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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;
struct RDKIT_FMCS_EXPORT MCSAtomCompareParameters {
bool MatchValences;
bool MatchChiralTag;
bool MatchFormalCharge;
bool RingMatchesRingOnly;
public:
MCSAtomCompareParameters()
: MatchValences(false),
MatchChiralTag(false),
MatchFormalCharge(false),
RingMatchesRingOnly(false) {}
};
struct RDKIT_FMCS_EXPORT MCSBondCompareParameters {
bool RingMatchesRingOnly;
bool CompleteRingsOnly;
bool MatchStereo;
public:
MCSBondCompareParameters()
: RingMatchesRingOnly(false),
CompleteRingsOnly(false),
MatchStereo(false) {}
};
typedef bool (*MCSFinalMatchCheckFunction)(
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);
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 MCSAtomCompareAny(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 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;
unsigned NumBonds;
unsigned SeedProcessed;
public:
MCSProgressData() : NumAtoms(0), NumBonds(0), SeedProcessed(0) {}
};
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;
double Threshold;
unsigned Timeout; // in seconds
bool Verbose;
MCSAtomCompareParameters AtomCompareParameters;
MCSBondCompareParameters BondCompareParameters;
MCSAtomCompareFunction AtomTyper;
MCSBondCompareFunction BondTyper;
void* CompareFunctionsUserData;
MCSProgressCallback ProgressCallback; // return false to interrupt execution
void* ProgressCallbackUserData;
MCSFinalMatchCheckFunction
FinalMatchChecker; // FinalChiralityCheckFunction() to check chirality
std::string InitialSeed; // user defined or empty string (default)
public:
MCSParameters()
: MaximizeBonds(true),
Threshold(1.0) // match to all
,
Timeout(-1),
Verbose(false),
AtomTyper(MCSAtomCompareElements),
BondTyper(MCSBondCompareOrder),
CompareFunctionsUserData(0),
ProgressCallback(0),
ProgressCallbackUserData(0),
FinalMatchChecker(0),
InitialSeed("") {}
};
struct RDKIT_FMCS_EXPORT MCSResult {
unsigned NumAtoms;
unsigned NumBonds;
std::string SmartsString;
bool Canceled; // interrupted by timeout or user defined progress callback.
// Contains valid current MCS !
public:
MCSResult() : NumAtoms(0), NumBonds(0), Canceled(false) {}
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 = 0);
RDKIT_FMCS_EXPORT MCSResult findMCS_P(const std::vector<ROMOL_SPTR>& mols,
const char* params_json);
typedef enum {
AtomCompareAny,
AtomCompareElements,
AtomCompareIsotopes
} AtomComparator;
typedef enum {
BondCompareAny,
BondCompareOrder,
BondCompareOrderExact
} BondComparator;
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
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