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libcifpp
Commit 1e4e0638 by maarten
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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
void PreParseInput(istream& is);
void GetNextRecord();
void Match(const string& expected);
void Match(const string& expected, bool throwIfMissing);
void ParseTitle();
void ParseCitation(const string& id);
......@@ -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)
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)
......@@ -1224,7 +1228,7 @@ void PDBFileParser::ParseTitle()
// coordinates were received at the PDB.
// 63 - 66 IDcode idCode This identifier is unique within the PDB.
Match("HEADER");
Match("HEADER", true);
mStructureId = vS(63, 66);
string keywords = vS(11, 50);
......@@ -1270,7 +1274,7 @@ void PDBFileParser::ParseTitle()
}
// TITLE
// Match("TITLE ");
Match("TITLE ", false);
string title;
if (mRec->is("TITLE ")) // 1 - 6 Record name "TITLE "
{ // 9 - 10 Continuation continuation Allows concatenation of multiple records.
......@@ -1301,7 +1305,7 @@ void PDBFileParser::ParseTitle()
}
// COMPND
Match("COMPND");
Match("COMPND", false);
// 1 - 6 Record name "COMPND"
// 8 - 10 Continuation continuation Allows concatenation of multiple records.
// 11 - 80 Specification compound Description of the molecular components.
......@@ -1356,7 +1360,7 @@ void PDBFileParser::ParseTitle()
GetNextRecord();
// SOURCE
// Match("SOURCE");
Match("SOURCE", false);
if (mRec->is("SOURCE"))
{
......@@ -1415,7 +1419,7 @@ void PDBFileParser::ParseTitle()
}
// KEYWDS
// Match("KEYWDS");
Match("KEYWDS", false);
string pdbxKeywords;
if (mRec->is("KEYWDS")) // 1 - 6 Record name "KEYWDS"
......@@ -1435,7 +1439,7 @@ void PDBFileParser::ParseTitle()
}
// EXPDTA
// Match("EXPDTA");
Match("EXPDTA", false);
if (mRec->is("EXPDTA"))
{
mExpMethod = vS(11);
......@@ -1482,7 +1486,7 @@ void PDBFileParser::ParseTitle()
}
// AUTHOR
// Match("AUTHOR");
Match("AUTHOR", false);
if (mRec->is("AUTHOR"))
{
int n = 1;
......@@ -4761,7 +4765,7 @@ void PDBFileParser::ParseMiscellaneousFeatures()
void PDBFileParser::ParseCrystallographic()
{
Match("CRYST1");
Match("CRYST1", true);
getCategory("cell")->emplace({
{ "entry_id", mStructureId }, // 1 - 6 Record name "CRYST1"
......@@ -4805,11 +4809,11 @@ void PDBFileParser::ParseCoordinateTransformation()
{
int x = stoi(n) - 1;
Match("ORIGX" + n); // 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][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
v[x] = vF(46, 55); // 46 - 55 Real(10.5) t[n] Tn
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][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
v[x] = vF(46, 55); // 46 - 55 Real(10.5) t[n] Tn
GetNextRecord();
}
......@@ -4837,11 +4841,11 @@ void PDBFileParser::ParseCoordinateTransformation()
{
int x = stoi(n) - 1;
Match("SCALE" + n); // 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][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
v[x] = vF(46, 55); // 46 - 55 Real(10.5) u[n] Un
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][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
v[x] = vF(46, 55); // 46 - 55 Real(10.5) u[n] Un
GetNextRecord();
}
......@@ -4871,7 +4875,7 @@ void PDBFileParser::ParseCoordinateTransformation()
{
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.
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
......@@ -4935,7 +4939,7 @@ void PDBFileParser::ParseCoordinate(int modelNr)
/*if?... */ while (mRec->is("TER "))
{
Match("TER ");
Match("TER ", true);
GetNextRecord();
}
}
......@@ -5114,10 +5118,10 @@ void PDBFileParser::ParseBookkeeping()
{
if (mRec->is("MASTER"))
{
Match("MASTER");
Match("MASTER", false);
GetNextRecord();
}
Match("END ");
Match("END ", false);
}
void PDBFileParser::Parse(istream& is, cif::File& result)
......@@ -5164,7 +5168,7 @@ void PDBFileParser::Parse(istream& is, cif::File& result)
if (model)
{
Match("ENDMDL");
Match("ENDMDL", true);
GetNextRecord();
}
}
......
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