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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 <RDGeneral/export.h>
#pragma once
#include <vector>
#include <string>
#include <stdexcept>
#include "../RDKitBase.h"
#include "FMCS.h"
#include "DebugTrace.h" // algorithm filter definitions
#include "SeedSet.h"
#include "Target.h"
#include "SubstructureCache.h"
#include "DuplicatedSeedCache.h"
#include "MatchTable.h"
#include "TargetMatch.h"
#include "RingMatchTableSet.h"
namespace RDKit {
bool FinalChiralityCheckFunction(const short unsigned c1[],
const short unsigned c2[], const ROMol& mol1,
const FMCS::Graph& query, const ROMol& mol2,
const FMCS::Graph& target,
const MCSParameters* p);
namespace FMCS {
class RDKIT_FMCS_EXPORT MaximumCommonSubgraph {
struct MCS { // current result. Reference to a fragment of source molecule
std::vector<const Atom*> Atoms;
std::vector<const Bond*> Bonds;
std::vector<unsigned> AtomsIdx;
std::vector<unsigned> BondsIdx; // need for results and size() only !
const ROMol* QueryMolecule;
std::vector<Target> Targets;
};
unsigned long long To;
MCSProgressData Stat;
MCSParameters Parameters;
unsigned ThresholdCount; // min number of matching
std::vector<const ROMol*> Molecules;
#ifdef FAST_SUBSTRUCT_CACHE
std::vector<unsigned> QueryAtomLabels; // for code Morgan. Value based on
// current functor and parameters
std::vector<unsigned> QueryBondLabels; // for code Morgan. Value based on
// current functor and parameters
SubstructureCache HashCache;
MatchTable QueryAtomMatchTable;
MatchTable QueryBondMatchTable;
RingMatchTableSet RingMatchTables;
#endif
#ifdef DUP_SUBSTRUCT_CACHE
DuplicatedSeedCache DuplicateCache;
#endif
const ROMol* QueryMolecule;
unsigned QueryMoleculeMatchedBonds;
unsigned QueryMoleculeMatchedAtoms;
std::vector<Target> Targets;
SeedSet Seeds;
MCS McsIdx;
public:
#ifdef VERBOSE_STATISTICS_ON
ExecStatistics VerboseStatistics;
#endif
MaximumCommonSubgraph(const MCSParameters* params);
~MaximumCommonSubgraph() { clear(); }
MCSResult find(const std::vector<ROMOL_SPTR>& mols);
const ROMol& getQueryMolecule() const { return *QueryMolecule; }
unsigned getMaxNumberBonds() const { return McsIdx.BondsIdx.size(); }
unsigned getMaxNumberAtoms() const { return McsIdx.AtomsIdx.size(); }
// internal:
bool checkIfMatchAndAppend(Seed& seed);
private:
void clear() {
Targets.clear();
Molecules.clear();
To = nanoClock();
}
void init();
void makeInitialSeeds();
bool createSeedFromMCS(size_t newQueryTarget, Seed& seed);
bool growSeeds(); // returns false if canceled
std::string generateResultSMARTS(const MCS& McsIdx) const;
bool match(Seed& seed);
bool matchIncrementalFast(Seed& seed, unsigned itarget);
};
}
} // namespace RDKit
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