C++ OBMol::IsReaction方法代码示例

  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";
//.........这里部分代码省略.........

bool RXNFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
    OBMol* pmol = dynamic_cast<OBMol*>(pOb);
    if (pmol == NULL || !pmol->IsReaction())
      return false;

    pConv->AddOption("no$$$$",OBConversion::OUTOPTIONS);

    OBFormat* pMolFormat = pConv->FindFormat("MOL");
    if(pMolFormat==NULL)
    {
      obErrorLog.ThrowError(__FUNCTION__, "MDL MOL format not available", obError);
        return false;
    }

    OBReactionFacade rxnfacade(pmol);

    HandleAgent handleagent = ReadAgentOption(pConv->IsOption("G"));
    bool hasAgent = rxnfacade.NumComponents(AGENT) > 0;
    bool agentInReactants, agentInProducts;
    if (hasAgent && (handleagent==BOTH_REACT_AND_PROD || handleagent==AS_REACT))
      agentInReactants = true;
    else
      agentInReactants = false;
    if (hasAgent && (handleagent==BOTH_REACT_AND_PROD || handleagent==AS_PROD))
      agentInProducts = true;
    else
      agentInProducts = false;

    ostream &ofs = *pConv->GetOutStream();

    ofs << "$RXN" << '\n';
    ofs << pmol->GetTitle() << '\n';
    ofs << "      OpenBabel" << '\n';
    //ofs << pReact->GetComment() << '\n';
    ofs << "\n";

    ofs << setw(3);
    if (agentInReactants)
      ofs << rxnfacade.NumComponents(REACTANT) + rxnfacade.NumComponents(AGENT);
    else
      ofs << rxnfacade.NumComponents(REACTANT);
    ofs << setw(3);
    if (agentInProducts)
      ofs << rxnfacade.NumComponents(PRODUCT) + rxnfacade.NumComponents(AGENT);
    else
      ofs << rxnfacade.NumComponents(PRODUCT);
    if (hasAgent && handleagent==AS_AGENT)
      ofs << setw(3) << rxnfacade.NumComponents(AGENT);
    ofs << '\n';

    // Write reactants
    OBMol mol;
    for(unsigned int i=0; i<rxnfacade.NumComponents(REACTANT); i++) {
      mol.Clear();
      rxnfacade.GetComponent(&mol, REACTANT, i);
      WriteMolFile(&mol, pConv, pMolFormat);
    }
    if (agentInReactants)
      WriteAgents(mol, rxnfacade, pConv, pMolFormat);

    // Write products
    for(unsigned int i=0; i<rxnfacade.NumComponents(PRODUCT); i++) {
      mol.Clear();
      rxnfacade.GetComponent(&mol, PRODUCT, i);
      WriteMolFile(&mol, pConv, pMolFormat);
    }
    if (agentInProducts)
      WriteAgents(mol, rxnfacade, pConv, pMolFormat);

    // Write agent out (if treating AS_AGENT)
    if(hasAgent && handleagent==AS_AGENT)
      WriteAgents(mol, rxnfacade, pConv, pMolFormat);
    
    return true;
}

  bool OBMoleculeFormat::ReadChemObjectImpl(OBConversion* pConv, OBFormat* pFormat)
  {
    std::istream *ifs = pConv->GetInStream();
    if (!ifs || !ifs->good())
      return false;

    OBMol* pmol = new OBMol;

    if(pConv->IsOption("C",OBConversion::GENOPTIONS))
      return DeferMolOutput(pmol, pConv, pFormat);

    bool ret=true;
   if(pConv->IsOption("separate",OBConversion::GENOPTIONS))
   {
     //On first call, separate molecule and put fragments in MolArray.
     //On subsequent calls, remove a fragment from MolArray and send it for writing
     //Done this way so that each fragment can be written to its own file (with -m option)
     if(!StoredMolsReady)
     {
       while(ret) //do all the molecules in the file
       {
         ret = pFormat->ReadMolecule(pmol,pConv);

         if(ret && (pmol->NumAtoms() > 0 || (pFormat->Flags()&ZEROATOMSOK)))
         {
           vector<OBMol> SepArray = pmol->Separate(); //use un-transformed molecule
           //Add an appropriate title to each fragment
           if(SepArray.size()>1)
             for (unsigned int i=0; i<SepArray.size(); ++i)
             {
               stringstream ss;
               ss << pmol->GetTitle() << '#' << i+1;
               string title = ss.str();
               SepArray[i].SetTitle(title);
             }
           else
              SepArray[0].SetTitle(pmol->GetTitle());

           copy(SepArray.begin(),SepArray.end(),back_inserter(MolArray));
         }
       }
       reverse(MolArray.begin(),MolArray.end());
       StoredMolsReady = true;
       //Clear the flags of the input stream(which may have found eof) to ensure will
       //try to read anothe molecule and allow the stored ones to be sent for output.
       pConv->GetInStream()->clear();
     }

     if(MolArray.empty()) //normal end of fragments
       ret =false;
     else
     {
       // Copying is needed because the OBMol passed to AddChemObject will be deleted.
       // The OBMol in the vector is deleted here.
       OBMol* pMolCopy = new OBMol( MolArray.back());
       MolArray.pop_back();
       ret = pConv->AddChemObject(
           pMolCopy->DoTransformations(pConv->GetOptions(OBConversion::GENOPTIONS), pConv))!=0;
     }
     if(!ret)
       StoredMolsReady = false;

     delete pmol;
     return ret;
   }

    ret=pFormat->ReadMolecule(pmol,pConv);

    OBMol* ptmol = NULL;
    //Molecule is valid if it has some atoms
    //or it represents a reaction
    //or the format allows zero-atom molecules and it has a title or properties
    if(ret && (pmol->NumAtoms() > 0 
      || pmol->IsReaction()
      || (pFormat->Flags()&ZEROATOMSOK && (*pmol->GetTitle() || pmol->HasData(1)))))
    {
      ptmol = static_cast<OBMol*>(pmol->DoTransformations(pConv->GetOptions(OBConversion::GENOPTIONS),pConv));
      if(ptmol && (pConv->IsOption("j",OBConversion::GENOPTIONS)
                || pConv->IsOption("join",OBConversion::GENOPTIONS)))
      {
        //With j option, accumulate all mols in one stored in this class
        if(pConv->IsFirstInput())
          _jmol = new OBMol;
        pConv->AddChemObject(_jmol);
        //will be discarded in WriteChemObjectImpl until the last input mol. This complication
        //is needed to allow joined molecules to be from different files. pOb1 in AddChem Object
        //is zeroed at the end of a file and _jmol is in danger of not being output.
        *_jmol += *ptmol;
        delete ptmol;
        return true;
      }
    }
    else
      delete pmol;

    // Normal operation - send molecule to be written
    ret = ret && (pConv->AddChemObject(ptmol)!=0); //success of both writing and reading
    return ret;
  }