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();
}
/******************************************
*
* ======= MAIN =======
*
******************************************/
int main(int argc, char *argv[]) {
// store start time
time(&start_time);
cout << "Start: " << ctime(&start_time);
cout << "Program: " << programName << endl;
cout << "Program description: " << programDescription << endl;
cout << "Program author: " << programAuthor << endl;
cout << "Program version: " << programVersion << " " << programDate << endl;
cout << "MSL version: " << mslVersion << " " << mslDate << endl;
/******************************************************************************
* === SETTINGS THE DEFAULTS ===
*
* Put here the defaults for some options that are
* not always required
******************************************************************************/
Options defaults;
defaults.noAlign = false;
defaults.noOutputPdb = false;
defaults.writeAllModels = false;
/******************************************************************************
* === OPTION PARSING ===
*
* Parse the command line (and possibly input file)
* options. It will also create an input file based
* on the current options in the output directory
* that can be used to re-run the program with the same
* configuration
******************************************************************************/
Options opt = parseOptions(argc, argv, defaults);
if (opt.errorFlag) {
cerr << endl;
cerr << "The program terminated with errors:" << endl;
cerr << endl;
cerr << opt.errorMessages << endl;
cerr << endl;
cerr << opt.OPerrors << endl;
//printErrors(opt);
usage();
exit(1);
}
cout << "Read pdb 1: " << opt.pdb1 << endl;
System sys1;
if (!sys1.readPdb(opt.pdb1)) {
cerr << "Unable to open pdb " << opt.pdb1 << endl;
exit(1);
}
if (opt.setModel1) {
// set the current NMR model
sys1.setActiveModel(opt.model1);
}
cout << "Read pdb 2: " << opt.pdb2 << endl;
System sys2;
if (!sys2.readPdb(opt.pdb2)) {
cerr << "Unable to open pdb " << opt.pdb2 << endl;
exit(1);
}
if (opt.setModel2) {
// set the current NMR model
sys2.setActiveModel(opt.model2);
}
AtomPointerVector av1 = sys1.getAtomPointers();
AtomPointerVector av2 = sys2.getAtomPointers();
AtomPointerVector alignAtoms1;
if (opt.sele1.size() == 0) {
// select all atoms
alignAtoms1.insert(alignAtoms1.end(), av1.begin(), av1.end());
} else {
AtomSelection sel1(av1);
for (unsigned int i=0; i<opt.sele1.size(); i++) {
char c [1000];
sprintf(c, "keyatoms, %s", opt.sele1[i].c_str());
AtomPointerVector selAtom = sel1.select(c);
alignAtoms1.insert(alignAtoms1.end(), selAtom.begin(), selAtom.end());
}
}
cout << "Selected " << alignAtoms1.size() << " reference atoms for pdb " << opt.pdb1 << endl;
AtomPointerVector alignAtoms2;
if (opt.sele2.size() == 0) {
// select all atoms
alignAtoms2.insert(alignAtoms2.end(), av2.begin(), av2.end());
} else {
AtomSelection sel2(av2);
for (unsigned int i=0; i<opt.sele2.size(); i++) {
char c [1000];
sprintf(c, "keyatoms, %s", opt.sele2[i].c_str());
AtomPointerVector selAtom = sel2.select(c);
alignAtoms2.insert(alignAtoms2.end(), selAtom.begin(), selAtom.end());
}
}
cout << "Selected " << alignAtoms2.size() << " reference atoms for pdb " << opt.pdb2 << endl;
if (alignAtoms1.size() != alignAtoms2.size()) {
cerr << "The number of atoms selected for pdb 1 (" << alignAtoms1.size() << ") does not match the number of atoms selected for pdb 2 (" << alignAtoms2.size() << ")" << endl;
exit(1);
}
cout << endl;
cout << "Set 1 ================================" << endl;
cout << endl;
cout << alignAtoms1;
cout << endl;
cout << "Set 2 ================================" << endl;
cout << endl;
cout << alignAtoms2;
cout << endl;
cout << " ================================" << endl;
if (opt.noAlign) {
// only calc the rmsd
double rmsd = alignAtoms2.rmsd(alignAtoms1);
cout << endl;
cout << opt.pdb2 << " was NOT aligned to " << opt.pdb1 << "." << endl;
cout << "RMSD " << rmsd << endl;
} else {
Transforms tm;
if (!tm.rmsdAlignment(alignAtoms2,alignAtoms1,av2)) {
cerr << "Alignment failed!" << endl;
exit(1);
}
//double rmsd = tm.getRMSD();
double rmsd = alignAtoms2.rmsd(alignAtoms1);
Matrix rotMatrix = tm.getLastRotationMatrix();
CartesianPoint translation = tm.getLastTranslation();
cout << rotMatrix << endl;
cout << translation << endl;
cout << endl;
cout << "Aligned " << opt.pdb2;
if (opt.setModel2) {
cout << " (model " << opt.model2 << ")";
}
cout << " to " << opt.pdb1;
if (opt.setModel1) {
cout << " (model " << opt.model1 << ")";
}
cout << "." << endl;
cout << "RMSD " << rmsd << endl;
if (!opt.noOutputPdb) {
if (!sys2.writePdb(opt.outputPdb2, opt.writeAllModels)) {
cerr << "Cannot open " << opt.outputPdb2 << " for writing" << endl;
exit(1);
}
cout << "Written to " << opt.outputPdb2 << endl;
} else {
cout << "Aligned PDB not written" << endl;
}
}
return 0;
}