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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 ¶ms,
void *userData);
RDKIT_FMCS_EXPORT bool MCSProgressCallbackTimeout(const MCSProgressData &stat,
const MCSParameters ¶ms,
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() {}
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
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