FMCS.h
Go to the documentation of this file.
//
// 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 (*MCSFinalMatchCheckFunction)(
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);
typedef bool (*MCSAtomCompareFunction)(const MCSAtomCompareParameters& p,
const ROMol& mol1, unsigned int atom1,
const ROMol& mol2, unsigned int atom2,
void* userData);
typedef bool (*MCSBondCompareFunction)(const MCSBondCompareParameters& p,
const ROMol& mol1, unsigned int bond1,
const ROMol& mol2, unsigned int bond2,
void* userData);
// 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 checkBondRingMatch(const MCSBondCompareParameters& p,
const ROMol& mol1, unsigned int bond1,
const ROMol& mol2, unsigned int bond2,
void* v_ringMatchMatrixSet);
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 NumAtoms{0};
unsigned NumBonds{0};
unsigned 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 {
bool MaximizeBonds = true;
double Threshold = 1.0; // match all molecules
unsigned Timeout = -1; // 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;
MCSFinalMatchCheckFunction FinalMatchChecker =
nullptr; // FinalMatchCheckFunction() to check chirality and ring fusion
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);
};
struct RDKIT_FMCS_EXPORT MCSResult {
unsigned NumAtoms{0};
unsigned NumBonds{0};
std::string SmartsString;
bool Canceled{false}; // interrupted by timeout or user defined progress
// callback. Contains valid current MCS !
ROMOL_SPTR QueryMol;
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 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 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
RDKit::FMCS::Graph
Definition: Graph.h:26
RDKit::ROMol
Definition: ROMol.h:178
export.h
RDKIT_FMCS_EXPORT
#define RDKIT_FMCS_EXPORT
Definition: export.h:145
RDKit
Std stuff.
Definition: Abbreviations.h:18
RDKit::MCSAtomCompareFunction
bool(* MCSAtomCompareFunction)(const MCSAtomCompareParameters &p, const ROMol &mol1, unsigned int atom1, const ROMol &mol2, unsigned int atom2, void *userData)
Definition: FMCS.h:62
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:21
RDKit::AtomCompareElements
@ AtomCompareElements
Definition: FMCS.h:23
RDKit::AtomCompareAnyHeavyAtom
@ AtomCompareAnyHeavyAtom
Definition: FMCS.h:25
RDKit::AtomCompareAny
@ AtomCompareAny
Definition: FMCS.h:22
RDKit::AtomCompareIsotopes
@ AtomCompareIsotopes
Definition: FMCS.h:24
RDKit::BondComparator
BondComparator
Definition: FMCS.h:28
RDKit::BondCompareOrderExact
@ BondCompareOrderExact
Definition: FMCS.h:31
RDKit::BondCompareAny
@ BondCompareAny
Definition: FMCS.h:29
RDKit::BondCompareOrder
@ BondCompareOrder
Definition: FMCS.h:30
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::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::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::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:34
RDKit::StrictRingFusion
@ StrictRingFusion
Definition: FMCS.h:37
RDKit::IgnoreRingFusion
@ IgnoreRingFusion
Definition: FMCS.h:35
RDKit::PermissiveRingFusion
@ PermissiveRingFusion
Definition: FMCS.h:36
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::checkBondRingMatch
RDKIT_FMCS_EXPORT bool checkBondRingMatch(const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *v_ringMatchMatrixSet)
RDKit::ROMOL_SPTR
boost::shared_ptr< ROMol > ROMOL_SPTR
Definition: ChemTransforms.h:22
RDKit::MCSBondCompareFunction
bool(* MCSBondCompareFunction)(const MCSBondCompareParameters &p, const ROMol &mol1, unsigned int bond1, const ROMol &mol2, unsigned int bond2, void *userData)
Definition: FMCS.h:66
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:131
RDKit::MCSProgressCallbackTimeout
RDKIT_FMCS_EXPORT bool MCSProgressCallbackTimeout(const MCSProgressData &stat, const MCSParameters &params, void *userData)
RDKit::MCSFinalMatchCheckFunction
bool(* MCSFinalMatchCheckFunction)(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)
Definition: FMCS.h:58
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:40
RDKit::MCSBondCompareParameters
Definition: FMCS.h:50
RDKit::MCSParameters
Definition: FMCS.h:138
RDKit::MCSParameters::setMCSBondTyperFromEnum
void setMCSBondTyperFromEnum(BondComparator bondComp)
RDKit::MCSParameters::setMCSBondTyperFromConstChar
void setMCSBondTyperFromConstChar(const char *bondComp)
RDKit::MCSParameters::setMCSAtomTyperFromConstChar
void setMCSAtomTyperFromConstChar(const char *atomComp)
RDKit::MCSParameters::setMCSAtomTyperFromEnum
void setMCSAtomTyperFromEnum(AtomComparator atomComp)
RDKit::MCSParameters::AtomCompareParameters
MCSAtomCompareParameters AtomCompareParameters
Definition: FMCS.h:143
RDKit::MCSParameters::BondCompareParameters
MCSBondCompareParameters BondCompareParameters
Definition: FMCS.h:144
RDKit::MCSProgressData
Definition: FMCS.h:122
RDKit::MCSProgressData::MCSProgressData
MCSProgressData()
Definition: FMCS.h:128
RDKit::MCSResult
Definition: FMCS.h:160
RDKit::MCSResult::QueryMol
ROMOL_SPTR QueryMol
Definition: FMCS.h:166
RDKit::MCSResult::SmartsString
std::string SmartsString
Definition: FMCS.h:163
RDKit::MCSResult::isCompleted
bool isCompleted() const
Definition: FMCS.h:170
RDKit::MCSResult::MCSResult
MCSResult()
Definition: FMCS.h:169