MaximumCommonSubgraph.h
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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.
//
#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 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
SeedSet.h
RDKit::FMCS::DuplicatedSeedCache
Definition: DuplicatedSeedCache.h:18
RDKit::FMCS::Seed
Definition: Seed.h:44
FMCS.h
RDKit::FMCS::TArray2D< bool >
RDKit::MCSProgressData
Definition: FMCS.h:50
DuplicatedSeedCache.h
RDKit::FMCS::SeedSet
Definition: SeedSet.h:18
SubstructureCache.h
RDKit::FMCS::MaximumCommonSubgraph::find
MCSResult find(const std::vector< ROMOL_SPTR > &mols)
RDKit::FMCS::SubstructureCache
Definition: SubstructureCache.h:23
RDKit::ROMol
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:105
TargetMatch.h
RDKit::FMCS::MaximumCommonSubgraph::getQueryMolecule
const ROMol & getQueryMolecule() const
Definition: MaximumCommonSubgraph.h:74
DebugTrace.h
RDKit::FMCS::MaximumCommonSubgraph::getMaxNumberBonds
unsigned getMaxNumberBonds() const
Definition: MaximumCommonSubgraph.h:77
RDKit::FinalChiralityCheckFunction
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)
RDKit::FMCS::ExecStatistics
Definition: DebugTrace.h:102
nanoClock
static unsigned long long nanoClock(void)
Definition: DebugTrace.h:87
RDKit
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:28
RDKit::FMCS::MaximumCommonSubgraph
Definition: MaximumCommonSubgraph.h:32
RDKit::FMCS::RingMatchTableSet
Definition: RingMatchTableSet.h:17
RDKit::FMCS::MaximumCommonSubgraph::getMaxNumberAtoms
unsigned getMaxNumberAtoms() const
Definition: MaximumCommonSubgraph.h:81
RDKit::FMCS::MaximumCommonSubgraph::VerboseStatistics
ExecStatistics VerboseStatistics
Definition: MaximumCommonSubgraph.h:66
RDKit::MCSParameters
Definition: FMCS.h:61
Target.h
MatchTable.h
RDKit::FMCS::MaximumCommonSubgraph::~MaximumCommonSubgraph
~MaximumCommonSubgraph()
Definition: MaximumCommonSubgraph.h:70
RDKit::FMCS::MaximumCommonSubgraph::MaximumCommonSubgraph
MaximumCommonSubgraph(const MCSParameters *params)
RDKit::MCSResult
Definition: FMCS.h:88
RingMatchTableSet.h
RDKit::FMCS::MaximumCommonSubgraph::checkIfMatchAndAppend
bool checkIfMatchAndAppend(Seed &seed)