bool OpConformer::Do(OBBase* pOb, const char* OptionText, OpMap* pmap, OBConversion*)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(!pmol)
return false;
pmol->AddHydrogens(false, false);
OpMap::const_iterator iter;
bool log = false;
bool systematic = false;
bool random = false;
bool weighted = false;
int numConformers = 30;
iter = pmap->find("log");
if(iter!=pmap->end())
log=true;
iter = pmap->find("nconf");
if(iter!=pmap->end())
getInteger(iter->second, numConformers);
iter = pmap->find("systematic");
if(iter!=pmap->end())
systematic = true;
iter = pmap->find("random");
if(iter!=pmap->end())
random = true;
iter = pmap->find("weighted");
if(iter!=pmap->end())
weighted = true;
if (systematic || random || weighted) {
std::string ff = "MMFF94";
iter = pmap->find("ff");
if(iter!=pmap->end())
ff = iter->second;
OBForceField* pFF = OBForceField::FindForceField(ff);
// set some force field variables
pFF->SetLogFile(&clog);
pFF->SetLogLevel(log ? OBFF_LOGLVL_MEDIUM : OBFF_LOGLVL_NONE);
if (!pFF->Setup(*pmol)) {
cerr << "Could not setup force field." << endl;
return false;
}
} else {
int numChildren = 5;
int mutability = 5;
int convergence = 25;
std::string score = "rmsd";
iter = pmap->find("children");
if(iter!=pmap->end())
getInteger(iter->second, numChildren);
iter = pmap->find("mutability");
if(iter!=pmap->end())
getInteger(iter->second, mutability);
iter = pmap->find("convergence");
if(iter!=pmap->end())
getInteger(iter->second, convergence);
iter = pmap->find("score");
if(iter!=pmap->end())
score = iter->second;
OBConformerSearch cs;
if (score == "energy")
cs.SetScore(new OBEnergyConformerScore);
if (cs.Setup(*pmol, numConformers, numChildren, mutability, convergence)) {
cs.Search();
cs.GetConformers(*pmol);
}
}
return true;
}
bool OpConformer::Do(OBBase* pOb, const char* OptionText, OpMap* pmap, OBConversion*)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(!pmol)
return false;
pmol->AddHydrogens(false, false);
OpMap::const_iterator iter;
bool log = false;
bool systematic = false;
bool random = false;
bool weighted = false;
bool fast = false;
int numConformers = 30;
iter = pmap->find("log");
if(iter!=pmap->end())
log=true;
iter = pmap->find("nconf");
if(iter!=pmap->end())
getInteger(iter->second, numConformers);
iter = pmap->find("systematic");
if(iter!=pmap->end())
systematic = true;
iter = pmap->find("random");
if(iter!=pmap->end())
random = true;
iter = pmap->find("fast");
if(iter!=pmap->end())
fast = true;
iter = pmap->find("weighted");
if(iter!=pmap->end())
weighted = true;
if (systematic || random || fast || weighted) {
std::string ff = "MMFF94";
iter = pmap->find("ff");
if(iter!=pmap->end())
ff = iter->second;
OBForceField* pFF = OBForceField::FindForceField(ff);
// set some force field variables
pFF->SetLogFile(&clog);
pFF->SetLogLevel(log ? OBFF_LOGLVL_MEDIUM : OBFF_LOGLVL_NONE);
// Add cut-offs for faster conformer searching
// Generally people will perform further optimization on a final conformer
pFF->EnableCutOff(true);
pFF->SetVDWCutOff(10.0);
pFF->SetElectrostaticCutOff(20.0);
pFF->SetUpdateFrequency(10); // delay updates of non-bonded distances
if (!pFF->Setup(*pmol)) {
cerr << "Could not setup force field." << endl;
return false;
}
// Perform search
if (systematic) {
pFF->SystematicRotorSearch(10); // 10 steepest-descent forcfield steps per conformer
} else if (fast) {
pFF->FastRotorSearch(true); // permute rotors
} else if (random) {
pFF->RandomRotorSearch(numConformers, 10);
} else if (weighted) {
pFF->WeightedRotorSearch(numConformers, 10);
}
pFF->GetConformers(*pmol);
} else { // GA-based searching
int numChildren = 5;
int mutability = 5;
int convergence = 5;
std::string score = "rmsd";
iter = pmap->find("children");
if(iter!=pmap->end())
getInteger(iter->second, numChildren);
iter = pmap->find("mutability");
if(iter!=pmap->end())
getInteger(iter->second, mutability);
iter = pmap->find("convergence");
if(iter!=pmap->end())
getInteger(iter->second, convergence);
iter = pmap->find("score");
if(iter!=pmap->end())
score = iter->second;
OBConformerSearch cs;
if (score == "energy")
cs.SetScore(new OBEnergyConformerScore);
else if (score == "mine" || score == "minenergy")
cs.SetScore(new OBMinimizingEnergyConformerScore);
else if (score == "minr" || score == "minrmsd")
cs.SetScore(new OBMinimizingRMSDConformerScore);
if (cs.Setup(*pmol, numConformers, numChildren, mutability, convergence)) {
cs.Search();
cs.GetConformers(*pmol);
}
}
return true;
}