Shape::GaussianShapeOverlapFunction implementation that uses two approximation techniques to trade some accuracy for a substantial speedup compared to Shape::ExactGaussianShapeOverlapFunction. More...

#include <FastGaussianShapeOverlapFunction.hpp>

Inheritance diagram for CDPL::Shape::FastGaussianShapeOverlapFunction:

Public Types
typedef std::shared_ptr< FastGaussianShapeOverlapFunction >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `FastGaussianShapeOverlapFunction` instances. More...

Public Types inherited from CDPL::Shape::GaussianShapeOverlapFunction
typedef std::shared_ptr< GaussianShapeOverlapFunction >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `GaussianShapeOverlapFunction` instances. More...

typedef std::function< bool(std::size_t)>	ColorFilterFunction
	Type of the function used to filter color (pharmacophore) features by type. More...

typedef std::function< bool(std::size_t, std::size_t)>	ColorMatchFunction
	Type of the function used to decide whether two color features match. More...

Public Member Functions
	FastGaussianShapeOverlapFunction ()
	Constructs the `FastGaussianShapeOverlapFunction` instance without associated shape functions. More...

	FastGaussianShapeOverlapFunction (const FastGaussianShapeOverlapFunction &func)
	Constructs a copy of the `FastGaussianShapeOverlapFunction` instance func. More...

	FastGaussianShapeOverlapFunction (const GaussianShapeFunction &ref_shape_func, const GaussianShapeFunction &ovl_shape_func)
	Constructs the `FastGaussianShapeOverlapFunction` instance with the given reference and aligned shape functions. More...

	~FastGaussianShapeOverlapFunction ()
	Destructor. More...

void	proximityOptimization (bool enable)
	Enables or disables the proximity-check pruning of Gaussian-product pair contributions. More...

bool	proximityOptimization () const
	Tells whether the proximity-check pruning is enabled. More...

void	setRadiusScalingFactor (double factor)
	Sets the scaling factor applied to Van der Waals radii during the proximity check. More...

double	getRadiusScalingFactor () const
	Returns the currently configured radius scaling factor. More...

void	fastExpFunction (bool enable)
	Enables or disables the use of a fast approximation for the exponential function. More...

bool	fastExpFunction () const
	Tells whether the fast-exponential approximation is enabled. More...

void	setShapeFunction (const GaussianShapeFunction &func, bool is_ref)
	Specifies the reference or aligned shape function used by the overlap evaluation. More...

const GaussianShapeFunction *	getShapeFunction (bool ref) const
	Returns the reference or aligned shape function. More...

void	setColorMatchFunction (const ColorMatchFunction &func)
	Specifies the function used to decide whether two color features match. More...

const ColorMatchFunction &	getColorMatchFunction () const
	Returns the currently configured color-match function. More...

void	setColorFilterFunction (const ColorFilterFunction &func)
	Specifies the function used to filter color features by type. More...

const ColorFilterFunction &	getColorFilterFunction () const
	Returns the currently configured color-filter function. More...

double	calcSelfOverlap (bool ref) const
	Calculates the shape-only self-overlap of the reference or aligned shape function. More...

double	calcColorSelfOverlap (bool ref) const
	Calculates the color self-overlap of the reference or aligned shape function. More...

double	calcOverlap () const
	Calculates the shape-only overlap of the reference and aligned shape functions. More...

double	calcColorOverlap () const
	Calculates the color overlap of the reference and aligned shape functions. More...

double	calcOverlap (const Math::Vector3DArray &coords) const
	Calculates the shape-only overlap with the aligned shape element positions taken from coords. More...

double	calcColorOverlap (const Math::Vector3DArray &coords) const
	Calculates the color overlap with the aligned shape element positions taken from coords. More...

double	calcOverlapGradient (const Math::Vector3DArray &coords, Math::Vector3DArray &grad) const
	Calculates the shape overlap with the aligned shape element positions taken from coords and returns the gradient with respect to those positions. More...

FastGaussianShapeOverlapFunction &	operator= (const FastGaussianShapeOverlapFunction &func)
	Copy assignment operator. More...

Public Member Functions inherited from CDPL::Shape::GaussianShapeOverlapFunction
virtual	~GaussianShapeOverlapFunction ()
	Virtual destructor. More...

Static Public Attributes
static constexpr double	DEF_RADIUS_SCALING_FACTOR = 1.4
	Default scaling factor applied to Van der Waals radii for the proximity-check pruning. More...

Additional Inherited Members
Protected Member Functions inherited from CDPL::Shape::GaussianShapeOverlapFunction
	GaussianShapeOverlapFunction ()

	GaussianShapeOverlapFunction (const GaussianShapeOverlapFunction &func)

GaussianShapeOverlapFunction &	operator= (const GaussianShapeOverlapFunction &func)

Detailed Description

Shape::GaussianShapeOverlapFunction implementation that uses two approximation techniques to trade some accuracy for a substantial speedup compared to Shape::ExactGaussianShapeOverlapFunction.

Two independent acceleration features can be enabled:

Proximity optimization prunes Gaussian-product pair contributions based on a scaled van-der-Waals proximity test (see setRadiusScalingFactor()).
Fast exponential function replaces the expensive std::exp call with a fast approximation that is accurate enough for screening-style overlap evaluation.

Member Typedef Documentation

◆ SharedPointer

typedef std::shared_ptr<FastGaussianShapeOverlapFunction> CDPL::Shape::FastGaussianShapeOverlapFunction::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated FastGaussianShapeOverlapFunction instances.

Constructor & Destructor Documentation

◆ FastGaussianShapeOverlapFunction() [1/3]

CDPL::Shape::FastGaussianShapeOverlapFunction::FastGaussianShapeOverlapFunction ( )

Constructs the FastGaussianShapeOverlapFunction instance without associated shape functions.

◆ FastGaussianShapeOverlapFunction() [2/3]

CDPL::Shape::FastGaussianShapeOverlapFunction::FastGaussianShapeOverlapFunction ( const FastGaussianShapeOverlapFunction & func )

Constructs a copy of the FastGaussianShapeOverlapFunction instance func.

Parameters

func	The `FastGaussianShapeOverlapFunction` to copy.

◆ FastGaussianShapeOverlapFunction() [3/3]

CDPL::Shape::FastGaussianShapeOverlapFunction::FastGaussianShapeOverlapFunction	(	const GaussianShapeFunction &	ref_shape_func,
		const GaussianShapeFunction &	ovl_shape_func
	)

Constructs the FastGaussianShapeOverlapFunction instance with the given reference and aligned shape functions.

Parameters

ref_shape_func	The reference shape function.
ovl_shape_func	The aligned shape function.

◆ ~FastGaussianShapeOverlapFunction()

CDPL::Shape::FastGaussianShapeOverlapFunction::~FastGaussianShapeOverlapFunction ( )

Destructor.

Member Function Documentation

◆ proximityOptimization() [1/2]

void CDPL::Shape::FastGaussianShapeOverlapFunction::proximityOptimization ( bool enable )

Enables or disables the proximity-check pruning of Gaussian-product pair contributions.

Parameters

enable true to enable the proximity check, and false to disable it.

◆ proximityOptimization() [2/2]

bool CDPL::Shape::FastGaussianShapeOverlapFunction::proximityOptimization ( ) const

Tells whether the proximity-check pruning is enabled.

Returns: true if the proximity check is enabled, and false otherwise.

◆ setRadiusScalingFactor()

void CDPL::Shape::FastGaussianShapeOverlapFunction::setRadiusScalingFactor ( double factor )

Sets the scaling factor applied to Van der Waals radii during the proximity check.

Parameters

factor The new radius scaling factor.

◆ getRadiusScalingFactor()

double CDPL::Shape::FastGaussianShapeOverlapFunction::getRadiusScalingFactor ( ) const

Returns the currently configured radius scaling factor.

Returns: The radius scaling factor.

◆ fastExpFunction() [1/2]

void CDPL::Shape::FastGaussianShapeOverlapFunction::fastExpFunction ( bool enable )

Enables or disables the use of a fast approximation for the exponential function.

Parameters

enable true to enable the fast-exponential approximation, and false to use the standard exponential.

◆ fastExpFunction() [2/2]

bool CDPL::Shape::FastGaussianShapeOverlapFunction::fastExpFunction ( ) const

Tells whether the fast-exponential approximation is enabled.

Returns: true if the fast-exponential approximation is enabled, and false otherwise.

◆ setShapeFunction()

void CDPL::Shape::FastGaussianShapeOverlapFunction::setShapeFunction	(	const GaussianShapeFunction &	func,
		bool	is_ref
	)

virtual

Specifies the reference or aligned shape function used by the overlap evaluation.

Parameters

func	The shape function.
is_ref	If `true`, func is the reference shape function; otherwise the aligned shape function.

Implements CDPL::Shape::GaussianShapeOverlapFunction.

◆ getShapeFunction()

const GaussianShapeFunction* CDPL::Shape::FastGaussianShapeOverlapFunction::getShapeFunction ( bool ref ) const

virtual

Returns the reference or aligned shape function.

Parameters

ref	If `true`, the reference shape function is returned; otherwise the aligned shape function.

Returns: A pointer to the requested shape function (or nullptr if none is associated).

Implements CDPL::Shape::GaussianShapeOverlapFunction.

◆ setColorMatchFunction()

void CDPL::Shape::FastGaussianShapeOverlapFunction::setColorMatchFunction ( const ColorMatchFunction & func )

virtual

Specifies the function used to decide whether two color features match.

Parameters

func	The color-match function.

Implements CDPL::Shape::GaussianShapeOverlapFunction.

◆ getColorMatchFunction()

const ColorMatchFunction& CDPL::Shape::FastGaussianShapeOverlapFunction::getColorMatchFunction ( ) const

virtual

Returns the currently configured color-match function.

Returns: A const reference to the color-match function.

Implements CDPL::Shape::GaussianShapeOverlapFunction.

◆ setColorFilterFunction()

void CDPL::Shape::FastGaussianShapeOverlapFunction::setColorFilterFunction ( const ColorFilterFunction & func )

virtual

Specifies the function used to filter color features by type.

Parameters

func	The color-filter function.

Implements CDPL::Shape::GaussianShapeOverlapFunction.

◆ getColorFilterFunction()

const ColorFilterFunction& CDPL::Shape::FastGaussianShapeOverlapFunction::getColorFilterFunction ( ) const

virtual

Returns the currently configured color-filter function.

Returns: A const reference to the color-filter function.

Implements CDPL::Shape::GaussianShapeOverlapFunction.

◆ calcSelfOverlap()

double CDPL::Shape::FastGaussianShapeOverlapFunction::calcSelfOverlap ( bool ref ) const

virtual

Calculates the shape-only self-overlap of the reference or aligned shape function.

Parameters

ref	If `true`, the reference self-overlap is returned; otherwise the aligned self-overlap.

Returns: The self-overlap value.

Implements CDPL::Shape::GaussianShapeOverlapFunction.

◆ calcColorSelfOverlap()

double CDPL::Shape::FastGaussianShapeOverlapFunction::calcColorSelfOverlap ( bool ref ) const

virtual

Calculates the color self-overlap of the reference or aligned shape function.

Parameters

ref	If `true`, the reference color self-overlap is returned; otherwise the aligned color self-overlap.

Returns: The color self-overlap value.

Implements CDPL::Shape::GaussianShapeOverlapFunction.

◆ calcOverlap() [1/2]

double CDPL::Shape::FastGaussianShapeOverlapFunction::calcOverlap ( ) const

virtual

Calculates the shape-only overlap of the reference and aligned shape functions.

Returns: The shape overlap value.

Implements CDPL::Shape::GaussianShapeOverlapFunction.

◆ calcColorOverlap() [1/2]

double CDPL::Shape::FastGaussianShapeOverlapFunction::calcColorOverlap ( ) const

virtual

Calculates the color overlap of the reference and aligned shape functions.

Returns: The color overlap value.

Implements CDPL::Shape::GaussianShapeOverlapFunction.

◆ calcOverlap() [2/2]

double CDPL::Shape::FastGaussianShapeOverlapFunction::calcOverlap ( const Math::Vector3DArray & coords ) const

virtual

Calculates the shape-only overlap with the aligned shape element positions taken from coords.

Parameters

coords The element 3D positions of the aligned shape.

Returns: The shape overlap value.

Implements CDPL::Shape::GaussianShapeOverlapFunction.

◆ calcColorOverlap() [2/2]

double CDPL::Shape::FastGaussianShapeOverlapFunction::calcColorOverlap ( const Math::Vector3DArray & coords ) const

virtual

Calculates the color overlap with the aligned shape element positions taken from coords.

Parameters

coords The element 3D positions of the aligned shape.

Returns: The color overlap value.

Implements CDPL::Shape::GaussianShapeOverlapFunction.

◆ calcOverlapGradient()

double CDPL::Shape::FastGaussianShapeOverlapFunction::calcOverlapGradient	(	const Math::Vector3DArray &	coords,
		Math::Vector3DArray &	grad
	)		const

virtual

Calculates the shape overlap with the aligned shape element positions taken from coords and returns the gradient with respect to those positions.

Parameters

coords	The element 3D positions of the aligned shape.
grad	The output element-wise gradient of the overlap.

Returns: The shape overlap value.

Implements CDPL::Shape::GaussianShapeOverlapFunction.

◆ operator=()

FastGaussianShapeOverlapFunction& CDPL::Shape::FastGaussianShapeOverlapFunction::operator= ( const FastGaussianShapeOverlapFunction & func )

Copy assignment operator.

Parameters

func	The other `FastGaussianShapeOverlapFunction` instance.

Returns: A reference to itself.

Member Data Documentation

◆ DEF_RADIUS_SCALING_FACTOR

constexpr double CDPL::Shape::FastGaussianShapeOverlapFunction::DEF_RADIUS_SCALING_FACTOR = 1.4

staticconstexpr

Default scaling factor applied to Van der Waals radii for the proximity-check pruning.

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

FastGaussianShapeOverlapFunction.hpp

Public Types

Public Member Functions

Static Public Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ SharedPointer

Constructor & Destructor Documentation

◆ FastGaussianShapeOverlapFunction() [1/3]

◆ FastGaussianShapeOverlapFunction() [2/3]

◆ FastGaussianShapeOverlapFunction() [3/3]

◆ ~FastGaussianShapeOverlapFunction()

Member Function Documentation

◆ proximityOptimization() [1/2]

◆ proximityOptimization() [2/2]

◆ setRadiusScalingFactor()

◆ getRadiusScalingFactor()

◆ fastExpFunction() [1/2]

◆ fastExpFunction() [2/2]

◆ setShapeFunction()

◆ getShapeFunction()

◆ setColorMatchFunction()

◆ getColorMatchFunction()

◆ setColorFilterFunction()

◆ getColorFilterFunction()

◆ calcSelfOverlap()

◆ calcColorSelfOverlap()

◆ calcOverlap() [1/2]

◆ calcColorOverlap() [1/2]

◆ calcOverlap() [2/2]

◆ calcColorOverlap() [2/2]

◆ calcOverlapGradient()

◆ operator=()

Member Data Documentation

◆ DEF_RADIUS_SCALING_FACTOR