int main(int argc, char **argv)
{
if (argc < 2) {
std::cout << "Usage: " << argv[0] << " <filename>" << std::endl;
return 1;
}
// Read the file
shared_ptr<OBMol> mol = GetMol(argv[1]);
// Create the OBConformerSearch object
OBConformerSearch cs;
// Setup
std::cout << "Setting up conformer searching..." << std::endl
<< " conformers: 30" << std::endl
<< " children: 5" << std::endl
<< " mutability: 5" << std::endl
<< " convergence: 25" << std::endl;
cs.Setup(*mol.get(),
30, // numConformers
5, // numChildren
5, // mutability
25); // convergence
// Perform searching
cs.Search();
// Print the rotor keys
RotorKeys keys = cs.GetRotorKeys();
for (RotorKeys::iterator key = keys.begin(); key != keys.end(); ++key) {
for (unsigned int i = 1; i < key->size(); ++i)
std::cout << key->at(i) << " ";
std::cout << std::endl;
}
// Get the conformers
cs.GetConformers(*mol.get());
std::cout << mol->NumConformers() << std::endl;
OBConversion conv;
conv.SetOutFormat("sdf");
for (unsigned int c = 0; c < mol->NumConformers(); ++c) {
mol->SetConformer(c);
conv.Write(mol.get(), &std::cerr);
}
}
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;
}