//
//  Copyright (C) 2003-2009 Greg Landrum and Rational Discovery LLC
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
#ifndef _RD_SUBGRAPHUTILS_H_
#define _RD_SUBGRAPHUTILS_H_

#include "Subgraphs.h"
#include <boost/tuple/tuple.hpp>
#include <boost/cstdint.hpp>

namespace RDKit{
  class ROMol;

  namespace Subgraphs {
    //! used to return path discriminators (three unsigned ints):
    typedef boost::tuples::tuple<boost::uint32_t,boost::uint32_t,boost::uint32_t> DiscrimTuple;

    
    DiscrimTuple calcPathDiscriminators(const ROMol &mol,const PATH_TYPE &path,
                                        bool useBO=true,
					std::vector<boost::uint32_t> *extraInvars=0);
    PATH_LIST uniquifyPaths (const ROMol &mol, const PATH_LIST &allPathsb,
                             bool useBO=true);

    // Return the list of bond that connect a list of atoms
    // ASSUMPTION: the atoms specified in the list are connected
    PATH_TYPE bondListFromAtomList(const ROMol &mol, const PATH_TYPE &atomIds);

    // create a new molecule object from a part of molecule "mol". The part of
    // of the molecule is specified as a list of bonds in "path".
    // the optional argument "useQuery" will set all the bond and atoms in the 
    // the new molecule to "QueryAtoms" and "QueryBonds" instead of regular Atoms and Bonds
    //  atomIdxMap provides a mapping between the atomsIds in mol to the atomIds in
    // the newly created sub-molecule (the molecule that is returned)
    ROMol *pathToSubmol(const ROMol &mol, const PATH_TYPE &path, 
                        bool useQuery,
                        std::map<int,int> &atomIdxMap);
    ROMol *pathToSubmol(const ROMol &mol, const PATH_TYPE &path, 
                        bool useQuery=false);
  } // end of namespace Subgraphs
}


#endif