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19c9a3905c
* - generateDepictionMatching2DStructure can be used with referencePattern smaller than reference to only use part of a scaffold - adds generateDepictionMatching2DStructure overload to pass a matchVect instead of doing a substructure match - adds allowRGroups parameter to enable using a scaffold bearing R groups as reference * changes in response to review * added comments * fixes failing doctest * - reverted change committed accidentally - fixed get_sss_json for the case where R groups are not included in the match - added tests for the return value of generate_aligned_coords * Documented the value returned by GenerateDepictionMatching2DStructure (Python) * changes in response to review * - changes in response to review - fixed sortMatchesByDegreeOfCoreSubstitution that was not working - added Python wrappers for sortMatchesByDegreeOfCoreSubstitution and getMostSubstitutedCoreMatch - added C++ and Pyhon unit tests for the above * added missing variable initialization Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
45 lines
1.8 KiB
C++
45 lines
1.8 KiB
C++
//
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// Copyright (C) 2003-2019 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_SUBSTRUCT_UTILS_H
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#define RD_SUBSTRUCT_UTILS_H
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#include "SubstructMatch.h"
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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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RDKIT_SUBSTRUCTMATCH_EXPORT double toPrime(const MatchVectType& v);
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RDKIT_SUBSTRUCTMATCH_EXPORT void removeDuplicates(std::vector<MatchVectType>& v,
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unsigned int nAtoms);
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RDKIT_SUBSTRUCTMATCH_EXPORT bool atomCompat(const Atom* a1, const Atom* a2,
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const SubstructMatchParameters& ps);
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RDKIT_SUBSTRUCTMATCH_EXPORT bool chiralAtomCompat(const Atom* a1,
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const Atom* a2);
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RDKIT_SUBSTRUCTMATCH_EXPORT bool bondCompat(const Bond* b1, const Bond* b2,
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const SubstructMatchParameters& ps);
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//! This postprocesses the passed substruct matches and returns
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//! the match that has the largest number of non-hydrogen atoms
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//! in correspondence of terminal dummy atoms
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RDKIT_SUBSTRUCTMATCH_EXPORT const MatchVectType& getMostSubstitutedCoreMatch(
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const ROMol& mol, const ROMol& core,
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const std::vector<MatchVectType>& matches);
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//! This returns a copy of the passed substruct matches sorted by decreasing
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//! number of non-hydrogen atoms in correspondence of terminal dummy atoms
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RDKIT_SUBSTRUCTMATCH_EXPORT std::vector<MatchVectType>
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sortMatchesByDegreeOfCoreSubstitution(
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const ROMol& mol, const ROMol& core,
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const std::vector<MatchVectType>& matches);
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} // namespace RDKit
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#endif
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