RDKit
Open-source cheminformatics and machine learning.
RDKit::RGroupDecompositionParameters Struct Reference

#include <RGroupDecomp.h>

Public Member Functions

unsigned int autoGetLabels (const RWMol &)
 
bool prepareCore (RWMol &, const RWMol *alignCore)
 
 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 More...
 
bool removeAllHydrogenRGroups = true
 remove all user-defined rgroups that only have hydrogens More...
 
bool removeAllHydrogenRGroupsAndLabels = true
 
bool removeHydrogensPostMatch = true
 remove all hydrogens from the output molecules More...
 
bool allowNonTerminalRGroups = false
 allow labelled Rgroups of degree 2 or more More...
 
double timeout = -1.0
 timeout in seconds. <=0 indicates no timeout More...
 
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 75 of file RGroupDecomp.h.

Constructor & Destructor Documentation

◆ RGroupDecompositionParameters()

RDKit::RGroupDecompositionParameters::RGroupDecompositionParameters ( )
inline

Definition at line 125 of file RGroupDecomp.h.

References RDKit::SubstructMatchParameters::useChirality.

Member Function Documentation

◆ 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 80 of file RGroupDecomp.h.

◆ allowNonTerminalRGroups

bool RDKit::RGroupDecompositionParameters::allowNonTerminalRGroups = false

allow labelled Rgroups of degree 2 or more

Definition at line 93 of file RGroupDecomp.h.

◆ chunkSize

unsigned int RDKit::RGroupDecompositionParameters::chunkSize = 5

Definition at line 82 of file RGroupDecomp.h.

◆ gaMaximumOperations

int RDKit::RGroupDecompositionParameters::gaMaximumOperations = -1

Definition at line 108 of file RGroupDecomp.h.

◆ gaNumberOperationsWithoutImprovement

int RDKit::RGroupDecompositionParameters::gaNumberOperationsWithoutImprovement = -1

Definition at line 111 of file RGroupDecomp.h.

◆ gaNumberRuns

int RDKit::RGroupDecompositionParameters::gaNumberRuns = 1

Definition at line 115 of file RGroupDecomp.h.

Referenced by RDKit::RGroupDecompData::process().

◆ gaParallelRuns

bool RDKit::RGroupDecompositionParameters::gaParallelRuns = false

Definition at line 120 of file RGroupDecomp.h.

◆ gaPopulationSize

int RDKit::RGroupDecompositionParameters::gaPopulationSize = -1

Definition at line 106 of file RGroupDecomp.h.

◆ gaRandomSeed

int RDKit::RGroupDecompositionParameters::gaRandomSeed = -1

Definition at line 113 of file RGroupDecomp.h.

◆ labels

unsigned int RDKit::RGroupDecompositionParameters::labels = AutoDetect

Definition at line 76 of file RGroupDecomp.h.

◆ matchingStrategy

unsigned int RDKit::RGroupDecompositionParameters::matchingStrategy = GreedyChunks

◆ onlyMatchAtRGroups

bool RDKit::RGroupDecompositionParameters::onlyMatchAtRGroups = false

only allow rgroup decomposition at the specified rgroups

Definition at line 84 of file RGroupDecomp.h.

Referenced by RDKit::RGroupDecompData::relabel().

◆ removeAllHydrogenRGroups

bool RDKit::RGroupDecompositionParameters::removeAllHydrogenRGroups = true

remove all user-defined rgroups that only have hydrogens

Definition at line 86 of file RGroupDecomp.h.

Referenced by RDKit::RGroupDecompData::GetCurrentBestPermutation().

◆ 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 89 of file RGroupDecomp.h.

Referenced by RDKit::RGroupDecompData::GetCurrentBestPermutation().

◆ removeHydrogensPostMatch

bool RDKit::RGroupDecompositionParameters::removeHydrogensPostMatch = true

remove all hydrogens from the output molecules

Definition at line 91 of file RGroupDecomp.h.

Referenced by RDKit::RGroupDecompData::relabelRGroup().

◆ rgroupLabelling

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

Definition at line 79 of file RGroupDecomp.h.

Referenced by RDKit::RGroupDecompData::setRlabel().

◆ scoreMethod

unsigned int RDKit::RGroupDecompositionParameters::scoreMethod = Match

◆ substructmatchParams

SubstructMatchParameters RDKit::RGroupDecompositionParameters::substructmatchParams

Definition at line 123 of file RGroupDecomp.h.

◆ timeout

double RDKit::RGroupDecompositionParameters::timeout = -1.0

timeout in seconds. <=0 indicates no timeout

Definition at line 95 of file RGroupDecomp.h.

Referenced by RDKit::RGroupDecompData::process().


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