RDKit
Open-source cheminformatics and machine learning.
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Public Member Functions | Public Attributes | List of all members
RDKit::RGroupDecompositionParameters Struct Reference

#include <RGroupDecompParams.h>

Public Member Functions

unsigned int autoGetLabels (const RWMol &)
 
bool prepareCore (RWMol &, const RWMol *alignCore)
 
void addDummyAtomsToUnlabelledCoreAtoms (RWMol &core)
 
 RGroupDecompositionParameters ()
 

Public Attributes

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
 
bool onlyMatchAtRGroups = false
 only allow rgroup decomposition at the specified rgroups
 
bool removeAllHydrogenRGroups = true
 remove all user-defined rgroups that only have hydrogens
 
bool removeAllHydrogenRGroupsAndLabels = true
 
bool removeHydrogensPostMatch = true
 remove all hydrogens from the output molecules
 
bool allowNonTerminalRGroups = false
 allow labelled Rgroups of degree 2 or more
 
bool allowMultipleRGroupsOnUnlabelled = false
 unlabelled core atoms can have multiple rgroups
 
bool doTautomers = false
 
bool doEnumeration = false
 
bool includeTargetMolInResults = false
 
double timeout = -1.0
 timeout in seconds. <=0 indicates no timeout
 
int gaPopulationSize = -1
 
int gaMaximumOperations = -1
 
int gaNumberOperationsWithoutImprovement = -1
 
int gaRandomSeed = -1
 
int gaNumberRuns = 1
 
bool gaParallelRuns = false
 
SubstructMatchParameters substructmatchParams
 

Detailed Description

Definition at line 64 of file RGroupDecompParams.h.

Constructor & Destructor Documentation

◆ RGroupDecompositionParameters()

RDKit::RGroupDecompositionParameters::RGroupDecompositionParameters ( )
inline

Definition at line 129 of file RGroupDecompParams.h.

References RDKit::SubstructMatchParameters::useChirality.

Member Function Documentation

◆ addDummyAtomsToUnlabelledCoreAtoms()

void RDKit::RGroupDecompositionParameters::addDummyAtomsToUnlabelledCoreAtoms ( RWMol &  core)

◆ autoGetLabels()

unsigned int RDKit::RGroupDecompositionParameters::autoGetLabels ( const RWMol &  )

◆ prepareCore()

bool RDKit::RGroupDecompositionParameters::prepareCore ( RWMol &  ,
const RWMol *  alignCore 
)

Member Data Documentation

◆ alignment

unsigned int RDKit::RGroupDecompositionParameters::alignment = MCS

Definition at line 69 of file RGroupDecompParams.h.

◆ allowMultipleRGroupsOnUnlabelled

bool RDKit::RGroupDecompositionParameters::allowMultipleRGroupsOnUnlabelled = false

unlabelled core atoms can have multiple rgroups

Definition at line 84 of file RGroupDecompParams.h.

◆ allowNonTerminalRGroups

bool RDKit::RGroupDecompositionParameters::allowNonTerminalRGroups = false

allow labelled Rgroups of degree 2 or more

Definition at line 82 of file RGroupDecompParams.h.

◆ chunkSize

unsigned int RDKit::RGroupDecompositionParameters::chunkSize = 5

Definition at line 71 of file RGroupDecompParams.h.

◆ doEnumeration

bool RDKit::RGroupDecompositionParameters::doEnumeration = false

Definition at line 87 of file RGroupDecompParams.h.

◆ doTautomers

bool RDKit::RGroupDecompositionParameters::doTautomers = false

Definition at line 86 of file RGroupDecompParams.h.

◆ gaMaximumOperations

int RDKit::RGroupDecompositionParameters::gaMaximumOperations = -1

Definition at line 112 of file RGroupDecompParams.h.

◆ gaNumberOperationsWithoutImprovement

int RDKit::RGroupDecompositionParameters::gaNumberOperationsWithoutImprovement = -1

Definition at line 115 of file RGroupDecompParams.h.

◆ gaNumberRuns

int RDKit::RGroupDecompositionParameters::gaNumberRuns = 1

Definition at line 119 of file RGroupDecompParams.h.

◆ gaParallelRuns

bool RDKit::RGroupDecompositionParameters::gaParallelRuns = false

Definition at line 124 of file RGroupDecompParams.h.

◆ gaPopulationSize

int RDKit::RGroupDecompositionParameters::gaPopulationSize = -1

Definition at line 110 of file RGroupDecompParams.h.

◆ gaRandomSeed

int RDKit::RGroupDecompositionParameters::gaRandomSeed = -1

Definition at line 117 of file RGroupDecompParams.h.

◆ includeTargetMolInResults

bool RDKit::RGroupDecompositionParameters::includeTargetMolInResults = 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)

Definition at line 94 of file RGroupDecompParams.h.

◆ labels

unsigned int RDKit::RGroupDecompositionParameters::labels = AutoDetect

Definition at line 65 of file RGroupDecompParams.h.

◆ matchingStrategy

unsigned int RDKit::RGroupDecompositionParameters::matchingStrategy = GreedyChunks

Definition at line 66 of file RGroupDecompParams.h.

◆ onlyMatchAtRGroups

bool RDKit::RGroupDecompositionParameters::onlyMatchAtRGroups = false

only allow rgroup decomposition at the specified rgroups

Definition at line 73 of file RGroupDecompParams.h.

◆ removeAllHydrogenRGroups

bool RDKit::RGroupDecompositionParameters::removeAllHydrogenRGroups = true

remove all user-defined rgroups that only have hydrogens

Definition at line 75 of file RGroupDecompParams.h.

◆ removeAllHydrogenRGroupsAndLabels

bool RDKit::RGroupDecompositionParameters::removeAllHydrogenRGroupsAndLabels = true

remove all user-defined rgroups that only have hydrogens, and also remove the corresponding labels from the core

Definition at line 78 of file RGroupDecompParams.h.

◆ removeHydrogensPostMatch

bool RDKit::RGroupDecompositionParameters::removeHydrogensPostMatch = true

remove all hydrogens from the output molecules

Definition at line 80 of file RGroupDecompParams.h.

◆ rgroupLabelling

unsigned int RDKit::RGroupDecompositionParameters::rgroupLabelling = AtomMap | MDLRGroup

Definition at line 68 of file RGroupDecompParams.h.

◆ scoreMethod

unsigned int RDKit::RGroupDecompositionParameters::scoreMethod = Match

Definition at line 67 of file RGroupDecompParams.h.

◆ substructmatchParams

SubstructMatchParameters RDKit::RGroupDecompositionParameters::substructmatchParams

Definition at line 127 of file RGroupDecompParams.h.

◆ timeout

double RDKit::RGroupDecompositionParameters::timeout = -1.0

timeout in seconds. <=0 indicates no timeout

Definition at line 96 of file RGroupDecompParams.h.

The documentation for this struct was generated from the following file: