int mode_pdb(int argument_c, char **argument_v)
{
if(argument_c < 2) throw std::invalid_argument("too few commands");
const std::string command(argument_v[1]);
if(command == "seq")
{
if(argument_c < 3) throw std::invalid_argument("too few commands");
const std::string fname(argument_v[2]);
PDBReader<vectorT> reader;
const auto atoms = reader.read(fname);
const auto chains = reader.parse(atoms);
SequenceExtractor<vectorT> extr;
for(auto iter = chains.cbegin(); iter != chains.cend(); ++iter)
std::cout << "chain " << iter->chain_id() << ": "
<< extr.extract(*iter) << std::endl;
return 0;
}
else
{
throw std::invalid_argument("command not found");
}
}
int main(int argc, char *argv[]){
// Option Parser
Options opt = setupOptions(argc,argv);
ifstream fs2;
//create system and dm for first PDB
PDBReader reader;
reader.open(opt.inputPDB);
reader.read();
reader.close();
System *constSys = new System(reader.getAtoms());
DistanceMatrix constDM;
//add CA atoms to the atom vectors
for (int j=0; j<constSys->residueSize(); j++){
Residue &tempRes=constSys->getResidue(j);
if (tempRes.exists("CA")){
constDM.addAtom(tempRes("CA"));
}
}//end for on j
//fill the DistanceMatrix and set window size
constDM.setGeneralWinSize(opt.windowSize);
constDM.createDistanceMatrix();
constDM.setIntraChain(opt.intraChainCompare);
constDM.setPDBid(opt.inputPDB);
constDM.setDebug(opt.debug);
//create matrix windows
constDM.createMatrixWindows();
delete(constSys);
if (constDM.getMatrixWindows().size()==0){
cout<<"Uh-oh.All the windows got filtered in the PDB you wanted to compare against."<<endl;
exit(111);
}
// COMMMENT OUT BEGINS
/*
//read in list of PDBs to compare to first PDB
vector<string> list;
ifstream fs;
fs.open(opt.pdbList.c_str());
if (fs.fail()){
cerr<<"Cannot open file "<<opt.pdbList<<endl;
exit(1);
}
while(true){
string line;
getline(fs, line);
if(fs.fail()){
//no more lines to read, quite the while.
break;
}
if(line==""){
continue;
}
list.push_back(line);
}
fs.close();
// List of distance matrices, one for each PDB
vector<DistanceMatrix> DMVec(list.size());
// A system object for each PDB
vector<System*> sysVec(list.size(), NULL);
// Create DistanceMatrix and System Objects for list of PDBs
for(int i=0; i<list.size(); i++){
cout<<i<<"create sys and dm."<<endl;
PDBReader rAv;
rAv.open(list[i]);
rAv.read();
rAv.close();
sysVec[i] =new System(rAv.getAtoms());
//add CA atoms to the atom vectors
for (int j=0; j<sysVec[i]->residueSize(); j++){
Residue &tempRes=sysVec[i]->getResidue(j);
if (tempRes.exists("CA")){
//only add CA if it is on a helix
string segID = tempRes("CA").getSegID();
//if(segID == "" || segID.at(0) == 'H'){
DMVec[i].addAtom(tempRes("CA"));
// }
}
}//end for on j
//fill the DistanceMatrix and set window size
DMVec[i].setGeneralWinSize(opt.windowSize);
DMVec[i].createDistanceMatrix();
DMVec[i].setIntraChain(opt.intraChainCompare);
DMVec[i].setPDBid(list[i]);
//create matrix windows
DMVec[i].createMatrixWindows();
delete(sysVec[i]);
}//end for on i
*/
// COMMMENT OUT ENDS
// NEW BEGINS
// load distance matrix database from an external binary file
DistanceMatrixDatabase dmd;
dmd.load_checkpoint("try.bin");
// List of distance matrices, one for each PDB
//************* from now on, all DMVec become pointers ****************//
vector<DistanceMatrix *> &DMVec = dmd.getDistanceMatrixList();
/*
for (uint i = 0;i < dms.size();i++){
cout << "DM["<<i<<"]: "<<dms[i]->getPDBid()<<endl;
}
cout << "Done"<<endl;
*/
//ManageResults to take care of printing/sorting at end
ManageDistanceMatrixResults resultManager;
for(int i=0; i<DMVec.size(); i++){
cout<< "Trying "<<DMVec[i]->getPDBid()<<" ("<<i<<") # Residues: "<<DMVec.size()<<" Number of MatrixWindows to compare: "<<DMVec[i]->getMatrixWindows().size();
//don't compare if all of the windows got filtered out
if (DMVec[i]->getMatrixWindows().size() == 0){
cout << " Sorry Zero Matrix Windows !"<<endl;
continue;
}
cout <<endl;
vector<DistanceMatrixResult> resultsToAdd;
if(opt.searchCriteria=="standard"){
resultsToAdd = constDM.multiCompareAllWindows(*DMVec[i], DistanceMatrix::standard, opt.numberOfIterations);
}//end if
if(opt.searchCriteria=="diagonal"){
resultsToAdd = constDM.multiCompareAllWindows(*DMVec[i], DistanceMatrix::diag, opt.numberOfIterations);
}
if(opt.searchCriteria=="doubleDiagonal"){
resultsToAdd = constDM.multiCompareAllWindows(*DMVec[i], DistanceMatrix::doubleDiag, opt.numberOfIterations);
}
if(opt.searchCriteria=="minDistance"){
resultsToAdd = constDM.multiCompareAllWindows(*DMVec[i], DistanceMatrix::minDist, opt.numberOfIterations);
}
if(opt.searchCriteria=="minDistanceRow"){
resultsToAdd = constDM.multiCompareAllWindows(*DMVec[i], DistanceMatrix::minDistRow, opt.numberOfIterations);
}
bool addFlag = false;
for (uint j = 0; j< resultsToAdd.size();j++){
if (opt.likenessTolerance == MslTools::doubleMax || resultsToAdd[j].getLikeness() <= opt.likenessTolerance){
addFlag = true;
break;
}
}
if (addFlag && resultsToAdd.size() > 0){
resultManager.addResults(resultsToAdd);
}
}//end for on i
// NEW ENDS
cout << "Printing"<<endl;
resultManager.setAlignPdbs(opt.alignPdbs);
// cout << "hello"<<endl;
resultManager.setRmsdTol(opt.rmsdTol);
// cout << "hello again"<<endl;
resultManager.printResults();
cout << "Done."<<endl;
return 0;
}
JNIEXPORT void JNICALL Java_jp_sfjp_webglmol_NDKmol_NDKmolActivity_test(JNIEnv *, jobject) {
PDBReader pdb;
protein = pdb.parsePDB("/mnt/sdcard/2POR-porin.pdb");
__android_log_print(ANDROID_LOG_DEBUG,"Ndkmol","model loaded");
return;
}
