.
// 72 - 76 Integer length Length of this helix.
std::string begAsymID, endAsymID;
......@@ -4661,22 +4702,22 @@ void PDBFileParser::ParseConnectivtyAnnotation()
if (cif::VERBOSE and mRec->is("LINKR "))
std::cerr << "Accepting non-standard LINKR record, but ignoring extra information" << std::endl;
// 1 - 6 Record name "LINK "
// 1 - 6 Record name "LINK "
std::string name1 = vS(13, 16); // 13 - 16 Atom name1 Atom name.
// 17 Character altLoc1 Alternate location indicator.
// 17 Character altLoc1 Alternate location indicator.
std::string resName1 = vS(18,20); // 18 - 20 Residue name resName1 Residue name.
// 22 Character chainID1 Chain identifier.
// 23 - 26 Integer resSeq1 Residue sequence number.
// 27 AChar iCode1 Insertion code.
// 22 Character chainID1 Chain identifier.
// 23 - 26 Integer resSeq1 Residue sequence number.
// 27 AChar iCode1 Insertion code.
std::string name2 = vS(43, 46); // 43 - 46 Atom name2 Atom name.
// 47 Character altLoc2 Alternate location indicator.
// 47 Character altLoc2 Alternate location indicator.
std::string resName2 = vS(48, 50); // 48 - 50 Residue name resName2 Residue name.
// 52 Character chainID2 Chain identifier.
// 53 - 56 Integer resSeq2 Residue sequence number.
// 57 AChar iCode2 Insertion code.
// 60 - 65 SymOP sym1 Symmetry operator atom 1.
// 67 - 72 SymOP sym2 Symmetry operator atom 2.
// 74 – 78 Real(5.2) Length Link distance
// 52 Character chainID2 Chain identifier.
// 53 - 56 Integer resSeq2 Residue sequence number.
// 57 AChar iCode2 Insertion code.
// 60 - 65 SymOP sym1 Symmetry operator atom 1.
// 67 - 72 SymOP sym2 Symmetry operator atom 2.
// 74 – 78 Real(5.2) Length Link distance
std::string type = "covale";
if (IsMetal(resName1, name1) or IsMetal(resName2, name2))
......@@ -4789,17 +4830,17 @@ void PDBFileParser::ParseConnectivtyAnnotation()
if (mRec->is("CISPEP"))
{
// 1 - 6 Record name "CISPEP"
int serNum = vI(8, 10); // 8 - 10 Integer serNum Record serial number.
// 1 - 6 Record name "CISPEP"
int serNum = vI(8, 10); // 8 - 10 Integer serNum Record serial number.
std::string pep1 = vS(12, 14); // 12 - 14 LString(3) pep1 Residue name.
char chainID1 = vC(16); // 16 Character chainID1 Chain identifier.
int seqNum1 = vI(18, 21); // 18 - 21 Integer seqNum1 Residue sequence number.
char iCode1 = vC(22); // 22 AChar icode1 Insertion code.
char chainID1 = vC(16); // 16 Character chainID1 Chain identifier.
int seqNum1 = vI(18, 21); // 18 - 21 Integer seqNum1 Residue sequence number.
char iCode1 = vC(22); // 22 AChar icode1 Insertion code.
std::string pep2 = vS(26, 28); // 26 - 28 LString(3) pep2 Residue name.
char chainID2 = vC(30); // 30 Character chainID2 Chain identifier.
int seqNum2 = vI(32, 35); // 32 - 35 Integer seqNum2 Residue sequence number.
char iCode2 = vC(36); // 36 AChar icode2 Insertion code.
int modNum = vI(44, 46); // 44 - 46 Integer modNum Identifies the specific model.
char chainID2 = vC(30); // 30 Character chainID2 Chain identifier.
int seqNum2 = vI(32, 35); // 32 - 35 Integer seqNum2 Residue sequence number.
char iCode2 = vC(36); // 36 AChar icode2 Insertion code.
int modNum = vI(44, 46); // 44 - 46 Integer modNum Identifies the specific model.
std::string measure = vF(54, 59); // 54 - 59 Real(6.2) measure Angle measurement in degrees.
if (modNum == 0)
......@@ -4858,7 +4899,7 @@ void PDBFileParser::ParseMiscellaneousFeatures()
while (mRec->is("SITE "))
{ // 1 - 6 Record name "SITE "
// 8 - 10 Integer seqNum Sequence number.
std::string siteID = vS(12, 14); // 12 - 14 LString(3) siteID Site name.
std::string siteID = vS(12, 14);// 12 - 14 LString(3) siteID Site name.
int numRes = vI(16, 17); // 16 - 17 Integer numRes Number of residues that compose the site.
int o = 19;
......@@ -4868,11 +4909,11 @@ void PDBFileParser::ParseMiscellaneousFeatures()
for (int i = 0; i < numRes; ++i)
{
std::string resName = vS(o, o + 2); // 19 - 21 Residue name resName1 Residue name for first residue that
// creates the site.
char chainID = vC(o + 4); // 23 Character chainID1 Chain identifier for first residue of site.
int seq = vI(o + 5, o + 8); // 24 - 27 Integer seq1 Residue sequence number for first residue
// of the site.
char iCode = vC(o + 9); // 28 AChar iCode1 Insertion code for first residue of the site.
// creates the site.
char chainID = vC(o + 4); // 23 Character chainID1 Chain identifier for first residue of site.
int seq = vI(o + 5, o + 8); // 24 - 27 Integer seq1 Residue sequence number for first residue
// of the site.
char iCode = vC(o + 9); // 28 AChar iCode1 Insertion code for first residue of the site.
int labelSeq;
std::string asym;
......@@ -4915,14 +4956,14 @@ void PDBFileParser::ParseCrystallographic()
getCategory("cell")->emplace({
{ "entry_id", mStructureID }, // 1 - 6 Record name "CRYST1"
{ "length_a", vF(7, 15) }, // 7 - 15 Real(9.3) a a (Angstroms).
{ "length_b", vF(16, 24) }, // 16 - 24 Real(9.3) b b (Angstroms).
{ "length_c", vF(25, 33) }, // 25 - 33 Real(9.3) c c (Angstroms).
{ "angle_alpha", vF(34, 40) }, // 34 - 40 Real(7.2) alpha alpha (degrees).
{ "angle_beta", vF(41, 47) }, // 41 - 47 Real(7.2) beta beta (degrees).
{ "angle_gamma", vF(48, 54) }, // 48 - 54 Real(7.2) gamma gamma (degrees).
{ "length_a", vF(7, 15) }, // 7 - 15 Real(9.3) a a (Angstroms).
{ "length_b", vF(16, 24) }, // 16 - 24 Real(9.3) b b (Angstroms).
{ "length_c", vF(25, 33) }, // 25 - 33 Real(9.3) c c (Angstroms).
{ "angle_alpha", vF(34, 40) }, // 34 - 40 Real(7.2) alpha alpha (degrees).
{ "angle_beta", vF(41, 47) }, // 41 - 47 Real(7.2) beta beta (degrees).
{ "angle_gamma", vF(48, 54) }, // 48 - 54 Real(7.2) gamma gamma (degrees).
/* goes into symmetry */ // 56 - 66 LString sGroup Space group.
{ "Z_PDB", vF(67, 70) } // 67 - 70 Integer z Z value.
{ "Z_PDB", vF(67, 70) } // 67 - 70 Integer z Z value.
});
std::string spaceGroup, intTablesNr;
......@@ -5027,9 +5068,9 @@ void PDBFileParser::ParseCoordinateTransformation()
m[x][2] = vF(31, 40); // 31 - 40 Real(10.6) m[n][3] Mn3
v[x] = vF(46, 55); // 46 - 55 Real(10.5) v[n] Vn
igiven = vC(60) == '1'; // 60 Integer iGiven 1 if coordinates for the representations
// which are approximately related by the
GetNextRecord(); // transformations of the molecule are
} // contained in the datablock. Otherwise, blank.
// which are approximately related by the
GetNextRecord(); // transformations of the molecule are
} // contained in the datablock. Otherwise, blank.
getCategory("struct_ncs_oper")->emplace({
{ "id", serial },
......@@ -5058,10 +5099,10 @@ void PDBFileParser::ParseCoordinate(int modelNr)
typedef std::tuple<std::string,int,bool,PDBRecord*,PDBRecord*> atomRec;
std::vector<atomRec> atoms;
while (mRec->is("ATOM ") or mRec->is("HETATM")) // 1 - 6 Record name "ATOM "
while (mRec->is("ATOM ") or mRec->is("HETATM")) // 1 - 6 Record name "ATOM "
{
char chainID = vC(22); // 22 Character chainID Chain identifier.
int resSeq = vI(23, 26); // 23 - 26 Integer resSeq Residue sequence number.
char chainID = vC(22); // 22 Character chainID Chain identifier.
int resSeq = vI(23, 26); // 23 - 26 Integer resSeq Residue sequence number.
char iCode = vC(27);
std::string asymID;
......@@ -5166,20 +5207,20 @@ void PDBFileParser::ParseCoordinate(int modelNr)
++mAtomID;
std::string groupPDB = mRec->is("ATOM ") ? "ATOM" : "HETATM";
// int serial = vI(7, 11); // 7 - 11 Integer serial Atom serial number.
// int serial = vI(7, 11); // 7 - 11 Integer serial Atom serial number.
std::string name = vS(13, 16); // 13 - 16 Atom name Atom name.
char altLoc = vC(17); // 17 Character altLoc Alternate location indicator.
char altLoc = vC(17); // 17 Character altLoc Alternate location indicator.
std::string resName = vS(18, 20); // 18 - 20 Residue name resName Residue name.
char chainID = vC(22); // 22 Character chainID Chain identifier.
int resSeq = vI(23, 26); // 23 - 26 Integer resSeq Residue sequence number.
char iCode = vC(27); // 27 AChar iCode Code for insertion of residues.
char chainID = vC(22); // 22 Character chainID Chain identifier.
int resSeq = vI(23, 26); // 23 - 26 Integer resSeq Residue sequence number.
char iCode = vC(27); // 27 AChar iCode Code for insertion of residues.
std::string x = vF(31, 38); // 31 - 38 Real(8.3) x Orthogonal coordinates for X in Angstroms.
std::string y = vF(39, 46); // 39 - 46 Real(8.3) y Orthogonal coordinates for Y in Angstroms.
std::string z = vF(47, 54); // 47 - 54 Real(8.3) z Orthogonal coordinates for Z in Angstroms.
std::string occupancy = vF(55, 60); // 55 - 60 Real(6.2) occupancy Occupancy.
std::string tempFactor = vF(61, 66); // 61 - 66 Real(6.2) tempFactor Temperature factor.
std::string tempFactor = vF(61, 66);// 61 - 66 Real(6.2) tempFactor Temperature factor.
std::string element = vS(77, 78); // 77 - 78 LString(2) element Element symbol, right-justified.
std::string charge = vS(79, 80); // 79 - 80 LString(2) charge Charge on the atom.
std::string charge = vS(79, 80); // 79 - 80 LString(2) charge Charge on the atom.
std::string entityID = mAsymID2EntityID[asymID];
......
test/pdb2cif-test.cpp 0 → 100644
/*-
* SPDX-License-Identifier: BSD-2-Clause
*
* Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include <stdexcept>
#include "cif++/Cif++.hpp"
#include <cif++/Structure.hpp>
int main(int argc, char* const argv[])
{
cif::rsrc_loader::init({
{ cif::rsrc_loader_type::file, "." },
{ cif::rsrc_loader_type::file, "rsrc" },
#if USE_RSRC
{ cif::rsrc_loader_type::mrsrc, "", { gResourceIndex, gResourceData, gResourceName } }
#endif
});
mmcif::File file("pdb2b8h.ent.gz");
return 0;
}
\ No newline at end of file
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