rdkit/Code/GraphMol/ChemReactions/ReactionWriter.cpp

// $Id$
//
//  Copyright (c) 2010-2014, Novartis Institutes for BioMedical Research Inc.
//  All rights reserved.
// 
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met: 
//
//     * Redistributions of source code must retain the above copyright 
//       notice, this list of conditions and the following disclaimer.
//     * Redistributions in binary form must reproduce the above
//       copyright notice, this list of conditions and the following 
//       disclaimer in the documentation and/or other materials provided 
//       with the distribution.
//     * Neither the name of Novartis Institutes for BioMedical Research Inc. 
//       nor the names of its contributors may be used to endorse or promote 
//       products derived from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//

#include <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/ChemReactions/ReactionParser.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("molRxnRole", role);
  }
}

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

std::string ChemicalReactionToRxnToString(RDKit::ChemicalReaction &rxn, bool toSmiles)
{
  std::string res="";
  for(RDKit::MOL_SPTR_VECT::const_iterator iter=rxn.beginReactantTemplates();
  iter != rxn.endReactantTemplates();++iter){
    if(iter!=rxn.beginReactantTemplates()){
    	res +=".";
    }
    res += molToString(**iter, toSmiles);
  }
  res += ">";
  for(RDKit::MOL_SPTR_VECT::const_iterator iter=rxn.beginAgentTemplates();
  iter != rxn.endAgentTemplates();++iter){
    if(iter!=rxn.beginAgentTemplates()){
      res +=".";
    }
    res += molToString(**iter, toSmiles);
  }
  res += ">";
  for(RDKit::MOL_SPTR_VECT::const_iterator iter=rxn.beginProductTemplates();
  iter != rxn.endProductTemplates();++iter){
    if(iter!=rxn.beginProductTemplates()){
      res +=".";
    }
    res += molToString(**iter, toSmiles);
  }
  return res;
}
}

namespace RDKit {

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

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

#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;
  }

}