int main(int argc, char *argv[]) {
Options opt = setupOptions(argc, argv);
cout << "READING: "<<opt.pdblist<<endl;
vector<string> lines;
MslTools::readTextFile(lines,opt.pdblist);
map<string,bool> residueCombinations;
PhiPsiStatistics pps;
for (uint i = 0; i < lines.size();i++){
System sys;
sys.readPdb(lines[i]);
bool brokenChain = false;
// Each chain
int loopCount = 1;
for (uint c = 0; c < sys.chainSize();c++){
// Walk through residues
Chain &ch = sys.getChain(c);
int startIndex = 0;
int endIndex = ch.positionSize();
for (uint r = startIndex; r < endIndex;r++){
// Skip first and last residues
if (r == 0 || r == ch.positionSize()-1) {continue;}
Residue &resm1 = ch.getResidue(r-1);
Residue &res = ch.getResidue(r);
Residue &resp1 = ch.getResidue(r+1);
// Skip if no backbone atoms
if (!(resm1.atomExists("N") && res.atomExists("N") && resp1.atomExists("N"))) {continue;}
if (!(resm1.atomExists("CA") && res.atomExists("CA") && resp1.atomExists("CA"))) {continue;}
if (!(resm1.atomExists("C") && res.atomExists("C") && resp1.atomExists("C"))) {continue;}
// Only look for loop residues
if (!(res("CA").getSegID() == "LLLL" || res("CA").getSegID() == "TTTT")) {continue;}
double psi1 = PhiPsiStatistics::getPsi(resm1,res);
double phi2 = PhiPsiStatistics::getPhi(resm1,res);
double psi2 = PhiPsiStatistics::getPsi(res,resp1);
double phi3 = PhiPsiStatistics::getPhi(res,resp1);
stringstream ss1;
ss1 << resm1.getResidueName()<<"-"<<res.getResidueName();
double psi1round = MslTools::smartRound(psi1,20);
if (abs(psi1round) > 180){
cerr << "ERROR psi1 = "<<psi1<<" rounded: "<<psi1round<<endl;
cerr << "\t"<<res.toString()<<endl;
exit(0);
}
stringstream psi1ss;
psi1ss << psi1round;
double phi2round = MslTools::smartRound(phi2,20);
if (abs(phi2round) > 180){
cerr << "ERROR phi2 = "<<phi2<<" rounded: "<<phi2round<<endl;
cerr << "\t"<<res.toString()<<endl;
exit(0);
}
stringstream phi2ss;
phi2ss << phi2round;
//cout << "ADDING "<<ss1.str()<<" "<<psi1ss.str()<<" "<<phi2ss.str()<<endl;
pps.addStatisitics(ss1.str(),psi1ss.str(),phi2ss.str(),1);
residueCombinations[ss1.str()] = true;
}
}
}//lines[i]
map<string,int> counts = pps.getPhiPsiCounts();
RandomNumberGenerator rng;
rng.setTimeBasedSeed();
ofstream fout;
fout.open("shiftedRamaStats.txt");
stringstream ss;
map<string,bool>::iterator it;
for (it = residueCombinations.begin();it != residueCombinations.end();it++){
vector<string> toks = MslTools::tokenize(it->first,"-");
cout << "PAIR: "<<it->first<<" has "<<counts[it->first]<<" counts."<<endl;
for (uint i = 0; i < opt.numSamples;i++){
// Get a random pair of Phi/Psi values
std::pair<double,double> angles = pps.getRandomPhiPsi(it->first);
// Add some noise into the angles.. (random angle 1/2 the width of a bin)
angles.first += (rng.getRandomDouble() * (20/2) * (rng.getRandomDouble() < 0.5 ? -1 : 1));
angles.second += (rng.getRandomDouble() * (20/2) * (rng.getRandomDouble() < 0.5 ? -1 : 1));
while (abs(angles.first) > 180){
angles.first = pps.getRandomPhiPsi(it->first).first + (rng.getRandomDouble() * (20/2) * (rng.getRandomDouble() < 0.5 ? -1 : 1));
}
while (abs(angles.second) > 180){
angles.second = pps.getRandomPhiPsi(it->first).second + (rng.getRandomDouble() * (20/2) * (rng.getRandomDouble() < 0.5 ? -1 : 1));
}
char tmp[300];
sprintf(tmp, "%3s %8.3f %3s %8.3f\n",
toks[0].c_str(),
angles.first,
toks[1].c_str(),
angles.second);
fout << tmp;
}
}
fout.close();
//cout << ss.str()<<endl;
}
void runSaltBridgeMC(
subSeq &_exposedPositions,
map<string,map<string,map<int, map<string,map<string, double> > > > > &_sbScoreTable,
System &_sys,
Options &_opt,
std::priority_queue< std::pair<saltBridgeResult,subSeq>, std::vector< std::pair<saltBridgeResult,subSeq> >, compareScores> &_mcData){
// WT score
saltBridgeResult wt_sbresult = scoreSaltBridgePositions(_exposedPositions,_sbScoreTable,_sys);
// Map to insure we don't fill priority queue with duplicates
map<string,bool> mcDataMap;
string possibleMutations = "KREDH";
RandomNumberGenerator rng;
rng.setTimeBasedSeed();
MSLOUT.stream() << "RNG SEED: "<<rng.getSeed()<<endl;
//MonteCarloManager MCMngr(_startingTemperature, _endingTemperature,_scheduleCycles, _scheduleShape, _maxRejectionsNumber, _convergedSteps, _convergedE);
MonteCarloManager MCMngr(_opt.startMCtemp,_opt.endMCtemp,_opt.numMCcycles, MonteCarloManager::EXPONENTIAL,100,0,0.0);
MCMngr.setRandomNumberGenerator(&rng);
MCMngr.setEner(wt_sbresult.score);
subSeq current = _exposedPositions;
string wtSeq = _exposedPositions.seq;
// TODO add options to Options opt; to take care of MC-related options..... get rid of hard-coded values.
while (!MCMngr.getComplete()) {
// Make change
int mutIndex = rng.getRandomInt(0,possibleMutations.size()-1);
int seqPosIndex = rng.getRandomInt(0,_exposedPositions.seq.size()-1);
string mutAA = possibleMutations.substr(mutIndex,1);
string previousAA = current.seq.substr(seqPosIndex,1);
current.seq.replace(seqPosIndex,1,mutAA);
// Eval
saltBridgeResult sbResult = scoreSaltBridgePositions(current,_sbScoreTable,_sys);
//MSLOUT.stream() << "SCORE: "<<score<<" wt: "<<wt_score<<endl;
// MC test for Acceptance:
if (MCMngr.accept(sbResult.score)){
//cout << "New SEQ: "<<current.seq<<" score: "<<score<<endl;
//cout << "WT SEQ: "<<wtSeq<<" score: "<<wt_score<<endl;
bool keepIt = false;
map<string, bool>::iterator it;
it = mcDataMap.find(sbResult.sbId);
if (it == mcDataMap.end()){
mcDataMap[sbResult.sbId] = true;
if (_mcData.size() >= _opt.numSequenceModels){
if (sbResult.score < _mcData.top().first.score){
// Remove highest score, then add
_mcData.pop();
_mcData.push(pair<saltBridgeResult,subSeq>(sbResult,current));
keepIt = true;
}
} else {
_mcData.push(pair<saltBridgeResult,subSeq>(sbResult,current));
keepIt = true;
}
}
if (!keepIt){
current.seq.replace(seqPosIndex,1,previousAA);
}
} else {
current.seq.replace(seqPosIndex,1,previousAA);
}
}
MSLOUT.stream() << "MC Completed -> "<<MCMngr.getReasonCompleted()<<endl;
}
