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f43677b978
as conjugated like their oxygen analogs
- fixed an issue with large numbers of resonance structures exceeding
the unsigned int allowance
- implemented the uniquify feature properly
- uniquify now defaults to false when using the ResonanceMolSupplier-
enabled SubstructMatch() version
- the concept of 'laziness' is now clearer
- TODO:
* remove some debugging info
* move classes from .h to .cpp
* SWIG wrappers
* improve resonance structure sorting for degenerate resonance
structures
I will do all of the above ASAP
128 lines
5.3 KiB
C++
128 lines
5.3 KiB
C++
//
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// Copyright (C) 2001-2015 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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#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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//! \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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bool SubstructMatch(const ROMol &mol,const ROMol &query,
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MatchVectType &matchVect,
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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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//! 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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bool SubstructMatch(const ResonanceMolSupplier &resMolSuppl,
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const ROMol &query,
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MatchVectType &matchVect,
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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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//! 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 very
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easy to end up with a combinatorial explosion in the 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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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 very
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easy to end up with a combinatorial explosion in the 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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unsigned int SubstructMatch(const ResonanceMolSupplier &resMolSuppl,
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const ROMol &query,
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std::vector< MatchVectType > &matchVect,
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bool uniquify=false, 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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