#include <RGroupDecomp.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 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...

bool	allowMultipleRGroupsOnUnlabelled = false

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 130 of file RGroupDecomp.h.

References RDKit::SubstructMatchParameters::useChirality.

Member Function Documentation

◆ addDummyAtomsToUnlabelledCoreAtoms()

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

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

◆ autoGetLabels()

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

◆ prepareCore()

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

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

Member Data Documentation

◆ alignment

unsigned int RDKit::RGroupDecompositionParameters::alignment = MCS

Definition at line 80 of file RGroupDecomp.h.

◆ allowMultipleRGroupsOnUnlabelled

bool RDKit::RGroupDecompositionParameters::allowMultipleRGroupsOnUnlabelled = false

Definition at line 95 of file RGroupDecomp.h.

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

◆ 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 113 of file RGroupDecomp.h.

◆ gaNumberOperationsWithoutImprovement

int RDKit::RGroupDecompositionParameters::gaNumberOperationsWithoutImprovement = -1

Definition at line 116 of file RGroupDecomp.h.

◆ gaNumberRuns

int RDKit::RGroupDecompositionParameters::gaNumberRuns = 1

Definition at line 120 of file RGroupDecomp.h.

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

◆ gaParallelRuns

bool RDKit::RGroupDecompositionParameters::gaParallelRuns = false

Definition at line 125 of file RGroupDecomp.h.

◆ gaPopulationSize

int RDKit::RGroupDecompositionParameters::gaPopulationSize = -1

Definition at line 111 of file RGroupDecomp.h.

◆ gaRandomSeed

int RDKit::RGroupDecompositionParameters::gaRandomSeed = -1

Definition at line 118 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

Definition at line 77 of file RGroupDecomp.h.

Referenced by RDKit::RGroupDecompData::process(), and RDKit::RGroupDecompData::prune().

◆ 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::getRlabel(), and RDKit::RGroupDecompData::setRlabel().

◆ scoreMethod

unsigned int RDKit::RGroupDecompositionParameters::scoreMethod = Match

Definition at line 78 of file RGroupDecomp.h.

Referenced by RDKit::RGroupDecompData::process(), RDKit::RGroupDecompData::prune(), RDKit::RGroupDecompData::score(), and RDKit::RGroupDecompData::scoreFromPrunedData().

◆ substructmatchParams

SubstructMatchParameters RDKit::RGroupDecompositionParameters::substructmatchParams

Definition at line 128 of file RGroupDecomp.h.

◆ timeout

double RDKit::RGroupDecompositionParameters::timeout = -1.0

timeout in seconds. <=0 indicates no timeout

Definition at line 97 of file RGroupDecomp.h.