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* run clang-format-18 across Code/*.cpp and Code/*.h * run clang-format-18 across External
107 lines
3.4 KiB
C++
107 lines
3.4 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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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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// current result. Reference to a fragment of source molecule
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struct MCS {
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std::vector<const Atom *> Atoms;
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std::vector<const Bond *> Bonds;
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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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detail::MCSParametersInternal Parameters;
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// min number of matches
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unsigned int ThresholdCount;
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std::vector<const ROMol *> Molecules;
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#ifdef FAST_SUBSTRUCT_CACHE
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// for Morgan code. Value based on current functor and parameters
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std::vector<unsigned int> QueryAtomLabels;
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// for Morgan code. Value based on current functor and parameters
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std::vector<unsigned int> QueryBondLabels;
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SubstructureCache HashCache;
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MatchTable QueryAtomMatchTable;
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MatchTable QueryBondMatchTable;
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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 int QueryMoleculeMatchedBonds;
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unsigned int 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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std::map<std::vector<unsigned int>, MCS> DegenerateMcsMap;
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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 int getMaxNumberBonds() const { return McsIdx.Bonds.size(); }
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unsigned int getMaxNumberAtoms() const { return McsIdx.Atoms.size(); }
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bool checkIfMatchAndAppend(Seed &seed);
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bool match(Seed &seed);
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const MCSParameters ¶meters() const { return Parameters; }
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MCSParameters ¶meters() { return Parameters; }
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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(size_t startIdx);
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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, ROMOL_SPTR> generateResultSMARTSAndQueryMol(
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const MCS &mcsIdx) const;
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bool matchIncrementalFast(Seed &seed, unsigned int itarget);
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};
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} // namespace FMCS
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} // namespace RDKit
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