/usr/include/rdkit/GraphMol/FMCS/FMCS.h is in librdkit-dev 201503-3.
This file is owned by root:root, with mode 0o644.
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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.
//
#pragma once
#include <vector>
#include <string>
#include <stdexcept>
#include "../RDKitBase.h"
#include "Graph.h"
namespace RDKit {
struct MCSParameters;
struct MCSAtomCompareParameters {
bool MatchValences;
bool MatchChiralTag;
public:
MCSAtomCompareParameters() : MatchValences(false), MatchChiralTag(false) {}
};
struct 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:
bool MCSAtomCompareAny (const MCSAtomCompareParameters& p, const ROMol& mol1, unsigned int atom1, const ROMol& mol2, unsigned int atom2, void* userData);
bool MCSAtomCompareElements (const MCSAtomCompareParameters& p, const ROMol& mol1, unsigned int atom1, const ROMol& mol2, unsigned int atom2, void* userData);
bool MCSAtomCompareIsotopes (const MCSAtomCompareParameters& p, const ROMol& mol1, unsigned int atom1, const ROMol& mol2, unsigned int atom2, void* userData);
bool MCSBondCompareAny (const MCSBondCompareParameters& p, const ROMol& mol1, unsigned int bond1, const ROMol& mol2, unsigned int bond2, void* userData);
bool MCSBondCompareOrder (const MCSBondCompareParameters& p, const ROMol& mol1, unsigned int bond1, const ROMol& mol2, unsigned int bond2, void* userData); // ignore Aromatization
bool MCSBondCompareOrderExact(const MCSBondCompareParameters&p, const ROMol& mol1, unsigned int bond1, const ROMol& mol2, unsigned int bond2, void* userData);
struct MCSProgressData {
unsigned NumAtoms;
unsigned NumBonds;
unsigned SeedProcessed;
public:
MCSProgressData() : NumAtoms(0), NumBonds(0), SeedProcessed(0) {}
};
typedef bool (*MCSProgressCallback)(const MCSProgressData& stat, const MCSParameters ¶ms, void* userData);
bool MCSProgressCallbackTimeout(const MCSProgressData& stat, const MCSParameters ¶ms, void* userData);
struct 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
public:
MCSParameters(): MaximizeBonds(true)
, Threshold(1.0) // match to all
, Timeout(-1)
, Verbose(false)
, AtomTyper(MCSAtomCompareElements)
, BondTyper(MCSBondCompareOrder)
, CompareFunctionsUserData(0)
, ProgressCallback(MCSProgressCallbackTimeout)
, ProgressCallbackUserData(0)
, FinalMatchChecker(0)
{}
};
struct 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;
}
};
void parseMCSParametersJSON (const char* json, MCSParameters* params);
MCSResult findMCS (const std::vector<ROMOL_SPTR>& mols, const MCSParameters* params=0);
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;
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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