Generator that produces alignment starting transformations by aligning the principal axes of the aligned shape to those of the reference shape. More...

#include <PrincipalAxesAlignmentStartGenerator.hpp>

Inheritance diagram for CDPL::Shape::PrincipalAxesAlignmentStartGenerator:

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

unsigned int	setupReference (GaussianShapeFunction &func, Math::Matrix4D &xform) const
	Prepares the reference shape function for use by the start generator. More...

unsigned int	setupAligned (GaussianShapeFunction &func, Math::Matrix4D &xform) const
	Prepares the aligned shape function for use by the start generator. More...

void	genShapeCenterStarts (bool generate)
	Enables or disables the generation of a starting transformation at the shape centroid. More...

bool	genShapeCenterStarts () const
	Tells whether a starting transformation at the shape centroid is generated. More...

void	genColorCenterStarts (bool generate)
	Enables or disables the generation of starting transformations at color (pharmacophore) feature centers. More...

bool	genColorCenterStarts () const
	Tells whether starting transformations at color (pharmacophore) feature centers are generated. More...

void	genNonColorCenterStarts (bool generate)
	Enables or disables the generation of starting transformations at non-color (shape) element centers. More...

bool	genNonColorCenterStarts () const
	Tells whether starting transformations at non-color (shape) element centers are generated. More...

void	genRandomStarts (bool generate)
	Enables or disables the generation of random starting transformations. More...

bool	genRandomStarts () const
	Tells whether random starting transformations are generated. More...

void	genForAlignedShapeCenters (bool generate)
	Specifies whether element-/color-center starts shall be generated for centers of the aligned shape. More...

bool	genForAlignedShapeCenters () const
	Tells whether element-/color-center starts are generated for centers of the aligned shape. More...

void	genForReferenceShapeCenters (bool generate)
	Specifies whether element-/color-center starts shall be generated for centers of the reference shape. More...

bool	genForReferenceShapeCenters () const
	Tells whether element-/color-center starts are generated for centers of the reference shape. More...

void	genForLargerShapeCenters (bool generate)
	Specifies whether element-/color-center starts shall be generated for centers of the shape with more elements (instead of both shapes). More...

bool	genForLargerShapeCenters () const
	Tells whether element-/color-center starts are generated for centers of the shape with more elements (instead of both shapes). More...

void	setSymmetryThreshold (double thresh)
	Sets the relative threshold for treating two principal moments as equal. More...

double	getSymmetryThreshold ()
	Returns the currently configured symmetry threshold. More...

void	setMaxRandomTranslation (double max_trans)
	Sets the maximum random translation magnitude applied to random starts. More...

double	getMaxRandomTranslation () const
	Returns the currently configured maximum random translation. More...

void	setNumRandomStarts (std::size_t num_starts)
	Sets the number of random starting transformations. More...

std::size_t	getNumRandomStarts () const
	Returns the currently configured number of random starts. More...

void	setRandomSeed (unsigned int seed)
	Sets the seed used by the random number generator that produces the random starts. More...

void	setReference (const GaussianShapeFunction &func, unsigned int sym_class)
	Specifies the reference shape function and its symmetry class. More...

bool	generate (const GaussianShapeFunction &func, unsigned int sym_class)
	Generates the starting transformations for the alignment of func against the previously configured reference shape. More...

std::size_t	getNumStartTransforms () const
	Returns the total number of starting transformations produced by the last generate() call. More...

std::size_t	getNumStartSubTransforms () const
	Returns the number of sub-transformations applied per generated starting transformation (e.g. axes-swap variants). More...

const QuaternionTransformation &	getStartTransform (std::size_t idx) const
	Returns the starting transformation at index idx. More...

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

Static Public Attributes
static constexpr double	DEF_SYMMETRY_THRESHOLD = 0.15
	Default relative threshold for treating two principal moments as equal. More...

static constexpr std::size_t	DEF_NUM_RANDOM_STARTS = 4
	Default number of random starting transformations. More...

static constexpr double	DEF_MAX_RANDOM_TRANSLATION = 2.0
	Default maximum random translation magnitude applied to random starts. More...

Detailed Description

Generator that produces alignment starting transformations by aligning the principal axes of the aligned shape to those of the reference shape.

Starting transformations can be derived from any combination of (a) the shape centroid, (b) shape element (atom) centers, (c) color (pharmacophore) feature centers, and (d) random rotations applied to translated centers. The exact combination of starts is configured via the various gen* setter methods.

Constructor & Destructor Documentation

◆ PrincipalAxesAlignmentStartGenerator()

CDPL::Shape::PrincipalAxesAlignmentStartGenerator::PrincipalAxesAlignmentStartGenerator ( )

Constructs the PrincipalAxesAlignmentStartGenerator instance.

Member Function Documentation

◆ setupReference()

unsigned int CDPL::Shape::PrincipalAxesAlignmentStartGenerator::setupReference	(	GaussianShapeFunction &	func,
		Math::Matrix4D &	xform
	)		const

virtual

Prepares the reference shape function for use by the start generator.

Parameters

func	The reference shape function (may be modified, e.g. centered).
xform	The output transformation that maps the reference shape from its prepared frame back to its original frame.

Returns: The perceived symmetry class of the reference shape (see namespace Shape::SymmetryClass).

Reimplemented from CDPL::Shape::GaussianShapeAlignmentStartGenerator.

◆ setupAligned()

unsigned int CDPL::Shape::PrincipalAxesAlignmentStartGenerator::setupAligned	(	GaussianShapeFunction &	func,
		Math::Matrix4D &	xform
	)		const

virtual

Prepares the aligned shape function for use by the start generator.

Parameters

func	The aligned shape function (may be modified, e.g. centered).
xform	The output transformation that maps the aligned shape from its prepared frame back to its original frame.

Returns: The perceived symmetry class of the aligned shape (see namespace Shape::SymmetryClass).

Reimplemented from CDPL::Shape::GaussianShapeAlignmentStartGenerator.

◆ genShapeCenterStarts() [1/2]

void CDPL::Shape::PrincipalAxesAlignmentStartGenerator::genShapeCenterStarts ( bool generate )

Enables or disables the generation of a starting transformation at the shape centroid.

Parameters

generate true to enable the shape-centroid start, and false to disable it.

◆ genShapeCenterStarts() [2/2]

bool CDPL::Shape::PrincipalAxesAlignmentStartGenerator::genShapeCenterStarts ( ) const

Tells whether a starting transformation at the shape centroid is generated.

Returns: true if a shape-centroid start is generated, and false otherwise.

◆ genColorCenterStarts() [1/2]

void CDPL::Shape::PrincipalAxesAlignmentStartGenerator::genColorCenterStarts ( bool generate )

Enables or disables the generation of starting transformations at color (pharmacophore) feature centers.

Parameters

generate true to enable the color-center starts, and false to disable them.

◆ genColorCenterStarts() [2/2]

bool CDPL::Shape::PrincipalAxesAlignmentStartGenerator::genColorCenterStarts ( ) const

Tells whether starting transformations at color (pharmacophore) feature centers are generated.

Returns: true if color-center starts are generated, and false otherwise.

◆ genNonColorCenterStarts() [1/2]

void CDPL::Shape::PrincipalAxesAlignmentStartGenerator::genNonColorCenterStarts ( bool generate )

Enables or disables the generation of starting transformations at non-color (shape) element centers.

Parameters

generate true to enable the non-color-center starts, and false to disable them.

◆ genNonColorCenterStarts() [2/2]

bool CDPL::Shape::PrincipalAxesAlignmentStartGenerator::genNonColorCenterStarts ( ) const

Tells whether starting transformations at non-color (shape) element centers are generated.

Returns: true if non-color-center starts are generated, and false otherwise.

◆ genRandomStarts() [1/2]

void CDPL::Shape::PrincipalAxesAlignmentStartGenerator::genRandomStarts ( bool generate )

Enables or disables the generation of random starting transformations.

Parameters

generate true to enable the random starts, and false to disable them.

◆ genRandomStarts() [2/2]

bool CDPL::Shape::PrincipalAxesAlignmentStartGenerator::genRandomStarts ( ) const

Tells whether random starting transformations are generated.

Returns: true if random starts are generated, and false otherwise.

◆ genForAlignedShapeCenters() [1/2]

void CDPL::Shape::PrincipalAxesAlignmentStartGenerator::genForAlignedShapeCenters ( bool generate )

Specifies whether element-/color-center starts shall be generated for centers of the aligned shape.

Parameters

generate true to consider aligned-shape centers, and false to ignore them.

◆ genForAlignedShapeCenters() [2/2]

bool CDPL::Shape::PrincipalAxesAlignmentStartGenerator::genForAlignedShapeCenters ( ) const

Tells whether element-/color-center starts are generated for centers of the aligned shape.

Returns: true if aligned-shape centers are considered, and false otherwise.

◆ genForReferenceShapeCenters() [1/2]

void CDPL::Shape::PrincipalAxesAlignmentStartGenerator::genForReferenceShapeCenters ( bool generate )

Specifies whether element-/color-center starts shall be generated for centers of the reference shape.

Parameters

generate true to consider reference-shape centers, and false to ignore them.

◆ genForReferenceShapeCenters() [2/2]

bool CDPL::Shape::PrincipalAxesAlignmentStartGenerator::genForReferenceShapeCenters ( ) const

Tells whether element-/color-center starts are generated for centers of the reference shape.

Returns: true if reference-shape centers are considered, and false otherwise.

◆ genForLargerShapeCenters() [1/2]

void CDPL::Shape::PrincipalAxesAlignmentStartGenerator::genForLargerShapeCenters ( bool generate )

Specifies whether element-/color-center starts shall be generated for centers of the shape with more elements (instead of both shapes).

Parameters

generate true to use only the centers of the larger shape, and false to use the centers of all configured shapes.

◆ genForLargerShapeCenters() [2/2]

bool CDPL::Shape::PrincipalAxesAlignmentStartGenerator::genForLargerShapeCenters ( ) const

Tells whether element-/color-center starts are generated for centers of the shape with more elements (instead of both shapes).

Returns: true if only the centers of the larger shape are used, and false otherwise.

◆ setSymmetryThreshold()

void CDPL::Shape::PrincipalAxesAlignmentStartGenerator::setSymmetryThreshold ( double thresh )

Sets the relative threshold for treating two principal moments as equal.

Parameters

thresh The new symmetry threshold.

◆ getSymmetryThreshold()

double CDPL::Shape::PrincipalAxesAlignmentStartGenerator::getSymmetryThreshold ( )

Returns the currently configured symmetry threshold.

Returns: The symmetry threshold.

◆ setMaxRandomTranslation()

void CDPL::Shape::PrincipalAxesAlignmentStartGenerator::setMaxRandomTranslation ( double max_trans )

Sets the maximum random translation magnitude applied to random starts.

Parameters

max_trans The new maximum random translation magnitude.

◆ getMaxRandomTranslation()

double CDPL::Shape::PrincipalAxesAlignmentStartGenerator::getMaxRandomTranslation ( ) const

Returns the currently configured maximum random translation.

Returns: The maximum random translation magnitude.

◆ setNumRandomStarts()

void CDPL::Shape::PrincipalAxesAlignmentStartGenerator::setNumRandomStarts ( std::size_t num_starts )

Sets the number of random starting transformations.

Parameters

num_starts The new number of random starts.

◆ getNumRandomStarts()

std::size_t CDPL::Shape::PrincipalAxesAlignmentStartGenerator::getNumRandomStarts ( ) const

Returns the currently configured number of random starts.

Returns: The number of random starts.

◆ setRandomSeed()

void CDPL::Shape::PrincipalAxesAlignmentStartGenerator::setRandomSeed ( unsigned int seed )

Sets the seed used by the random number generator that produces the random starts.

Parameters

seed	The new random seed.

◆ setReference()

void CDPL::Shape::PrincipalAxesAlignmentStartGenerator::setReference	(	const GaussianShapeFunction &	func,
		unsigned int	sym_class
	)

virtual

Specifies the reference shape function and its symmetry class.

Parameters

func	The reference shape function.
sym_class	The symmetry class of the reference shape (see namespace Shape::SymmetryClass).

Implements CDPL::Shape::GaussianShapeAlignmentStartGenerator.

◆ generate()

bool CDPL::Shape::PrincipalAxesAlignmentStartGenerator::generate	(	const GaussianShapeFunction &	func,
		unsigned int	sym_class
	)

virtual

Generates the starting transformations for the alignment of func against the previously configured reference shape.

Parameters

func	The aligned shape function.
sym_class	The symmetry class of the aligned shape (see namespace Shape::SymmetryClass).

Returns: true if at least one starting transformation has been generated, and false otherwise.

Implements CDPL::Shape::GaussianShapeAlignmentStartGenerator.

◆ getNumStartTransforms()

std::size_t CDPL::Shape::PrincipalAxesAlignmentStartGenerator::getNumStartTransforms ( ) const

virtual

Returns the total number of starting transformations produced by the last generate() call.

Returns: The number of starting transformations.

Implements CDPL::Shape::GaussianShapeAlignmentStartGenerator.

◆ getNumStartSubTransforms()

std::size_t CDPL::Shape::PrincipalAxesAlignmentStartGenerator::getNumStartSubTransforms ( ) const

virtual

Returns the number of sub-transformations applied per generated starting transformation (e.g. axes-swap variants).

Returns: The number of sub-transformations.

Implements CDPL::Shape::GaussianShapeAlignmentStartGenerator.

◆ getStartTransform()

const QuaternionTransformation& CDPL::Shape::PrincipalAxesAlignmentStartGenerator::getStartTransform ( std::size_t idx ) const

virtual

Returns the starting transformation at index idx.

Parameters

idx	The zero-based index of the starting transformation.

Returns: A const reference to the starting transformation.

Exceptions

Base::IndexError if the number of starting transformations is zero or idx is not in the range [0, getNumStartTransforms() - 1].

Implements CDPL::Shape::GaussianShapeAlignmentStartGenerator.

Member Data Documentation

◆ DEF_SYMMETRY_THRESHOLD

constexpr double CDPL::Shape::PrincipalAxesAlignmentStartGenerator::DEF_SYMMETRY_THRESHOLD = 0.15

staticconstexpr

Default relative threshold for treating two principal moments as equal.

◆ DEF_NUM_RANDOM_STARTS

constexpr std::size_t CDPL::Shape::PrincipalAxesAlignmentStartGenerator::DEF_NUM_RANDOM_STARTS = 4

staticconstexpr

Default number of random starting transformations.

◆ DEF_MAX_RANDOM_TRANSLATION

constexpr double CDPL::Shape::PrincipalAxesAlignmentStartGenerator::DEF_MAX_RANDOM_TRANSLATION = 2.0

staticconstexpr

Default maximum random translation magnitude applied to random starts.

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

PrincipalAxesAlignmentStartGenerator.hpp

Public Member Functions

Static Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PrincipalAxesAlignmentStartGenerator()

Member Function Documentation

◆ setupReference()

◆ setupAligned()

◆ genShapeCenterStarts() [1/2]

◆ genShapeCenterStarts() [2/2]

◆ genColorCenterStarts() [1/2]

◆ genColorCenterStarts() [2/2]

◆ genNonColorCenterStarts() [1/2]

◆ genNonColorCenterStarts() [2/2]

◆ genRandomStarts() [1/2]

◆ genRandomStarts() [2/2]

◆ genForAlignedShapeCenters() [1/2]

◆ genForAlignedShapeCenters() [2/2]

◆ genForReferenceShapeCenters() [1/2]

◆ genForReferenceShapeCenters() [2/2]

◆ genForLargerShapeCenters() [1/2]

◆ genForLargerShapeCenters() [2/2]

◆ setSymmetryThreshold()

◆ getSymmetryThreshold()

◆ setMaxRandomTranslation()

◆ getMaxRandomTranslation()

◆ setNumRandomStarts()

◆ getNumRandomStarts()

◆ setRandomSeed()

◆ setReference()

◆ generate()

◆ getNumStartTransforms()

◆ getNumStartSubTransforms()

◆ getStartTransform()

Member Data Documentation

◆ DEF_SYMMETRY_THRESHOLD

◆ DEF_NUM_RANDOM_STARTS

◆ DEF_MAX_RANDOM_TRANSLATION