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>
 
namespace RDKit {
 
typedef enum {
  IsotopeLabels = 0x01,
  AtomMapLabels = 0x02,
  AtomIndexLabels = 0x04,
  RelabelDuplicateLabels = 0x08,
  MDLRGroupLabels = 0x10,
  DummyAtomLabels = 0x20,  // These are rgroups but will get relabelled
  AutoDetect = 0xFF,
} RGroupLabels;
 
typedef enum {
  Greedy = 0x01,
  GreedyChunks = 0x02,
  Exhaustive = 0x04,  // not really useful for large sets
  NoSymmetrization = 0x08,
  GA = 0x10,
} RGroupMatching;
 
typedef enum {
  AtomMap = 0x01,
  Isotope = 0x02,
  MDLRGroup = 0x04,
} RGroupLabelling;
 
typedef enum {
  // DEPRECATED, remove the following line in release 2021.03
  None = 0x0,
  NoAlignment = 0x0,
  MCS = 0x01,
} RGroupCoreAlignment;
 
typedef enum {
  Match = 0x1,
  FingerprintVariance = 0x4,
} RGroupScore;
 
struct RDKIT_RGROUPDECOMPOSITION_EXPORT RGroupDecompositionParameters {
  unsigned int labels = AutoDetect;
  unsigned int matchingStrategy = GreedyChunks;
  unsigned int scoreMethod = Match;
  unsigned int rgroupLabelling = AtomMap | MDLRGroup;
  unsigned int alignment = 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;
 
  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