// $Id$
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#include <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/ROMol.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/ChemReactions/ReactionParser.h>

namespace{

bool testForSameRXNRoleOfAllMoleculeAtoms(const RDKit::ROMol &mol, int role)
{
  RDKit::ROMol::ATOM_ITER_PAIR atItP = mol.getVertices();
  while(atItP.first != atItP.second ){
    const RDKit::Atom *oAtom=mol[*(atItP.first++)].get();
    int current_role;
    if(oAtom->getPropIfPresent(RDKit::common_properties::molRxnRole, current_role) &&
       current_role!=role){
  	  return false;
    }
  }
  return true;
}

int getRXNRoleOfMolecule(const RDKit::ROMol &mol)
{
  RDKit::ROMol::ATOM_ITER_PAIR atItP = mol.getVertices();
  while(atItP.first != atItP.second ){
    const RDKit::Atom *oAtom=mol[*(atItP.first++)].get();
    int molRxnRole;
    if(oAtom->getPropIfPresent(RDKit::common_properties::molRxnRole, molRxnRole)){
      return molRxnRole;
    }
  }
  return -1;
}

}

namespace RDKit {
  
  ChemicalReaction * RxnMolToChemicalReaction(const ROMol &mol)
  {
	ChemicalReaction *rxn=new ChemicalReaction();

	MOL_SPTR_VECT fragments = MolOps::getMolFrags(mol);

	unsigned countFragments = 0;
	for(MOL_SPTR_VECT::iterator iter = fragments.begin();
		    iter != fragments.end(); ++iter, countFragments++){
	  int role = getRXNRoleOfMolecule(*iter->get());
      if(!testForSameRXNRoleOfAllMoleculeAtoms(*iter->get(), role)){
    	BOOST_LOG(rdWarningLog)<<">> Atoms within one molecule have different RXN roles.\n";
        continue;
      }
      switch(role){
      case 1:
    	rxn->addReactantTemplate(*iter);
        break;
      case 2:
    	rxn->addProductTemplate(*iter);
        break;
      case 3:
    	rxn->addAgentTemplate(*iter);
        break;
      default:
    	BOOST_LOG(rdWarningLog)<<">> Fragment "<< countFragments <<" not included in the reaction, atoms do not have a correct RXN role.\n";
      }
	}
    return rxn;    
  }

}
