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FMCS.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 "Graph.h"
namespace RDKit {
struct MCSParameters;
typedef enum {
AtomCompareAny,
AtomCompareElements,
AtomCompareIsotopes,
AtomCompareAnyHeavyAtom
} AtomComparator;
typedef enum {
BondCompareAny,
BondCompareOrder,
BondCompareOrderExact
} BondComparator;
typedef enum {
IgnoreRingFusion,
PermissiveRingFusion,
StrictRingFusion
} RingComparator;
struct RDKIT_FMCS_EXPORT MCSAtomCompareParameters {
bool MatchValences = false;
bool MatchChiralTag = false;
bool MatchFormalCharge = false;
bool RingMatchesRingOnly = false;
bool CompleteRingsOnly = false;
bool MatchIsotope = false;
double MaxDistance = -1.0;
};
struct RDKIT_FMCS_EXPORT MCSBondCompareParameters {
bool RingMatchesRingOnly = false;
bool CompleteRingsOnly = false;
bool MatchFusedRings = false;
bool MatchFusedRingsStrict = false;
bool MatchStereo = false;
};
typedef bool (*MCSAtomCompareFunction)(const MCSAtomCompareParameters &,
const ROMol &, unsigned int,
const ROMol &, unsigned int, void *);
typedef bool (*MCSBondCompareFunction)(const MCSBondCompareParameters &,
const ROMol &, unsigned int,
const ROMol &, unsigned int, void *);
typedef bool (*MCSAcceptanceFunction)(const ROMol &, const ROMol &,
const std::vector<std::pair<int, int>> &,
const std::vector<std::pair<int, int>> &,
const MCSParameters *);
typedef bool (*MCSFinalMatchCheckFunction)(const std::uint32_t[],
const std::uint32_t[], const ROMol &,
const FMCS::Graph &, const ROMol &,
const FMCS::Graph &,
const MCSParameters *);
// Some predefined functors:
RDKIT_FMCS_EXPORT bool checkAtomRingMatch(const MCSAtomCompareParameters &p,
const ROMol &mol1, unsigned int atom1,
const ROMol &mol2,
unsigned int atom2);
RDKIT_FMCS_EXPORT bool checkAtomCharge(const MCSAtomCompareParameters &p,
const ROMol &mol1, unsigned int atom1,
const ROMol &mol2, unsigned int atom2);
RDKIT_FMCS_EXPORT bool checkAtomChirality(const MCSAtomCompareParameters &p,
const ROMol &mol1, unsigned int atom1,
const ROMol &mol2,
unsigned int atom2);
RDKIT_FMCS_EXPORT bool checkAtomDistance(const MCSAtomCompareParameters &p,
const ROMol &mol1, unsigned int atom1,
const ROMol &mol2, unsigned int atom2);
RDKIT_FMCS_EXPORT bool MCSAtomCompareAny(const MCSAtomCompareParameters &p,
const ROMol &mol1, unsigned int atom1,
const ROMol &mol2, unsigned int atom2,
void *userData);
RDKIT_FMCS_EXPORT bool MCSAtomCompareAnyHeavyAtom(
const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1,
const ROMol &mol2, unsigned int atom2, void *userData);
RDKIT_FMCS_EXPORT bool MCSAtomCompareElements(
const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1,
const ROMol &mol2, unsigned int atom2, void *userData);
RDKIT_FMCS_EXPORT bool MCSAtomCompareIsotopes(
const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1,
const ROMol &mol2, unsigned int atom2, void *userData);
RDKIT_FMCS_EXPORT bool checkBondStereo(const MCSBondCompareParameters &p,
const ROMol &mol1, unsigned int bond1,
const ROMol &mol2, unsigned int bond2);
RDKIT_FMCS_EXPORT bool havePairOfCompatibleRings(
const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1,
const ROMol &mol2, unsigned int bond2);
RDKIT_FMCS_EXPORT bool checkBondRingMatch(const MCSBondCompareParameters &p,
const ROMol &mol1, unsigned int bond1,
const ROMol &mol2,
unsigned int bond2);
RDKIT_FMCS_EXPORT bool MCSBondCompareAny(const MCSBondCompareParameters &p,
const ROMol &mol1, unsigned int bond1,
const ROMol &mol2, unsigned int bond2,
void *userData);
RDKIT_FMCS_EXPORT bool MCSBondCompareOrder(
const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1,
const ROMol &mol2, unsigned int bond2,
void *userData); // ignore Aromatization
RDKIT_FMCS_EXPORT bool MCSBondCompareOrderExact(
const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1,
const ROMol &mol2, unsigned int bond2, void *userData);
struct RDKIT_FMCS_EXPORT MCSProgressData {
unsigned int NumAtoms{0};
unsigned int NumBonds{0};
unsigned int SeedProcessed{0};
public:
MCSProgressData() {}
};
typedef bool (*MCSProgressCallback)(const MCSProgressData &stat,
const MCSParameters &params,
void *userData);
RDKIT_FMCS_EXPORT bool MCSProgressCallbackTimeout(const MCSProgressData &stat,
const MCSParameters &params,
void *userData);
struct RDKIT_FMCS_EXPORT MCSParameters {
MCSParameters() {}
MCSParameters(const MCSParameters *other) : MCSParameters() {
if (other) {
*this = *other;
}
}
MCSParameters(const MCSParameters &other) = default;
MCSParameters &operator=(const MCSParameters &other) = default;
virtual ~MCSParameters() {}
bool StoreAll = false;
bool MaximizeBonds = true;
double Threshold = 1.0; // match all molecules
unsigned int Timeout = 0; // in seconds
bool Verbose = false;
MCSAtomCompareParameters AtomCompareParameters;
MCSBondCompareParameters BondCompareParameters;
MCSAtomCompareFunction AtomTyper = MCSAtomCompareElements;
MCSBondCompareFunction BondTyper = MCSBondCompareOrder;
void *CompareFunctionsUserData = nullptr;
MCSProgressCallback ProgressCallback =
nullptr; // return false to interrupt execution
void *ProgressCallbackUserData = nullptr;
// FinalMatchCheckFunction() to accept/reject a growing MCS candidate based on
// user-defined criteria
MCSFinalMatchCheckFunction FinalMatchChecker = nullptr;
void *FinalMatchCheckerUserData = nullptr;
// ShouldAcceptMCS() to accept/reject a fully-grown MCS candidate based on
// user-defined criteria
MCSAcceptanceFunction ShouldAcceptMCS = nullptr;
void *ShouldAcceptMCSUserData = nullptr;
std::string InitialSeed = ""; // user defined or empty string (default)
void setMCSAtomTyperFromEnum(AtomComparator atomComp);
void setMCSAtomTyperFromConstChar(const char *atomComp);
void setMCSBondTyperFromEnum(BondComparator bondComp);
void setMCSBondTyperFromConstChar(const char *bondComp);
};
namespace detail {
struct MCSParametersInternal : public MCSParameters {
MCSParametersInternal() {}
~MCSParametersInternal() override {}
MCSParametersInternal(const MCSParameters *params);
MCSFinalMatchCheckFunction UserFinalMatchChecker = nullptr;
};
} // end namespace detail
struct RDKIT_FMCS_EXPORT MCSResult {
unsigned int NumAtoms{0};
unsigned int NumBonds{0};
std::string SmartsString;
bool Canceled{false}; // interrupted by timeout or user defined progress
// callback. Contains valid current MCS !
ROMOL_SPTR QueryMol;
std::map<std::string, ROMOL_SPTR> DegenerateSmartsQueryMolDict;
public:
MCSResult() {}
bool isCompleted() const { return !Canceled; }
};
RDKIT_FMCS_EXPORT void parseMCSParametersJSON(const char *json,
MCSParameters *params);
RDKIT_FMCS_EXPORT MCSResult findMCS(const std::vector<ROMOL_SPTR> &mols,
const MCSParameters *params = nullptr);
RDKIT_FMCS_EXPORT MCSResult findMCS_P(const std::vector<ROMOL_SPTR> &mols,
const char *params_json);
RDKIT_FMCS_EXPORT MCSResult findMCS(
const std::vector<ROMOL_SPTR> &mols, bool maximizeBonds, double threshold,
unsigned int timeout, bool verbose, bool matchValences,
bool ringMatchesRingOnly, bool completeRingsOnly, bool matchChiralTag,
AtomComparator atomComp, BondComparator bondComp, RingComparator ringComp);
RDKIT_FMCS_EXPORT MCSResult findMCS(
const std::vector<ROMOL_SPTR> &mols, bool maximizeBonds,
double threshold = 1.0, unsigned int timeout = 3600, bool verbose = false,
bool matchValences = false, bool ringMatchesRingOnly = false,
bool completeRingsOnly = false, bool matchChiralTag = false,
AtomComparator atomComp = AtomCompareElements,
BondComparator bondComp = BondCompareOrder);
} // namespace RDKit
Graph.h
RDKitBase.h
pulls in the core RDKit functionality
RDKit::FMCS::Graph
Definition Graph.h:26
RDKit::ROMol
Definition ROMol.h:319
export.h
RDKIT_FMCS_EXPORT
#define RDKIT_FMCS_EXPORT
Definition export.h:169
RDKit::detail
Definition FMCS.h:185
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::findMCS_P
RDKIT_FMCS_EXPORT MCSResult findMCS_P(const std::vector< ROMOL_SPTR > &mols, const char *params_json)
RDKit::MCSAtomCompareAnyHeavyAtom
RDKIT_FMCS_EXPORT bool MCSAtomCompareAnyHeavyAtom(const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData)
RDKit::AtomComparator
AtomComparator
Definition FMCS.h:22
RDKit::AtomCompareElements
@ AtomCompareElements
Definition FMCS.h:24
RDKit::AtomCompareAnyHeavyAtom
@ AtomCompareAnyHeavyAtom
Definition FMCS.h:26
RDKit::AtomCompareAny
@ AtomCompareAny
Definition FMCS.h:23
RDKit::AtomCompareIsotopes
@ AtomCompareIsotopes
Definition FMCS.h:25
RDKit::BondComparator
BondComparator
Definition FMCS.h:29
RDKit::BondCompareOrderExact
@ BondCompareOrderExact
Definition FMCS.h:32
RDKit::BondCompareAny
@ BondCompareAny
Definition FMCS.h:30
RDKit::BondCompareOrder
@ BondCompareOrder
Definition FMCS.h:31
RDKit::checkBondRingMatch
RDKIT_FMCS_EXPORT bool checkBondRingMatch(const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2)
RDKit::MCSAtomCompareElements
RDKIT_FMCS_EXPORT bool MCSAtomCompareElements(const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData)
RDKit::MCSFinalMatchCheckFunction
bool(* MCSFinalMatchCheckFunction)(const std::uint32_t[], const std::uint32_t[], const ROMol &, const FMCS::Graph &, const ROMol &, const FMCS::Graph &, const MCSParameters *)
Definition FMCS.h:69
RDKit::checkAtomDistance
RDKIT_FMCS_EXPORT bool checkAtomDistance(const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2)
RDKit::checkBondStereo
RDKIT_FMCS_EXPORT bool checkBondStereo(const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2)
RDKit::parseMCSParametersJSON
RDKIT_FMCS_EXPORT void parseMCSParametersJSON(const char *json, MCSParameters *params)
RDKit::MCSBondCompareFunction
bool(* MCSBondCompareFunction)(const MCSBondCompareParameters &, const ROMol &, unsigned int, const ROMol &, unsigned int, void *)
Definition FMCS.h:62
RDKit::MCSBondCompareAny
RDKIT_FMCS_EXPORT bool MCSBondCompareAny(const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *userData)
RDKit::findMCS
RDKIT_FMCS_EXPORT MCSResult findMCS(const std::vector< ROMOL_SPTR > &mols, const MCSParameters *params=nullptr)
RDKit::MCSAtomCompareAny
RDKIT_FMCS_EXPORT bool MCSAtomCompareAny(const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData)
RDKit::MCSAtomCompareFunction
bool(* MCSAtomCompareFunction)(const MCSAtomCompareParameters &, const ROMol &, unsigned int, const ROMol &, unsigned int, void *)
Definition FMCS.h:59
RDKit::MCSBondCompareOrder
RDKIT_FMCS_EXPORT bool MCSBondCompareOrder(const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *userData)
RDKit::checkAtomRingMatch
RDKIT_FMCS_EXPORT bool checkAtomRingMatch(const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2)
RDKit::RingComparator
RingComparator
Definition FMCS.h:35
RDKit::StrictRingFusion
@ StrictRingFusion
Definition FMCS.h:38
RDKit::IgnoreRingFusion
@ IgnoreRingFusion
Definition FMCS.h:36
RDKit::PermissiveRingFusion
@ PermissiveRingFusion
Definition FMCS.h:37
RDKit::checkAtomCharge
RDKIT_FMCS_EXPORT bool checkAtomCharge(const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2)
RDKit::MCSAtomCompareIsotopes
RDKIT_FMCS_EXPORT bool MCSAtomCompareIsotopes(const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData)
RDKit::ROMOL_SPTR
boost::shared_ptr< ROMol > ROMOL_SPTR
Definition ChemTransforms.h:23
RDKit::havePairOfCompatibleRings
RDKIT_FMCS_EXPORT bool havePairOfCompatibleRings(const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2)
RDKit::checkAtomChirality
RDKIT_FMCS_EXPORT bool checkAtomChirality(const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2)
RDKit::MCSProgressCallback
bool(* MCSProgressCallback)(const MCSProgressData &stat, const MCSParameters &params, void *userData)
Definition FMCS.h:140
RDKit::MCSProgressCallbackTimeout
RDKIT_FMCS_EXPORT bool MCSProgressCallbackTimeout(const MCSProgressData &stat, const MCSParameters &params, void *userData)
RDKit::MCSAcceptanceFunction
bool(* MCSAcceptanceFunction)(const ROMol &, const ROMol &, const std::vector< std::pair< int, int > > &, const std::vector< std::pair< int, int > > &, const MCSParameters *)
Definition FMCS.h:65
RDKit::MCSBondCompareOrderExact
RDKIT_FMCS_EXPORT bool MCSBondCompareOrderExact(const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *userData)
RDKit::MCSAtomCompareParameters
Definition FMCS.h:41
RDKit::MCSAtomCompareParameters::MatchChiralTag
bool MatchChiralTag
Definition FMCS.h:43
RDKit::MCSAtomCompareParameters::MaxDistance
double MaxDistance
Definition FMCS.h:48
RDKit::MCSAtomCompareParameters::MatchValences
bool MatchValences
Definition FMCS.h:42
RDKit::MCSAtomCompareParameters::MatchIsotope
bool MatchIsotope
Definition FMCS.h:47
RDKit::MCSAtomCompareParameters::MatchFormalCharge
bool MatchFormalCharge
Definition FMCS.h:44
RDKit::MCSAtomCompareParameters::CompleteRingsOnly
bool CompleteRingsOnly
Definition FMCS.h:46
RDKit::MCSAtomCompareParameters::RingMatchesRingOnly
bool RingMatchesRingOnly
Definition FMCS.h:45
RDKit::MCSBondCompareParameters
Definition FMCS.h:51
RDKit::MCSBondCompareParameters::MatchFusedRings
bool MatchFusedRings
Definition FMCS.h:54
RDKit::MCSBondCompareParameters::RingMatchesRingOnly
bool RingMatchesRingOnly
Definition FMCS.h:52
RDKit::MCSBondCompareParameters::MatchFusedRingsStrict
bool MatchFusedRingsStrict
Definition FMCS.h:55
RDKit::MCSBondCompareParameters::CompleteRingsOnly
bool CompleteRingsOnly
Definition FMCS.h:53
RDKit::MCSBondCompareParameters::MatchStereo
bool MatchStereo
Definition FMCS.h:56
RDKit::MCSParameters
Definition FMCS.h:147
RDKit::MCSParameters::ProgressCallbackUserData
void * ProgressCallbackUserData
Definition FMCS.h:169
RDKit::MCSParameters::StoreAll
bool StoreAll
Definition FMCS.h:157
RDKit::MCSParameters::InitialSeed
std::string InitialSeed
Definition FMCS.h:178
RDKit::MCSParameters::MCSParameters
MCSParameters(const MCSParameters *other)
Definition FMCS.h:149
RDKit::MCSParameters::setMCSBondTyperFromEnum
void setMCSBondTyperFromEnum(BondComparator bondComp)
RDKit::MCSParameters::FinalMatchChecker
MCSFinalMatchCheckFunction FinalMatchChecker
Definition FMCS.h:172
RDKit::MCSParameters::ShouldAcceptMCSUserData
void * ShouldAcceptMCSUserData
Definition FMCS.h:177
RDKit::MCSParameters::setMCSBondTyperFromConstChar
void setMCSBondTyperFromConstChar(const char *bondComp)
RDKit::MCSParameters::~MCSParameters
virtual ~MCSParameters()
Definition FMCS.h:156
RDKit::MCSParameters::AtomTyper
MCSAtomCompareFunction AtomTyper
Definition FMCS.h:164
RDKit::MCSParameters::MCSParameters
MCSParameters(const MCSParameters &other)=default
RDKit::MCSParameters::FinalMatchCheckerUserData
void * FinalMatchCheckerUserData
Definition FMCS.h:173
RDKit::MCSParameters::operator=
MCSParameters & operator=(const MCSParameters &other)=default
RDKit::MCSParameters::MCSParameters
MCSParameters()
Definition FMCS.h:148
RDKit::MCSParameters::MaximizeBonds
bool MaximizeBonds
Definition FMCS.h:158
RDKit::MCSParameters::Timeout
unsigned int Timeout
Definition FMCS.h:160
RDKit::MCSParameters::Threshold
double Threshold
Definition FMCS.h:159
RDKit::MCSParameters::BondTyper
MCSBondCompareFunction BondTyper
Definition FMCS.h:165
RDKit::MCSParameters::setMCSAtomTyperFromConstChar
void setMCSAtomTyperFromConstChar(const char *atomComp)
RDKit::MCSParameters::Verbose
bool Verbose
Definition FMCS.h:161
RDKit::MCSParameters::setMCSAtomTyperFromEnum
void setMCSAtomTyperFromEnum(AtomComparator atomComp)
RDKit::MCSParameters::ShouldAcceptMCS
MCSAcceptanceFunction ShouldAcceptMCS
Definition FMCS.h:176
RDKit::MCSParameters::AtomCompareParameters
MCSAtomCompareParameters AtomCompareParameters
Definition FMCS.h:162
RDKit::MCSParameters::CompareFunctionsUserData
void * CompareFunctionsUserData
Definition FMCS.h:166
RDKit::MCSParameters::ProgressCallback
MCSProgressCallback ProgressCallback
Definition FMCS.h:167
RDKit::MCSParameters::BondCompareParameters
MCSBondCompareParameters BondCompareParameters
Definition FMCS.h:163
RDKit::MCSProgressData
Definition FMCS.h:131
RDKit::MCSProgressData::NumAtoms
unsigned int NumAtoms
Definition FMCS.h:132
RDKit::MCSProgressData::NumBonds
unsigned int NumBonds
Definition FMCS.h:133
RDKit::MCSProgressData::SeedProcessed
unsigned int SeedProcessed
Definition FMCS.h:134
RDKit::MCSProgressData::MCSProgressData
MCSProgressData()
Definition FMCS.h:137
RDKit::MCSResult
Definition FMCS.h:194
RDKit::MCSResult::NumBonds
unsigned int NumBonds
Definition FMCS.h:196
RDKit::MCSResult::QueryMol
ROMOL_SPTR QueryMol
Definition FMCS.h:200
RDKit::MCSResult::SmartsString
std::string SmartsString
Definition FMCS.h:197
RDKit::MCSResult::Canceled
bool Canceled
Definition FMCS.h:198
RDKit::MCSResult::DegenerateSmartsQueryMolDict
std::map< std::string, ROMOL_SPTR > DegenerateSmartsQueryMolDict
Definition FMCS.h:201
RDKit::MCSResult::NumAtoms
unsigned int NumAtoms
Definition FMCS.h:195
RDKit::MCSResult::isCompleted
bool isCompleted() const
Definition FMCS.h:205
RDKit::MCSResult::MCSResult
MCSResult()
Definition FMCS.h:204
RDKit::detail::MCSParametersInternal::MCSParametersInternal
MCSParametersInternal()
Definition FMCS.h:187
RDKit::detail::MCSParametersInternal::MCSParametersInternal
MCSParametersInternal(const MCSParameters *params)
RDKit::detail::MCSParametersInternal::~MCSParametersInternal
~MCSParametersInternal() override
Definition FMCS.h:188
RDKit::detail::MCSParametersInternal::UserFinalMatchChecker
MCSFinalMatchCheckFunction UserFinalMatchChecker
Definition FMCS.h:190