Calculation of an RDF descriptor of a molecular graph partitioned by specific atom types. More...

#include <MoleculeRDFDescriptorCalculator.hpp>

Public Types
typedef RDFCodeCalculator::Entity3DCoordinatesFunction	Atom3DCoordinatesFunction
	Type of the function used to retrieve the 3D coordinates of an atom. More...

typedef std::function< double(const Chem::Atom &, const Chem::Atom &, unsigned int)>	AtomPairWeightFunction
	Type of the generic functor used to retrieve the weight of an atom pair. More...

Public Member Functions
	MoleculeRDFDescriptorCalculator ()
	Constructs the `MoleculeRDFDescriptorCalculator` instance. More...

	MoleculeRDFDescriptorCalculator (const Chem::AtomContainer &cntnr, Math::DVector &descr)
	Constructs the `MoleculeRDFDescriptorCalculator` instance and calculates the RDF descriptor of the atoms in cntnr. More...

void	setSmoothingFactor (double factor)
	Allows to specify the smoothing factor used in the calculation of atom pair RDF contributions. More...

double	getSmoothingFactor () const
	Returns the smoothing factor used in the calculation of atom pair RDF contributions. More...

void	setScalingFactor (double factor)
	Allows to specify the scaling factor for the RDF code elements. More...

double	getScalingFactor () const
	Returns the scaling factor applied to the RDF code elements. More...

void	setStartRadius (double start_radius)
	Sets the starting value of the radius. More...

double	getStartRadius () const
	Returns the starting value of the radius. More...

void	setRadiusIncrement (double radius_inc)
	Sets the radius step size between successive RDF code elements. More...

double	getRadiusIncrement () const
	Returns the radius step size between successive RDF code elements. More...

void	setNumSteps (std::size_t num_steps)
	Sets the number of desired radius incrementation steps. More...

std::size_t	getNumSteps () const
	Returns the number of performed radius incrementation steps. More...

void	setAtom3DCoordinatesFunction (const Atom3DCoordinatesFunction &func)
	Allows to specify the atom coordinates function. More...

void	setAtomPairWeightFunction (const AtomPairWeightFunction &func)
	Allows to specify a custom atom pair weight function. More...

void	enableDistanceToIntervalCenterRounding (bool enable)
	Allows to specify whether atom pair distances should be rounded to the nearest radius interval center. More...

bool	distanceToIntervalsCenterRoundingEnabled () const
	Tells whether atom pair distances get rounded to the nearest radius interval centers. More...

void	calculate (const Chem::AtomContainer &cntnr, Math::DVector &descr)
	Calculates the RDF descriptor of the atoms in cntnr. More...

Detailed Description

Calculation of an RDF descriptor of a molecular graph partitioned by specific atom types.

Atom types considered for partitioning are:

See also: [CITB, HBMD]

Member Typedef Documentation

◆ Atom3DCoordinatesFunction

typedef RDFCodeCalculator::Entity3DCoordinatesFunction CDPL::Descr::MoleculeRDFDescriptorCalculator::Atom3DCoordinatesFunction

Type of the function used to retrieve the 3D coordinates of an atom.

◆ AtomPairWeightFunction

typedef std::function<double(const Chem::Atom&, const Chem::Atom&, unsigned int)> CDPL::Descr::MoleculeRDFDescriptorCalculator::AtomPairWeightFunction

Type of the generic functor used to retrieve the weight of an atom pair.

The function receives the two atoms and a single atom type specifying the descriptor partition.

Constructor & Destructor Documentation

◆ MoleculeRDFDescriptorCalculator() [1/2]

CDPL::Descr::MoleculeRDFDescriptorCalculator::MoleculeRDFDescriptorCalculator ( )

Constructs the MoleculeRDFDescriptorCalculator instance.

◆ MoleculeRDFDescriptorCalculator() [2/2]

CDPL::Descr::MoleculeRDFDescriptorCalculator::MoleculeRDFDescriptorCalculator	(	const Chem::AtomContainer &	cntnr,
		Math::DVector &	descr
	)

Constructs the MoleculeRDFDescriptorCalculator instance and calculates the RDF descriptor of the atoms in cntnr.

Parameters

cntnr	The container with the atoms for which to calculate the descriptor.
descr	The output descriptor vector.

Member Function Documentation

◆ setSmoothingFactor()

void CDPL::Descr::MoleculeRDFDescriptorCalculator::setSmoothingFactor ( double factor )

Allows to specify the smoothing factor used in the calculation of atom pair RDF contributions.

Parameters

factor The smoothing factor.

Note: The default value of the smoothing factor is 1.0.

◆ getSmoothingFactor()

double CDPL::Descr::MoleculeRDFDescriptorCalculator::getSmoothingFactor ( ) const

Returns the smoothing factor used in the calculation of atom pair RDF contributions.

Returns: The applied smoothing factor.

◆ setScalingFactor()

void CDPL::Descr::MoleculeRDFDescriptorCalculator::setScalingFactor ( double factor )

Allows to specify the scaling factor for the RDF code elements.

Parameters

factor The scaling factor.

Note: The default scaling factor is 1.0.

◆ getScalingFactor()

double CDPL::Descr::MoleculeRDFDescriptorCalculator::getScalingFactor ( ) const

Returns the scaling factor applied to the RDF code elements.

Returns: The applied scaling factor.

◆ setStartRadius()

void CDPL::Descr::MoleculeRDFDescriptorCalculator::setStartRadius ( double start_radius )

Sets the starting value of the radius.

Parameters

start_radius The starting value of the radius.

Note: The default starting radius is 0.0Å.

◆ getStartRadius()

double CDPL::Descr::MoleculeRDFDescriptorCalculator::getStartRadius ( ) const

Returns the starting value of the radius.

Returns: The current radius starting value.

◆ setRadiusIncrement()

void CDPL::Descr::MoleculeRDFDescriptorCalculator::setRadiusIncrement ( double radius_inc )

Sets the radius step size between successive RDF code elements.

Parameters

radius_inc The radius step size.

Note: The default radius step size is 0.1Å.

◆ getRadiusIncrement()

double CDPL::Descr::MoleculeRDFDescriptorCalculator::getRadiusIncrement ( ) const

Returns the radius step size between successive RDF code elements.

Returns: The applied radius step size.

◆ setNumSteps()

void CDPL::Descr::MoleculeRDFDescriptorCalculator::setNumSteps ( std::size_t num_steps )

Sets the number of desired radius incrementation steps.

The number of performed radius incrementation steps defines the size of the calculated RDF code vector which is equal to the number of steps plus 1 times 10.

Parameters

num_steps The number of radius incrementation steps.

Note: The default number of steps is 99.

◆ getNumSteps()

std::size_t CDPL::Descr::MoleculeRDFDescriptorCalculator::getNumSteps ( ) const

Returns the number of performed radius incrementation steps.

Returns: The number of performed radius incrementation steps.

◆ setAtom3DCoordinatesFunction()

void CDPL::Descr::MoleculeRDFDescriptorCalculator::setAtom3DCoordinatesFunction ( const Atom3DCoordinatesFunction & func )

Allows to specify the atom coordinates function.

Parameters

func	A Atom3DCoordinatesFunction instance that wraps the target function.

◆ setAtomPairWeightFunction()

void CDPL::Descr::MoleculeRDFDescriptorCalculator::setAtomPairWeightFunction ( const AtomPairWeightFunction & func )

Allows to specify a custom atom pair weight function.

Parameters

func	A AtomPairWeightFunction instance that wraps the target function.

◆ enableDistanceToIntervalCenterRounding()

void CDPL::Descr::MoleculeRDFDescriptorCalculator::enableDistanceToIntervalCenterRounding ( bool enable )

Allows to specify whether atom pair distances should be rounded to the nearest radius interval center.

Parameters

enable true if pair distances should be rounded, and false otherwise.

Note: The default setting is not to round the atom pair distances.

◆ distanceToIntervalsCenterRoundingEnabled()

bool CDPL::Descr::MoleculeRDFDescriptorCalculator::distanceToIntervalsCenterRoundingEnabled ( ) const

Tells whether atom pair distances get rounded to the nearest radius interval centers.

Returns: true if pair distances get rounded, and false otherwise.

◆ calculate()

void CDPL::Descr::MoleculeRDFDescriptorCalculator::calculate	(	const Chem::AtomContainer &	cntnr,
		Math::DVector &	descr
	)

Calculates the RDF descriptor of the atoms in cntnr.

Parameters

cntnr	The container with the atoms for which to calculate the descriptor.
descr	The output descriptor vector.

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

MoleculeRDFDescriptorCalculator.hpp

Public Types

Public Member Functions

Detailed Description

Member Typedef Documentation

◆ Atom3DCoordinatesFunction

◆ AtomPairWeightFunction

Constructor & Destructor Documentation

◆ MoleculeRDFDescriptorCalculator() [1/2]

◆ MoleculeRDFDescriptorCalculator() [2/2]

Member Function Documentation

◆ setSmoothingFactor()

◆ getSmoothingFactor()

◆ setScalingFactor()

◆ getScalingFactor()

◆ setStartRadius()

◆ getStartRadius()

◆ setRadiusIncrement()

◆ getRadiusIncrement()

◆ setNumSteps()

◆ getNumSteps()

◆ setAtom3DCoordinatesFunction()

◆ setAtomPairWeightFunction()

◆ enableDistanceToIntervalCenterRounding()

◆ distanceToIntervalsCenterRoundingEnabled()

◆ calculate()