CDPL.GRAIL.GRAILDataSetGenerator Class Reference

GRAILDataSetGenerator. More...

Inheritance diagram for CDPL.GRAIL.GRAILDataSetGenerator:

Public Member Functions
None	__init__ ()
	Initializes 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)
None	removeScoringFunction (int ftr_type, int tgt_ftr_type)
DoubleVector3DFeatureFunctor	getScoringFunction (int ftr_type, int tgt_ftr_type)
None	setGridName (int ftr_type, int tgt_ftr_type, str name)
None	removeGridName (int ftr_type, int tgt_ftr_type)
str	getGridName (int ftr_type, int tgt_ftr_type)
None	enableInteraction (int ftr_type, int tgt_ftr_type, bool enable)
bool	isInteractionEnabled (int ftr_type, int tgt_ftr_type)
bool	clearEnabledInteractions (int arg2, int self)
None	setScoreCombinationFunction (Math.DoubleDVectorFunctor func)
Math.DoubleDVectorFunctor	getScoreCombinationFunction ()
None	normalizeScores (bool normalize)
bool	scoresNormalized ()
None	diminishScoresByAtomDensity (bool diminish)
bool	scoresDiminishedByAtomDensity ()
None	storeEnvironmentAtomDensityGrid (bool store)
bool	environmentAtomDensityGridStored ()
None	setEnvironmentAtomDensityGridName ()
str	getEnvironmentAtomDensityGridName ()
float	getGridStepSize ()
None	setGridStepSize (float size)
int	getGridXSize ()
None	setGridXSize (int size)
int	getGridYSize ()
None	setGridYSize (int size)
int	getGridZSize ()
None	setGridZSize (int size)
Math.Matrix4D	getGridTransform ()
None	setGridTransform (Math.Matrix4D xform)
None	setGridParamsForBoundingBox (Math.Vector3D bbox_min, Math.Vector3D bbox_max, float step_size=0.5)
Pharm.DefaultPharmacophoreGenerator	getPharmacophoreGenerator ()
None	setPharmacophoreProcessingFunction (VoidPharmacophoreFunctor func)
VoidPharmacophoreFunctor	getPharmacophoreProcessingFunction ()
None	calcInteractionGrids (Chem.MolecularGraph tgt_env, Chem.Atom3DCoordinatesFunction coords_func, Grid.DRegularGridSet grid_set, bool append=False)
Grid.DRegularGrid	calcAtomDensityGrid (Chem.AtomContainer atoms, Chem.Atom3DCoordinatesFunction coords_func, str grid_name)

Static Public Attributes
float	DEF_GRID_STEP_SIZE = 0.5

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

GRAILDataSetGenerator.

See also

[GRAIL]

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
	)

Parameters

ftr_type
tgt_ftr_type
func

removeScoringFunction()

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

Parameters

ftr_type
tgt_ftr_type

getScoringFunction()

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

Parameters

ftr_type
tgt_ftr_type

Returns

setGridName()

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

Parameters

ftr_type
tgt_ftr_type
name

removeGridName()

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

Parameters

ftr_type
tgt_ftr_type

getGridName()

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

Parameters

ftr_type
tgt_ftr_type

Returns

enableInteraction()

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

Parameters

ftr_type
tgt_ftr_type
enable

isInteractionEnabled()

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

Parameters

ftr_type
tgt_ftr_type

Returns

clearEnabledInteractions()

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

Parameters

arg1
arg2

Returns

setScoreCombinationFunction()

None CDPL.GRAIL.GRAILDataSetGenerator.setScoreCombinationFunction

(

Math.DoubleDVectorFunctor

func

)

Parameters

func

getScoreCombinationFunction()

Math.DoubleDVectorFunctor CDPL.GRAIL.GRAILDataSetGenerator.getScoreCombinationFunction

(

)

Returns

normalizeScores()

None CDPL.GRAIL.GRAILDataSetGenerator.normalizeScores

(

bool

normalize

)

Parameters

normalize

scoresNormalized()

bool CDPL.GRAIL.GRAILDataSetGenerator.scoresNormalized

(

)

Returns

diminishScoresByAtomDensity()

None CDPL.GRAIL.GRAILDataSetGenerator.diminishScoresByAtomDensity

(

bool

diminish

)

Parameters

diminish

scoresDiminishedByAtomDensity()

bool CDPL.GRAIL.GRAILDataSetGenerator.scoresDiminishedByAtomDensity

(

)

Returns

storeEnvironmentAtomDensityGrid()

None CDPL.GRAIL.GRAILDataSetGenerator.storeEnvironmentAtomDensityGrid

(

bool

store

)

Parameters

store

environmentAtomDensityGridStored()

bool CDPL.GRAIL.GRAILDataSetGenerator.environmentAtomDensityGridStored

(

)

Returns

setEnvironmentAtomDensityGridName()

None CDPL.GRAIL.GRAILDataSetGenerator.setEnvironmentAtomDensityGridName

(

)

Parameters

<br>

getEnvironmentAtomDensityGridName()

str CDPL.GRAIL.GRAILDataSetGenerator.getEnvironmentAtomDensityGridName

(

)

Returns

getGridStepSize()

float CDPL.GRAIL.GRAILDataSetGenerator.getGridStepSize

(

)

Returns

setGridStepSize()

None CDPL.GRAIL.GRAILDataSetGenerator.setGridStepSize

(

float

size

)

Parameters

size

getGridXSize()

int CDPL.GRAIL.GRAILDataSetGenerator.getGridXSize

(

)

Returns

setGridXSize()

None CDPL.GRAIL.GRAILDataSetGenerator.setGridXSize

(

int

size

)

Parameters

size

getGridYSize()

int CDPL.GRAIL.GRAILDataSetGenerator.getGridYSize

(

)

Returns

setGridYSize()

None CDPL.GRAIL.GRAILDataSetGenerator.setGridYSize

(

int

size

)

Parameters

size

getGridZSize()

int CDPL.GRAIL.GRAILDataSetGenerator.getGridZSize

(

)

Returns

setGridZSize()

None CDPL.GRAIL.GRAILDataSetGenerator.setGridZSize

(

int

size

)

Parameters

size

getGridTransform()

Math.Matrix4D CDPL.GRAIL.GRAILDataSetGenerator.getGridTransform

(

)

Returns

setGridTransform()

None CDPL.GRAIL.GRAILDataSetGenerator.setGridTransform

(

Math.Matrix4D

xform

)

Parameters

xform

setGridParamsForBoundingBox()

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

Parameters

bbox_min
bbox_max
step_size

getPharmacophoreGenerator()

Pharm.DefaultPharmacophoreGenerator CDPL.GRAIL.GRAILDataSetGenerator.getPharmacophoreGenerator

(

)

Returns

setPharmacophoreProcessingFunction()

None CDPL.GRAIL.GRAILDataSetGenerator.setPharmacophoreProcessingFunction

(

VoidPharmacophoreFunctor

func

)

Parameters

func

getPharmacophoreProcessingFunction()

VoidPharmacophoreFunctor CDPL.GRAIL.GRAILDataSetGenerator.getPharmacophoreProcessingFunction

(

)

Returns

calcInteractionGrids()

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

Parameters

tgt_env
coords_func
grid_set
append

calcAtomDensityGrid()

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

Parameters

atoms
coords_func
grid_name

Returns