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RGroupDecompParams.h
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//
// Copyright (c) 2017-2023, Novartis Institutes for BioMedical Research Inc.
// and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#ifndef RDKIT_RGROUPDECOMPPARAMS_H
#define RDKIT_RGROUPDECOMPPARAMS_H
#include "../RDKitBase.h"
#include <GraphMol/Substruct/SubstructMatch.h>
#include <RDGeneral/BetterEnums.h>
namespace RDKit {
BETTER_ENUM(
RGroupLabels, unsigned int, IsotopeLabels = 0x01, AtomMapLabels = 0x02,
AtomIndexLabels = 0x04, RelabelDuplicateLabels = 0x08,
MDLRGroupLabels = 0x10,
DummyAtomLabels = 0x20, // These are rgroups but will get relabelled
AutoDetect = 0xFF);
BETTER_ENUM(RGroupMatching, unsigned int, Greedy = 0x01, GreedyChunks = 0x02,
Exhaustive = 0x04, // not really useful for large sets
NoSymmetrization = 0x08, GA = 0x10);
BETTER_ENUM(RGroupLabelling, unsigned int, AtomMap = 0x01, Isotope = 0x02,
MDLRGroup = 0x04);
BETTER_ENUM(RGroupCoreAlignment, unsigned int, NoAlignment = 0x0, MCS = 0x01);
BETTER_ENUM(RGroupScore, unsigned int, Match = 0x1, FingerprintVariance = 0x4);
struct RDKIT_RGROUPDECOMPOSITION_EXPORT RGroupDecompositionParameters {
unsigned int labels = RGroupLabels::AutoDetect;
unsigned int matchingStrategy = RGroupMatching::GreedyChunks;
unsigned int scoreMethod = RGroupScore::Match;
unsigned int rgroupLabelling =
RGroupLabelling::AtomMap | RGroupLabelling::MDLRGroup;
unsigned int alignment = RGroupCoreAlignment::MCS;
unsigned int chunkSize = 5;
//! only allow rgroup decomposition at the specified rgroups
bool onlyMatchAtRGroups = false;
//! remove all user-defined rgroups that only have hydrogens
bool removeAllHydrogenRGroups = true;
//! remove all user-defined rgroups that only have hydrogens,
//! and also remove the corresponding labels from the core
bool removeAllHydrogenRGroupsAndLabels = true;
//! remove all hydrogens from the output molecules
bool removeHydrogensPostMatch = true;
//! allow labelled Rgroups of degree 2 or more
bool allowNonTerminalRGroups = false;
//! unlabelled core atoms can have multiple rgroups
bool allowMultipleRGroupsOnUnlabelled = false;
//! Permit a core to match more than once in the same molecule if the sets of
// matched atoms are not equal.
bool allowMultipleCoresInSameMol = false;
// extended query settings for core matching
bool doTautomers = false;
bool doEnumeration = false;
//! include target molecule (featuring explicit hydrogens where they
//! coincide with R groups in the core) into RGD results,
//! and set _rgroupTargetAtoms and _rgroupTargetBonds properties
//! on R groups and core as vectors of target atom and bond indices
//! to enable highlighting for SAR analysis (see
//! https://greglandrum.github.io/rdkit-blog/posts/2021-08-07-rgd-and-highlighting.html)
bool includeTargetMolInResults = false;
double timeout = -1.0; ///< timeout in seconds. <=0 indicates no timeout
// Determine how to assign the rgroup labels from the given core
unsigned int autoGetLabels(const RWMol &);
// Prepare the core for substructure searching and rgroup assignment
bool prepareCore(RWMol &, const RWMol *alignCore);
// Add r groups to unlabelled atoms if allowMultipleRGroupsOnUnlabelled is set
void addDummyAtomsToUnlabelledCoreAtoms(RWMol &core);
// Parameters specific to GA
// GA population size or -1 to use best guess
int gaPopulationSize = -1;
// GA maximum number of operations or -1 to use best guess
int gaMaximumOperations = -1;
// GA number of operations permitted without improvement before exiting (-1
// for best guess)
int gaNumberOperationsWithoutImprovement = -1;
// GA random number seed (-1 for default, -2 for random seed)
int gaRandomSeed = -1;
// Number of runs
int gaNumberRuns = 1;
// Sequential or parallel runs?
#ifdef RDK_BUILD_THREADSAFE_SSS
bool gaParallelRuns = true;
#else
bool gaParallelRuns = false;
#endif
// Controls the way substructure matching with the core is done
SubstructMatchParameters substructmatchParams;
RGroupDecompositionParameters() { substructmatchParams.useChirality = true; }
private:
int indexOffset{-1};
void checkNonTerminal(const Atom &atom) const;
};
} // namespace RDKit
#endif // RDKIT_RGROUPDECOMPPARAMS_H
BetterEnums.h
BETTER_ENUM
#define BETTER_ENUM(Enum, Underlying,...)
Definition BetterEnums.h:17
RDKitBase.h
pulls in the core RDKit functionality
SubstructMatch.h
RDKit::RWMol
RWMol is a molecule class that is intended to be edited.
Definition RWMol.h:32
RDKIT_RGROUPDECOMPOSITION_EXPORT
#define RDKIT_RGROUPDECOMPOSITION_EXPORT
Definition export.h:481
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::RGroupDecompositionParameters::removeAllHydrogenRGroupsAndLabels
bool removeAllHydrogenRGroupsAndLabels
Definition RGroupDecompParams.h:54
RDKit::RGroupDecompositionParameters::gaNumberRuns
int gaNumberRuns
Definition RGroupDecompParams.h:98
RDKit::RGroupDecompositionParameters::allowNonTerminalRGroups
bool allowNonTerminalRGroups
allow labelled Rgroups of degree 2 or more
Definition RGroupDecompParams.h:58
RDKit::RGroupDecompositionParameters::gaPopulationSize
int gaPopulationSize
Definition RGroupDecompParams.h:89
RDKit::RGroupDecompositionParameters::matchingStrategy
unsigned int matchingStrategy
Definition RGroupDecompParams.h:41
RDKit::RGroupDecompositionParameters::gaRandomSeed
int gaRandomSeed
Definition RGroupDecompParams.h:96
RDKit::RGroupDecompositionParameters::allowMultipleRGroupsOnUnlabelled
bool allowMultipleRGroupsOnUnlabelled
unlabelled core atoms can have multiple rgroups
Definition RGroupDecompParams.h:60
RDKit::RGroupDecompositionParameters::addDummyAtomsToUnlabelledCoreAtoms
void addDummyAtomsToUnlabelledCoreAtoms(RWMol &core)
RDKit::RGroupDecompositionParameters::labels
unsigned int labels
Definition RGroupDecompParams.h:40
RDKit::RGroupDecompositionParameters::onlyMatchAtRGroups
bool onlyMatchAtRGroups
only allow rgroup decomposition at the specified rgroups
Definition RGroupDecompParams.h:49
RDKit::RGroupDecompositionParameters::removeAllHydrogenRGroups
bool removeAllHydrogenRGroups
remove all user-defined rgroups that only have hydrogens
Definition RGroupDecompParams.h:51
RDKit::RGroupDecompositionParameters::gaMaximumOperations
int gaMaximumOperations
Definition RGroupDecompParams.h:91
RDKit::RGroupDecompositionParameters::alignment
unsigned int alignment
Definition RGroupDecompParams.h:45
RDKit::RGroupDecompositionParameters::doEnumeration
bool doEnumeration
Definition RGroupDecompParams.h:66
RDKit::RGroupDecompositionParameters::autoGetLabels
unsigned int autoGetLabels(const RWMol &)
RDKit::RGroupDecompositionParameters::timeout
double timeout
timeout in seconds. <=0 indicates no timeout
Definition RGroupDecompParams.h:75
RDKit::RGroupDecompositionParameters::removeHydrogensPostMatch
bool removeHydrogensPostMatch
remove all hydrogens from the output molecules
Definition RGroupDecompParams.h:56
RDKit::RGroupDecompositionParameters::chunkSize
unsigned int chunkSize
Definition RGroupDecompParams.h:47
RDKit::RGroupDecompositionParameters::includeTargetMolInResults
bool includeTargetMolInResults
Definition RGroupDecompParams.h:73
RDKit::RGroupDecompositionParameters::gaNumberOperationsWithoutImprovement
int gaNumberOperationsWithoutImprovement
Definition RGroupDecompParams.h:94
RDKit::RGroupDecompositionParameters::allowMultipleCoresInSameMol
bool allowMultipleCoresInSameMol
Permit a core to match more than once in the same molecule if the sets of.
Definition RGroupDecompParams.h:63
RDKit::RGroupDecompositionParameters::scoreMethod
unsigned int scoreMethod
Definition RGroupDecompParams.h:42
RDKit::RGroupDecompositionParameters::rgroupLabelling
unsigned int rgroupLabelling
Definition RGroupDecompParams.h:43
RDKit::RGroupDecompositionParameters::doTautomers
bool doTautomers
Definition RGroupDecompParams.h:65
RDKit::RGroupDecompositionParameters::prepareCore
bool prepareCore(RWMol &, const RWMol *alignCore)
RDKit::RGroupDecompositionParameters::RGroupDecompositionParameters
RGroupDecompositionParameters()
Definition RGroupDecompParams.h:108
RDKit::RGroupDecompositionParameters::substructmatchParams
SubstructMatchParameters substructmatchParams
Definition RGroupDecompParams.h:106
RDKit::RGroupDecompositionParameters::gaParallelRuns
bool gaParallelRuns
Definition RGroupDecompParams.h:103
RDKit::SubstructMatchParameters
Definition SubstructMatch.h:42