CDPL.Descr.KuvekPocketDescriptorCalculator Class Reference

Implements the algorithm devised by Kuvek et al. More...

Inheritance diagram for CDPL.Descr.KuvekPocketDescriptorCalculator:

Public Member Functions
None	__init__ (float sphere_radius=20.0, int num_test_vecs=492, float max_atom_to_sphr_surf_dist=2.0)
	Initializes the KuvekPocketDescriptorCalculator instance. More...
None	__init__ (KuvekPocketDescriptorCalculator calc)
	Initializes a copy of the KuvekPocketDescriptorCalculator instance calc. More...
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
KuvekPocketDescriptorCalculator	assign (KuvekPocketDescriptorCalculator calc)
	Replaces the current state of self with a copy of the state of the KuvekPocketDescriptorCalculator instance calc. More...
None	setAtom3DCoordinatesFunction (Chem.Atom3DCoordinatesFunction func)
	Specifies a function for the retrieval of atom 3D-coordinates. More...
Chem.Atom3DCoordinatesFunction	getAtom3DCoordinatesFunction ()
None	setAtomChargeFunction (ForceField.MMFF94AtomChargeFunction func)
	Specifies a function for the retrieval of atom charges. More...
ForceField.MMFF94AtomChargeFunction	getAtomChargeFunction ()
None	setSphereRadius (float radius)
float	getSphereRadius ()
None	setMaxAtomToSphereSurfaceDistance (float radius)
float	getMaxAtomToSphereSurfaceDistance ()
None	setNumTestVectors (int num_vectors)
int	getNumTestVectors ()
Math.Vector3D	getTestVector (int idx)
None	calculate (Math.Vector3D sphere_ctr, Chem.AtomContainer atoms, Math.DVector descr)

Static Public Attributes
float	DEF_PROBE_RADIUS = 20.0
float	DEF_MAX_ATOM_TO_SPHERE_SURF_DIST = 2.0
int	DEF_NUM_TEST_VECTORS = 492

Properties
	objectID = property(getObjectID)
	sphereRadius = property(getSphereRadius, setSphereRadius)
	maxAtomToSphereSurfaceDistance = property(getMaxAtomToSphereSurfaceDistance, setMaxAtomToSphereSurfaceDistance)
	numTestVectors = property(getNumTestVectors, setNumTestVectors)
	atomCoordsFunction = property(getAtom3DCoordinatesFunction, setAtom3DCoordinatesFunction)
	atomChargeFunction = property(getAtomChargeFunction, setAtomChargeFunction)

Detailed Description

Implements the algorithm devised by Kuvek et al.

[KBPD] for the calculation of receptor binding pocket shape and surface electrostatics descriptors.

Since

1.3

Constructor & Destructor Documentation

__init__() [1/2]

None CDPL.Descr.KuvekPocketDescriptorCalculator.__init__	(	float	sphere_radius = 20.0,
		int	num_test_vecs = 492,
		float	max_atom_to_sphr_surf_dist = 2.0
	)

Initializes the KuvekPocketDescriptorCalculator instance.

Parameters

sphere_radius
num_test_vecs
max_atom_to_sphr_surf_dist

__init__() [2/2]

None CDPL.Descr.KuvekPocketDescriptorCalculator.__init__

(

KuvekPocketDescriptorCalculator

calc

)

Initializes a copy of the KuvekPocketDescriptorCalculator instance calc.

Parameters

calc	The KuvekPocketDescriptorCalculator instance to copy.

Member Function Documentation

getObjectID()

int CDPL.Descr.KuvekPocketDescriptorCalculator.getObjectID

(

)

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

Different Python KuvekPocketDescriptorCalculator 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 KuvekPocketDescriptorCalculator 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()

KuvekPocketDescriptorCalculator CDPL.Descr.KuvekPocketDescriptorCalculator.assign

(

KuvekPocketDescriptorCalculator

calc

)

Replaces the current state of self with a copy of the state of the KuvekPocketDescriptorCalculator instance calc.

Parameters

calc	The KuvekPocketDescriptorCalculator instance to copy.

Returns

self

setAtom3DCoordinatesFunction()

None CDPL.Descr.KuvekPocketDescriptorCalculator.setAtom3DCoordinatesFunction

(

Chem.Atom3DCoordinatesFunction

func

)

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

Parameters

func	The atom 3D-coordinates function.

getAtom3DCoordinatesFunction()

Chem.Atom3DCoordinatesFunction CDPL.Descr.KuvekPocketDescriptorCalculator.getAtom3DCoordinatesFunction

(

)

Returns

setAtomChargeFunction()

None CDPL.Descr.KuvekPocketDescriptorCalculator.setAtomChargeFunction

(

ForceField.MMFF94AtomChargeFunction

func

)

Specifies a function for the retrieval of atom charges.

Parameters

func	The atom charge retrieval function.

Note

By default, formal charges will be used.

getAtomChargeFunction()

ForceField.MMFF94AtomChargeFunction CDPL.Descr.KuvekPocketDescriptorCalculator.getAtomChargeFunction

(

)

Returns

setSphereRadius()

None CDPL.Descr.KuvekPocketDescriptorCalculator.setSphereRadius

(

float

radius

)

Parameters

radius

getSphereRadius()

float CDPL.Descr.KuvekPocketDescriptorCalculator.getSphereRadius

(

)

Returns

setMaxAtomToSphereSurfaceDistance()

None CDPL.Descr.KuvekPocketDescriptorCalculator.setMaxAtomToSphereSurfaceDistance

(

float

radius

)

Parameters

radius

getMaxAtomToSphereSurfaceDistance()

float CDPL.Descr.KuvekPocketDescriptorCalculator.getMaxAtomToSphereSurfaceDistance

(

)

Returns

setNumTestVectors()

None CDPL.Descr.KuvekPocketDescriptorCalculator.setNumTestVectors

(

int

num_vectors

)

Parameters

num_vectors

getNumTestVectors()

int CDPL.Descr.KuvekPocketDescriptorCalculator.getNumTestVectors

(

)

Returns

getTestVector()

Math.Vector3D CDPL.Descr.KuvekPocketDescriptorCalculator.getTestVector

(

int

idx

)

Parameters

idx

Returns

calculate()

None CDPL.Descr.KuvekPocketDescriptorCalculator.calculate	(	Math.Vector3D	sphere_ctr,
		Chem.AtomContainer	atoms,
		Math.DVector	descr
	)

Parameters

sphere_ctr
atoms
descr