Contains classes and functions related to the GRAIL method [GRAIL, GRADE]. More...

Classes
class	AtomDensityGridCalculator
	Calculator that fills a spatial grid with combined per-atom density contributions. More...

class	AttributedGridProperty
	Provides keys for built-in Grid.AttributedGrid properties. More...

class	AttributedGridPropertyDefault
	Provides default values for built-in Grid.AttributedGrid properties. More...

class	BindingAffinityCalculator
	Predicts the binding affinity of a ligand pose from its GRAIL descriptor vector. More...

class	BuriednessGridCalculator
	Calculator that fills a spatial grid with per-cell buriedness scores derived from GRAIL.BuriednessScore. More...

class	BuriednessScore
	Functor for the calculation of the buriedness of a 3D query position with respect to the surrounding atoms. More...

class	DoubleVector3DFeatureFunctor

class	FeatureInteractionScoreGridCalculator
	Calculator that fills a spatial grid with per-cell feature-interaction scores against a set of target pharmacophore features. More...

class	FeatureType
	Provides constants for the specification of GRAIL-specific extended pharmacophore feature types that refine H-bond donor and acceptor categories by the chemical environment (atom element + SYBYL-like type) of the participating heavy atom. More...

class	GRAILDataSetGenerator
	Generator that pre-computes the per-cell interaction-score grids and the atom-density grid used by GRAIL scoring of ligand poses against a target environment. More...

class	GRAILDescriptorCalculator
	Calculation of GRAIL descriptors for protein-ligand complexes. More...

class	GRAILXDescriptorCalculator
	Calculation of the extended GRAIL-X descriptor for protein-ligand complexes. More...

class	GeneralizedBellAtomDensity
	Functor for the evaluation of the generalized-bell atom density contribution of an atom at a query position. More...

class	VoidPharmacophoreFunctor

Functions
None	setFeatureType (Grid.AttributedGrid grid, int type)
	Sets the value of the GRAIL.AttributedGridProperty.FEATURE_TYPE property of the grid grid. More...

bool	hasFeatureType (Grid.AttributedGrid grid)
	Tells whether grid carries an explicit GRAIL.AttributedGridProperty.FEATURE_TYPE property. More...

int	getFeatureType (Grid.AttributedGrid grid)
	Returns the value of the GRAIL.AttributedGridProperty.FEATURE_TYPE property of the grid grid. More...

None	clearFeatureType (Grid.AttributedGrid grid)
	Clears the value of the GRAIL.AttributedGridProperty.FEATURE_TYPE property of the grid grid. More...

None	setTargetFeatureType (Grid.AttributedGrid grid, int type)
	Sets the value of the GRAIL.AttributedGridProperty.TARGET_FEATURE_TYPE property of the grid grid. More...

bool	hasTargetFeatureType (Grid.AttributedGrid grid)
	Tells whether grid carries an explicit GRAIL.AttributedGridProperty.TARGET_FEATURE_TYPE property. More...

int	getTargetFeatureType (Grid.AttributedGrid grid)
	Returns the value of the GRAIL.AttributedGridProperty.TARGET_FEATURE_TYPE property of the grid grid. More...

None	clearTargetFeatureType (Grid.AttributedGrid grid)
	Clears the value of the GRAIL.AttributedGridProperty.TARGET_FEATURE_TYPE property of the grid grid. More...

int	perceiveExtendedType (Pharm.Feature feature, bool ligand)

None	prepareForGRAILDescriptorCalculation (Chem.Molecule mol, bool std_prot_state=False)
	Prepares the molecule mol for GRAIL descriptor calculation. More...

Detailed Description

Contains classes and functions related to the GRAIL method [GRAIL, GRADE].

Function Documentation

◆ setFeatureType()

None CDPL.GRAIL.setFeatureType	(	Grid.AttributedGrid	grid,
		int	type
	)

Sets the value of the GRAIL.AttributedGridProperty.FEATURE_TYPE property of the grid grid.

Parameters

grid	The grid for which to set the property value.
type	The new feature type value.

◆ hasFeatureType()

bool CDPL.GRAIL.hasFeatureType ( Grid.AttributedGrid grid )

Tells whether grid carries an explicit GRAIL.AttributedGridProperty.FEATURE_TYPE property.

Parameters

grid	The grid for which to query the property value.

Returns: True if the property is set, and False otherwise.

◆ getFeatureType()

int CDPL.GRAIL.getFeatureType ( Grid.AttributedGrid grid )

Returns the value of the GRAIL.AttributedGridProperty.FEATURE_TYPE property of the grid grid.

Parameters

grid	The grid for which to return the property value.

Returns: The feature type value.

◆ clearFeatureType()

None CDPL.GRAIL.clearFeatureType ( Grid.AttributedGrid grid )

Clears the value of the GRAIL.AttributedGridProperty.FEATURE_TYPE property of the grid grid.

Parameters

grid	The grid for which to clear the property value.

◆ setTargetFeatureType()

None CDPL.GRAIL.setTargetFeatureType	(	Grid.AttributedGrid	grid,
		int	type
	)

Sets the value of the GRAIL.AttributedGridProperty.TARGET_FEATURE_TYPE property of the grid grid.

Parameters

grid	The grid for which to set the property value.
type	The new target feature type value.

◆ hasTargetFeatureType()

bool CDPL.GRAIL.hasTargetFeatureType ( Grid.AttributedGrid grid )

Tells whether grid carries an explicit GRAIL.AttributedGridProperty.TARGET_FEATURE_TYPE property.

Parameters

grid	The grid for which to query the property value.

Returns: True if the property is set, and False otherwise.

◆ getTargetFeatureType()

int CDPL.GRAIL.getTargetFeatureType ( Grid.AttributedGrid grid )

Returns the value of the GRAIL.AttributedGridProperty.TARGET_FEATURE_TYPE property of the grid grid.

Parameters

grid	The grid for which to return the property value.

Returns: The target feature type value.

◆ clearTargetFeatureType()

None CDPL.GRAIL.clearTargetFeatureType ( Grid.AttributedGrid grid )

Clears the value of the GRAIL.AttributedGridProperty.TARGET_FEATURE_TYPE property of the grid grid.

Parameters

grid	The grid for which to clear the property value.

◆ perceiveExtendedType()

int CDPL.GRAIL.perceiveExtendedType	(	Pharm.Feature	feature,
		bool	ligand
	)

Parameters

feature
ligand

Returns

◆ prepareForGRAILDescriptorCalculation()

None CDPL.GRAIL.prepareForGRAILDescriptorCalculation	(	Chem.Molecule	mol,
		bool	std_prot_state = `False`
	)

Prepares the molecule mol for GRAIL descriptor calculation.

Performs all molecular structure preprocessing steps (e.g. ring perception, atom typing, hydrogen handling) required by the descriptor calculation procedure (implemented by GRAIL.GRAILDescriptorCalculator).

Parameters

mol	The molecule to prepare. The molecule is modified in place.
std_prot_state	If `True`, the standard protonation state of the molecule is assigned prior to the GRAIL-specific preprocessing.

Classes

Functions

Detailed Description

Function Documentation

◆ setFeatureType()

◆ hasFeatureType()

◆ getFeatureType()

◆ clearFeatureType()

◆ setTargetFeatureType()

◆ hasTargetFeatureType()

◆ getTargetFeatureType()

◆ clearTargetFeatureType()

◆ perceiveExtendedType()

◆ prepareForGRAILDescriptorCalculation()