//
//  Copyright (C) 2003-2006 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_FRAG_CATALOG_UTILS_H_
#define _RD_FRAG_CATALOG_UTILS_H_

#include <GraphMol/Subgraphs/Subgraphs.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include "FragCatParams.h"
#include <iostream>

namespace RDKit {

// get the functional groups from file or stream
// each functional groups is read in as a molecule with queryatoms and
// querybonds
MOL_SPTR_VECT readFuncGroups(std::string fileName);
MOL_SPTR_VECT readFuncGroups(std::istream &inStream, int nToRead = -1);

// REVIEW: should this return a vector of pairs or a map?
// mark the functional groups of interest on the molecule
// and return a vector os std::pair <aid, fid>
//    aid - is the atom id in mol that connect to a functional (fid)
//    fid - the functional groups in the list maintained in params
// ARGUMENTS:
//  mol - molecule of interest
//  params - fragment catalog paramter object (contains a list of functional
//             groups of interest
//  fgBonds - container for bondIds in mol that are part of the functional
//  groups
//            the connection bond is included. these need to be chopped from
//            the molecule later

MatchVectType findFuncGroupsOnMol(const ROMol &mol, const FragCatParams *params,
                                  INT_VECT &fgBonds);

// This functions is called before either adding the fragments from a molecule
// to a fragment catalog or generating the fincgerprint for this molecule
// using a fragment catalog. These are the things this function does
// - recognize the function groups (and their location) on the molecule
// - chop these functional groups of the molecule to create a core molecule
//   "coreMol"
// - map the function group locations onto this "coreMol" (bacause the atom ids
//   on coreMol are different from the original molecule
// - return coreMol to the caller of this function and the enter the atom ids to
// func
//   group ids mapping into aToFmap argument
ROMol *prepareMol(const ROMol &mol, const FragCatParams *fparams,
                  MatchVectType &aToFmap);
}

#endif
