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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;
// 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
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