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)
	Constructs a KuvekPocketDescriptorCalculator instance with the given configuration. 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 ()
	Returns the function used for the retrieval of atom 3D-coordinates. More...
None	setAtomChargeFunction (ForceField.MMFF94AtomChargeFunction func)
	Specifies a function for the retrieval of atom charges. More...
ForceField.MMFF94AtomChargeFunction	getAtomChargeFunction ()
	Returns the function used for the retrieval of atom charges. More...
None	setSphereRadius (float radius)
	Sets the probe sphere radius. More...
float	getSphereRadius ()
	Returns the currently configured probe sphere radius. More...
None	setMaxAtomToSphereSurfaceDistance (float radius)
float	getMaxAtomToSphereSurfaceDistance ()
	Returns the currently configured maximum atom-to-sphere-surface distance. More...
None	setNumTestVectors (int num_vectors)
	Sets the number of test vectors used to sample the probe sphere surface. More...
int	getNumTestVectors ()
	Returns the currently configured number of test vectors. More...
Math.Vector3D	getTestVector (int idx)
	Returns the test vector at index idx (generated on demand). More...
None	calculate (Math.Vector3D sphere_ctr, Chem.AtomContainer atoms, Math.DVector descr)
	Calculates the Kuvek pocket descriptor at the given query position. More...

Static Public Attributes
float	DEF_PROBE_RADIUS = 20.0
	Default radius of the probe sphere centered at the query position.
float	DEF_MAX_ATOM_TO_SPHERE_SURF_DIST = 2.0
	Default maximum distance between an atom and the probe sphere surface for the atom to contribute.
int	DEF_NUM_TEST_VECTORS = 492
	Default number of test vectors used to sample the probe sphere surface.

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
	)

Constructs a KuvekPocketDescriptorCalculator instance with the given configuration.

Parameters

sphere_radius	The probe sphere radius.
num_test_vecs	The number of test vectors used to sample the probe sphere surface.
max_atom_to_sphr_surf_dist	The maximum distance between an atom and the probe sphere surface for the atom to contribute.

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

Returns

The configured atom 3D-coordinates function.

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 the function used for the retrieval of atom charges.

Returns

The configured atom charge function.

setSphereRadius()

None CDPL.Descr.KuvekPocketDescriptorCalculator.setSphereRadius

(

float

radius

)

Sets the probe sphere radius.

Parameters

radius

The probe sphere radius.

getSphereRadius()

float CDPL.Descr.KuvekPocketDescriptorCalculator.getSphereRadius

(

)

Returns the currently configured probe sphere radius.

Returns

The configured probe sphere radius.

setMaxAtomToSphereSurfaceDistance()

None CDPL.Descr.KuvekPocketDescriptorCalculator.setMaxAtomToSphereSurfaceDistance

(

float

radius

)

Parameters

radius

getMaxAtomToSphereSurfaceDistance()

float CDPL.Descr.KuvekPocketDescriptorCalculator.getMaxAtomToSphereSurfaceDistance

(

)

Returns the currently configured maximum atom-to-sphere-surface distance.

Returns

The configured maximum distance.

setNumTestVectors()

None CDPL.Descr.KuvekPocketDescriptorCalculator.setNumTestVectors

(

int

num_vectors

)

Sets the number of test vectors used to sample the probe sphere surface.

Parameters

num_vectors

The number of test vectors.

getNumTestVectors()

int CDPL.Descr.KuvekPocketDescriptorCalculator.getNumTestVectors

(

)

Returns the currently configured number of test vectors.

Returns

The configured number of test vectors.

getTestVector()

Math.Vector3D CDPL.Descr.KuvekPocketDescriptorCalculator.getTestVector

(

int

idx

)

Returns the test vector at index idx (generated on demand).

Parameters

idx	The test vector index.

Returns

A reference to the test vector.

Exceptions

Base.IndexError

if the number of test vectors is zero or idx is not in the range [0, getNumTestVectors() - 1].

calculate()

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

Calculates the Kuvek pocket descriptor at the given query position.

Parameters

sphere_ctr	The 3D position of the probe sphere center.
atoms	The atoms used as the environment for the calculation.
descr	The output descriptor vector.