CDPL.GRAIL.BuriednessGridCalculator Class Reference

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

Inheritance diagram for CDPL.GRAIL.BuriednessGridCalculator:

Public Member Functions
None	__init__ ()
	Constructs the BuriednessGridCalculator instance.
None	__init__ (BuriednessGridCalculator calc)
	Constructs a copy of the BuriednessGridCalculator instance calc. More...
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
BuriednessGridCalculator	assign (BuriednessGridCalculator calc)
	Copy assignment operator. More...
None	setMinVdWSurfaceDistance (float dist)
	Sets the minimum required distance between a ray and the Van der Waals surface of an atom. More...
float	getMinVdWSurfaceDistance ()
	Returns the currently configured minimum distance to the Van der Waals surface of an atom. More...
None	setProbeRadius (float radius)
	Sets the probe sphere radius used by the underlying GRAIL.BuriednessScore. More...
float	getProbeRadius ()
	Returns the currently configured probe sphere radius. More...
None	setNumTestRays (int num_rays)
	Sets the number of test rays cast from each grid cell. More...
int	getNumTestRays ()
	Returns the currently configured number of test rays. More...
None	setAtom3DCoordinatesFunction (Chem.Atom3DCoordinatesFunction func)
	Specifies a function for the retrieval of atom 3D-coordinates for grid calculation. More...
Chem.Atom3DCoordinatesFunction	getAtom3DCoordinatesFunction ()
	Returns the function used for the retrieval of atom 3D-coordinates. More...
None	calculate (Chem.AtomContainer atoms, Grid.DSpatialGrid grid)
	Calculates the buriedness value at each cell of grid for the given atoms. More...

Properties
	objectID = property(getObjectID)
	probeRadius = property(getProbeRadius, setProbeRadius)
	minVdWSurfaceDistance = property(getMinVdWSurfaceDistance, setMinVdWSurfaceDistance)
	numTestRays = property(getNumTestRays, setNumTestRays)
	atom3DCoordinatesFunction = property(getAtom3DCoordinatesFunction, setAtom3DCoordinatesFunction)

Detailed Description

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

For each grid cell, the buriedness score with respect to the surrounding atoms is computed and stored. The configurable parameters (probe radius, minimum Van der Waals surface distance, number of test rays) are forwarded to the underlying BuriednessScore instance.

Constructor & Destructor Documentation

__init__()

None CDPL.GRAIL.BuriednessGridCalculator.__init__

(

BuriednessGridCalculator

calc

)

Constructs a copy of the BuriednessGridCalculator instance calc.

Parameters

calc	The BuriednessGridCalculator to copy.

Member Function Documentation

getObjectID()

int CDPL.GRAIL.BuriednessGridCalculator.getObjectID

(

)

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

Different Python BuriednessGridCalculator 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 BuriednessGridCalculator 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()

BuriednessGridCalculator CDPL.GRAIL.BuriednessGridCalculator.assign

(

BuriednessGridCalculator

calc

)

Copy assignment operator.

Parameters

calc	The other BuriednessGridCalculator instance.

Returns

self

setMinVdWSurfaceDistance()

None CDPL.GRAIL.BuriednessGridCalculator.setMinVdWSurfaceDistance

(

float

dist

)

Sets the minimum required distance between a ray and the Van der Waals surface of an atom.

Parameters

dist	The minimum distance to the Van der Waals surface.

getMinVdWSurfaceDistance()

float CDPL.GRAIL.BuriednessGridCalculator.getMinVdWSurfaceDistance

(

)

Returns the currently configured minimum distance to the Van der Waals surface of an atom.

Returns

The configured minimum distance to the Van der Waals surface.

setProbeRadius()

None CDPL.GRAIL.BuriednessGridCalculator.setProbeRadius

(

float

radius

)

Sets the probe sphere radius used by the underlying GRAIL.BuriednessScore.

Parameters

radius

The probe sphere radius.

getProbeRadius()

float CDPL.GRAIL.BuriednessGridCalculator.getProbeRadius

(

)

Returns the currently configured probe sphere radius.

Returns

The configured probe sphere radius.

setNumTestRays()

None CDPL.GRAIL.BuriednessGridCalculator.setNumTestRays

(

int

num_rays

)

Sets the number of test rays cast from each grid cell.

Parameters

num_rays

The number of test rays.

getNumTestRays()

int CDPL.GRAIL.BuriednessGridCalculator.getNumTestRays

(

)

Returns the currently configured number of test rays.

Returns

The configured number of test rays.

setAtom3DCoordinatesFunction()

None CDPL.GRAIL.BuriednessGridCalculator.setAtom3DCoordinatesFunction

(

Chem.Atom3DCoordinatesFunction

func

)

Specifies a function for the retrieval of atom 3D-coordinates for grid calculation.

Parameters

func	The atom 3D-coordinates function.

getAtom3DCoordinatesFunction()

Chem.Atom3DCoordinatesFunction CDPL.GRAIL.BuriednessGridCalculator.getAtom3DCoordinatesFunction

(

)

Returns the function used for the retrieval of atom 3D-coordinates.

Returns

The configured atom 3D-coordinates function.

calculate()

None CDPL.GRAIL.BuriednessGridCalculator.calculate	(	Chem.AtomContainer	atoms,
		Grid.DSpatialGrid	grid
	)

Calculates the buriedness value at each cell of grid for the given atoms.

Parameters

atoms	The atoms used as the environment for the buriedness calculation.
grid	The output grid populated with per-cell buriedness scores.