CDPL::Descr::KuvekPocketDescriptorCalculator Class Reference

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

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)
void	setSphereRadius (double radius)
double	getSphereRadius () const
void	setMaxAtomToSphereSurfaceDistance (double dist)
double	getMaxAtomToSphereSurfaceDistance () const
void	setNumTestVectors (std::size_t num_vectors)
std::size_t	getNumTestVectors () const
const Math::Vector3D &	getTestVector (std::size_t idx)
void	setAtom3DCoordinatesFunction (const Chem::Atom3DCoordinatesFunction &func)
	Specifies a function for the retrieval of atom 3D-coordinates. More...
const Chem::Atom3DCoordinatesFunction &	getAtom3DCoordinatesFunction () const
void	setAtomChargeFunction (const AtomChargeFunction &func)
	Specifies a function for the retrieval of atom charges. More...
const AtomChargeFunction &	getAtomChargeFunction () const
void	calculate (const Math::Vector3D &sphere_ctr, const Chem::AtomContainer &atoms, Math::DVector &descr)

Static Public Attributes
static constexpr double	DEF_PROBE_RADIUS = 20.0
static constexpr double	DEF_MAX_ATOM_TO_SPHERE_SURF_DIST = 2.0
static constexpr std::size_t	DEF_NUM_TEST_VECTORS = 492

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

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
	)

Member Function Documentation

setSphereRadius()

void CDPL::Descr::KuvekPocketDescriptorCalculator::setSphereRadius

(

double

radius

)

getSphereRadius()

double CDPL::Descr::KuvekPocketDescriptorCalculator::getSphereRadius

(

)

const

setMaxAtomToSphereSurfaceDistance()

void CDPL::Descr::KuvekPocketDescriptorCalculator::setMaxAtomToSphereSurfaceDistance

(

double

dist

)

getMaxAtomToSphereSurfaceDistance()

double CDPL::Descr::KuvekPocketDescriptorCalculator::getMaxAtomToSphereSurfaceDistance

(

)

const

setNumTestVectors()

void CDPL::Descr::KuvekPocketDescriptorCalculator::setNumTestVectors

(

std::size_t

num_vectors

)

getNumTestVectors()

std::size_t CDPL::Descr::KuvekPocketDescriptorCalculator::getNumTestVectors

(

)

const

getTestVector()

const Math::Vector3D& CDPL::Descr::KuvekPocketDescriptorCalculator::getTestVector

(

std::size_t

idx

)

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

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

calculate()

void CDPL::Descr::KuvekPocketDescriptorCalculator::calculate	(	const Math::Vector3D &	sphere_ctr,
		const Chem::AtomContainer &	atoms,
		Math::DVector &	descr
	)

Member Data Documentation

DEF_PROBE_RADIUS

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

staticconstexpr

DEF_MAX_ATOM_TO_SPHERE_SURF_DIST

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

staticconstexpr

DEF_NUM_TEST_VECTORS

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

staticconstexpr

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

• KuvekPocketDescriptorCalculator.hpp