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();
}
int main(){
writePdbFile();
System sys;
sys.readPdb("/tmp/xtalLattice.pdb");
BackRub br;
br.localSample(sys.getChain("A"), 8, 15, 10);
System newSystem;
newSystem.addAtoms(br.getAtomPointers());
newSystem.writePdb("/tmp/brEnsemble.pdb",true);
cout << "Done."<<endl;
}
int main(int argc, char *argv[]) {
// Parse commandline options
Options opt = setupOptions(argc,argv);
// Read multiple sequence alignment and create a PSSM
PSSMCreator pssm;
MSLOUT.stream() << "Add FASTA to PSSM"<<endl;
pssm.addMultipleSequenceAlignment(opt.fasta,opt.regexForFasta);
if (opt.refAACounts != ""){
MSLOUT.stream() << "Add refAACounts to PSSM"<<endl;
pssm.readReferenceCounts(opt.refAACounts);
}
MSLOUT.stream() << "Create the PSSM"<<endl;
if (opt.logodds){
pssm.create(PSSMCreator::logodds);
} else {
pssm.create(PSSMCreator::freq);
}
if (opt.pdb != ""){
// Read in the reference pdb file
System sys;
sys.readPdb(opt.pdb);
AtomSelection select(sys.getAtomPointers());
AtomPointerVector ats = select.select(opt.sel);
string seq = PolymerSequence::toOneLetterCode(ats);
MSLOUT.stream() << "Getting scoring function for sequence: "<<seq<<endl;
MSLOUT.stream() << "refSeqName is: "<<opt.refSeqName<<endl;
string scoreType = "";
switch (opt.valueType) {
case Options::freq:
scoreType = "";
break;
case Options::entropy:
scoreType = "entropy";
break;
case Options::mostfreq:
scoreType = "mostfreq";
break;
}
vector<double> scores = pssm.getScoreFunction(seq,opt.refSeqName,opt.refSeqOffset,scoreType);
MSLOUT.stream() << "Add score to pdb file"<<endl;
System selSys;
selSys.addAtoms(ats);
if (selSys.positionSize() != scores.size()){
cerr << "ERROR 234 Selection position size is : "<<selSys.positionSize()<< " score vector is size: "<<scores.size()<<" "<<seq.length()<<endl;
selSys.writePdb("sel.pdb");
exit(234);
}
// Clear all temp-factors
for (uint i = 0; i < sys.positionSize();i++){
Position &pos = sys.getPosition(i);
for (uint a = 0; a < pos.atomSize();a++){
pos.getAtom(a).setTempFactor(0.0);
}
}
selSys.writePdb("foo.pdb");
// Re-assign with score
for (uint i = 0; i < selSys.positionSize();i++){
Position &pos = sys.getPosition(selSys.getPosition(i).getPositionId());
for (uint c = 0; c < sys.chainSize();c++){
if (!(opt.applyToAllChains || sys.getChain(c).getChainId() == pos.getChainId())) continue;
Position &chainPos = sys.getPosition(MslTools::stringf("%s,%d%s",sys.getChain(c).getChainId().c_str(),pos.getResidueNumber(),pos.getResidueIcode().c_str()));
cout << "Setting chainPos "<<chainPos.getCurrentIdentity().getIdentityId()<<" "<<i<<endl;
for (uint a = 0; a < chainPos.atomSize();a++){
chainPos.getAtom(a).setTempFactor(scores[i]);
}
MSLOUT.fprintf(stdout,"%8s %8.3f\n", chainPos.getPositionId().c_str(),scores[i]);
}
}
sys.writePdb(opt.outPdb);
} // IF opt.pdb
if (opt.seq != ""){
vector<string> toks = MslTools::tokenize(opt.seq, ",");
if (toks.size() != 3){
cerr << "ERROR opt.seq needs to be in the format REFNAME,STARTINDEX,ENDINDEX and it is: "<<opt.seq<<endl;
}
string refName = toks[0];
int start = MslTools::toInt(toks[1]);
int end = MslTools::toInt(toks[2]);
MSLOUT.stream() << "Get frequencies of "<<refName<<" "<<start<<" "<<end<<endl;
vector<map<string,double> > freqs = pssm.getFrequencies(refName,start,end);
MSLOUT.stream() << "Get sequence of "<<refName<<" "<<start<<" "<<end<<endl;
string seq = pssm.getSequence(refName,start,end);
MSLOUT.stream() << "Got sequence "<<seq<<endl;
// ****** CRAZY FORMATTING CODE.... THIS SUCKS ***** //
// For each position
int largestVariation = 0;
for (uint i = 0;i < freqs.size();i++){
if (freqs[i].size() > largestVariation){
largestVariation = freqs[i].size();
}
}
MSLOUT.stream() << "Make output largest variation: "<<largestVariation<<endl;
int resNum = start;
vector<string> rows;
rows.resize(21,"");
for (uint i = 0;i < freqs.size();i++){
priority_queue<aaDat> orderedMap = orderMap(freqs[i]);
int blanks = largestVariation - orderedMap.size();
for (uint v = 0; v < blanks;v++){
if (v <= blanks) {
rows[v] += MslTools::stringf("%1s %6.2f\t", "-", 00.00);
continue;
}
}
int v = blanks;
while (orderedMap.size() > 0){
aaDat data = orderedMap.top();
orderedMap.pop();
if (data.aa == "entropy" || data.aa == "mostfreq") continue;
rows[v++] += MslTools::stringf("%1s %6.2f\t", data.aa.c_str(), data.freq*100);
//cout << "ROW IS: "<<MslTools::stringf("%1s %8.2f ", data.aa.c_str(), data.freq*100)<<endl;
}
// Add residue number at very end
rows[20] += MslTools::stringf("=%c-%-4d=\t",seq[i],resNum++);
} // FOR freqs.size()
MSLOUT.stream() << "Make output2"<<endl;
for (uint r = 0; r < rows.size();r++){
if (rows[r] == "") continue;
if (r == 20){
fprintf(stdout,"\n");
}
fprintf(stdout, "%s\n",rows[r].c_str());
}
} // IF opt.seq
MSLOUT.stream() << "Done."<<endl;
}
int main(int argc, char *argv[]) {
// Parse commandline options
Options opt = setupOptions(argc,argv);
// Read multiple sequence alignment and create a PSSM
PSSMCreator pssm;
MSLOUT.stream() << "Add FASTA to PSSM"<<endl;
pssm.addMultipleSequenceAlignment(opt.fasta,opt.regexForFasta);
MSLOUT.stream() << "Add refAACounts to PSSM"<<endl;
pssm.readReferenceCounts(opt.refAACounts);
MSLOUT.stream() << "Create the PSSM"<<endl;
if (opt.freq){
pssm.createUsingMultipleSequenceAlignment(PSSMCreator::freq);
} else {
pssm.createUsingMultipleSequenceAlignment(PSSMCreator::logodds);
}
if (opt.pdb != ""){
// Read in the reference pdb file
System sys;
sys.readPdb(opt.pdb);
AtomSelection select(sys.getAtomPointers());
AtomPointerVector ats = select.select(opt.sel);
string seq = PolymerSequence::toOneLetterCode(ats);
MSLOUT.stream() << "Getting scoring function for sequence: "<<seq<<endl;
MSLOUT.stream() << "refSeqName is: "<<opt.refSeqName<<endl;
vector<double> scores = pssm.getScoreFunction(seq,opt.refSeqName,opt.refSeqOffset);
System selSys;
selSys.addAtoms(ats);
if (selSys.positionSize() != scores.size()){
cerr << "ERROR 234 Selection position size is : "<<selSys.positionSize()<< " score vector is size: "<<scores.size()<<endl;
exit(234);
}
// Clear all temp-factors
for (uint i = 0; i < sys.positionSize();i++){
Position &pos = sys.getPosition(i);
for (uint a = 0; a < pos.atomSize();a++){
pos.getAtom(a).setTempFactor(0.0);
}
}
// Re-assign with score
for (uint i = 0; i < selSys.positionSize();i++){
Position &pos = sys.getPosition(selSys.getPosition(i).getPositionId());
for (uint c = 0; c < sys.chainSize();c++){
if (!(opt.applyToAllChains || sys.getChain(c).getChainId() == pos.getChainId())) continue;
Position &chainPos = sys.getPosition(MslTools::stringf("%s,%d%s",sys.getChain(c).getChainId().c_str(),pos.getResidueNumber(),pos.getResidueIcode().c_str()));
for (uint a = 0; a < chainPos.atomSize();a++){
chainPos.getAtom(a).setTempFactor(scores[i]);
}
}
}
sys.writePdb(opt.outPdb);
} // IF opt.pdb
if (opt.seq != ""){
vector<string> toks = MslTools::tokenize(opt.seq, ",");
if (toks.size() != 3){
cerr << "ERROR opt.seq needs to be in the format REFNAME,STARTINDEX,ENDINDEX and it is: "<<opt.seq<<endl;
}
string refName = toks[0];
int start = MslTools::toInt(toks[1]);
int end = MslTools::toInt(toks[2]);
vector<map<string,double> > freqs = pssm.getFrequencies(refName,start,end);
string seq = pssm.getSequence(refName,start,end);
// ****** CRAZY FORMATTING CODE.... THIS SUCKS ***** //
// For each position
int largestVariation = 0;
for (uint i = 0;i < freqs.size();i++){
if (freqs[i].size() > largestVariation){
largestVariation = freqs[i].size();
}
}
int resNum = start;
vector<vector<string> > output;
for (uint i = 0;i < freqs.size();i++){
vector<string> rows;
priority_queue<pair<double,string> > orderedMap = orderMap(freqs[i]);
int blankRows = largestVariation - orderedMap.size();
for (uint v = 0; v < largestVariation;v++){
if (v <= blankRows) {
rows.push_back(MslTools::stringf(" "));
continue;
}
while (orderedMap.size() > 0){
pair<double,string> data = orderedMap.top();
orderedMap.pop();
rows.push_back(MslTools::stringf("%1s %3d ", data.second.c_str(), data.first));
}
}
// Add residue number at very end
rows.push_back(MslTools::stringf(" %4d ",resNum++));
output.push_back(rows);
}
for (uint r = 0; r < output.size();r++){
string outrow = "";
for (uint c = 0; c < output[r].size();c++){
outrow += output[r][c];
}
fprintf(stdout,"%s\n",outrow.c_str());
}
}
MSLOUT.stream() << "Done."<<endl;
}
