Skip to content

L
libcifpp
Commit 1e4e0638 by maarten
Options

less strict parsing 

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@234 a1961a4f-ab94-4bcc-80e8-33b5a54de466
parent 724c8346
Showing with 30 additions and 26 deletions
src/PDB2Cif.cpp
...@@ -652,7 +652,7 @@ class PDBFileParser ...@@ -652,7 +652,7 @@ class PDBFileParser
void PreParseInput(istream& is); void PreParseInput(istream& is);
void GetNextRecord(); void GetNextRecord();
void Match(const string& expected); void Match(const string& expected, bool throwIfMissing);
void ParseTitle(); void ParseTitle();
void ParseCitation(const string& id); void ParseCitation(const string& id);
...@@ -1198,10 +1198,14 @@ void PDBFileParser::GetNextRecord() ...@@ -1198,10 +1198,14 @@ void PDBFileParser::GetNextRecord()
} }
} }
void PDBFileParser::Match(const string& expected) void PDBFileParser::Match(const string& expected, bool throwIfMissing)
{ {
if (mRec->mName != expected) if (mRec->mName != expected)
throw runtime_error("Expected record " + expected + " but found " + mRec->mName); {
if (throwIfMissing)
throw runtime_error("Expected record " + expected + " but found " + mRec->mName);
cerr << "Expected record " + expected + " but found " + mRec->mName << endl;
}
} }
vector<string> PDBFileParser::SplitCSV(const string& value) vector<string> PDBFileParser::SplitCSV(const string& value)
...@@ -1224,7 +1228,7 @@ void PDBFileParser::ParseTitle() ...@@ -1224,7 +1228,7 @@ void PDBFileParser::ParseTitle()
// coordinates were received at the PDB. // coordinates were received at the PDB.
// 63 - 66 IDcode idCode This identifier is unique within the PDB. // 63 - 66 IDcode idCode This identifier is unique within the PDB.
Match("HEADER"); Match("HEADER", true);
mStructureId = vS(63, 66); mStructureId = vS(63, 66);
string keywords = vS(11, 50); string keywords = vS(11, 50);
...@@ -1270,7 +1274,7 @@ void PDBFileParser::ParseTitle() ...@@ -1270,7 +1274,7 @@ void PDBFileParser::ParseTitle()
} }
// TITLE // TITLE
// Match("TITLE "); Match("TITLE ", false);
string title; string title;
if (mRec->is("TITLE ")) // 1 - 6 Record name "TITLE " if (mRec->is("TITLE ")) // 1 - 6 Record name "TITLE "
{ // 9 - 10 Continuation continuation Allows concatenation of multiple records. { // 9 - 10 Continuation continuation Allows concatenation of multiple records.
...@@ -1301,7 +1305,7 @@ void PDBFileParser::ParseTitle() ...@@ -1301,7 +1305,7 @@ void PDBFileParser::ParseTitle()
} }
// COMPND // COMPND
Match("COMPND"); Match("COMPND", false);
// 1 - 6 Record name "COMPND" // 1 - 6 Record name "COMPND"
// 8 - 10 Continuation continuation Allows concatenation of multiple records. // 8 - 10 Continuation continuation Allows concatenation of multiple records.
// 11 - 80 Specification compound Description of the molecular components. // 11 - 80 Specification compound Description of the molecular components.
...@@ -1356,7 +1360,7 @@ void PDBFileParser::ParseTitle() ...@@ -1356,7 +1360,7 @@ void PDBFileParser::ParseTitle()
GetNextRecord(); GetNextRecord();
// SOURCE // SOURCE
// Match("SOURCE"); Match("SOURCE", false);
if (mRec->is("SOURCE")) if (mRec->is("SOURCE"))
{ {
...@@ -1415,7 +1419,7 @@ void PDBFileParser::ParseTitle() ...@@ -1415,7 +1419,7 @@ void PDBFileParser::ParseTitle()
} }
// KEYWDS // KEYWDS
// Match("KEYWDS"); Match("KEYWDS", false);
string pdbxKeywords; string pdbxKeywords;
if (mRec->is("KEYWDS")) // 1 - 6 Record name "KEYWDS" if (mRec->is("KEYWDS")) // 1 - 6 Record name "KEYWDS"
...@@ -1435,7 +1439,7 @@ void PDBFileParser::ParseTitle() ...@@ -1435,7 +1439,7 @@ void PDBFileParser::ParseTitle()
} }
// EXPDTA // EXPDTA
// Match("EXPDTA"); Match("EXPDTA", false);
if (mRec->is("EXPDTA")) if (mRec->is("EXPDTA"))
{ {
mExpMethod = vS(11); mExpMethod = vS(11);
...@@ -1482,7 +1486,7 @@ void PDBFileParser::ParseTitle() ...@@ -1482,7 +1486,7 @@ void PDBFileParser::ParseTitle()
} }
// AUTHOR // AUTHOR
// Match("AUTHOR"); Match("AUTHOR", false);
if (mRec->is("AUTHOR")) if (mRec->is("AUTHOR"))
{ {
int n = 1; int n = 1;
...@@ -4761,7 +4765,7 @@ void PDBFileParser::ParseMiscellaneousFeatures() ...@@ -4761,7 +4765,7 @@ void PDBFileParser::ParseMiscellaneousFeatures()
void PDBFileParser::ParseCrystallographic() void PDBFileParser::ParseCrystallographic()
{ {
Match("CRYST1"); Match("CRYST1", true);
getCategory("cell")->emplace({ getCategory("cell")->emplace({
{ "entry_id", mStructureId }, // 1 - 6 Record name "CRYST1" { "entry_id", mStructureId }, // 1 - 6 Record name "CRYST1"
...@@ -4805,11 +4809,11 @@ void PDBFileParser::ParseCoordinateTransformation() ...@@ -4805,11 +4809,11 @@ void PDBFileParser::ParseCoordinateTransformation()
{ {
int x = stoi(n) - 1; int x = stoi(n) - 1;
Match("ORIGX" + n); // 1 - 6 Record name "ORIGXn" n=1, 2, or 3 Match("ORIGX" + n, true); // 1 - 6 Record name "ORIGXn" n=1, 2, or 3
m[x][0] = vF(11, 20); // 11 - 20 Real(10.6) o[n][1] On1 m[x][0] = vF(11, 20); // 11 - 20 Real(10.6) o[n][1] On1
m[x][1] = vF(21, 30); // 21 - 30 Real(10.6) o[n][2] On2 m[x][1] = vF(21, 30); // 21 - 30 Real(10.6) o[n][2] On2
m[x][2] = vF(31, 40); // 31 - 40 Real(10.6) o[n][3] On3 m[x][2] = vF(31, 40); // 31 - 40 Real(10.6) o[n][3] On3
v[x] = vF(46, 55); // 46 - 55 Real(10.5) t[n] Tn v[x] = vF(46, 55); // 46 - 55 Real(10.5) t[n] Tn
GetNextRecord(); GetNextRecord();
} }
...@@ -4837,11 +4841,11 @@ void PDBFileParser::ParseCoordinateTransformation() ...@@ -4837,11 +4841,11 @@ void PDBFileParser::ParseCoordinateTransformation()
{ {
int x = stoi(n) - 1; int x = stoi(n) - 1;
Match("SCALE" + n); // 1 - 6 Record name "SCALEn" n=1, 2, or 3 Match("SCALE" + n, true); // 1 - 6 Record name "SCALEn" n=1, 2, or 3
m[x][0] = vF(11, 20); // 11 - 20 Real(10.6) s[n][1] Sn1 m[x][0] = vF(11, 20); // 11 - 20 Real(10.6) s[n][1] Sn1
m[x][1] = vF(21, 30); // 21 - 30 Real(10.6) s[n][2] Sn2 m[x][1] = vF(21, 30); // 21 - 30 Real(10.6) s[n][2] Sn2
m[x][2] = vF(31, 40); // 31 - 40 Real(10.6) s[n][3] Sn3 m[x][2] = vF(31, 40); // 31 - 40 Real(10.6) s[n][3] Sn3
v[x] = vF(46, 55); // 46 - 55 Real(10.5) u[n] Un v[x] = vF(46, 55); // 46 - 55 Real(10.5) u[n] Un
GetNextRecord(); GetNextRecord();
} }
...@@ -4871,7 +4875,7 @@ void PDBFileParser::ParseCoordinateTransformation() ...@@ -4871,7 +4875,7 @@ void PDBFileParser::ParseCoordinateTransformation()
{ {
int x = stoi(n) - 1; int x = stoi(n) - 1;
Match("MTRIX" + n); // 1 - 6 Record name "MTRIXn" n=1, 2, or 3 Match("MTRIX" + n, true); // 1 - 6 Record name "MTRIXn" n=1, 2, or 3
serial = vI(8, 10); // 8 - 10 Integer serial Serial number. serial = vI(8, 10); // 8 - 10 Integer serial Serial number.
m[x][0] = vF(11, 20); // 11 - 20 Real(10.6) m[n][1] Mn1 m[x][0] = vF(11, 20); // 11 - 20 Real(10.6) m[n][1] Mn1
m[x][1] = vF(21, 30); // 21 - 30 Real(10.6) m[n][2] Mn2 m[x][1] = vF(21, 30); // 21 - 30 Real(10.6) m[n][2] Mn2
...@@ -4935,7 +4939,7 @@ void PDBFileParser::ParseCoordinate(int modelNr) ...@@ -4935,7 +4939,7 @@ void PDBFileParser::ParseCoordinate(int modelNr)
/*if?... */ while (mRec->is("TER ")) /*if?... */ while (mRec->is("TER "))
{ {
Match("TER "); Match("TER ", true);
GetNextRecord(); GetNextRecord();
} }
} }
...@@ -5114,10 +5118,10 @@ void PDBFileParser::ParseBookkeeping() ...@@ -5114,10 +5118,10 @@ void PDBFileParser::ParseBookkeeping()
{ {
if (mRec->is("MASTER")) if (mRec->is("MASTER"))
{ {
Match("MASTER"); Match("MASTER", false);
GetNextRecord(); GetNextRecord();
} }
Match("END "); Match("END ", false);
} }
void PDBFileParser::Parse(istream& is, cif::File& result) void PDBFileParser::Parse(istream& is, cif::File& result)
...@@ -5164,7 +5168,7 @@ void PDBFileParser::Parse(istream& is, cif::File& result) ...@@ -5164,7 +5168,7 @@ void PDBFileParser::Parse(istream& is, cif::File& result)
if (model) if (model)
{ {
Match("ENDMDL"); Match("ENDMDL", true);
GetNextRecord(); GetNextRecord();
} }
} }
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment