void runSDFile(std::string fileName,int checkEvery=10){ SDMolSupplier suppl(fileName,false); RWMol *mol; mol = (RWMol *)suppl.next(); while(mol){ std::string name; mol->getProp("_Name",name); std::cerr << "Mol: " << name << std::endl; try{ MolOps::sanitizeMol(*mol); } catch (...) { std::cerr << " sanitization failed" << std::endl; delete mol; mol = 0; } if(mol){ ROMol *mol2=MolOps::addHs(*mol,false,true); delete mol; runMol(mol2,checkEvery,false); delete mol2; } mol = (RWMol *)suppl.next(); } }
int main(int argc, char *argv[]) { RDLog::InitLogs(); std::string fname; if (argc > 1) { fname = argv[1]; } else { BOOST_LOG(rdErrorLog) << "Pass in the list of smiles\n"; } std::ifstream inStream(fname.c_str()); const int MAX_LINE_LEN = 256; char inLine[MAX_LINE_LEN]; std::string tmpstr; std::string smi; inStream.getline(inLine, MAX_LINE_LEN, '\n'); tmpstr = inLine; // MolOps molop; while (tmpstr.size() > 0) { getSmiles(tmpstr, smi); RWMol *m = SmilesToMol(smi, 0, 0); try { // testKekule(*m); MolOps::sanitizeMol(*m); int nar; m->getProp(common_properties::numArom, nar); BOOST_LOG(rdInfoLog) << nar << "\n"; // MolOps::setHybridization(*m); delete m; } catch (MolSanitizeException) { BOOST_LOG(rdErrorLog) << smi << "\n"; delete m; } inStream.getline(inLine, MAX_LINE_LEN, '\n'); tmpstr = inLine; } return 1; }
// ------------------------------------------------------------------ // // Enumerates the library around a template and returns the result. // // // ------------------------------------------------------------------ RWMOL_SPTR_VECT enumerateLibrary(RWMol *templateMol, VECT_RWMOL_SPTR_VECT &sidechains, bool orientSidechains){ PRECONDITION(templateMol,"bad molecule"); RWMOL_SPTR_VECT res,tmp; res.push_back(RWMOL_SPTR(new RWMol(*templateMol))); // if there's no attachment point on the molecule or no // sidechains, return now: if(!templateMol->hasProp(common_properties::maxAttachIdx) || sidechains.size()==0 ) return res; int maxIdx; templateMol->getProp(common_properties::maxAttachIdx,maxIdx); tmp.clear(); // loop over the sidechains and attach them for(unsigned int i=0;i<sidechains.size();i++){ int tgtMark=CONNECT_BOOKMARK_START+i; // here's another boundary condition if(tgtMark>maxIdx) break; /// loop over all atoms with the appropriate mark // This means that if a mol has two attachment points with the // same name (e.g. two Xa's) they'll always have the same // sidechain attached to them. This is a feature. RWMOL_SPTR_VECT::iterator sidechainIt; for(sidechainIt=sidechains[i].begin(); sidechainIt!=sidechains[i].end(); sidechainIt++){ // we've got our sidechain, find the atom it attaches from if( (*sidechainIt)->hasAtomBookmark(CONNECT_BOOKMARK_START) ){ // // NOTE: If there's more than one marked atom in the sidechain, /// we'll only use the first for the moment. // int sidechainAtomIdx = (*sidechainIt)->getAtomWithBookmark(CONNECT_BOOKMARK_START)->getIdx(); // now add the sidechain to each molecule RWMOL_SPTR_VECT::iterator templMolIt; // loop over all the mols we've generated to this point for(templMolIt=res.begin();templMolIt!=res.end();templMolIt++){ RWMol *templ = new RWMol(**templMolIt); std::string name,tmpStr; if(templ->hasProp(common_properties::_Name)){ templ->getProp(common_properties::_Name,tmpStr); name = name + " " + tmpStr; } while(templ->hasAtomBookmark(tgtMark)){ // this is the atom we'll be replacing in the template Atom *at = templ->getAtomWithBookmark(tgtMark); // copy and transform the sidechain: RWMol *sidechain; if(orientSidechains){ sidechain = new RWMol(*(sidechainIt->get())); orientSidechain(templ,sidechain, at->getIdx(),sidechainAtomIdx); } else { sidechain = sidechainIt->get(); } // FIX: need to use the actual bond order here: molAddSidechain(templ,sidechain, at->getIdx(),sidechainAtomIdx, Bond::SINGLE); if(sidechain->hasProp(common_properties::_Name)){ sidechain->getProp(common_properties::_Name,tmpStr); name = name + " " + tmpStr; } templ->clearAtomBookmark(tgtMark,at); if(orientSidechains){ delete sidechain; } } //std::cout << templ << "> " << MolToSmiles(*templ) << std::endl; if(name != "") templ->setProp(common_properties::_Name,name); tmp.push_back(RWMOL_SPTR(templ)); } } } // // if we just made any molecules, free up the memory used by the // existing result set and move the molecules we just generated // over if(tmp.size()){ #if 0 RWMOL_SPTR_VECT::iterator tmpMolIt; for(tmpMolIt=res.begin();tmpMolIt!=res.end();tmpMolIt++){ delete *tmpMolIt; } #endif res = tmp; tmp.clear(); } } return res; }