int main(int argc, char *argv[]) {
Options opt = setupOptions(argc, argv);
vector<string> lines;
MslTools::readTextFile(lines,opt.pdblist);
for (uint i = 0; i < lines.size();i++){
System sys;
sys.readPdb(lines[i]);
// Each chain
for (uint c = 0; c < sys.chainSize();c++){
stringstream ss;
// Walk through residues
Chain &ch = sys.getChain(c);
char tmp[100];
sprintf(tmp,"%s_%1s.pdb",MslTools::getFileName(lines[i]).c_str(),ch.getChainId().c_str());
ss << tmp;
PDBWriter pout;
pout.open(ss.str());
pout.write(ch.getAtomPointers());
pout.close();
}
}
}
int main(){
cout << "Read a string pdb 'fourHelixBundle'"<<endl;
PDBReader pdbin;
pdbin.read(fourHelixBundle);
pdbin.close();
System sys;
sys.addAtoms(pdbin.getAtomPointers());
sys.writePdb("/tmp/preFusion.pdb");
HelixFusion hf;
cout << "Chain Sizes: "<<sys("A").positionSize()<<" "<<sys("B").positionSize()<<endl;
hf.setChains(sys("A"),sys("B"));
hf.fusionByAtomicAlignment(0.3);
for (uint f = 0; f< hf.getNumberFusions();f++){
Chain &newChain = hf.getFusedChain(f);
PDBWriter pdbout;
char name[80];
sprintf(name,"/tmp/fusedChain-%04d.pdb",f);
pdbout.open((string)name);
pdbout.write(newChain.getAtomPointers());
pdbout.close();
}
hf.fusionByHelicalFrames();
}
void OutputFinalPDBPos::doFinalize(long step) {
PDBWriter writer;
if (!writer.open(filename))
THROWS("Can't open " << getId() << " '" << filename << "'.");
writer.setComment("Time : " + toString(app->outputCache.getTime()) +
", step : " + toString(step) +
(minimalImage ? ", minimal Image" : "") + ".");
const Vector3DBlock *pos =
(minimalImage ? app->outputCache.getMinimalPositions() : &app->positions);
if (!writer.write(*pos, app->outputCache.getAtoms()))
THROWS("Could not write " << getId() << " '" << filename << "'.");
}
int main(int argc, char *argv[]){
// Option Parser
Options opt = setupOptions(argc,argv);
// Read PDB
System sys;
sys.readPdb(opt.pdb);
if (!sys.getPDBReader()->doesFileExist()) {
cerr << "Pdb file does not exist, failing.\n";
exit(1111);
}
AtomPointerVector centerAtoms;
if (opt.sele != "") {
AtomSelection as(sys.getAtomPointers());
char selStr[80];
sprintf(selStr,"%s",opt.sele.c_str());
centerAtoms = as.select(selStr);
}
else {
centerAtoms = sys.getAtomPointers();
}
AtomPointerVector allAtoms = sys.getAtomPointers();
CartesianPoint total(0.,0.,0.);
for (uint i = 0; i < centerAtoms.size(); i++) {
total += centerAtoms[i]->getCoor();
}
CartesianPoint avg = total/centerAtoms.size();
cout << "Average: " << avg.getX() << "\t" << avg.getY() << "\t" << avg.getZ() << endl;
CartesianPoint newCenter(opt.x, opt.y, opt.z);
for (uint i = 0; i < allAtoms.size(); i++) {
allAtoms[i]->getCoor() -= avg;
allAtoms[i]->getCoor() += newCenter;
}
PDBWriter writer;
writer.open(opt.outfile);
if (!writer.write(allAtoms)) {
cerr << "Problem writing " << opt.outfile << endl;
}
writer.close();
exit(0);
}
int main(int argc, char *argv[]){
// Option Parser
Options opt = setupOptions(argc,argv);
System initialSystem;
initialSystem.readPdb(opt.pdb);
Quench quencher(opt.topfile, opt.parfile, opt.rotlib);
// Set the number of rotamers you want for large and small side chains, respectively
quencher.setVariableNumberRotamers(50,5);
//System sys = quencher.runQuench(initialSystem);
// Set which positions you want to repack (optional)
vector<int> variablePositions;
variablePositions.push_back(0);
variablePositions.push_back(1);
variablePositions.push_back(2);
variablePositions.push_back(3);
variablePositions.push_back(4);
// Could instead use: variablePositions.push_back(initialSystem.getPositionIndex("A", "73");
System sys = quencher.runQuench(initialSystem, variablePositions);
// For all positions, use: System sys = quencher.runQuench(initialSystem);
stringstream ss;
ss << "/tmp/currentConformation.pdb";
string filename = ss.str();
cout << "Write pdb " << filename << endl;
PDBWriter writer;
writer.open(filename);
if (!writer.write(sys.getAtomPointers())) {
cerr << "Problem writing " << filename << endl;
}
writer.close();
}
int main(int argc, char *argv[]){
// Option Parser
Options opt = setupOptions(argc,argv);
Transforms tr;
// Super-helical Radius Loop
for (double sr = opt.superHelicalRadius[0]; sr <= opt.superHelicalRadius[1]; sr += opt.superHelicalRadius[2]){
// Alpha-helical Phase Angle Loop
for (double aph = opt.alphaHelicalPhaseAngle[0]; aph < opt.alphaHelicalPhaseAngle[1];aph+=opt.alphaHelicalPhaseAngle[2]){
// Super-helical Pitch Angle loop added by David Slochower
for(double shpa = opt.superHelicalPitchAngle[0]; shpa < opt.superHelicalPitchAngle[1]; shpa+=opt.superHelicalPitchAngle[2]) {
double shPitch = (2*M_PI*sr)/tan(M_PI*shpa/180);
// Generate a coiled helix
CoiledCoils cc;
// Values used for previous work: cc.northCoiledCoils(sr, 1.5232, shPitch, 2.25, opt.numberOfResidues, 103.195, aph);
// March 31, 2010: Jason Donald
// Hard code values of h (rise/residue) = 1.51, r1 (alpha-helical radius), and theta (alpha helical frequency)
// based on median values observed by Gevorg Grigoryan
//cc.northCoiledCoils(sr, 1.51, shPitch, 2.26, opt.numberOfResidues, 102.8, aph);
AtomPointerVector coil = cc.getCoiledCoil(sr, 1.51, shPitch, 2.26, 102.8, aph, 0.0,opt.numberOfResidues);
// Apply symmetry operations to create a bundle
int C_axis = atoi(opt.symmetry.substr(1,(opt.symmetry.length()-1)).c_str());
if (opt.symmetry.substr(0,1) == "C"){
Symmetry sym;
sym.applyCN(coil,C_axis);
// Write out bundle
char filename[80];
sprintf(filename, "%s_%s_%03d_%05.2f_%05.2f_shp%05.2f.pdb", opt.name.c_str(),opt.symmetry.c_str(),opt.numberOfResidues, sr, aph, shpa);
cout << "Writing "<<filename<<endl;
PDBWriter pout;
pout.open(filename);
pout.write(sym.getAtomPointers());
pout.close();
}
else if (opt.symmetry.substr(0,1) == "D"){
// Z Rotate
for (double spa = opt.superHelicalPhaseAngle[0]; spa < opt.superHelicalPhaseAngle[1]; spa += opt.superHelicalPhaseAngle[2]){
coil.clearSavedCoor();
coil.saveCoor("preSPA");
Matrix zRot = CartesianGeometry::getZRotationMatrix(spa);
//coil.rotate(zRot);
tr.rotate(coil, zRot);
// Z Trans
for (double ztrans = opt.d2zTranslation[0];ztrans < opt.d2zTranslation[1]; ztrans += opt.d2zTranslation[2]){
coil.saveCoor("preZtrans");
CartesianPoint z(0,0,ztrans);
//coil.translate(z);
tr.translate(coil, z);
Symmetry sym;
sym.applyDN(coil,C_axis);
// Write out bundle
char filename[80];
sprintf(filename, "%s_%s_%03d_%05.2f_%05.2f_shp%05.2f_%05.2f_%05.2f.pdb", opt.name.c_str(),opt.symmetry.c_str(),opt.numberOfResidues,sr, aph, shpa, spa, ztrans);
cout << "Writing "<<filename<<endl;
PDBWriter pout;
pout.open(filename);
pout.write(sym.getAtomPointers());
pout.close();
coil.applySavedCoor("preZtrans");
} // Ztrans
coil.applySavedCoor("preSPA");
} // SHA
}
}
}
}
}
/******************************************
*
* ======= MAIN =======
*
******************************************/
int main(int argc, char *argv[]) {
// Define Objects for the test
CoiledCoils cc;
CoiledCoilFitter ccf;
PDBWriter pout;
/******************************************************************************
*
* === GEVORG/CRICKS CC GENERATION ===
*
******************************************************************************/
//sys.writePdb(opt.fileName);
cc.getCoiledCoilCricks(4.910, -4.027, -13.530, 2.267, 102.806, 149.984, 0.0, 26);
AtomPointerVector cricks = cc.getAtomPointers();
pout.open("/tmp/cricks.pdb");
pout.write(cricks);
pout.close();
double shr = 4.910;
double risePerRes = 1.51;
double shp = 128.206;
double ahr = 2.26;
double ahp = 102.8;
double ahphase = 149.984;
double dZ = 0.0; //meaningless parameter at the moment.
cc.getCoiledCoil(shr, risePerRes, shp, ahr, ahp, ahphase, dZ, 26);
AtomPointerVector norths = cc.getAtomPointers();
pout.open("/tmp/norths.pdb");
pout.write(norths);
pout.close();
Symmetry sym;
sym.applyCN(norths,2);
pout.open("/tmp/northC2.pdb");
pout.write(sym.getAtomPointers());
pout.close();
System sys;
sys.readPdb("/tmp/northC2.pdb");
// Fitting procedure..
// Add helix chain A
ccf.addNextHelix(&sys.getChain("A").getAtomPointers());
// Add helix chain B
ccf.addNextHelix(&sys.getChain("B").getAtomPointers());
// Set symmetry
ccf.setSymmetry("C");
// Do fittin procedure
ccf.fit();
// Do something else..
vector<double> params = ccf.getMinimizedParameters();
if ( abs(params[0] - shr) > 0.1){
cerr << "ERROR Super-helical radius is off. Target = "<<shr<<" MinValue = "<<params[0]<<endl;
} else if (abs(params[1] - risePerRes) > 0.1){
cerr << "ERROR RisePerRes is off. Target = "<<risePerRes<<" MinValue = "<<params[1]<<endl;
} else if (abs(params[2] - shp) > 0.1){
cerr << "ERROR Super-helical pitch is off. Target = "<<shp<<" MinValue = "<<params[2]<<endl;
} else if (abs(params[3] - ahr) > 0.1){
cerr << "ERROR Alpha-helical radius is off. Target = "<<ahr<<" MinValue = "<<params[3]<<endl;
} else if (abs(params[4] - ahp) > 0.1){
cerr << "ERROR Alpha-helical pitch is off. Target = "<<ahp<<" MinValue = "<<params[4]<<endl;
} else if (abs(params[5] - ahphase) > 0.1){
cerr << "ERROR Alpha-helical phase is off. Target = "<<ahphase<<" MinValue = "<<params[5]<<endl;
} else if (abs(params[6] - dZ) > 0.1){
cerr << "ERROR deltaZ offset is off. Target = "<<dZ<<" MinValue = "<<params[6]<<endl;
} else {
cout << "LEAD";
}
}
void ManageDistanceMatrixResults::printResults(){
cout << "Number of results to print: "<<allResults.size()<<endl;
int numberAligned = 0;
ofstream seqOut1;
ofstream seqOut2;
if (alignPdbs){
seqOut1.open("seqAlignment1.txt", ios::out|ios::app);
seqOut2.open("seqAlignment2.txt", ios::out|ios::app);
}
for (int i=0; i<allResults.size(); i++){
//retrieve distance matrices
DistanceMatrix dm1 = allResults[i][0].getDistanceMatrix1();
DistanceMatrix dm2 = allResults[i][0].getDistanceMatrix2();
//retrieve lists of matrix windows
//print the name of PDBs we're comparing
string PDBName1 = getFileName(dm1.getPDBid());
string PDBName1Short = PDBName1.substr(0,17);
string PDBName2 = getFileName(dm2.getPDBid());
string PDBName2Short = PDBName2.substr(0,17);
cout<<"Comparing PDBs: "<<PDBName1Short<<", "<<PDBName2Short<<endl;
//for two fixed DM's (dm1, dm2), access and print the multiCompare results
for(int j=0; j<allResults[i].size(); j++){
//retrieve winning MWs and score from the Result
DistanceMatrixResult & currentResult = allResults[i][j];
double minLikeness = currentResult.getLikeness();
// compare function failed. Nothing to print--result has null windows.
if(minLikeness==1000000){
cout<<"Badness, badness everywhere."<<endl;
continue; //the compareFunction didn't find any matches
}
MatrixWindow & minWindow1 = currentResult.getMatrixWindow1();
MatrixWindow & minWindow2 = currentResult.getMatrixWindow2();
//print information
int i1 = (minWindow1).getLeftR();
int j1 = (minWindow1).getLeftC();
int i2 = (minWindow2).getLeftR();
int j2 = (minWindow2).getLeftC();
string i1ID = dm1.getAtomVector()[i1]->getSegID().c_str();
string j1ID = dm1.getAtomVector()[j1]->getSegID().c_str();
string i2ID = dm2.getAtomVector()[i2]->getSegID().c_str();
string j2ID = dm2.getAtomVector()[j2]->getSegID().c_str();
if(i1ID=="" || j1ID=="" || i2ID=="" ||j2ID==""){
i1ID = dm1.getAtomVector()[i1]->getChainId().c_str();
j1ID = dm1.getAtomVector()[j1]->getChainId().c_str();
i2ID = dm2.getAtomVector()[i2]->getChainId().c_str();
j2ID = dm2.getAtomVector()[j2]->getChainId().c_str();
}//end if
int i1res = dm1.getAtomVector()[i1]->getResidueNumber();
int j1res = dm1.getAtomVector()[j1]->getResidueNumber();
int i2res = dm2.getAtomVector()[i2]->getResidueNumber();
int j2res = dm2.getAtomVector()[j2]->getResidueNumber();
fprintf(stdout, "\t\tWindow1 %3d,%3d (Residues: %1s %3d, %1s %3d)\tWindow2 %3d,%3d (Residues: %1s %3d, %1s %3d)\t%8.3f\n", i1, j1, i1ID.c_str(), i1res, j1ID.c_str(), j1res, i2, j2, i2ID.c_str(), i2res, j2ID.c_str(), j2res, minLikeness);
if (alignPdbs){
// Get AtomVectors of matching windows
AtomPointerVector ca1 = minWindow1.getSmallAVec();
AtomPointerVector ca2 = minWindow2.getSmallAVec();
//for(int i=0; i<ca2.size();i++) cout<<*ca2[i]<<endl;
// Read PDB1 in
PDBReader r1;
r1.open(dm1.getPDBid());
r1.read();
r1.close();
AtomPointerVector &ref = r1.getAtomPointers();
if (ref.size() == 0){
cerr << "ERRROR 3453 in ManageDistanceMatrixResults::printResults while aligning pdbs, ref pdb not found?: "<<dm1.getPDBid()<<endl;
exit(3453);
}
PDBReader r2;
r2.open(dm2.getPDBid());
r2.read();
r2.close();
AtomPointerVector &vec = r2.getAtomPointers();
Transforms t;
//for(int i=0; i<vec.size();i++) cout<<*vec[i]<<endl;
//cout<<endl;
// cout << ca2.size() << "\t" << ca1.size() << "\t" << vec.size() << endl;
bool result = t.rmsdAlignment(ca2,ca1, vec);
// This align is to a get vec (full pdb coordinates)
//ca2,ca1 did not changed; vec changed
if (!result){
cerr << "Alignment has failed!"<<endl;
exit(1211);
}
ca2.saveCoor("pre");
// here record old ca2 coordinates
result = t.rmsdAlignment(ca2,ca1);
// this align is to get a new ca2 to calculate rmsd
if (!result){
cerr << "Alignment has failed!"<<endl;
exit(1212);
}
double rmsd=ca1.rmsd(ca2);
cout << "RMSD: "<<rmsd<<endl;
if (rmsd <= rmsdTol){
// a smaller rmsd is to get optimized structures
numberAligned++;
/*
// Write out aligned PDB for dm2
char a[80];
sprintf(a, "%s.aligned.%5.3f.pdb",MslTools::getFileName(dm2.getPDBid()).c_str(),rmsd);
PDBWriter w;
w.open(a);
w.write(vec);
w.close();
*/
// Setup a Polymer Sequence to print out the alignment...
/*
Since chain A in dm1 can match chain A or chain B in dm2 , everything is named chain1 and chain2.
Procedure:
1. Get chain1 and chain2 from all AtomVectors (ca1,ca2,ref) ; ref = ca1 , but includes all of the residues.
2. Create sequences for chain1s
3. Create a PolymerSequence for chain1s and print out.
.. chain2s
*/
AtomSelection selWin1(ca1);
AtomPointerVector win1Ch1 = selWin1.select("chain "+ca1(0).getChainId());
AtomPointerVector win1Ch2 = selWin1.select("chain "+ca1(ca1.size()/2).getChainId());
AtomSelection selWin2(ca2);
AtomPointerVector win2Ch1 = selWin2.select("chain "+ca2(0).getChainId());
AtomPointerVector win2Ch2 = selWin2.select("chain "+ca2(ca2.size()/2).getChainId());
AtomSelection selRef(ref);
AtomPointerVector refCh1 = selRef.select("chain "+ca1(0).getChainId());
AtomPointerVector refCh2 = selRef.select("chain "+ca1(ca2.size()/2).getChainId());
// Write out aligned PDB for dm2
char a[80];
sprintf(a, "%s.aligned.%5.3f.pdb",MslTools::getFileName(dm2.getPDBid()).c_str(),rmsd);
// sprintf(a, "SEQ.%s.SEQ.%s.%s.aligned.%5.3f.pdb",refCh1(0).getChainId().c_str(),refCh2(0).getChainId().c_str(),MslTools::getFileName(dm2.getPDBid()).c_str(),rmsd);
PDBWriter w;
w.open(a);
w.write(vec);
// w.write(ca2);
w.close();
// Create an input sequence for chain 1
stringstream seqStr1;
seqStr1 << win2Ch1(0).getChainId()<<" "<<win2Ch1(0).getResidueNumber()<<": ";
seqStr1 << PolymerSequence::toThreeLetterCode(win2Ch1);
//seqStr1 << PolymerSequence::toOneLetterCode(win2Ch1); // it does not work as the whole one-letter code and "X" will be printed out as an unrecognized amino acid
//cout<<seqStr1.str()<<endl;
//for(int i=0; i<win2Ch1.size();i++) cout<<win2Ch1[i]->getResidueNumber()<<" "<<*win2Ch1[i]<<endl;
// Create a polymer sequence for chain A
PolymerSequence poly1;
poly1.setName("SEQ"+refCh1(0).getChainId()+"-"+MslTools::getFileName(dm2.getPDBid()));
poly1.setSequence(seqStr1.str());
poly1.setReferenceSequence(PolymerSequence::toOneLetterCode(refCh1).c_str(),"SEQ"+refCh1(0).getChainId()+"-REF-"+MslTools::getFileName(dm1.getPDBid()).c_str(),1,win1Ch1[0]->getResidueNumber(),win2Ch1[0]->getResidueNumber());
//cout <<"win1Ch1[0]->getResidueNumber(): "<<win1Ch1[0]->getResidueNumber()<<" win2Ch1([0]->getResidueNumber(): "<<win2Ch1[0]->getResidueNumber()<<endl;
// poly1.setReferenceSequence(MslTools::getOneLetterCode(refCh1),"SEQ"+refCh1(0).getChainId().c_str()+"-REF",refCh1(0).getResidueNumber(),win1Ch1(0).getResidueNumber());
//cout<<poly1<<endl;
/*
vector<vector<vector<string> > > sequences = poly1.getSequence();
for(vector<vector<vector<string> > >::iterator it = sequences.begin(); it != sequences.end(); ++it) {
for(vector<vector<string> >::iterator it2 = it->begin(); it2 != it->end(); ++it2) {
for(vector<string>::iterator it3 = it2->begin(); it3 != it2->end(); ++it3) {
cout << *it3 <<" ";
}
}
}
cout <<endl;
*/
stringstream seqStr2;
seqStr2 << win2Ch2(0).getChainId()<<" "<<win2Ch2(0).getResidueNumber()<<": ";
seqStr2 << PolymerSequence::toThreeLetterCode(win2Ch2);
//seqStr2 << PolymerSequence::toOneLetterCode(win2Ch2);
// Create a polymer sequence for chain A
PolymerSequence poly2;
poly2.setName("SEQ"+refCh2(0).getChainId()+"-"+MslTools::getFileName(dm2.getPDBid()));
poly2.setSequence(seqStr2.str());
// poly2.setReferenceSequence(MslTools::getOneLetterCode(refCh2),"SEQ"+refCh2(0).getChainId()+"-REF", refCh2(0).getResidueNumber(),win1Ch2(0).getResidueNumber());
poly2.setReferenceSequence(PolymerSequence::toOneLetterCode(refCh2),"SEQ"+refCh2(0).getChainId()+"-REF-"+MslTools::getFileName(dm1.getPDBid()).c_str(),1,win1Ch2[0]->getResidueNumber(),win2Ch2[0]->getResidueNumber());
if (numberAligned == 1){
seqOut1 << poly1.getReferenceHeader();
seqOut2 << poly2.getReferenceHeader();
}
seqOut1 << poly1;
seqOut2 << poly2;
}
ca2.applySavedCoor("pre");
// ca2 is changed to its former value
}
}//end for on j
}//end for on i
seqOut1.close();
seqOut2.close();
}
int main(int argc, char *argv[]) {
// the program requires the location of the "exampleFiles" as an argument
if (argc < 1) {
cerr << "USAGE:\nexample_coiled_coil_and_symmetric_bundles" << endl;
exit(0);
}
cout << " ***************************************************************************************" << endl;
cout << "" << endl;
cout << " How to generate coiled-coils in MSL (" << MslTools::getMSLversion() << ") " << endl;
cout << "" << endl;
cout << " ***************************************************************************************" << endl;
cout << endl;
cout << endl;
// CoiledCoils object used to create a coiled helix (by a number of algorithms)
CoiledCoils cc;
// A super-helical radius
double sr = 6.5;
// An alpha-helical phase angle
double aph = 0.0;
// A super-helical pitch angle, and pitch distance
double shpa = 190;
double shPitch = (2*M_PI*sr)/tan(M_PI*shpa/180);
// Hard code values of h (rise/residue) = 1.51, r1 (alpha-helical radius), and theta (alpha helical frequency)
double risePerResidue = 1.51;
// Use observed medians by Gevorg Grigoryan (Probing Deisgnability via a Generalized Model of Helical Bundle Geometry, JMB 2010)
double alphaHelicalRadius = 2.26;
double alphaHelicalFrequency = 102.8;
// Number of residues in coil ( lets do 4 heptads = 28 residues )
double numberOfResidues = 28;
// Generate a coiled coil, using specified parameters
//cc.northCoiledCoils(sr, risePerResidue, shPitch, alphaHelicalRadius, numberOfResidues, alphaHelicalFrequency, aph);
// dZ
double dZ = 0.0;
// Get the atoms from the CoiledCoils object back (this is a single coiled-coil helix)
AtomPointerVector coil = cc.getCoiledCoil(sr, risePerResidue, shPitch, alphaHelicalRadius, alphaHelicalFrequency,dZ, aph,numberOfResidues);
cout << "Writing /tmp/singleHelixCoil.pdb"<<endl;
PDBWriter pout;
pout.open("/tmp/singleHelixCoil.pdb");
pout.write(coil);
pout.close();
// Create a symmtery object to generate a coiled bundle ( C4 symmetric )
Symmetry sym;
// Apply C4 to "coil"
sym.applyCN(coil,4);
cout << "Writing /tmp/C4HelixCoil.pdb"<<endl;
pout.open("/tmp/C4HelixCoil.pdb");
pout.write(sym.getAtomPointers());
pout.close();
}
int main(int argc, char *argv[]) {
Options opt = setupOptions(argc, argv);
cout << "Read in PDB structure"<<endl;
System initSys;
initSys.readPdb(opt.pdb);
initSys.writePdb("/tmp/init.pdb");
// Read through and mark positions that don't have full side chains?
CharmmTopologyReader CTR(opt.topfile);
CTR.read();
vector<int> residuesToFill;
for (uint r = 0; r < initSys.positionSize();r++){
Residue &res = initSys.getResidue(r);
// Default to HSD for HIS
if (res.getResidueName() == "HIS") res.setResidueName("HSD");
if (!CTR.residueExists(res.getResidueName())){
cerr << "ERROR 2222 Residue: "<<res.toString()<<" ; residue type does not exist in topology file: "<<opt.topfile<<endl;
exit(2222);
}
vector<string> topologyAtoms = CTR.getResidue(res.getResidueName()).getAllTopoAtomNames();
for (uint t = 0; t < topologyAtoms.size();t++){
// Skip over hydrogen atoms..
if (topologyAtoms[t].substr(0,1) == "H") continue;
// If ILE and CD, look for CD1
if (res.getResidueName() == "ILE" && topologyAtoms[t] == "CD" && !res.atomExists(topologyAtoms[t]) && res.atomExists("CD1")){
//res.getAtom("CD1").setName("CD");
//res.updateAtomMap(res.getAtom("CD1"));
continue;
}
if (!res.atomExists(topologyAtoms[t])){
residuesToFill.push_back(r);
cout << "*** Residue to fill: "<<res.toString()<<" due to atom from topology not found in pdb: "<<topologyAtoms[t]<<endl;
break;
}
}
}
PolymerSequence seq(initSys);
cout << "Build Charmm System"<<endl;
System sys;
CharmmSystemBuilder CSB(sys,opt.topfile,opt.parfile);
CSB.setBuildNonBondedInteractions(false);
CSB.buildSystem(seq);
int numAssignedAtoms = sys.assignCoordinates(initSys.getAtomPointers());
fprintf(stdout, "\tNumber of assigned atoms: %8d\n",numAssignedAtoms);
if (numAssignedAtoms == 0){
cerr << "ERROR 2222 zero assigned atoms, means after re-building from sequence we can not match chain,residue numbers with original coordinates.\n";
exit(2222);
}
sys.buildAllAtoms();
if (opt.debug) {
string filename = "/tmp/initialBuild.pdb";
cout << "Write initial build pdb " << filename << endl;
PDBWriter writer;
writer.open(filename);
if (!writer.write(sys.getAtomPointers())) {
cerr << "Problem writing " << filename << endl;
}
writer.close();
}
cout << "Read rotamer library " << opt.rotlib << " and load rotamers"<<endl;
SystemRotamerLoader sysRot(sys, opt.rotlib);
// For each residue to fill add 100 rotamers
for (uint r = 0; r < residuesToFill.size();r++){
Residue &res = sys.getResidue(residuesToFill[r]);
Position *pos = res.getParentPosition();
//sysRot.loadRotamers(pos, "BALANCED-200",res.getResidueName(),0,99);
sysRot.loadRotamers(pos,res.getResidueName(),0,99,"");
}
// Quencher-type
CharmmEnergyCalculator calculator(opt.parfile);
for (uint p = 0; p < sys.positionSize();p++){
Position &pos = sys.getPosition(p);
if (pos.getTotalNumberOfRotamers() > 1){
double minEnergy = MslTools::doubleMax;
int minIndex = -1;
for (uint c = 0; c < pos.getTotalNumberOfRotamers();c++){
double self = calculator.calculateSelfEnergy(sys,p,c);
double temp = calculator.calculateTemplateEnergy(sys,p,c);
if (temp+self < minEnergy){
minEnergy = temp+self;
minIndex = c;
}
}
if (minIndex == -1){
cerr << "ERROR 8754 on position "<<pos.getCurrentIdentity().toString()<< " no low energy rotamer ? .. do nothing and continue."<<endl;
continue;
}
// Set to lowest self+template energy rotamer.
cout << "*** Setting "<<pos.getCurrentIdentity().toString()<<" to rotamer "<<minIndex<<" with self+template energy = "<<minEnergy<<endl;
pos.setActiveRotamer(minIndex);
}
}
sys.writePdb(opt.outpdb);
}