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133 lines
3.7 KiB
C++
133 lines
3.7 KiB
C++
//
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// Copyright (C) 2014 Novartis Institutes for BioMedical Research
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#pragma once
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#include <vector>
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#include <string>
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#include <stdexcept>
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#include "../RDKitBase.h"
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#include "FMCS.h"
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#include "DebugTrace.h" // algorithm filter definitions
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#include "SeedSet.h"
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#include "Target.h"
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#include "SubstructureCache.h"
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#include "DuplicatedSeedCache.h"
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#include "MatchTable.h"
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#ifdef FAST_INCREMENTAL_MATCH
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#include "TargetMatch.h"
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#endif
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#ifdef MULTI_THREAD
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#include "ThreadPool.h"
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#endif
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#include "RingMatchTableSet.h"
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namespace RDKit
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{
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namespace FMCS
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{
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class MaximumCommonSubgraph
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#ifdef MULTI_THREAD
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: private Mutex
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#endif
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{
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struct MCS // current result. Reference to a fragment of source molecule
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{
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std::vector<const Atom*> Atoms;
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std::vector<const Bond*> Bonds;
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std::vector<unsigned> AtomsIdx;
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std::vector<unsigned> BondsIdx; // need for results and size() only !
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const ROMol* QueryMolecule;
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std::vector<Target> Targets;
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};
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unsigned long long To;
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MCSProgressData Stat;
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MCSParameters Parameters;
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unsigned ThresholdCount; // min number of matching
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std::vector<const ROMol*> Molecules;
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#ifdef FAST_SUBSTRUCT_CACHE
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std::vector<unsigned> QueryAtomLabels; // for code Morgan. Value based on current functor and parameters
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std::vector<unsigned> QueryBondLabels; // for code Morgan. Value based on current functor and parameters
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SubstructureCache HashCache;
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#ifdef PRECOMPUTED_TABLES_MATCH
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MatchTable QueryAtomMatchTable;
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MatchTable QueryBondMatchTable;
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#endif
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RingMatchTableSet RingMatchTables;
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#endif
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#ifdef DUP_SUBSTRUCT_CACHE
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DuplicatedSeedCache DuplicateCache;
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#endif
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const ROMol* QueryMolecule;
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unsigned QueryMoleculeMatchedBonds;
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unsigned QueryMoleculeMatchedAtoms;
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std::vector<Target> Targets;
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SeedSet Seeds;
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MCS McsIdx;
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public:
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#ifdef VERBOSE_STATISTICS_ON
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ExecStatistics VerboseStatistics;
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#ifdef MULTI_THREAD
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Mutex StatisticsMutex;
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#endif
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#endif
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MaximumCommonSubgraph(const MCSParameters* params);
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~MaximumCommonSubgraph() {clear();}
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MCSResult find (const std::vector<ROMOL_SPTR>& mols);
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const ROMol& getQueryMolecule()const { return *QueryMolecule;}
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/* optional
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unsigned getMaxNumberBonds()
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#ifdef MULTI_THREAD
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{
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Guard lock(*this);
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#else
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const
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{
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#endif
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*/ unsigned getMaxNumberBonds() const
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{
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return McsIdx.BondsIdx.size();
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}
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/* optional
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unsigned getMaxNumberAtoms()
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#ifdef MULTI_THREAD
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{
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Guard lock(*this);
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#else
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const
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{
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#endif
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*/ unsigned getMaxNumberAtoms() const
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{
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return McsIdx.AtomsIdx.size();
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}
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//internal:
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bool checkIfMatchAndAppend(Seed& seed);//, const std::vector<char>& excludedBonds); // REPLACE with Swap !!!
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private:
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void clear()
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{
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Targets.clear();
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Molecules.clear();
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To = nanoClock();
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}
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void init();
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void makeInitialSeeds();
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bool createSeedFromMCS(size_t newQueryTarget, Seed& seed);
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bool growSeeds(); //returns false if canceled
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std::string generateResultSMARTS(const MCS& McsIdx)const;
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bool match(Seed& seed);
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bool matchIncrementalFast(Seed& seed, unsigned itarget);
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};
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}
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} // namespace RDKit
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