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//
// 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 {
const FMCS::Graph& QueryTopology;
const FMCS::Graph& TargetTopology;
const ROMol& d_query;
const ROMol& d_mol;
const MCSParameters* Parameters;
public:
MolMatchFinalCheckFunctor(const FMCS::Graph& query, const FMCS::Graph& target,
const ROMol& querySrc, const ROMol& mol // target
,
const MCSParameters* parameters)
: QueryTopology(query),
TargetTopology(target),
d_query(querySrc),
d_mol(mol),
Parameters(parameters){};
bool operator()(const boost::detail::node_id c1[],
const boost::detail::node_id c2[]) const {
if ((unsigned)c1[0] >= boost::num_vertices(QueryTopology))
return false; // invalid index - match failed, see v2f implementation
MCSFinalMatchCheckFunction compare =
Parameters ? Parameters->FinalMatchChecker : nullptr;
return compare ? compare(c1, c2, d_query, QueryTopology, d_mol,
TargetTopology, Parameters)
: 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 ROMol& mol,
const FMCS::Graph& query, const ROMol& querySrc,
const MatchTable& atomMatchTable,
const MatchTable& bondMatchTable,
const MCSParameters* p, 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;
MolMatchFinalCheckFunctor mc(query, target, querySrc, mol, p);
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,
MCSFinalMatchCheckFunction finalCompare,
const MCSAtomCompareParameters& acp, const MCSBondCompareParameters& bcp,
void* ud, match_V_t* match) {
RDUNUSED_PARAM(finalCompare);
MolMatchFinalCheckFunctor matchChecker(query, target, querySrc, mol, nullptr);
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);
}
}
}
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