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...

Inheritance diagram for CDPL.GRAIL.GRAILDataSetGenerator:

Public Member Functions
None	__init__ ()
	Constructs the `GRAILDataSetGenerator` instance.

None	__init__ (GRAILDataSetGenerator gen)
	Initializes a copy of the `GRAILDataSetGenerator` instance gen. More...

int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...

GRAILDataSetGenerator	assign (GRAILDataSetGenerator gen)
	Replaces the current state of self with a copy of the state of the `GRAILDataSetGenerator` instance gen. More...

None	setScoringFunction (int ftr_type, int tgt_ftr_type, DoubleVector3DFeatureFunctor func)
	Sets the scoring function for the given (ligand feature type, target feature type) pair. More...

None	removeScoringFunction (int ftr_type, int tgt_ftr_type)
	Removes the scoring function configured for the given (ligand feature type, target feature type) pair. More...

DoubleVector3DFeatureFunctor	getScoringFunction (int ftr_type, int tgt_ftr_type)
	Returns the scoring function configured for the given (ligand feature type, target feature type) pair. More...

None	setGridName (int ftr_type, int tgt_ftr_type, str name)
	Sets the grid name associated with the given (ligand feature type, target feature type) pair. More...

None	removeGridName (int ftr_type, int tgt_ftr_type)
	Removes the grid name associated with the given (ligand feature type, target feature type) pair. More...

str	getGridName (int ftr_type, int tgt_ftr_type)
	Returns the grid name associated with the given (ligand feature type, target feature type) pair. More...

None	enableInteraction (int ftr_type, int tgt_ftr_type, bool enable)
	Enables or disables interaction-grid generation for the given (ligand feature type, target feature type) pair. More...

bool	isInteractionEnabled (int ftr_type, int tgt_ftr_type)
	Tells whether interaction-grid generation is enabled for the given (ligand feature type, target feature type) pair. More...

bool	clearEnabledInteractions (int arg2, int self)

None	setScoreCombinationFunction (Math.DoubleDVectorFunctor func)
	Sets the function used to combine per-feature scores into a single grid cell value. More...

Math.DoubleDVectorFunctor	getScoreCombinationFunction ()
	Returns the currently configured score-combination function. More...

None	normalizeScores (bool normalize)
	Enables or disables normalization of the combined per-cell scores to the range [0, 1]. More...

bool	scoresNormalized ()
	Tells whether the combined per-cell scores are normalized. More...

None	diminishScoresByAtomDensity (bool diminish)
	Enables or disables multiplicative diminishing of interaction scores by the (normalized) atom density of the target environment. More...

bool	scoresDiminishedByAtomDensity ()
	Tells whether the interaction scores are diminished by the atom density of the target environment. More...

None	storeEnvironmentAtomDensityGrid (bool store)
	Specifies whether the target environment atom-density grid shall be added to the produced grid set. More...

bool	environmentAtomDensityGridStored ()
	Tells whether the target environment atom-density grid is stored in the produced grid set. More...

None	setEnvironmentAtomDensityGridName ()

str	getEnvironmentAtomDensityGridName ()
	Returns the name assigned to the target environment atom-density grid. More...

float	getGridStepSize ()
	Returns the currently configured grid spacing. More...

None	setGridStepSize (float size)
	Sets the grid spacing (isotropic). More...

int	getGridXSize ()
	Returns the grid size in the x direction. More...

None	setGridXSize (int size)
	Sets the grid size in the x direction. More...

int	getGridYSize ()
	Returns the grid size in the y direction. More...

None	setGridYSize (int size)
	Sets the grid size in the y direction. More...

int	getGridZSize ()
	Returns the grid size in the z direction. More...

None	setGridZSize (int size)
	Sets the grid size in the z direction. More...

Math.Matrix4D	getGridTransform ()
	Returns the affine transformation matrix that places the grids in the target coordinate frame. More...

None	setGridTransform (Math.Matrix4D xform)
	Sets the affine transformation matrix that places the grids in the target coordinate frame. More...

None	setGridParamsForBoundingBox (Math.Vector3D bbox_min, Math.Vector3D bbox_max, float step_size=0.5)
	Convenience method that configures grid size, spacing and transformation so that the grid covers the given axis-aligned bounding box. More...

Pharm.DefaultPharmacophoreGenerator	getPharmacophoreGenerator ()
	Returns the internal pharmacophore generator used for the target environment. More...

None	setPharmacophoreProcessingFunction (VoidPharmacophoreFunctor func)
	Sets the function applied to the generated target pharmacophore before grid calculation (e.g. More...

VoidPharmacophoreFunctor	getPharmacophoreProcessingFunction ()
	Returns the currently configured pharmacophore processing function. More...

None	calcInteractionGrids (Chem.MolecularGraph tgt_env, Chem.Atom3DCoordinatesFunction coords_func, Grid.DRegularGridSet grid_set, bool append=False)
	Calculates the interaction-score grids for all enabled feature-type pairs and stores them in grid_set. More...

Grid.DRegularGrid	calcAtomDensityGrid (Chem.AtomContainer atoms, Chem.Atom3DCoordinatesFunction coords_func, str grid_name)
	Calculates an atom-density grid for the given atoms. More...

Static Public Attributes
float	DEF_GRID_STEP_SIZE = 0.5
	Default grid spacing (isotropic).

Properties
	objectID = property(getObjectID)

	normalizedScores = property(scoresNormalized, normalizeScores)

	scoreCombinationFunction = property(getScoreCombinationFunction, setScoreCombinationFunction)

	pharmProcessingFunction = property(getPharmacophoreProcessingFunction, setPharmacophoreProcessingFunction)

	gridStepSize = property(getGridStepSize, setGridStepSize)

	gridXSize = property(getGridXSize, setGridXSize)

	gridYSize = property(getGridYSize, setGridYSize)

	gridZSize = property(getGridZSize, setGridZSize)

	gridTransform = property(getGridTransform, setGridTransform)

	pharmGenerator = property(getPharmacophoreGenerator)

	dimScoresByAtomDensity = property(scoresDiminishedByAtomDensity, diminishScoresByAtomDensity)

	storeEnvAtomDensityGrid = property(environmentAtomDensityGridStored, storeEnvironmentAtomDensityGrid)

	envAtomDensityGridName = property(getEnvironmentAtomDensityGridName, setEnvironmentAtomDensityGridName)

Detailed Description

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.

For every enabled (ligand feature type, target feature type) pair the generator runs a GRAIL.FeatureInteractionScoreGridCalculator and stores the resulting grid in a Grid.DRegularGridSet. Optionally the generator also produces an atom-density grid of the target environment (e.g. for use as a buriedness or accessibility weight).

See also: [GRAIL]

Since: 1.1

Constructor & Destructor Documentation

◆ init()

None CDPL.GRAIL.GRAILDataSetGenerator.__init__ ( GRAILDataSetGenerator gen )

Initializes a copy of the GRAILDataSetGenerator instance gen.

Parameters

gen	The `GRAILDataSetGenerator` instance to copy.

Member Function Documentation

◆ getObjectID()

int CDPL.GRAIL.GRAILDataSetGenerator.getObjectID ( )

Returns the numeric identifier (ID) of the wrapped C++ class instance.

Different Python GRAILDataSetGenerator instances may reference the same underlying C++ class instance. The commonly used Python expression a is not b thus cannot tell reliably whether the two GRAILDataSetGenerator instances a and b reference different C++ objects. The numeric identifier returned by this method allows to correctly implement such an identity test via the simple expression a.getObjectID() != b.getObjectID().

Returns: The numeric ID of the internally referenced C++ class instance.

◆ assign()

GRAILDataSetGenerator CDPL.GRAIL.GRAILDataSetGenerator.assign ( GRAILDataSetGenerator gen )

Replaces the current state of self with a copy of the state of the GRAILDataSetGenerator instance gen.

Parameters

gen	The `GRAILDataSetGenerator` instance to copy.

Returns: self

◆ setScoringFunction()

None CDPL.GRAIL.GRAILDataSetGenerator.setScoringFunction	(	int	ftr_type,
		int	tgt_ftr_type,
		DoubleVector3DFeatureFunctor	func
	)

Sets the scoring function for the given (ligand feature type, target feature type) pair.

Parameters

ftr_type	The ligand feature type.
tgt_ftr_type	The target feature type.
func	The scoring function.

◆ removeScoringFunction()

None CDPL.GRAIL.GRAILDataSetGenerator.removeScoringFunction	(	int	ftr_type,
		int	tgt_ftr_type
	)

Removes the scoring function configured for the given (ligand feature type, target feature type) pair.

Parameters

ftr_type	The ligand feature type.
tgt_ftr_type	The target feature type.

◆ getScoringFunction()

DoubleVector3DFeatureFunctor CDPL.GRAIL.GRAILDataSetGenerator.getScoringFunction	(	int	ftr_type,
		int	tgt_ftr_type
	)

Returns the scoring function configured for the given (ligand feature type, target feature type) pair.

Parameters

ftr_type	The ligand feature type.
tgt_ftr_type	The target feature type.

Returns: The configured scoring function (or an empty function if no entry is registered).

◆ setGridName()

None CDPL.GRAIL.GRAILDataSetGenerator.setGridName	(	int	ftr_type,
		int	tgt_ftr_type,
		str	name
	)

Sets the grid name associated with the given (ligand feature type, target feature type) pair.

Parameters

ftr_type	The ligand feature type.
tgt_ftr_type	The target feature type.
name	The grid name.

◆ removeGridName()

None CDPL.GRAIL.GRAILDataSetGenerator.removeGridName	(	int	ftr_type,
		int	tgt_ftr_type
	)

Removes the grid name associated with the given (ligand feature type, target feature type) pair.

Parameters

ftr_type	The ligand feature type.
tgt_ftr_type	The target feature type.

◆ getGridName()

str CDPL.GRAIL.GRAILDataSetGenerator.getGridName	(	int	ftr_type,
		int	tgt_ftr_type
	)

Returns the grid name associated with the given (ligand feature type, target feature type) pair.

Parameters

ftr_type	The ligand feature type.
tgt_ftr_type	The target feature type.

Returns: The grid name.

◆ enableInteraction()

None CDPL.GRAIL.GRAILDataSetGenerator.enableInteraction	(	int	ftr_type,
		int	tgt_ftr_type,
		bool	enable
	)

Enables or disables interaction-grid generation for the given (ligand feature type, target feature type) pair.

Parameters

ftr_type	The ligand feature type.
tgt_ftr_type	The target feature type.
enable	If `True`, the interaction is enabled.

◆ isInteractionEnabled()

bool CDPL.GRAIL.GRAILDataSetGenerator.isInteractionEnabled	(	int	ftr_type,
		int	tgt_ftr_type
	)

Tells whether interaction-grid generation is enabled for the given (ligand feature type, target feature type) pair.

Parameters

ftr_type	The ligand feature type.
tgt_ftr_type	The target feature type.

Returns: True if the interaction is enabled, and False otherwise.

◆ clearEnabledInteractions()

bool CDPL.GRAIL.GRAILDataSetGenerator.clearEnabledInteractions	(	int	arg2,
		int	self
	)

Parameters

arg1
arg2

Returns

◆ setScoreCombinationFunction()

None CDPL.GRAIL.GRAILDataSetGenerator.setScoreCombinationFunction ( Math.DoubleDVectorFunctor func )

Sets the function used to combine per-feature scores into a single grid cell value.

Parameters

func	The score-combination function.

◆ getScoreCombinationFunction()

Math.DoubleDVectorFunctor CDPL.GRAIL.GRAILDataSetGenerator.getScoreCombinationFunction ( )

Returns the currently configured score-combination function.

Returns: The configured score-combination function.

◆ normalizeScores()

None CDPL.GRAIL.GRAILDataSetGenerator.normalizeScores ( bool normalize )

Enables or disables normalization of the combined per-cell scores to the range [0, 1].

Parameters

normalize If True, the combined scores are normalized.

◆ scoresNormalized()

bool CDPL.GRAIL.GRAILDataSetGenerator.scoresNormalized ( )

Tells whether the combined per-cell scores are normalized.

Returns: True if the combined scores are normalized, and False otherwise.

◆ diminishScoresByAtomDensity()

None CDPL.GRAIL.GRAILDataSetGenerator.diminishScoresByAtomDensity ( bool diminish )

Enables or disables multiplicative diminishing of interaction scores by the (normalized) atom density of the target environment.

Parameters

diminish If True, scores are diminished by atom density.

◆ scoresDiminishedByAtomDensity()

bool CDPL.GRAIL.GRAILDataSetGenerator.scoresDiminishedByAtomDensity ( )

Tells whether the interaction scores are diminished by the atom density of the target environment.

Returns: True if scores are diminished by atom density, and False otherwise.

◆ storeEnvironmentAtomDensityGrid()

None CDPL.GRAIL.GRAILDataSetGenerator.storeEnvironmentAtomDensityGrid ( bool store )

Specifies whether the target environment atom-density grid shall be added to the produced grid set.

Parameters

store If True, the atom-density grid is stored.

◆ environmentAtomDensityGridStored()

bool CDPL.GRAIL.GRAILDataSetGenerator.environmentAtomDensityGridStored ( )

Tells whether the target environment atom-density grid is stored in the produced grid set.

Returns: True if the atom-density grid is stored, and False otherwise.

◆ setEnvironmentAtomDensityGridName()

None CDPL.GRAIL.GRAILDataSetGenerator.setEnvironmentAtomDensityGridName ( )

Parameters

<br>

◆ getEnvironmentAtomDensityGridName()

str CDPL.GRAIL.GRAILDataSetGenerator.getEnvironmentAtomDensityGridName ( )

Returns the name assigned to the target environment atom-density grid.

Returns: The grid name.

◆ getGridStepSize()

float CDPL.GRAIL.GRAILDataSetGenerator.getGridStepSize ( )

Returns the currently configured grid spacing.

Returns: The configured grid spacing.

◆ setGridStepSize()

None CDPL.GRAIL.GRAILDataSetGenerator.setGridStepSize ( float size )

Sets the grid spacing (isotropic).

Parameters

size	The grid spacing.

◆ getGridXSize()

int CDPL.GRAIL.GRAILDataSetGenerator.getGridXSize ( )

Returns the grid size in the x direction.

Returns: The grid size in the x direction.

◆ setGridXSize()

None CDPL.GRAIL.GRAILDataSetGenerator.setGridXSize ( int size )

Sets the grid size in the x direction.

Parameters

size	The grid size.

◆ getGridYSize()

int CDPL.GRAIL.GRAILDataSetGenerator.getGridYSize ( )

Returns the grid size in the y direction.

Returns: The grid size in the y direction.

◆ setGridYSize()

None CDPL.GRAIL.GRAILDataSetGenerator.setGridYSize ( int size )

Sets the grid size in the y direction.

Parameters

size	The grid size.

◆ getGridZSize()

int CDPL.GRAIL.GRAILDataSetGenerator.getGridZSize ( )

Returns the grid size in the z direction.

Returns: The grid size in the z direction.

◆ setGridZSize()

None CDPL.GRAIL.GRAILDataSetGenerator.setGridZSize ( int size )

Sets the grid size in the z direction.

Parameters

size	The grid size.

◆ getGridTransform()

Math.Matrix4D CDPL.GRAIL.GRAILDataSetGenerator.getGridTransform ( )

Returns the affine transformation matrix that places the grids in the target coordinate frame.

Returns: The grid transformation matrix.

◆ setGridTransform()

None CDPL.GRAIL.GRAILDataSetGenerator.setGridTransform ( Math.Matrix4D xform )

Sets the affine transformation matrix that places the grids in the target coordinate frame.

Parameters

xform The transformation matrix.

◆ setGridParamsForBoundingBox()

None CDPL.GRAIL.GRAILDataSetGenerator.setGridParamsForBoundingBox	(	Math.Vector3D	bbox_min,
		Math.Vector3D	bbox_max,
		float	step_size = `0.5`
	)

Convenience method that configures grid size, spacing and transformation so that the grid covers the given axis-aligned bounding box.

Parameters

bbox_min	The bounding box minimum-corner coordinates.
bbox_max	The bounding box maximum-corner coordinates.
step_size	The grid spacing.

◆ getPharmacophoreGenerator()

Pharm.DefaultPharmacophoreGenerator CDPL.GRAIL.GRAILDataSetGenerator.getPharmacophoreGenerator ( )

Returns the internal pharmacophore generator used for the target environment.

Returns: A reference to the pharmacophore generator.

◆ setPharmacophoreProcessingFunction()

None CDPL.GRAIL.GRAILDataSetGenerator.setPharmacophoreProcessingFunction ( VoidPharmacophoreFunctor func )

Sets the function applied to the generated target pharmacophore before grid calculation (e.g.

for filtering or modification).

Parameters

func	The pharmacophore processing function.

◆ getPharmacophoreProcessingFunction()

VoidPharmacophoreFunctor CDPL.GRAIL.GRAILDataSetGenerator.getPharmacophoreProcessingFunction ( )

Returns the currently configured pharmacophore processing function.

Returns: The configured pharmacophore processing function.

◆ calcInteractionGrids()

None CDPL.GRAIL.GRAILDataSetGenerator.calcInteractionGrids	(	Chem.MolecularGraph	tgt_env,
		Chem.Atom3DCoordinatesFunction	coords_func,
		Grid.DRegularGridSet	grid_set,
		bool	append = `False`
	)

Calculates the interaction-score grids for all enabled feature-type pairs and stores them in grid_set.

Parameters

tgt_env	The target environment.
coords_func	The function used to retrieve atom 3D-coordinates from tgt_env.
grid_set	The output grid set.
append	If `True`, the new grids are appended to grid_set. Otherwise, grid_set is cleared first.

◆ calcAtomDensityGrid()

Grid.DRegularGrid CDPL.GRAIL.GRAILDataSetGenerator.calcAtomDensityGrid	(	Chem.AtomContainer	atoms,
		Chem.Atom3DCoordinatesFunction	coords_func,
		str	grid_name
	)

Calculates an atom-density grid for the given atoms.

Parameters

atoms	The atoms contributing to the density.
coords_func	The function used to retrieve atom 3D-coordinates.
grid_name	The name to assign to the resulting grid.

Returns: A smart reference to the calculated atom-density grid.

Public Member Functions

Static Public Attributes

Properties

Detailed Description

Constructor & Destructor Documentation

◆ __init__()

Member Function Documentation

◆ getObjectID()

◆ assign()

◆ setScoringFunction()

◆ removeScoringFunction()

◆ getScoringFunction()

◆ setGridName()

◆ removeGridName()

◆ getGridName()

◆ enableInteraction()

◆ isInteractionEnabled()

◆ clearEnabledInteractions()

◆ setScoreCombinationFunction()

◆ getScoreCombinationFunction()

◆ normalizeScores()

◆ scoresNormalized()

◆ diminishScoresByAtomDensity()

◆ scoresDiminishedByAtomDensity()

◆ storeEnvironmentAtomDensityGrid()

◆ environmentAtomDensityGridStored()

◆ setEnvironmentAtomDensityGridName()

◆ getEnvironmentAtomDensityGridName()

◆ getGridStepSize()

◆ setGridStepSize()

◆ getGridXSize()

◆ setGridXSize()

◆ getGridYSize()

◆ setGridYSize()

◆ getGridZSize()

◆ setGridZSize()

◆ getGridTransform()

◆ setGridTransform()

◆ setGridParamsForBoundingBox()

◆ getPharmacophoreGenerator()

◆ setPharmacophoreProcessingFunction()

◆ getPharmacophoreProcessingFunction()

◆ calcInteractionGrids()

◆ calcAtomDensityGrid()

◆ init()