//count and return the total number inter- peptide strand hydrogen bonds in a snapshot
int countInterpeptideHB(vector<Peptide*> &peptides, double box[3]){
int totalNumInter=0;
int totalNumPep = peptides.size();
for(int i=0; i < totalNumPep; i++) {
Peptide* pepA = peptides.at(i);
for(int n=0; n < numRes; n++) {
double NH_pepA[3], H_pepA[3], O_pepA[3], C_pepA[3];
pepA->getNH(n,NH_pepA);
pepA->getHofNH(n,H_pepA);
pepA->getO(n,O_pepA);
pepA->getC(n,C_pepA);
for(int j = i+1; j < totalNumPep; j++) {
Peptide* pepB = peptides.at(j);
for(int m=0; m < numRes; m++) {
if(pepB->isHbondedNH(m,O_pepA, C_pepA, box)){
totalNumInter++;
}
if(pepB->isHbondedCO(m,NH_pepA, H_pepA, box)){
totalNumInter++;
}
}
}
}
}
return totalNumInter;
}
int main(int argc, char* argv[]) {
if(argc < 5){
cerr<<"usage: peptide_analysis_testing_simple <gro-file> <num-pep> <num-ins> <base>"<<endl;
return 0;
}
ifstream gro(argv[1]);
int numPeptides = atoi(argv[2]); //number of peptides in the snapshot
int numIns = atoi(argv[3]); //number of inositols in the snapshot
string base(argv[4]);
vector<Peptide*> peptides;
vector<Inositol*> inositols;
vector<Water*> waters;
int time = 0;
double boxDims[3];
int total_bound_groups = numPeptides*16;
//assumes that max number of HB that can be made by an inositol to be 6
vector<int> distr_inos_numHB_tot(7, 0); //distribution of number of inositols over #HB
ofstream contactwat((base + "_water_contact").c_str());
//ofstream nonpolar((base + "_np_contact").c_str());
ofstream cmap((base + "_hb_contact_map").c_str());
ofstream inos((base + "_inos_contact").c_str());
//read each snapshot of the partial gro file
//build vector of peptides, inositols, detect hydrogen bonds,collect statistics
//delete memory allocated for the snapshots
while(!readGroFile(gro, peptides, inositols, waters, numPeptides, numIns, boxDims)){
#ifdef DEBUG
cout<<"################frame # "<<totalNumSnap<<" #####################"<<endl;
#endif
int* water_bound_res = new int[total_bound_groups];
//initialize all to 0
for(int i=0; i<total_bound_groups; i++){
water_bound_res[i]=0;
}
//calculate water contacts
waterContacts(peptides, inositols, waters, water_bound_res, boxDims);
//output to file
for(int i=0; i < total_bound_groups; i++){
contactwat<<water_bound_res[i]<<" ";
}
contactwat<<endl;
//de-allocate memory
delete [] water_bound_res;
Peptide* pep = peptides.at(0);
// Contact maps calculations
for(int n=0; n < numRes; n++){
double NH_pep[3], H_pep[3], O_pep[3], C_pep[3];
pep->getNH(n, NH_pep);
pep->getHofNH(n, H_pep);
pep->getO(n, O_pep);
pep->getC(n, C_pep);
for(int m=n+1; m < numRes; m++){
if(pep->isHbondedCO(m, NH_pep, H_pep, boxDims)){
cmap << n << " " << m <<endl;
}
if(pep->isHbondedNH(m, O_pep, C_pep, boxDims)){
cmap << m << " "<< n <<endl;
}
}
}
//inositol peptide contact calculations
//we only have 1 peptide in the system
for(int nres = 0; nres < numRes; nres++) {
PepGroup* bgroupNH = new PepGroup;
PepGroup* bgroupCO = new PepGroup;
for(int nins = 0; nins < numIns; nins++) {
Inositol* aInos = inositols.at(nins);
for(int noh = 0; noh < 6; noh++) {
double inosO[3], inosH[3];
aInos->getOCoords(noh,inosO);
aInos->getHCoords(noh,inosH);
if (pep->isHbondedNH(nres, inosO, inosH, boxDims)) {
//cinos<<nres<<" has "<<nins*6+noh<<" NH bound"<<endl;
bgroupNH->addPepGroup(nins,nins*6+noh,"OH");
}
if (pep->isHbondedCO(nres, inosO, inosH, boxDims)) {
//cinos<<nres<<" has "<<nins*6+noh<<" CO bound"<<endl;
bgroupCO->addPepGroup(nins,nins*6+noh,"OH");
}
}
}
pep->setBoundGroup(2*nres, bgroupNH);
pep->setBoundGroup(2*nres+1, bgroupCO);
//delete bgroupNH;
//delete bgroupCO;
}
//inosput the data computed above
for(int nbb = 0; nbb < 16; nbb++) {
PepGroup* bgroup=pep->getBoundGroup(nbb);
int numBoundGroups = bgroup->numGroups();
if(numBoundGroups){
for(int nbgroup=0; nbgroup<numBoundGroups; nbgroup++){
inos<<bgroup->getResId(nbgroup);
if(nbgroup<numBoundGroups-1){
inos<<" ";
}
}
}else{
inos<<"-";
}
if(nbb%2 == 0 && nbb < 16){
inos<<";";
}
if(nbb%2 && nbb < 15){
inos<<"|";
}
//cinos<<nbb<<" has " << bgroup->numGroups()<< " bound groups"<<endl;
}
inos<<endl;
time++;
delete_vectors(peptides, inositols, waters);
}
contactwat.close();
cmap.close();
//nonpolar.close();
inos.close();
return 0;
}