/usr/include/rdkit/GraphMol/FMCS/FMCS.h is in librdkit-dev 201603.5-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 | //
// 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"
#ifndef RDKIT_WRAP_DECL
#define RDKIT_WRAP_DECL
#endif
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:
RDKIT_WRAP_DECL bool MCSAtomCompareAny(const MCSAtomCompareParameters& p, const ROMol& mol1,
unsigned int atom1, const ROMol& mol2,
unsigned int atom2, void* userData);
RDKIT_WRAP_DECL bool MCSAtomCompareElements(const MCSAtomCompareParameters& p,
const ROMol& mol1, unsigned int atom1,
const ROMol& mol2, unsigned int atom2,
void* userData);
RDKIT_WRAP_DECL bool MCSAtomCompareIsotopes(const MCSAtomCompareParameters& p,
const ROMol& mol1, unsigned int atom1,
const ROMol& mol2, unsigned int atom2,
void* userData);
RDKIT_WRAP_DECL bool MCSBondCompareAny(const MCSBondCompareParameters& p, const ROMol& mol1,
unsigned int bond1, const ROMol& mol2,
unsigned int bond2, void* userData);
RDKIT_WRAP_DECL bool MCSBondCompareOrder(const MCSBondCompareParameters& p, const ROMol& mol1,
unsigned int bond1, const ROMol& mol2,
unsigned int bond2,
void* userData); // ignore Aromatization
RDKIT_WRAP_DECL 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& params,
void* userData);
bool MCSProgressCallbackTimeout(const MCSProgressData& stat,
const MCSParameters& params, 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
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(MCSProgressCallbackTimeout),
ProgressCallbackUserData(0),
FinalMatchChecker(0),
InitialSeed("") {}
};
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
|