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101 lines
4.1 KiB
C++
101 lines
4.1 KiB
C++
//
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// Copyright (C) 2014 Novartis Institutes for BioMedical Research
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#pragma once
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#include <vector>
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#include <string>
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#include <stdexcept>
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#include "../RDKitBase.h"
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namespace RDKit
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{
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struct MCSAtomCompareParameters
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{
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bool MatchValences;
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public:
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MCSAtomCompareParameters() : MatchValences(false) {}
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};
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struct MCSBondCompareParameters
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{
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bool RingMatchesRingOnly;
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bool CompleteRingsOnly;
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public:
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MCSBondCompareParameters() : RingMatchesRingOnly(false), CompleteRingsOnly(false) {}
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};
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typedef bool (*MCSAtomCompareFunction)(const MCSAtomCompareParameters& p, const ROMol& mol1, unsigned int atom1, const ROMol& mol2, unsigned int atom2, void* userData);
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typedef bool (*MCSBondCompareFunction)(const MCSBondCompareParameters& p, const ROMol& mol1, unsigned int bond1, const ROMol& mol2, unsigned int bond2, void* userData);
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// Some predefined functors:
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bool MCSAtomCompareAny (const MCSAtomCompareParameters& p, const ROMol& mol1, unsigned int atom1, const ROMol& mol2, unsigned int atom2, void* userData);
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bool MCSAtomCompareElements (const MCSAtomCompareParameters& p, const ROMol& mol1, unsigned int atom1, const ROMol& mol2, unsigned int atom2, void* userData);
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bool MCSAtomCompareIsotopes (const MCSAtomCompareParameters& p, const ROMol& mol1, unsigned int atom1, const ROMol& mol2, unsigned int atom2, void* userData);
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bool MCSBondCompareAny (const MCSBondCompareParameters& p, const ROMol& mol1, unsigned int bond1, const ROMol& mol2, unsigned int bond2, void* userData);
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bool MCSBondCompareOrder (const MCSBondCompareParameters& p, const ROMol& mol1, unsigned int bond1, const ROMol& mol2, unsigned int bond2, void* userData); // ignore Aromatization
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bool MCSBondCompareOrderExact(const MCSBondCompareParameters& p, const ROMol& mol1, unsigned int bond1, const ROMol& mol2, unsigned int bond2, void* userData);
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struct MCSProgressData
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{
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unsigned NumAtoms;
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unsigned NumBonds;
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unsigned SeedProcessed;
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// ...............
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public:
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MCSProgressData() : NumAtoms(0), NumBonds(0), SeedProcessed(0) {}
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};
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struct MCSParameters;
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typedef bool (*MCSProgressCallback)(const MCSProgressData& stat, const MCSParameters ¶ms, void* userData);
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bool MCSProgressCallbackTimeout(const MCSProgressData& stat, const MCSParameters ¶ms, void* userData);
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struct MCSParameters
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{
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bool MaximizeBonds;
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double Threshold;
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unsigned Timeout; // in seconds
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bool Verbose; // ?
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MCSAtomCompareParameters AtomCompareParameters;
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MCSBondCompareParameters BondCompareParameters;
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MCSAtomCompareFunction AtomTyper;
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MCSBondCompareFunction BondTyper;
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void* CompareFunctionsUserData;
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MCSProgressCallback ProgressCallback; // return false to interrupt execution
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void* ProgressCallbackUserData;
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unsigned ThreadNumber; // #ifdef MULTI_THREAD
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public:
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MCSParameters(): MaximizeBonds(true)
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, Threshold(1.0) // match to all
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, Timeout(-1)
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, Verbose(false)
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, AtomTyper(MCSAtomCompareElements)
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, BondTyper(MCSBondCompareOrder)
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, CompareFunctionsUserData(0)
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, ProgressCallback(MCSProgressCallbackTimeout)
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, ProgressCallbackUserData(0)
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, ThreadNumber(64) // 64 is optimal value for 4 kernels i7 CPU
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{}
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};
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struct MCSResult
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{
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unsigned NumAtoms;
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unsigned NumBonds;
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std::string SmartsString;
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bool Canceled; // interrupted by timeout or user defined progress callback. Contains valid current MCS !
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public:
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MCSResult() : NumAtoms(0), NumBonds(0), Canceled(false) {}
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bool isCompleted()const { return !Canceled; }
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};
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MCSResult findMCS (const std::vector<ROMOL_SPTR>& mols, const MCSParameters* params=0);
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} // namespace RDKit
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