CDPL::Descr::PharmacophoreRDFDescriptorCalculator Class Reference

PharmacophoreRDFDescriptorCalculator. More...

#include <PharmacophoreRDFDescriptorCalculator.hpp>

Public Types
typedef RDFCodeCalc::Entity3DCoordinatesFunction	Feature3DCoordinatesFunction
typedef std::function< double(const Pharm::Feature &, const Pharm::Feature &, unsigned int)>	FeaturePairWeightFunction

Public Member Functions
	PharmacophoreRDFDescriptorCalculator ()
	Constructs the PharmacophoreRDFDescriptorCalculator instance. More...
	PharmacophoreRDFDescriptorCalculator (const Pharm::FeatureContainer &cntnr, Math::DVector &descr)
void	setSmoothingFactor (double factor)
	Allows to specify the smoothing factor used in the calculation of feature pair RDF contributions. More...
double	getSmoothingFactor () const
	Returns the smoothing factor used in the calculation of feature 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	setFeature3DCoordinatesFunction (const Feature3DCoordinatesFunction &func)
	Allows to specify the feature coordinates function. More...
void	setFeaturePairWeightFunction (const FeaturePairWeightFunction &func)
	Allows to specify a custom feature pair weight function. More...
void	enableDistanceToIntervalCenterRounding (bool enable)
	Allows to specify whether feature pair distances should be rounded to the nearest radius interval center. More...
bool	distanceToIntervalsCenterRoundingEnabled () const
	Tells whether feature pair distances get rounded to the nearest radius interval centers. More...
void	calculate (const Pharm::FeatureContainer &cntnr, Math::DVector &descr)

Detailed Description

PharmacophoreRDFDescriptorCalculator.

See also

[CITB, HBMD]

Member Typedef Documentation

Feature3DCoordinatesFunction

typedef RDFCodeCalc::Entity3DCoordinatesFunction CDPL::Descr::PharmacophoreRDFDescriptorCalculator::Feature3DCoordinatesFunction

FeaturePairWeightFunction

typedef std::function<double(const Pharm::Feature&, const Pharm::Feature&, unsigned int)> CDPL::Descr::PharmacophoreRDFDescriptorCalculator::FeaturePairWeightFunction

Constructor & Destructor Documentation

PharmacophoreRDFDescriptorCalculator() [1/2]

CDPL::Descr::PharmacophoreRDFDescriptorCalculator::PharmacophoreRDFDescriptorCalculator

(

)

Constructs the PharmacophoreRDFDescriptorCalculator instance.

PharmacophoreRDFDescriptorCalculator() [2/2]

CDPL::Descr::PharmacophoreRDFDescriptorCalculator::PharmacophoreRDFDescriptorCalculator	(	const Pharm::FeatureContainer &	cntnr,
		Math::DVector &	descr
	)

Member Function Documentation

setSmoothingFactor()

void CDPL::Descr::PharmacophoreRDFDescriptorCalculator::setSmoothingFactor

(

double

factor

)

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

Parameters

factor

The smoothing factor.

Note

The default value of the smoothing factor is 1.0.

getSmoothingFactor()

double CDPL::Descr::PharmacophoreRDFDescriptorCalculator::getSmoothingFactor

(

)

const

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

Returns

The applied smoothing factor.

setScalingFactor()

void CDPL::Descr::PharmacophoreRDFDescriptorCalculator::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 100.0.

getScalingFactor()

double CDPL::Descr::PharmacophoreRDFDescriptorCalculator::getScalingFactor

(

)

const

Returns the scaling factor applied to the RDF code elements.

Returns

The applied scaling factor.

setStartRadius()

void CDPL::Descr::PharmacophoreRDFDescriptorCalculator::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::PharmacophoreRDFDescriptorCalculator::getStartRadius

(

)

const

Returns the starting value of the radius.

Returns

The current radius starting value.

setRadiusIncrement()

void CDPL::Descr::PharmacophoreRDFDescriptorCalculator::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::PharmacophoreRDFDescriptorCalculator::getRadiusIncrement

(

)

const

Returns the radius step size between successive RDF code elements.

Returns

The applied radius step size.

setNumSteps()

void CDPL::Descr::PharmacophoreRDFDescriptorCalculator::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.

Parameters

num_steps

The number of radius incrementation steps.

Note

The default number of steps is 99.

getNumSteps()

std::size_t CDPL::Descr::PharmacophoreRDFDescriptorCalculator::getNumSteps

(

)

const

Returns the number of performed radius incrementation steps.

Returns

The number of performed radius incrementation steps.

setFeature3DCoordinatesFunction()

void CDPL::Descr::PharmacophoreRDFDescriptorCalculator::setFeature3DCoordinatesFunction

(

const Feature3DCoordinatesFunction &

func

)

Allows to specify the feature coordinates function.

Parameters

func	A Feature3DCoordinatesFunction instance that wraps the target function.

Note

The coordinates function must be specified before calling calculate(), otherwise a zero distance for each feature pair will be used for the calculation.

setFeaturePairWeightFunction()

void CDPL::Descr::PharmacophoreRDFDescriptorCalculator::setFeaturePairWeightFunction

(

const FeaturePairWeightFunction &

func

)

Allows to specify a custom feature pair weight function.

Parameters

func	A FeaturePairWeightFunction instance that wraps the target function.

enableDistanceToIntervalCenterRounding()

void CDPL::Descr::PharmacophoreRDFDescriptorCalculator::enableDistanceToIntervalCenterRounding

(

bool

enable

)

Allows to specify whether feature 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 feature pair distances.

distanceToIntervalsCenterRoundingEnabled()

bool CDPL::Descr::PharmacophoreRDFDescriptorCalculator::distanceToIntervalsCenterRoundingEnabled

(

)

const

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

Returns

true if pair distances get rounded, and false otherwise.

calculate()

void CDPL::Descr::PharmacophoreRDFDescriptorCalculator::calculate	(	const Pharm::FeatureContainer &	cntnr,
		Math::DVector &	descr
	)

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

• PharmacophoreRDFDescriptorCalculator.hpp