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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.
//
#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"
namespace RDKit {
inline bool FinalChiralityCheckFunction(
const std::uint32_t c1[], const std::uint32_t c2[], const ROMol &mol1,
const FMCS::Graph &query, const ROMol &mol2, const FMCS::Graph &target,
const MCSParameters *p);
bool FinalMatchCheckFunction(const std::uint32_t c1[], const std::uint32_t 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 {
// current result. Reference to a fragment of source molecule
struct MCS {
std::vector<const Atom *> Atoms;
std::vector<const Bond *> Bonds;
const ROMol *QueryMolecule;
std::vector<Target> Targets;
};
unsigned long long To;
MCSProgressData Stat;
detail::MCSParametersInternal Parameters;
// min number of matches
unsigned int ThresholdCount;
std::vector<const ROMol *> Molecules;
#ifdef FAST_SUBSTRUCT_CACHE
// for Morgan code. Value based on current functor and parameters
std::vector<unsigned int> QueryAtomLabels;
// for Morgan code. Value based on current functor and parameters
std::vector<unsigned int> QueryBondLabels;
SubstructureCache HashCache;
MatchTable QueryAtomMatchTable;
MatchTable QueryBondMatchTable;
#endif
#ifdef DUP_SUBSTRUCT_CACHE
DuplicatedSeedCache DuplicateCache;
#endif
const ROMol *QueryMolecule;
unsigned int QueryMoleculeMatchedBonds;
unsigned int QueryMoleculeMatchedAtoms;
const Atom *QueryMoleculeSingleMatchedAtom;
std::vector<Target> Targets;
SeedSet Seeds;
MCS McsIdx;
std::map<std::vector<unsigned int>, MCS> DegenerateMcsMap;
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 int getMaxNumberBonds() const { return McsIdx.Bonds.size(); }
unsigned int getMaxNumberAtoms() const { return McsIdx.Atoms.size(); }
bool checkIfMatchAndAppend(Seed &seed);
bool match(Seed &seed);
const MCSParameters &parameters() const { return Parameters; }
MCSParameters &parameters() { return Parameters; }
private:
void clear() {
Targets.clear();
Molecules.clear();
To = nanoClock();
}
void init(size_t startIdx);
void makeInitialSeeds();
bool createSeedFromMCS(size_t newQueryTarget, Seed &seed);
bool growSeeds(); // returns false if canceled
std::pair<std::string, ROMOL_SPTR> generateResultSMARTSAndQueryMol(
const MCS &mcsIdx) const;
bool matchIncrementalFast(Seed &seed, unsigned int itarget);
};
} // namespace FMCS
} // namespace RDKit
DebugTrace.h
nanoClock
static unsigned long long nanoClock(void)
Definition DebugTrace.h:97
DuplicatedSeedCache.h
FMCS.h
MatchTable.h
RDKitBase.h
pulls in the core RDKit functionality
SeedSet.h
SubstructureCache.h
TargetMatch.h
Target.h
RDKit::Atom
The class for representing atoms.
Definition Atom.h:75
RDKit::FMCS::DuplicatedSeedCache
Definition DuplicatedSeedCache.h:19
RDKit::FMCS::Graph
Definition Graph.h:26
RDKit::FMCS::MaximumCommonSubgraph::~MaximumCommonSubgraph
~MaximumCommonSubgraph()
Definition MaximumCommonSubgraph.h:79
RDKit::FMCS::MaximumCommonSubgraph::getMaxNumberBonds
unsigned int getMaxNumberBonds() const
Definition MaximumCommonSubgraph.h:82
RDKit::FMCS::MaximumCommonSubgraph::MaximumCommonSubgraph
MaximumCommonSubgraph(const MCSParameters *params)
RDKit::FMCS::MaximumCommonSubgraph::getMaxNumberAtoms
unsigned int getMaxNumberAtoms() const
Definition MaximumCommonSubgraph.h:84
RDKit::FMCS::MaximumCommonSubgraph::match
bool match(Seed &seed)
RDKit::FMCS::MaximumCommonSubgraph::parameters
MCSParameters & parameters()
Definition MaximumCommonSubgraph.h:88
RDKit::FMCS::MaximumCommonSubgraph::checkIfMatchAndAppend
bool checkIfMatchAndAppend(Seed &seed)
RDKit::FMCS::MaximumCommonSubgraph::VerboseStatistics
ExecStatistics VerboseStatistics
Definition MaximumCommonSubgraph.h:75
RDKit::FMCS::MaximumCommonSubgraph::find
MCSResult find(const std::vector< ROMOL_SPTR > &mols)
RDKit::FMCS::MaximumCommonSubgraph::parameters
const MCSParameters & parameters() const
Definition MaximumCommonSubgraph.h:87
RDKit::FMCS::MaximumCommonSubgraph::getQueryMolecule
const ROMol & getQueryMolecule() const
Definition MaximumCommonSubgraph.h:81
RDKit::FMCS::SeedSet
Definition SeedSet.h:19
RDKit::FMCS::Seed
Definition Seed.h:61
RDKit::FMCS::SubstructureCache
Definition SubstructureCache.h:23
RDKit::ROMol
Definition ROMol.h:199
export.h
RDKIT_FMCS_EXPORT
#define RDKIT_FMCS_EXPORT
Definition export.h:169
RDKit::FMCS
Definition Composition2N.h:13
RDKit::FMCS::MatchTable
TArray2D< bool > MatchTable
Definition MatchTable.h:48
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::FinalChiralityCheckFunction
bool FinalChiralityCheckFunction(const std::uint32_t c1[], const std::uint32_t c2[], const ROMol &mol1, const FMCS::Graph &query, const ROMol &mol2, const FMCS::Graph &target, const MCSParameters *p)
RDKit::FinalMatchCheckFunction
bool FinalMatchCheckFunction(const std::uint32_t c1[], const std::uint32_t c2[], const ROMol &mol1, const FMCS::Graph &query, const ROMol &mol2, const FMCS::Graph &target, const MCSParameters *p)
RDKit::FMCS::ExecStatistics
Definition DebugTrace.h:114
RDKit::MCSParameters
Definition FMCS.h:147
RDKit::MCSProgressData
Definition FMCS.h:131
RDKit::MCSResult
Definition FMCS.h:194
RDKit::detail::MCSParametersInternal
Definition FMCS.h:186