Implements the algorithm devised by Kuvek et al. [KBPD] for the calculation of receptor binding pocket shape and surface electrostatics descriptors. More...

#include <KuvekPocketDescriptorCalculator.hpp>

Public Types
typedef std::function< double(const Chem::Atom &)>	AtomChargeFunction
	Type of the generic functor used to retrieve the partial charge of an atom. More...

Public Member Functions
	KuvekPocketDescriptorCalculator (double sphere_radius=DEF_PROBE_RADIUS, std::size_t num_test_vecs=DEF_NUM_TEST_VECTORS, double max_atom_to_sphr_surf_dist=DEF_MAX_ATOM_TO_SPHERE_SURF_DIST)
	Constructs a `KuvekPocketDescriptorCalculator` instance with the given configuration. More...

void	setSphereRadius (double radius)
	Sets the probe sphere radius. More...

double	getSphereRadius () const
	Returns the currently configured probe sphere radius. More...

void	setMaxAtomToSphereSurfaceDistance (double dist)
	Sets the maximum distance between an atom and the probe sphere surface for the atom to contribute. More...

double	getMaxAtomToSphereSurfaceDistance () const
	Returns the currently configured maximum atom-to-sphere-surface distance. More...

void	setNumTestVectors (std::size_t num_vectors)
	Sets the number of test vectors used to sample the probe sphere surface. More...

std::size_t	getNumTestVectors () const
	Returns the currently configured number of test vectors. More...

const Math::Vector3D &	getTestVector (std::size_t idx)
	Returns the test vector at index idx (generated on demand). More...

void	setAtom3DCoordinatesFunction (const Chem::Atom3DCoordinatesFunction &func)
	Specifies a function for the retrieval of atom 3D-coordinates. More...

const Chem::Atom3DCoordinatesFunction &	getAtom3DCoordinatesFunction () const
	Returns the function used for the retrieval of atom 3D-coordinates. More...

void	setAtomChargeFunction (const AtomChargeFunction &func)
	Specifies a function for the retrieval of atom charges. More...

const AtomChargeFunction &	getAtomChargeFunction () const
	Returns the function used for the retrieval of atom charges. More...

void	calculate (const Math::Vector3D &sphere_ctr, const Chem::AtomContainer &atoms, Math::DVector &descr)
	Calculates the Kuvek pocket descriptor at the given query position. More...

Static Public Attributes
static constexpr double	DEF_PROBE_RADIUS = 20.0
	Default radius of the probe sphere centered at the query position. More...

static constexpr double	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. More...

static constexpr std::size_t	DEF_NUM_TEST_VECTORS = 492
	Default number of test vectors used to sample the probe sphere surface. More...

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

Member Typedef Documentation

◆ AtomChargeFunction

typedef std::function<double(const Chem::Atom&)> CDPL::Descr::KuvekPocketDescriptorCalculator::AtomChargeFunction

Type of the generic functor used to retrieve the partial charge of an atom.

Constructor & Destructor Documentation

◆ KuvekPocketDescriptorCalculator()

CDPL::Descr::KuvekPocketDescriptorCalculator::KuvekPocketDescriptorCalculator	(	double	sphere_radius = `DEF_PROBE_RADIUS`,
		std::size_t	num_test_vecs = `DEF_NUM_TEST_VECTORS`,
		double	max_atom_to_sphr_surf_dist = `DEF_MAX_ATOM_TO_SPHERE_SURF_DIST`
	)

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.

Member Function Documentation

◆ setSphereRadius()

void CDPL::Descr::KuvekPocketDescriptorCalculator::setSphereRadius ( double radius )

Sets the probe sphere radius.

Parameters

radius The probe sphere radius.

◆ getSphereRadius()

double CDPL::Descr::KuvekPocketDescriptorCalculator::getSphereRadius ( ) const

Returns the currently configured probe sphere radius.

Returns: The configured probe sphere radius.

◆ setMaxAtomToSphereSurfaceDistance()

void CDPL::Descr::KuvekPocketDescriptorCalculator::setMaxAtomToSphereSurfaceDistance ( double dist )

Sets the maximum distance between an atom and the probe sphere surface for the atom to contribute.

Parameters

dist	The maximum distance to the probe sphere surface.

◆ getMaxAtomToSphereSurfaceDistance()

double CDPL::Descr::KuvekPocketDescriptorCalculator::getMaxAtomToSphereSurfaceDistance ( ) const

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

Returns: The configured maximum distance.

◆ setNumTestVectors()

void CDPL::Descr::KuvekPocketDescriptorCalculator::setNumTestVectors ( std::size_t num_vectors )

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

Parameters

num_vectors The number of test vectors.

◆ getNumTestVectors()

std::size_t CDPL::Descr::KuvekPocketDescriptorCalculator::getNumTestVectors ( ) const

Returns the currently configured number of test vectors.

Returns: The configured number of test vectors.

◆ getTestVector()

const Math::Vector3D& CDPL::Descr::KuvekPocketDescriptorCalculator::getTestVector ( std::size_t idx )

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

Parameters

idx	The test vector index.

Returns: A const 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].

◆ setAtom3DCoordinatesFunction()

void CDPL::Descr::KuvekPocketDescriptorCalculator::setAtom3DCoordinatesFunction ( const Chem::Atom3DCoordinatesFunction & func )

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

Parameters

func	The atom 3D-coordinates function.

◆ getAtom3DCoordinatesFunction()

const Chem::Atom3DCoordinatesFunction& CDPL::Descr::KuvekPocketDescriptorCalculator::getAtom3DCoordinatesFunction ( ) const

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

Returns: The configured atom 3D-coordinates function.

◆ setAtomChargeFunction()

void CDPL::Descr::KuvekPocketDescriptorCalculator::setAtomChargeFunction ( const AtomChargeFunction & 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()

const AtomChargeFunction& CDPL::Descr::KuvekPocketDescriptorCalculator::getAtomChargeFunction ( ) const

Returns the function used for the retrieval of atom charges.

Returns: The configured atom charge function.

◆ calculate()

void CDPL::Descr::KuvekPocketDescriptorCalculator::calculate	(	const Math::Vector3D &	sphere_ctr,
		const 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.

Member Data Documentation

◆ DEF_PROBE_RADIUS

constexpr double CDPL::Descr::KuvekPocketDescriptorCalculator::DEF_PROBE_RADIUS = 20.0

staticconstexpr

Default radius of the probe sphere centered at the query position.

◆ DEF_MAX_ATOM_TO_SPHERE_SURF_DIST

constexpr double CDPL::Descr::KuvekPocketDescriptorCalculator::DEF_MAX_ATOM_TO_SPHERE_SURF_DIST = 2.0

staticconstexpr

Default maximum distance between an atom and the probe sphere surface for the atom to contribute.

◆ DEF_NUM_TEST_VECTORS

constexpr std::size_t CDPL::Descr::KuvekPocketDescriptorCalculator::DEF_NUM_TEST_VECTORS = 492

staticconstexpr

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

The documentation for this class was generated from the following file:

KuvekPocketDescriptorCalculator.hpp

Public Types

Public Member Functions

Static Public Attributes

Detailed Description

Member Typedef Documentation

◆ AtomChargeFunction

Constructor & Destructor Documentation

◆ KuvekPocketDescriptorCalculator()

Member Function Documentation

◆ setSphereRadius()

◆ getSphereRadius()

◆ setMaxAtomToSphereSurfaceDistance()

◆ getMaxAtomToSphereSurfaceDistance()

◆ setNumTestVectors()

◆ getNumTestVectors()

◆ getTestVector()

◆ setAtom3DCoordinatesFunction()

◆ getAtom3DCoordinatesFunction()

◆ setAtomChargeFunction()

◆ getAtomChargeFunction()

◆ calculate()

Member Data Documentation

◆ DEF_PROBE_RADIUS

◆ DEF_MAX_ATOM_TO_SPHERE_SURF_DIST

◆ DEF_NUM_TEST_VECTORS