bool OpExtraOut::Do(OBBase* pOb, const char* OptionText, OpMap* pmap, OBConversion* pConv) { /* OptionText contains an output filename with a format extension. Make an OBConversion object with this as output destination. Make a copy the current OBConversion and replace the output format by an instance of ExtraFormat. This then does all the subsequent work. */ if(!pConv || !OptionText || *OptionText=='\0') return true; //silent no-op. false would prevent the main output if(pConv->IsFirstInput()) { OBConversion* pExtraConv = new OBConversion(*pConv); //copy ensures OBConversion::Index>-1 std::ofstream* ofs; if( (ofs = new std::ofstream(OptionText)) ) // extra parens to indicate truth value pExtraConv->SetOutStream(ofs); if(!ofs || !pExtraConv->SetOutFormat(OBConversion::FormatFromExt(OptionText))) { obErrorLog.ThrowError(__FUNCTION__, "Error setting up extra output file", obError); return true; } OBConversion* pOrigConv = new OBConversion(*pConv); //Make an instance of ExtraFormat and divert the output to it. It will delete itself. pConv->SetOutFormat(new ExtraFormat(pOrigConv, pExtraConv)); } return true; }
bool ReactionInChIFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv) { OBMol* pmol = dynamic_cast<OBMol*>(pOb); if (pmol == NULL || !pmol->IsReaction()) return false; ostream &ofs = *pConv->GetOutStream(); OBFormat* pInChIFormat = OBConversion::FindFormat("inchi"); if (!pInChIFormat) return false; bool isEquilibrium = pConv->IsOption("e"); OBConversion inchiconv; inchiconv.SetOutFormat(pInChIFormat); stringstream ss; inchiconv.SetOutStream(&ss); #define M_REACTANTS 0 #define M_PRODUCTS 1 #define M_AGENTS 2 OBReactionFacade facade(pmol); std::vector<std::vector<std::string> > inchis(3); unsigned int nonInchi[3] = { 0, 0, 0 }; bool hasNonInchi = false; OBMol mol; for (int part = 0; part <= 2; ++part) { unsigned int N; switch (part) { case M_REACTANTS: N = facade.NumComponents(REACTANT); break; case M_PRODUCTS: N = facade.NumComponents(PRODUCT); break; case M_AGENTS: N = facade.NumComponents(AGENT); break; } for (unsigned int i = 0; i < N; ++i) { mol.Clear(); switch (part) { case M_REACTANTS: facade.GetComponent(&mol, REACTANT, i); break; case M_PRODUCTS: facade.GetComponent(&mol, PRODUCT, i); break; case M_AGENTS: facade.GetComponent(&mol, AGENT, i); break; } if (mol.NumAtoms() == 1 && mol.GetFirstAtom()->GetAtomicNum() == 0) { // This represents an unknown component nonInchi[part]++; hasNonInchi = true; } else { bool ok = inchiconv.Write(&mol); if (!ok) { nonInchi[part]++; hasNonInchi = true; } else { string inchi = ss.str(); if (strncmp(inchi.c_str(), "InChI=1S/", 9) != 0) return false; inchis[part].push_back(TrimInChI(inchi.c_str())); } ss.str(""); } } } std::sort(inchis[M_REACTANTS].begin(), inchis[M_REACTANTS].end()); std::sort(inchis[M_PRODUCTS].begin(), inchis[M_PRODUCTS].end()); std::sort(inchis[M_AGENTS].begin(), inchis[M_AGENTS].end()); std::string reactants_string = ""; const int rsize = inchis[M_REACTANTS].size(); for (int i = 0; i < rsize; ++i) { if (i > 0) reactants_string += '!'; reactants_string += inchis[M_REACTANTS][i]; } std::string products_string = ""; const int psize = inchis[M_PRODUCTS].size(); for (int i = 0; i < psize; ++i) { if (i > 0) products_string += '!'; products_string += inchis[M_PRODUCTS][i]; } bool reactants_first = reactants_string <= products_string; ofs << RINCHI_VERSION_STRING; if (rsize > 0 || psize > 0 || !inchis[M_AGENTS].empty()) { ofs << (reactants_first ? reactants_string : products_string); ofs << "<>"; ofs << (reactants_first ? products_string : reactants_string); if (!inchis[M_AGENTS].empty()) { ofs << "<>"; for (std::vector<std::string>::const_iterator vit = inchis[M_AGENTS].begin(); vit != inchis[M_AGENTS].end(); ++vit) { if (vit != inchis[M_AGENTS].begin()) ofs << '!'; ofs << *vit; } } } ofs << "/d"; if (isEquilibrium) ofs << '='; else ofs << (reactants_first ? '+' : '-'); if (hasNonInchi) { ofs << "/u" << (reactants_first ? nonInchi[M_REACTANTS] : nonInchi[M_PRODUCTS]) << '-' << (reactants_first ? nonInchi[M_PRODUCTS] : nonInchi[M_REACTANTS]) << '-' << nonInchi[M_AGENTS]; } ofs << '\n'; return true; }