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b9a5be5a2d
* Remove accidentally tracked files and unset x flag * Ignore ComicNeue * Unify test tag to `reader` * Trivial destructors * Bump CMAKE_CXX_STANDARD to 14 (#4165)
109 lines
3.5 KiB
C++
109 lines
3.5 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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#include <RDGeneral/export.h>
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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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#include "TargetMatch.h"
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#include "RingMatchTableSet.h"
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namespace RDKit {
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inline bool FinalChiralityCheckFunction(
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const std::uint32_t c1[], const std::uint32_t c2[], const ROMol& mol1,
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const FMCS::Graph& query, const ROMol& mol2, const FMCS::Graph& target,
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const MCSParameters* p);
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bool FinalMatchCheckFunction(const std::uint32_t c1[], const std::uint32_t c2[],
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const ROMol& mol1, const FMCS::Graph& query,
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const ROMol& mol2, const FMCS::Graph& target,
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const MCSParameters* p);
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namespace FMCS {
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class RDKIT_FMCS_EXPORT MaximumCommonSubgraph {
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struct MCS { // current result. Reference to a fragment of source molecule
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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
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// current functor and parameters
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std::vector<unsigned> QueryBondLabels; // for code Morgan. Value based on
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// current functor and parameters
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SubstructureCache HashCache;
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MatchTable QueryAtomMatchTable;
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MatchTable QueryBondMatchTable;
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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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const Atom* QueryMoleculeSingleMatchedAtom;
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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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#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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unsigned getMaxNumberBonds() const { return McsIdx.BondsIdx.size(); }
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unsigned getMaxNumberAtoms() const { return McsIdx.AtomsIdx.size(); }
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// internal:
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bool checkIfMatchAndAppend(Seed& seed);
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private:
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void clear() {
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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::pair<std::string, RWMol*> generateResultSMARTSAndQueryMol(
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const MCS& mcsIdx) const;
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bool addFusedBondQueries(const MCS& McsIdx, RWMol* rwMol) 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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} // namespace FMCS
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} // namespace RDKit
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