mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
102 lines
3.2 KiB
C++
102 lines
3.2 KiB
C++
//
|
|
// 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
|