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179 lines
8.3 KiB
C++
179 lines
8.3 KiB
C++
//
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// Copyright (C) 2001-2017 Greg Landrum and Rational Discovery LLC
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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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#include <RDGeneral/export.h>
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#ifndef RD_SUBSTRUCTMATCH_H
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#define RD_SUBSTRUCTMATCH_H
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// std bits
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#include <vector>
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namespace RDKit {
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class ROMol;
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class Atom;
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class Bond;
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class ResonanceMolSupplier;
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class MolBundle;
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//! \brief used to return matches from substructure searching,
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//! The format is (queryAtomIdx, molAtomIdx)
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typedef std::vector<std::pair<int, int> > MatchVectType;
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//! Find a substructure match for a query in a molecule
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/*!
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\param mol The ROMol to be searched
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\param query The query ROMol
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\param matchVect Used to return the match
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(pre-existing contents will be deleted)
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\param recursionPossible flags whether or not recursive matches are allowed
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\param useChirality use atomic CIP codes as part of the comparison
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\param useQueryQueryMatches if set, the contents of atom and bond queries
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will be used as part of the matching
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\return whether or not a match was found
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*/
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RDKIT_SUBSTRUCTMATCH_EXPORT bool SubstructMatch(const ROMol &mol, const ROMol &query,
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MatchVectType &matchVect, bool recursionPossible = true,
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bool useChirality = false,
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bool useQueryQueryMatches = false);
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//! Find a substructure match for a query in a ResonanceMolSupplier object
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/*!
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\param resMolSuppl The ResonanceMolSupplier object to be searched
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\param query The query ROMol
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\param matchVect Used to return the match
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(pre-existing contents will be deleted)
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\param recursionPossible flags whether or not recursive matches are allowed
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\param useChirality use atomic CIP codes as part of the comparison
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\param useQueryQueryMatches if set, the contents of atom and bond queries
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will be used as part of the matching
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\return whether or not a match was found
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*/
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RDKIT_SUBSTRUCTMATCH_EXPORT bool SubstructMatch(ResonanceMolSupplier &resMolSuppl, const ROMol &query,
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MatchVectType &matchVect, bool recursionPossible = true,
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bool useChirality = false,
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bool useQueryQueryMatches = false);
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//! Find all substructure matches for a query in a molecule
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/*!
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\param mol The ROMol to be searched
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\param query The query ROMol
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\param matchVect Used to return the matches
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(pre-existing contents will be deleted)
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\param uniquify Toggles uniquification (by atom index) of the results
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\param recursionPossible flags whether or not recursive matches are allowed
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\param useChirality use atomic CIP codes as part of the comparison
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\param useQueryQueryMatches if set, the contents of atom and bond queries
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will be used as part of the matching
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\param maxMatches The maximum number of matches that will be returned.
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In high-symmetry cases with medium-sized molecules, it is
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very
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easy to end up with a combinatorial explosion in the
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number of
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possible matches. This argument prevents that from having
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unintended consequences
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\return the number of matches found
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*/
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RDKIT_SUBSTRUCTMATCH_EXPORT unsigned int SubstructMatch(const ROMol &mol, const ROMol &query,
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std::vector<MatchVectType> &matchVect,
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bool uniquify = true, bool recursionPossible = true,
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bool useChirality = false,
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bool useQueryQueryMatches = false,
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unsigned int maxMatches = 1000);
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//! Find all substructure matches for a query in a ResonanceMolSupplier object
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/*!
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\param resMolSuppl The ResonanceMolSupplier object to be searched
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\param query The query ROMol
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\param matchVect Used to return the matches
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(pre-existing contents will be deleted)
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\param uniquify Toggles uniquification (by atom index) of the results
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\param recursionPossible flags whether or not recursive matches are allowed
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\param useChirality use atomic CIP codes as part of the comparison
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\param useQueryQueryMatches if set, the contents of atom and bond queries
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will be used as part of the matching
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\param maxMatches The maximum number of matches that will be returned.
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In high-symmetry cases with medium-sized molecules, it is
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very
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easy to end up with a combinatorial explosion in the
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number of
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possible matches. This argument prevents that from having
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unintended consequences
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\param numThreads The number of threads used during the search
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(defaults to 1; 0 selects the number of
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concurrent threads supported by the hardware;
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negative values are added to the number of
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concurrent threads supported by the
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hardware)
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\return the number of matches found
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*/
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RDKIT_SUBSTRUCTMATCH_EXPORT unsigned int SubstructMatch(ResonanceMolSupplier &resMolSuppl,
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const ROMol &query,
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std::vector<MatchVectType> &matchVect,
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bool uniquify = false,
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bool recursionPossible = true,
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bool useChirality = false,
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bool useQueryQueryMatches = false,
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unsigned int maxMatches = 1000, int numThreads = 1);
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//! \overload
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//! finds the first match in the bundle
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RDKIT_SUBSTRUCTMATCH_EXPORT bool SubstructMatch(const MolBundle &bundle, const ROMol &query,
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MatchVectType &matchVect, bool recursionPossible = true,
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bool useChirality = false,
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bool useQueryQueryMatches = false);
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//! \overload
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//! finds the first match in the bundle
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RDKIT_SUBSTRUCTMATCH_EXPORT bool SubstructMatch(const ROMol &bundle, const MolBundle &query,
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MatchVectType &matchVect, bool recursionPossible = true,
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bool useChirality = false,
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bool useQueryQueryMatches = false);
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//! \overload
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//! finds the first match in the bundle
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RDKIT_SUBSTRUCTMATCH_EXPORT bool SubstructMatch(const MolBundle &bundle, const MolBundle &query,
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MatchVectType &matchVect, bool recursionPossible = true,
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bool useChirality = false,
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bool useQueryQueryMatches = false);
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//! \overload
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//! finds all matches in the first molecule of the bundle that matches the query
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RDKIT_SUBSTRUCTMATCH_EXPORT unsigned int SubstructMatch(const MolBundle &mol, const ROMol &query,
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std::vector<MatchVectType> &matchVect,
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bool uniquify = true, bool recursionPossible = true,
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bool useChirality = false,
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bool useQueryQueryMatches = false,
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unsigned int maxMatches = 1000);
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//! \overload
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//! finds all matches in the first molecule of the bundle that matches
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RDKIT_SUBSTRUCTMATCH_EXPORT unsigned int SubstructMatch(const MolBundle &mol, const MolBundle &query,
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std::vector<MatchVectType> &matchVect,
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bool uniquify = true, bool recursionPossible = true,
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bool useChirality = false,
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bool useQueryQueryMatches = false,
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unsigned int maxMatches = 1000);
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//! \overload
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//! finds all matches against the first molecule of the query bundle that
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//! matches
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RDKIT_SUBSTRUCTMATCH_EXPORT unsigned int SubstructMatch(const ROMol &mol, const MolBundle &query,
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std::vector<MatchVectType> &matchVect,
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bool uniquify = true, bool recursionPossible = true,
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bool useChirality = false,
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bool useQueryQueryMatches = false,
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unsigned int maxMatches = 1000);
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}
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#endif
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