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//
// 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
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