void test5() { // test working from SMILES std::cout << " ----------> Test5 " << std::endl; RWMol *m1 = SmilesToMol("[Xa]CC([Xb])CC", 0, 0); CHECK_INVARIANT(m1, ""); markAttachmentPoints(m1, 'X'); RWMOL_SPTR_VECT sidechains; sidechains.push_back(RWMOL_SPTR(SmilesToMol("[X]OC(=O)", 0, 0))); sidechains.push_back(RWMOL_SPTR(SmilesToMol("[X]OC(=O)C", 0, 0))); sidechains.push_back(RWMOL_SPTR(SmilesToMol("[X]OC(=O)CCC", 0, 0))); prepareSidechains(&sidechains, 'X'); VECT_RWMOL_SPTR_VECT allSideChains; allSideChains.push_back(sidechains); allSideChains.push_back(sidechains); RWMOL_SPTR_VECT library; library = enumerateLibrary(m1, allSideChains, false); CHECK_INVARIANT(library.size() == 9, ""); CHECK_INVARIANT(library[0]->getNumAtoms() == 10, ""); CHECK_INVARIANT(library[1]->getNumAtoms() == 11, ""); CHECK_INVARIANT(library[2]->getNumAtoms() == 13, ""); CHECK_INVARIANT(library[3]->getNumAtoms() == 11, ""); CHECK_INVARIANT(library[4]->getNumAtoms() == 12, ""); CHECK_INVARIANT(library[5]->getNumAtoms() == 14, ""); CHECK_INVARIANT(library[6]->getNumAtoms() == 13, ""); CHECK_INVARIANT(library[7]->getNumAtoms() == 14, ""); CHECK_INVARIANT(library[8]->getNumAtoms() == 16, ""); library.clear(); std::cout << " <---------- Done " << std::endl; }
// ------------------------------------------------------------------ // // Reads a template and library of sidechains from input files. // the template file should be a mol file and the sidechain files // SD files // // ------------------------------------------------------------------ RWMOL_SPTR_VECT enumFromFiles(const char *templateName, std::vector<const char *> &sidechainNames){ PRECONDITION(templateName,"bad template file name passed in"); // build and mark the template molecule RWMol *templ = MolFileToMol(templateName,false); if(!templ) throw EnumException("could not construct template molecule"); markAttachmentPoints(templ,'X'); // now build and mark each set of sidechains: RWMOL_SPTR_VECT sidechains; VECT_RWMOL_SPTR_VECT allSidechains; for(std::vector<const char*>::const_iterator i=sidechainNames.begin(); i!=sidechainNames.end();i++){ sidechains = SDFileToMols(*i,false); if(!sidechains.size()){ std::string err="no sidechains read from file: "; err += *i; throw EnumException(err.c_str()); } prepareSidechains(&sidechains,'X'); allSidechains.push_back(sidechains); } // enumerate the library: RWMOL_SPTR_VECT library=enumerateLibrary(templ,allSidechains); //-------------------------- // // Clean up the molecules and sidechains we constructed along the // way. // //-------------------------- delete templ; #if 0 VECT_RWMOL_SPTR_VECT::iterator vmpvI; for(vmpvI=allSidechains.begin();vmpvI!=allSidechains.end();vmpvI++){ RWMOL_SPTR_VECT::iterator mpvI; for(mpvI=vmpvI->begin();mpvI!=vmpvI->end();mpvI++){ delete *mpvI; } vmpvI->clear(); } #endif allSidechains.clear(); return library; }