Molecule createMeshZMolecules(Opls_Scan *scanner)
{
//1 S 200 0 0 0.000000 0 0.000000 0 0.000000 0
Atom atom1=scanner->getAtom("200");
atom1.id=1;
// 2 DUM -1 0 1 0.500000 0 0.000000 0 0.000000 0
Atom atom2=createAtom(2,-1,-1,-1,-1,-1,-1,NULL);
Bond bond2=createBond(2,1,0.5,false);
//3 DUM -1 0 2 0.500000 1 90.000000 0 0.000000 0
Atom atom3=createAtom(3,-1,-1,-1,-1,-1,-1,NULL);
Bond bond3=createBond(3,2,0.5,false);
Angle angle3=createAngle(3,1,90,false);
//4 hH 204 0 1 1.336532 2 90.000000 3 180.000000 0
Atom atom4=scanner->getAtom("204");
atom4.id=4;
Bond bond4=createBond(4,1,1.336532,true);
Angle angle4=createAngle(4,2,90,false);
Dihedral dihed4=createDihedral(4,3,180,false);
//5 C 217 0 1 1.811119 4 96.401770 2 180.000000 0
Atom atom5=scanner->getAtom("217");
atom5.id=5;
Bond bond5=createBond(5,1,1.811119,true);
Angle angle5=createAngle(5,4,96.401770,true);
Dihedral dihed5=createDihedral(5,2,180,false);
//6 HC 140 0 5 1.090187 1 110.255589 4 179.999947 0
Atom atom6=scanner->getAtom("140");
atom6.id=6;
Bond bond6=createBond(6,5,1.090187,true);
Angle angle6=createAngle(6,1,110.255589,true);
Dihedral dihed6=createDihedral(6,4,179.999947,true);
//7 HC 140 0 5 1.090135 6 108.527646 1 121.053891 0
Atom atom7=scanner->getAtom("140");
atom7.id=7;
Bond bond7=createBond(7,5,1.090135,true);
Angle angle7=createAngle(7,6,108.527646,true);
Dihedral dihed7=createDihedral(7,1,121.053891,true);
//8 HC 140 0 5 1.090135 6 108.527646 1 238.946114 0
Atom atom8=scanner->getAtom("140");
atom8.id=8;
Bond bond8=createBond(8,5,1.090135,true);
Angle angle8=createAngle(8,6,108.527646,true);
Dihedral dihed8=createDihedral(8,1,238.946114,true);
/* HOPS and BONDS Diagram of Mesh.z
// 1--2--3
// |\
// | \
// 4 5
// /|\
// / | \
// 6 7 8
*/
//All hops that have a hop distance >= 3
Hop hop1= createHop(2,6,3);
Hop hop2= createHop(2,7,3);
Hop hop3= createHop(2,8,3);
Hop hop4= createHop(3,4,3);
Hop hop5= createHop(3,5,3);
Hop hop6= createHop(3,6,4);
Hop hop7= createHop(3,7,4);
Hop hop8= createHop(3,8,4);
Hop hop9= createHop(4,6,3);
Hop hop10= createHop(4,7,3);
Hop hop11= createHop(4,8,3);
Atom *atomPtr = new Atom[8];
Bond *bondPtr = new Bond[7];
Angle *anglePtr = new Angle[6];
Dihedral *dihedPtr = new Dihedral[5];
Hop *hopPtr = new Hop[11];
atomPtr[0]=atom1; atomPtr[1]=atom2; atomPtr[2]=atom3; atomPtr[3]=atom4; atomPtr[4]=atom5; atomPtr[5]=atom6; atomPtr[6]=atom7; atomPtr[7]=atom8;
bondPtr[0]=bond2; bondPtr[1]=bond3; bondPtr[2]=bond4; bondPtr[3]=bond5; bondPtr[4]=bond6; bondPtr[5]=bond7; bondPtr[6]=bond8;
anglePtr[0]=angle3; anglePtr[1]=angle4; anglePtr[2]=angle5; anglePtr[3]=angle6; anglePtr[4]=angle7; anglePtr[5]=angle8;
dihedPtr[0]=dihed4; dihedPtr[1]=dihed5; dihedPtr[2]=dihed6; dihedPtr[3]=dihed7; dihedPtr[4]=dihed8;
hopPtr[0]=hop1; hopPtr[1]=hop2; hopPtr[2]=hop3; hopPtr[3]=hop4; hopPtr[4]=hop5; hopPtr[5]=hop6; hopPtr[6]=hop7; hopPtr[7]=hop8; hopPtr[8]=hop9;
hopPtr[9]=hop10; hopPtr[10]=hop11;
return createMolecule(1,atomPtr,anglePtr,bondPtr,dihedPtr,hopPtr,8,6,7,5,11);
}
vector<Molecule> createT3pdimMolecules(Opls_Scan *scanner)
{
// TIP3P Water Dimer Tot. E = -6.5396
//1 O 111 111 0 .000000 0 .000000 0 .000000 0
Atom atom1 = scanner->getAtom("111");
atom1.id=1;
//2 DU -1 -1 1 1.000000 0 .000000 0 .000000 0
Atom atom2=createAtom(2,-1,-1,-1,-1,-1,-1,NULL);
Bond bond2=createBond(2,1,1.0,false);
//3 DU -1 -1 2 1.000000 1 90.000000 0 .000000 0
Atom atom3=createAtom(3,-1,-1,-1,-1,-1,-1,NULL);
Bond bond3=createBond(3,2,1.0,false);
Angle angle3=createAngle(3,1,90.0,false);
//4 HO 112 112 1 .957200 2 127.740000 3 90.000000 0
Atom atom4=scanner->getAtom("112");
atom4.id=4;
Bond bond4=createBond(4,1,.957200,false);
Angle angle4=createAngle(4,2,127.740000,false);
Dihedral dihed4=createDihedral(4,3,90.00,false);
//5 HO 112 112 1 .957200 4 104.520000 2 180.000000 0
Atom atom5=scanner->getAtom("112");
atom5.id=5;
Bond bond5=createBond(5,1,.957200,false);
Angle angle5=createAngle(5,4,104.520000,false);
Dihedral dihed5=createDihedral(5,2,180.00,false);
//6 X -1 -1 1 .150000 4 52.260000 5 .000000 0
Atom atom6=createAtom(6,-1,-1,-1,-1,-1,-1,NULL);
Bond bond6=createBond(6,1,.150000,false);
Angle angle6=createAngle(6,4,52.260000,false);
Dihedral dihed6=createDihedral(6,5,.00,false);
//TERZ 2nd Bonded Molecule
//7 O 111 111 1 2.751259 2 131.716186 3 269.946364 0
Atom atom7=scanner->getAtom("111");
atom7.id=7;
Bond bond7=createBond(7,1,2.751259,false);
Angle angle7=createAngle(7,2,131.716186,false);
Dihedral dihed7=createDihedral(7,3,269.946364,false);
//8 DU -1 -1 7 1.000000 1 21.472391 2 179.887530 0
Atom atom8=createAtom(8,-1,-1,-1,-1,-1,-1,NULL);
Bond bond8=createBond(8,7,1.0,false);
Angle angle8=createAngle(8,1,21.472391,false);
Dihedral dihed8=createDihedral(8,2,179.887530,false);
//9 DU -1 -1 8 1.000000 7 90.000000 1 179.624613 0
Atom atom9=createAtom(9,-1,-1,-1,-1,-1,-1,NULL);
Bond bond9=createBond(9,8,1.0,false);
Angle angle9=createAngle(9,7,90.000000,false);
Dihedral dihed9=createDihedral(9,1,179.624613,false);
//10 HO 112 112 7 .957200 8 127.740000 9 90.000000 0
Atom atom10=scanner->getAtom("112");
atom10.id=10;
Bond bond10=createBond(10,7,0.957200,false);
Angle angle10=createAngle(10,8,127.74,false);
Dihedral dihed10=createDihedral(10,9,90.0,false);
//11 HO 112 112 7 .957200 10 104.520000 8 180.000000 0
Atom atom11=scanner->getAtom("112");
atom11.id=11;
Bond bond11=createBond(11,7,0.957200,false);
Angle angle11=createAngle(11,10,104.52,false);
Dihedral dihed11=createDihedral(11,8,180.0,false);
//12 X -1 -1 7 .150000 10 52.260000 11 .000000 0
Atom atom12=createAtom(12,-1,-1,-1,-1,-1,-1,NULL);
Bond bond12=createBond(12,7,0.15,false);
Angle angle12=createAngle(12,10,52.26,false);
Dihedral dihed12=createDihedral(12,11,0.0,false);
/* HOPS and BONDS Diagram of Mesh.z
//
//
// 10 11 12
// \ | /
// \|/
// 7--8--9
// |
// |
// 1--2--3
// /|\
// / | \
// 4 5 6
*/
//All intermolecular hops that have a hop distance >= 3
//bottom Molecule
Hop hop1=createHop(3,4,3);
Hop hop2=createHop(3,5,3);
Hop hop3=createHop(3,6,3);
//top Molecule
Hop hop4=createHop(9,10,3);
Hop hop5=createHop(9,11,3);
Hop hop6=createHop(9,12,3);
Atom *atomPtr = new Atom[6];
Bond *bondPtr = new Bond[5];
Angle *anglePtr = new Angle[4];
Dihedral *dihedPtr = new Dihedral[3];
Hop *hopPtr = new Hop[3];
vector<Molecule> retVect;
atomPtr[0]=atom1; atomPtr[1]=atom2; atomPtr[2]=atom3; atomPtr[3]=atom4; atomPtr[4]=atom5; atomPtr[5]=atom6;
bondPtr[0]=bond2; bondPtr[1]=bond3; bondPtr[2]=bond4; bondPtr[3]=bond5; bondPtr[4]=bond6;
anglePtr[0]=angle3; anglePtr[1]=angle4; anglePtr[2]=angle5; anglePtr[3]=angle6;
dihedPtr[0]=dihed4; dihedPtr[1]=dihed5; dihedPtr[2]=dihed6;
hopPtr[0]=hop1; hopPtr[1]=hop2; hopPtr[2]=hop3;
retVect.push_back( createMolecule(1,atomPtr,anglePtr,bondPtr,dihedPtr,hopPtr,6,4,5,3,3) );
Atom *atomPt = new Atom[6];
Bond *bondPt = new Bond[6];
Angle *anglePt = new Angle[6];
Dihedral *dihedPt = new Dihedral[6];
Hop *hopPt = new Hop[3];
atomPt[0]=atom7; atomPt[1]=atom8; atomPt[2]=atom9; atomPt[3]=atom10; atomPt[4]=atom11; atomPt[5]=atom12;
bondPt[0]=bond7; bondPt[1]=bond8; bondPt[2]=bond9; bondPt[3]=bond10; bondPt[4]=bond11; bondPt[5]=bond12;
anglePt[0]=angle7; anglePt[1]=angle8; anglePt[2]=angle9; anglePt[3]=angle10; anglePt[4]=angle11; anglePt[5]=angle12;
dihedPt[0]=dihed7; dihedPt[1]=dihed8; dihedPt[2]=dihed9; dihedPt[3]=dihed10; dihedPt[4]=dihed11; dihedPt[5]=dihed12;
hopPt[0]=hop4; hopPt[1]=hop5; hopPt[2]=hop6;
retVect.push_back( createMolecule(7,atomPt,anglePt,bondPt,dihedPt,hopPt,6,6,6,6,3) );
return retVect;
}
void PDBFormat::PDBParser::parseAtom(BioStruct3D& biostruct, U2OpStatus&)
{
/*
Record Format
COLUMNS DEFINITION
1 - 6 Record name "ATOM "
7 - 11 Atom serial number.
13 - 16 Atom name.
17 Alternate location indicator.
18 - 20 Residue name.
22 Chain identifier.
23 - 26 Residue sequence number.
27 Code for insertion of residues.
31 - 38 Orthogonal coordinates for X in Angstroms.
39 - 46 Orthogonal coordinates for Y in Angstroms.
47 - 54 Orthogonal coordinates for Z in Angstroms.
55 - 60 Occupancy.
61 - 66 Temperature factor.
77 - 78 Element symbol, right-justified.
79 - 80 Charge on the atom.
*/
if (!flagAtomRecordPresent)
flagAtomRecordPresent = true;
bool isHetero = false;
if (currentPDBLine.startsWith("HETATM")) {
isHetero = true;
}
int id = currentPDBLine.mid(6,5).toInt();
QByteArray atomName = currentPDBLine.mid(12,4).toLatin1().trimmed();
QByteArray residueName = currentPDBLine.mid(17,3).toLatin1().trimmed();
int resId = currentPDBLine.mid(22,4).toLatin1().toInt();
char insCode = currentPDBLine.at(26).toLatin1();
char residueAcronym = PDBFormat::getAcronymByName(residueName);
char chainIdentifier = currentPDBLine.at(21).toLatin1();
ResidueIndex residueIndex(resId,insCode);
bool atomIsInChain = !isHetero || seqResContains(chainIdentifier, residueIndex.toInt(), residueAcronym);
QByteArray elementName = currentPDBLine.mid(76,2).toLatin1().trimmed();
QByteArray element = elementName.isEmpty() ? atomName.mid(0,1) : elementName;
int atomicNumber = PDBFormat::getElementNumberByName(element);
int chainIndex = chainIndexMap.contains(chainIdentifier) ? chainIndexMap.value(chainIdentifier) : currentChainIndex;
if (currentModelIndex == 0 && atomIsInChain) {
// Process residue
if (!biostruct.moleculeMap.contains(chainIndex)) {
createMolecule(chainIdentifier, biostruct, chainIndex);
}
SharedMolecule& mol = biostruct.moleculeMap[chainIndex];
if (currentResidueIndex != residueIndex) {
SharedResidue residue(new ResidueData);
residue->name = residueName;
residue->acronym = residueAcronym;
if (residue->acronym == 'X') {
ioLog.details(tr("PDB warning: unknown residue name: %1").arg(residue->name.constData()));
}
residue->chainIndex = chainIndex;
currentResidueIndex = residueIndex;
residueOrder++;
residueIndex.setOrder(residueOrder);
mol->residueMap.insert(residueIndex, residue);
}
}
// Process atom
double x,y,z;
x = currentPDBLine.mid(30,8).toDouble();
y = currentPDBLine.mid(38,8).toDouble();
z = currentPDBLine.mid(46,8).toDouble();
double occupancy = currentPDBLine.mid(54,6).toDouble();
double temperature = currentPDBLine.mid(60,6).toDouble();
SharedAtom a(new AtomData);
a->chainIndex = chainIndex;
a->residueIndex = residueIndex;
a->atomicNumber = atomicNumber;
a->name = atomName;
a->coord3d = Vector3D(x,y,z);
a->occupancy = occupancy;
a->temperature = temperature;
biostruct.modelMap[currentModelIndex + 1].insert(id, a);
if (atomIsInChain) {
SharedMolecule& mol = biostruct.moleculeMap[chainIndex];
Molecule3DModel& model3D = mol->models[currentModelIndex];
model3D.atoms.insert(id, a);
}
}
int Zmatrix_Scan::scanInZmatrix(){
stringstream output;
int numOfLines=0;
ifstream zmatrixScanner(fileName.c_str());
if( !zmatrixScanner.is_open() )
return -1;
else {
string line;
while( zmatrixScanner.good() )
{
numOfLines++;
getline(zmatrixScanner,line);
Molecule workingMolecule;
//check if it is a commented line,
//or if it is a title line
try{
if(line.at(0) != '#' && numOfLines > 1)
parseLine(line,numOfLines);
}
catch(std::out_of_range& e){}
if (startNewMolecule){
Atom* atomArray;
Bond* bondArray;
Angle* angleArray;
Dihedral* dihedralArray;
atomArray = (Atom*) malloc(sizeof(Atom) * atomVector.size());
bondArray = (Bond*) malloc(sizeof(Bond) * bondVector.size());
angleArray = (Angle*) malloc(sizeof(Angle) * angleVector.size());
dihedralArray = (Dihedral*) malloc(sizeof(Dihedral) * dihedralVector.size());
for (int i = 0; i < atomVector.size(); i++){
atomArray[i] = atomVector[i];
}
for (int i = 0; i < bondVector.size(); i++){
bondArray[i] = bondVector[i];
}
for (int i = 0; i < angleVector.size(); i++){
angleArray[i] = angleVector[i];
}
for (int i = 0; i < dihedralVector.size(); i++){
dihedralArray[i] = dihedralVector[i];
}
moleculePattern.push_back(createMolecule(-1, atomArray, angleArray, bondArray, dihedralArray,
atomVector.size(), angleVector.size(), bondVector.size(), dihedralVector.size()));
atomVector.clear();
bondVector.clear();
angleVector.clear();
dihedralVector.clear();
startNewMolecule = false;
}
}
zmatrixScanner.close();
}
return 0;
}
bool ZmatrixScanner::readInZmatrix(string filename, OplsScanner* scanner) {
fileName = filename;
oplsScanner = scanner;
startNewMolecule = false;
if (fileName.empty()) {
std::cerr << "Error: readInZmatrix(): Given filename is NULL" << std::endl;
return false;
}
stringstream output;
int numOfLines=0;
ifstream zmatrixScanner(fileName.c_str());
if (!zmatrixScanner.is_open()) {
std::cerr << "Error: Unable to open Z-Matrix file (" << fileName << ")" << std::endl;
return false;
}
string line;
int moleculeNum = -1;
while (zmatrixScanner.good()) {
numOfLines++;
getline(zmatrixScanner, line);
Molecule workingMolecule;
workingMolecule.type = moleculeNum;
try {
if (line.at(0) != '#' && numOfLines > 1) {
parseLine(line,numOfLines);
}
} catch (std::out_of_range& e) {}
if (startNewMolecule) {
Atom* atomArray;
Bond* bondArray;
Angle* angleArray;
Dihedral* dihedralArray;
moleculeNum++;
workingMolecule.type = moleculeNum;
double atomVectorSize = atomVector.size();
atomArray = (Atom*) malloc(sizeof(Atom) * atomVector.size());
bondArray = (Bond*) malloc(sizeof(Bond) * bondVector.size());
angleArray = (Angle*) malloc(sizeof(Angle) * angleVector.size());
dihedralArray = (Dihedral*) malloc(sizeof(Dihedral) * dihedralVector.size());
for (int i = 0; i < atomVector.size(); i++) {
atomArray[i] = atomVector[i];
}
for (int i = 0; i < bondVector.size(); i++) {
bondArray[i] = bondVector[i];
}
for (int i = 0; i < angleVector.size(); i++) {
angleArray[i] = angleVector[i];
}
for (int i = 0; i < dihedralVector.size(); i++) {
dihedralArray[i] = dihedralVector[i];
}
moleculePattern.push_back(createMolecule(-1, moleculeNum, atomArray, angleArray, bondArray, dihedralArray,
atomVector.size(), angleVector.size(), bondVector.size(), dihedralVector.size()));
atomVector.clear();
bondVector.clear();
angleVector.clear();
dihedralVector.clear();
startNewMolecule = false;
}
}
zmatrixScanner.close();
return true;
}
int partTwo(Reps& replacements, std::string& molecule)
{
return createMolecule(reverseMap(replacements), molecule);
}
