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#include <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/ChemReactions/ReactionParser.h>
#include <GraphMol/ChemReactions/ReactionUtils.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/SmilesParse/SmartsWrite.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <sstream>

namespace{

void setRXNRoleOfAllMoleculeAtoms(RDKit::ROMol &mol, int role)
{
  RDKit::ROMol::ATOM_ITER_PAIR atItP = mol.getVertices();
  while(atItP.first != atItP.second ){
    RDKit::Atom *oAtom=mol[*(atItP.first++)].get();
  	oAtom->setProp(RDKit::common_properties::molRxnRole, role);
  }
}

std::string molToString(RDKit::ROMol &mol, bool toSmiles)
{
  if(toSmiles){
    return MolToSmiles(mol,true);
  }
    return MolToSmarts(mol,true);
}

std::string chemicalReactionTemplatesToString(
    const RDKit::ChemicalReaction &rxn, RDKit::ReactionMoleculeType type, bool toSmiles, bool canonical)
{
  std::string res="";
  std::vector<std::string> vfragsmi;
  RDKit::MOL_SPTR_VECT::const_iterator begin = getStartIterator(rxn, type);
  RDKit::MOL_SPTR_VECT::const_iterator end = getEndIterator(rxn, type);
  for(; begin != end; ++begin){
    vfragsmi.push_back(molToString(**begin, toSmiles));
  }
  if(canonical){
    std::sort(vfragsmi.begin(),vfragsmi.end());
  }
  for(unsigned i=0; i<vfragsmi.size(); ++i){
    res+=vfragsmi[i];
    if(i < vfragsmi.size()-1){
      res+=".";
    }
  }
  return res;
}

std::string chemicalReactionToRxnToString(const RDKit::ChemicalReaction &rxn, bool toSmiles, bool canonical)
{
  std::string res="";
  res += chemicalReactionTemplatesToString(rxn, RDKit::Reactant, toSmiles, canonical);
  res += ">";
  res += chemicalReactionTemplatesToString(rxn, RDKit::Agent, toSmiles, canonical);
  res += ">";
  res += chemicalReactionTemplatesToString(rxn, RDKit::Product, toSmiles, canonical);
  return res;
}
}

namespace RDKit {

  //! returns the reaction SMARTS for a reaction
  std::string ChemicalReactionToRxnSmarts(const ChemicalReaction &rxn){
	return chemicalReactionToRxnToString(rxn, false, false);
  };

  //! returns the reaction SMILES for a reaction
  std::string ChemicalReactionToRxnSmiles(const ChemicalReaction &rxn, bool canonical){
	  return chemicalReactionToRxnToString(rxn, true, canonical);
  };

#if 1
  //! returns an RXN block for a reaction
  std::string ChemicalReactionToRxnBlock(const ChemicalReaction &rxn, bool separateAgents){
    std::ostringstream res;
    res<<"$RXN\n\n      RDKit\n\n";
    if(separateAgents){
      res<<std::setw(3)<<rxn.getNumReactantTemplates()
    	 <<std::setw(3)<<rxn.getNumProductTemplates()
         <<std::setw(3)<<rxn.getNumAgentTemplates()<<"\n";
    }
    else{
      res<<std::setw(3)<<(rxn.getNumReactantTemplates()+rxn.getNumAgentTemplates())
    	 <<std::setw(3)<<rxn.getNumProductTemplates()<<"\n";
    }

    for(MOL_SPTR_VECT::const_iterator iter=rxn.beginReactantTemplates();
	iter != rxn.endReactantTemplates();++iter){
      // to write the mol block, we need ring information:
      MolOps::findSSSR(**iter);
      res<<"$MOL\n";
      res << MolToMolBlock(**iter,true,-1,false);
    }
    if(!separateAgents){
      for(MOL_SPTR_VECT::const_iterator iter=rxn.beginAgentTemplates();
          iter != rxn.endAgentTemplates();++iter){
        // to write the mol block, we need ring information:
        MolOps::findSSSR(**iter);
        res<<"$MOL\n";
        res << MolToMolBlock(**iter,true,-1,false);
      }
    }
    for(MOL_SPTR_VECT::const_iterator iter=rxn.beginProductTemplates();
	iter != rxn.endProductTemplates();++iter){
      // to write the mol block, we need ring information:
      MolOps::findSSSR(**iter);
      res<<"$MOL\n";
      res << MolToMolBlock(**iter,true,-1,false);
    }
    if(separateAgents){
      for(MOL_SPTR_VECT::const_iterator iter=rxn.beginAgentTemplates();
          iter != rxn.endAgentTemplates();++iter){
        // to write the mol block, we need ring information:
        MolOps::findSSSR(**iter);
        res<<"$MOL\n";
        res << MolToMolBlock(**iter,true,-1,false);
      }
    }
    return res.str();
  };
#endif

  //! returns a ROMol with RXNMolRole used for a reaction
  ROMol* ChemicalReactionToRxnMol(const ChemicalReaction &rxn)
  {
    RWMol *res=new RWMol();

    for(MOL_SPTR_VECT::const_iterator iter=rxn.beginReactantTemplates();
	iter != rxn.endReactantTemplates();++iter){
      setRXNRoleOfAllMoleculeAtoms(*iter->get(), 1);
      res->insertMol(*iter->get());
    }
    for(MOL_SPTR_VECT::const_iterator iter=rxn.beginProductTemplates();
	iter != rxn.endProductTemplates();++iter){
        setRXNRoleOfAllMoleculeAtoms(*iter->get(), 2);
        res->insertMol(*iter->get());
    }
    for(MOL_SPTR_VECT::const_iterator iter=rxn.beginAgentTemplates();
	iter != rxn.endAgentTemplates();++iter){
        setRXNRoleOfAllMoleculeAtoms(*iter->get(), 3);
        res->insertMol(*iter->get());
    }
    return (ROMol *)res;
  }

}