// $Id$
//
//  Copyright (c) 2014, Novartis Institutes for BioMedical Research Inc.
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#include <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/ChemReactions/ReactionUtils.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <GraphMol/ROMol.h>
#include <GraphMol/Descriptors/MolDescriptors.h>

namespace RDKit {

MOL_SPTR_VECT::const_iterator getStartIterator(
   const ChemicalReaction &rxn,
   ReactionMoleculeType t)
{
  MOL_SPTR_VECT::const_iterator begin;
  if(t == Reactant){
    begin = rxn.beginReactantTemplates();
  }
  if(t == Product){
    begin = rxn.beginProductTemplates();;
  }
  if(t == Agent){
    begin = rxn.beginAgentTemplates();
  }
  return begin;
}

MOL_SPTR_VECT::const_iterator getEndIterator(
   const ChemicalReaction &rxn,
   ReactionMoleculeType t)
{
  MOL_SPTR_VECT::const_iterator end;
  if(t == Reactant){
	end = rxn.endReactantTemplates();
  }
  if(t == Product){
	end = rxn.endProductTemplates();;
  }
  if(t == Agent){
    end = rxn.endAgentTemplates();
  }
  return end;
}


namespace {

bool hasReactionMoleculeTemplateSubstructMatch(
  const RDKit::ChemicalReaction &rxn,
  const RDKit::ChemicalReaction &query_rxn,
  RDKit::ReactionMoleculeType t)
{
  for(RDKit::MOL_SPTR_VECT::const_iterator begin = getStartIterator(rxn, t);
		  begin != getEndIterator(rxn, t); ++begin){
    for(RDKit::MOL_SPTR_VECT::const_iterator begin_query = getStartIterator(query_rxn, t);
    	  begin_query != getEndIterator(query_rxn, t); ++begin_query){
	  MatchVectType tvect;
	  if(SubstructMatch(*begin->get(), *begin_query->get(),tvect )){
		return true;
	  }
	}
  }
  return false;
}

}

bool hasReactantTemplateSubstructMatch(
  const ChemicalReaction &rxn,
  const ChemicalReaction &query_rxn)
{
  if(rxn.getNumReactantTemplates() < query_rxn.getNumReactantTemplates()){
    return false;
  }
  if(query_rxn.getNumReactantTemplates() == 0){
  	return true;
  }
  return hasReactionMoleculeTemplateSubstructMatch(rxn, query_rxn, Reactant);
}

bool hasProductTemplateSubstructMatch(
  const ChemicalReaction &rxn,
  const ChemicalReaction &query_rxn)
{
  if(rxn.getNumProductTemplates() < query_rxn.getNumProductTemplates()){
  	return false;
  }
  if(query_rxn.getNumProductTemplates() == 0){
  	return true;
  }
  return hasReactionMoleculeTemplateSubstructMatch(rxn, query_rxn, Product);
}

bool hasAgentTemplateSubstructMatch(
  const ChemicalReaction &rxn,
  const ChemicalReaction &query_rxn)
{
  if(rxn.getNumAgentTemplates() < query_rxn.getNumAgentTemplates()){
	return false;
  }
  if(query_rxn.getNumAgentTemplates() == 0){
	return true;
  }
  return hasReactionMoleculeTemplateSubstructMatch(rxn, query_rxn, Agent);
}

bool hasReactionSubstructMatch(
  const ChemicalReaction &rxn,
  const ChemicalReaction &query_rxn, bool includeAgents)
{
  if(includeAgents){
    return (hasReactantTemplateSubstructMatch(rxn, query_rxn) &&
    	  	  hasProductTemplateSubstructMatch(rxn, query_rxn) &&
  	  	      hasAgentTemplateSubstructMatch(rxn, query_rxn));
  }
  return (hasReactantTemplateSubstructMatch(rxn, query_rxn) &&
	  	  hasProductTemplateSubstructMatch(rxn, query_rxn));
}

bool hasReactionAtomMapping(const ChemicalReaction &rxn)
{
  RDKit::MOL_SPTR_VECT::const_iterator begin = getStartIterator(rxn, Reactant);
  RDKit::MOL_SPTR_VECT::const_iterator end = getEndIterator(rxn, Reactant);
  for(; begin != end; ++begin){
    const ROMol &reactant = *begin->get();
    if(MolOps::getNumAtomsWithDistinctProperty(reactant, common_properties::molAtomMapNumber)){
      return true;
    }
  }
  begin = getStartIterator(rxn, Product);
  end = getEndIterator(rxn, Product);
  for(; begin != end; ++begin){
    const ROMol &reactant = *begin->get();
    if(MolOps::getNumAtomsWithDistinctProperty(reactant, common_properties::molAtomMapNumber)){
      return true;
    }
  }
  return false;
}

bool isReactionTemplateMoleculeAgent(const ROMol &mol, double agentThreshold)
{
  unsigned numMappedAtoms = MolOps::getNumAtomsWithDistinctProperty(mol, common_properties::molAtomMapNumber);
  unsigned numAtoms = mol.getNumHeavyAtoms();
  if(numAtoms > 0 &&
       static_cast<double>(numMappedAtoms)/static_cast<double>(numAtoms) >= agentThreshold){
    return false;
  }
  return true;
}

namespace {

void getMappingNumAtomIdxMapReactants(ChemicalReaction *rxn, std::map<int,Atom::ChiralType>& reactantMapping){
  for(MOL_SPTR_VECT::const_iterator reactIt=rxn->beginReactantTemplates();
      reactIt!=rxn->endReactantTemplates();++reactIt){
    for(ROMol::AtomIterator reactAtomIt=(*reactIt)->beginAtoms();
        reactAtomIt!=(*reactIt)->endAtoms();++reactAtomIt){
      if(!(*reactAtomIt)->hasProp("molAtomMapNumber")){
        continue;
      }
      int reactMapNum;
      (*reactAtomIt)->getProp("molAtomMapNumber",reactMapNum);
      reactantMapping.insert(std::make_pair(reactMapNum,(*reactAtomIt)->getChiralTag()));
    }
  }
}

}

void updateProductsStereochem(ChemicalReaction *rxn)
{
  std::map<int,Atom::ChiralType> reactantMapping;
  getMappingNumAtomIdxMapReactants(rxn, reactantMapping);
  for(MOL_SPTR_VECT::const_iterator prodIt=rxn->beginProductTemplates();
      prodIt!=rxn->endProductTemplates();++prodIt){
    for(ROMol::AtomIterator prodAtomIt=(*prodIt)->beginAtoms();
        prodAtomIt!=(*prodIt)->endAtoms();++prodAtomIt){
      if((*prodAtomIt)->hasProp(common_properties::molInversionFlag)){
        continue;
      }
      if(!(*prodAtomIt)->hasProp(common_properties::molAtomMapNumber)){
        // if we have stereochemistry specified, it's automatically creating stereochem:
        (*prodAtomIt)->setProp(common_properties::molInversionFlag,4);
        continue;
      }
      int mapNum;
      (*prodAtomIt)->getProp(common_properties::molAtomMapNumber,mapNum);
      if(reactantMapping.find(mapNum) != reactantMapping.end()){
        if((*prodAtomIt)->getChiralTag()!=Atom::CHI_UNSPECIFIED &&
            (*prodAtomIt)->getChiralTag()!=Atom::CHI_OTHER) {
          if(reactantMapping[mapNum]!=Atom::CHI_UNSPECIFIED &&
              reactantMapping[mapNum]!=Atom::CHI_OTHER){
            // both have stereochem specified:
            if(reactantMapping[mapNum]==(*prodAtomIt)->getChiralTag()){
              (*prodAtomIt)->setProp(common_properties::molInversionFlag,2);
            }
            else{
              // FIX: this is technically fragile: it should be checking
              // if the atoms both have tetrahedral chirality. However,
              // at the moment that's the only chirality available, so there's
              // no need to go monkeying around.
              (*prodAtomIt)->setProp(common_properties::molInversionFlag,1);
            }
          }
          else{
            // stereochem in the product, but not in the reactant
            (*prodAtomIt)->setProp(common_properties::molInversionFlag,4);
          }
        }
        else if(reactantMapping[mapNum]!=Atom::CHI_UNSPECIFIED &&
            reactantMapping[mapNum]!=Atom::CHI_OTHER){
          // stereochem in the reactant, but not the product:
          (*prodAtomIt)->setProp(common_properties::molInversionFlag,3);
        }
      }
      else {
        // introduction of new stereocenter by the reaction
        (*prodAtomIt)->setProp(common_properties::molInversionFlag,4);
      }
    }
  }
}



} // end of RDKit namespace