rdkit/Code/GraphMol/FMCS/SubstructMatchCustom.cpp

// $Id$
//
//  Copyright (C) 2014 Novartis Institutes for BioMedical Research
//
//   @@ 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.
//
#include <map>
#include <RDGeneral/utils.h>
#include <RDGeneral/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include "SubstructMatchCustom.h"

#include "../Substruct/vf2.hpp"

namespace RDKit
{
 namespace FMCS
 {
    class MolMatchFinalCheckFunctor     // always TRUE. We DO NOT check Chirality
    {
    public:
        MolMatchFinalCheckFunctor(const ROMol &mol1, const ROMol &mol2)
        {};
        bool operator()(const boost::detail::node_id[], const boost::detail::node_id[])const
        {
            return true;
        }
    };
//=================================================================================================
// PRECOMPUTED_TABLES_MATCH much faster in overall even with very simple compare functions

    class AtomTableCompareFunctor
    {
        const FMCS::Graph&      QueryTopology;
        const FMCS::Graph&      TargetTopology;
        const FMCS::MatchTable& MatchTable;
    public:
        AtomTableCompareFunctor(const FMCS::Graph& query, const FMCS::Graph& target, const FMCS::MatchTable& targetMatch)
            : QueryTopology(query), TargetTopology(target), MatchTable(targetMatch) {};
        bool operator()(unsigned int i,unsigned int j)const
        {
            return MatchTable.at(QueryTopology[i], TargetTopology[j]);
        }
    };

    class BondTableCompareFunctor
    {
        const FMCS::Graph& QueryTopology;
        const FMCS::Graph& TargetTopology;
        const FMCS::MatchTable& MatchTable;
    public:
        BondTableCompareFunctor(const FMCS::Graph& query, const FMCS::Graph& target, const FMCS::MatchTable& targetMatch)
            : QueryTopology(query), TargetTopology(target), MatchTable(targetMatch) {};
        bool operator()(FMCS::Graph::edge_descriptor i, FMCS::Graph::edge_descriptor j)const
        {
            return MatchTable.at(QueryTopology[i], TargetTopology[j]);
        }
    };

bool SubstructMatchCustomTable(const FMCS::Graph& target, const FMCS::Graph& query, const MatchTable& atomMatchTable, const MatchTable& bondMatchTable, match_V_t* match)
{
    if(query.m_vertices.size() > target.m_vertices.size()   // query > target
     ||query.m_edges.size() > target.m_edges.size())
        return false;
    ROMol mo;
    MolMatchFinalCheckFunctor mc(mo, mo); // unused dummy item, just required by vf2() external implementation

    AtomTableCompareFunctor ac(query, target, atomMatchTable);
    BondTableCompareFunctor bc(query, target, bondMatchTable);

    match_V_t dummy_match;
    if(!match)
        match = &dummy_match;
    return boost::vf2(query, target, ac, bc, mc, *match);
}

//=========================================================================
// slow implementation with absolutely the same functionality
//=========================================================================

    class AtomLabelFunctor
    {
        const FMCS::Graph& QueryTopology;
        const FMCS::Graph& TargetTopology;
        const ROMol &d_query;
        const ROMol &d_mol;
        MCSAtomCompareFunction AtomCompare;
        const MCSAtomCompareParameters& Parameters;
        void* UserData;
    public:
      AtomLabelFunctor( const FMCS::Graph& query, const FMCS::Graph& target
                      , const ROMol &querySrc
                      , const ROMol &mol    // target
                      , MCSAtomCompareFunction atomCompare, const MCSAtomCompareParameters& p, void* ud
                      )
            : QueryTopology(query), TargetTopology(target)
            , d_query(querySrc)
            , d_mol(mol)
            , AtomCompare(atomCompare), Parameters(p), UserData(ud)
      {};
      bool operator()(unsigned int i,unsigned int j)const
      {
        return AtomCompare(Parameters, d_query, QueryTopology[i], d_mol, TargetTopology[j], UserData);
      }
    };

    class BondLabelFunctor
    {
        const FMCS::Graph& QueryTopology;
        const FMCS::Graph& TargetTopology;
        const ROMol &d_query;
        const ROMol &d_mol;
        MCSBondCompareFunction BondCompare;
        const MCSBondCompareParameters& Parameters;
        void* UserData;
    public:
      BondLabelFunctor(const FMCS::Graph& query, const FMCS::Graph& target
          , const ROMol &querySrc
          , const ROMol &mol
          , MCSBondCompareFunction bondCompare
          , const MCSBondCompareParameters& p, void* ud)
          : QueryTopology(query), TargetTopology(target)
          , d_query(querySrc)
          , d_mol(mol)
          , BondCompare(bondCompare), Parameters(p), UserData(ud)
      {};

      bool operator()(FMCS::Graph::edge_descriptor i, FMCS::Graph::edge_descriptor j)const
      {
        unsigned  ii =  QueryTopology[i]; //take actual Idx value for full source query molecule from index list
        unsigned  jj = TargetTopology[j]; // the same Idx
        return BondCompare(Parameters, d_query, ii, d_mol, jj, UserData);
      }
    };
  
bool SubstructMatchCustom(const FMCS::Graph& target, const ROMol &mol
            , const FMCS::Graph&  query, const ROMol &querySrc // seed and full source query molecule
            , MCSAtomCompareFunction atomCompare, MCSBondCompareFunction bondCompare
            , const MCSAtomCompareParameters& acp
            , const MCSBondCompareParameters& bcp
            , void* ud
            , match_V_t* match
            )
{
    MolMatchFinalCheckFunctor matchChecker(querySrc, mol);
    AtomLabelFunctor atomLabeler(query, target, querySrc, mol, atomCompare, acp, ud);
    BondLabelFunctor bondLabeler(query, target, querySrc, mol, bondCompare, bcp, ud);

    match_V_t dummy_match;
    if(!match)
        match = &dummy_match;
    return boost::vf2(query, target, atomLabeler, bondLabeler, matchChecker, *match);
}

}}