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a5347e725e
* Allow the same core to match more than once in a molecule. * Update annotation. * Changes after review. --------- Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
118 lines
4.4 KiB
C++
118 lines
4.4 KiB
C++
//
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// Copyright (c) 2017-2023, Novartis Institutes for BioMedical Research Inc.
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// and other RDKit contributors
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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 RDKIT_RGROUPDECOMPPARAMS_H
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#define RDKIT_RGROUPDECOMPPARAMS_H
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#include "../RDKitBase.h"
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#include <GraphMol/Substruct/SubstructMatch.h>
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#include <RDGeneral/BetterEnums.h>
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namespace RDKit {
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BETTER_ENUM(
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RGroupLabels, unsigned int, IsotopeLabels = 0x01, AtomMapLabels = 0x02,
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AtomIndexLabels = 0x04, RelabelDuplicateLabels = 0x08,
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MDLRGroupLabels = 0x10,
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DummyAtomLabels = 0x20, // These are rgroups but will get relabelled
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AutoDetect = 0xFF);
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BETTER_ENUM(RGroupMatching, unsigned int, Greedy = 0x01, GreedyChunks = 0x02,
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Exhaustive = 0x04, // not really useful for large sets
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NoSymmetrization = 0x08, GA = 0x10);
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BETTER_ENUM(RGroupLabelling, unsigned int, AtomMap = 0x01, Isotope = 0x02,
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MDLRGroup = 0x04);
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BETTER_ENUM(RGroupCoreAlignment, unsigned int, NoAlignment = 0x0, MCS = 0x01);
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BETTER_ENUM(RGroupScore, unsigned int, Match = 0x1, FingerprintVariance = 0x4);
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struct RDKIT_RGROUPDECOMPOSITION_EXPORT RGroupDecompositionParameters {
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unsigned int labels = RGroupLabels::AutoDetect;
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unsigned int matchingStrategy = RGroupMatching::GreedyChunks;
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unsigned int scoreMethod = RGroupScore::Match;
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unsigned int rgroupLabelling =
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RGroupLabelling::AtomMap | RGroupLabelling::MDLRGroup;
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unsigned int alignment = RGroupCoreAlignment::MCS;
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unsigned int chunkSize = 5;
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//! only allow rgroup decomposition at the specified rgroups
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bool onlyMatchAtRGroups = false;
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//! remove all user-defined rgroups that only have hydrogens
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bool removeAllHydrogenRGroups = true;
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//! remove all user-defined rgroups that only have hydrogens,
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//! and also remove the corresponding labels from the core
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bool removeAllHydrogenRGroupsAndLabels = true;
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//! remove all hydrogens from the output molecules
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bool removeHydrogensPostMatch = true;
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//! allow labelled Rgroups of degree 2 or more
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bool allowNonTerminalRGroups = false;
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//! unlabelled core atoms can have multiple rgroups
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bool allowMultipleRGroupsOnUnlabelled = false;
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//! Permit a core to match more than once in the same molecule if the sets of
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// matched atoms are not equal.
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bool allowMultipleCoresInSameMol = false;
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// extended query settings for core matching
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bool doTautomers = false;
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bool doEnumeration = false;
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//! include target molecule (featuring explicit hydrogens where they
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//! coincide with R groups in the core) into RGD results,
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//! and set _rgroupTargetAtoms and _rgroupTargetBonds properties
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//! on R groups and core as vectors of target atom and bond indices
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//! to enable highlighting for SAR analysis (see
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//! https://greglandrum.github.io/rdkit-blog/posts/2021-08-07-rgd-and-highlighting.html)
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bool includeTargetMolInResults = false;
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double timeout = -1.0; ///< timeout in seconds. <=0 indicates no timeout
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// Determine how to assign the rgroup labels from the given core
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unsigned int autoGetLabels(const RWMol &);
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// Prepare the core for substructure searching and rgroup assignment
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bool prepareCore(RWMol &, const RWMol *alignCore);
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// Add r groups to unlabelled atoms if allowMultipleRGroupsOnUnlabelled is set
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void addDummyAtomsToUnlabelledCoreAtoms(RWMol &core);
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// Parameters specific to GA
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// GA population size or -1 to use best guess
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int gaPopulationSize = -1;
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// GA maximum number of operations or -1 to use best guess
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int gaMaximumOperations = -1;
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// GA number of operations permitted without improvement before exiting (-1
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// for best guess)
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int gaNumberOperationsWithoutImprovement = -1;
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// GA random number seed (-1 for default, -2 for random seed)
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int gaRandomSeed = -1;
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// Number of runs
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int gaNumberRuns = 1;
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// Sequential or parallel runs?
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#ifdef RDK_BUILD_THREADSAFE_SSS
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bool gaParallelRuns = true;
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#else
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bool gaParallelRuns = false;
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#endif
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// Controls the way substructure matching with the core is done
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SubstructMatchParameters substructmatchParams;
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RGroupDecompositionParameters() { substructmatchParams.useChirality = true; }
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private:
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int indexOffset{-1};
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void checkNonTerminal(const Atom &atom) const;
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};
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} // namespace RDKit
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#endif // RDKIT_RGROUPDECOMPPARAMS_H
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