CDPL::Shape Namespace Reference

Contains classes and functions related to molecular shape representation and processing. More...

Namespaces
	AlignmentResultSelectionMode
	SymmetryClass

Classes
class	AlignmentResult
class	ExactGaussianShapeOverlapFunction
class	FastGaussianShapeAlignment
class	FastGaussianShapeOverlapFunction
class	GaussianShape
	A data type for the descripton of arbitrary shapes composed of spheres approximated by gaussian functions. More...
class	GaussianShapeAlignment
class	GaussianShapeAlignmentStartGenerator
class	GaussianShapeFunction
class	GaussianShapeFunctionAlignment
class	GaussianShapeGenerator
class	GaussianShapeOverlapFunction
class	GaussianShapeSet
class	PrincipalAxesAlignmentStartGenerator
class	TotalOverlapTanimotoScore
class	ShapeTanimotoScore
class	ColorTanimotoScore
class	TanimotoComboScore
class	TotalOverlapTverskyScore
class	ShapeTverskyScore
class	ColorTverskyScore
class	TverskyComboScore
class	ReferenceTotalOverlapTverskyScore
class	ReferenceShapeTverskyScore
class	ReferenceColorTverskyScore
class	ReferenceTverskyComboScore
class	AlignedTotalOverlapTverskyScore
class	AlignedShapeTverskyScore
class	AlignedColorTverskyScore
class	AlignedTverskyComboScore
class	ScreeningProcessor
class	ScreeningSettings

Typedefs
typedef Math::Vector7D	QuaternionTransformation
	A bounded 7 element vector specifying a quaternion-based rotation plus translation. More...

Functions
CDPL_SHAPE_API void	generateGaussianShape (const Chem::AtomContainer &atoms, GaussianShape &shape, bool append=false, double radius=-1.0, bool inc_h=false, double p=2.7)
CDPL_SHAPE_API void	generateGaussianShape (const Chem::AtomContainer &atoms, GaussianShape &shape, const Chem::Atom3DCoordinatesFunction &coords_func, bool append=false, double radius=-1.0, bool inc_h=false, double p=2.7)
CDPL_SHAPE_API void	generateGaussianShape (const Pharm::FeatureContainer &features, GaussianShape &shape, bool append=false, double radius=-1.0, bool inc_xv=false, double p=5.0)
CDPL_SHAPE_API void	transform (GaussianShape &shape, const Math::Matrix4D &xform)
CDPL_SHAPE_API unsigned int	centerAndAlignPrincipalAxes (GaussianShape &shape, const GaussianShapeFunction &func, Math::Matrix4D &back_xform, double mom_eq_thresh=0.15)
CDPL_SHAPE_API double	calcTotalOverlapTanimotoScore (const AlignmentResult &res)
CDPL_SHAPE_API double	calcShapeTanimotoScore (const AlignmentResult &res)
CDPL_SHAPE_API double	calcColorTanimotoScore (const AlignmentResult &res)
CDPL_SHAPE_API double	calcTanimotoComboScore (const AlignmentResult &res)
CDPL_SHAPE_API double	calcTotalOverlapTverskyScore (const AlignmentResult &res, double alpha=0.95, double beta=0.05)
CDPL_SHAPE_API double	calcShapeTverskyScore (const AlignmentResult &res, double alpha=0.95, double beta=0.05)
CDPL_SHAPE_API double	calcColorTverskyScore (const AlignmentResult &res, double alpha=0.95, double beta=0.05)
CDPL_SHAPE_API double	calcTverskyComboScore (const AlignmentResult &res, double alpha=0.95, double beta=0.05)
CDPL_SHAPE_API double	calcReferenceTotalOverlapTverskyScore (const AlignmentResult &res, double alpha=0.95)
CDPL_SHAPE_API double	calcReferenceShapeTverskyScore (const AlignmentResult &res, double alpha=0.95)
CDPL_SHAPE_API double	calcReferenceColorTverskyScore (const AlignmentResult &res, double alpha=0.95)
CDPL_SHAPE_API double	calcReferenceTverskyComboScore (const AlignmentResult &res, double alpha=0.95)
CDPL_SHAPE_API double	calcAlignedTotalOverlapTverskyScore (const AlignmentResult &res, double beta=0.95)
CDPL_SHAPE_API double	calcAlignedShapeTverskyScore (const AlignmentResult &res, double beta=0.95)
CDPL_SHAPE_API double	calcAlignedColorTverskyScore (const AlignmentResult &res, double beta=0.95)
CDPL_SHAPE_API double	calcAlignedTverskyComboScore (const AlignmentResult &res, double beta=0.95)
CDPL_SHAPE_API void	calcQuadrupoleTensorEigenDecomposition (const Math::Matrix3D &quad_tensor, Math::Matrix3D &eigen_vecs, Math::Vector3D &eigen_vals)
CDPL_SHAPE_API void	calcPrincipalAxes (const Math::Matrix3D &quad_tensor, Math::Vector3D &x_axis, Math::Vector3D &y_axis, Math::Vector3D &z_axis, Math::Vector3D &moments)
CDPL_SHAPE_API unsigned int	perceiveSymmetryClass (const Math::Vector3D &moments, double eq_thresh=0.15)
CDPL_SHAPE_API unsigned int	calcCenterAlignmentTransforms (const Shape::GaussianShapeFunction &func, Math::Matrix4D &to_ctr_xform, Math::Matrix4D &from_ctr_xform, double mom_eq_thresh=0.15)
CDPL_SHAPE_API void	matrixToQuaternion (const Math::Matrix4D &mtx, QuaternionTransformation &quat)
CDPL_SHAPE_API void	quaternionToMatrix (const QuaternionTransformation &quat, Math::Matrix4D &mtx)

Detailed Description

Contains classes and functions related to molecular shape representation and processing.

Typedef Documentation

QuaternionTransformation

typedef Math::Vector7D CDPL::Shape::QuaternionTransformation

A bounded 7 element vector specifying a quaternion-based rotation plus translation.

Function Documentation

generateGaussianShape() [1/3]

CDPL_SHAPE_API void CDPL::Shape::generateGaussianShape	(	const Chem::AtomContainer &	atoms,
		GaussianShape &	shape,
		bool	append = false,
		double	radius = -1.0,
		bool	inc_h = false,
		double	p = 2.7
	)

generateGaussianShape() [2/3]

CDPL_SHAPE_API void CDPL::Shape::generateGaussianShape	(	const Chem::AtomContainer &	atoms,
		GaussianShape &	shape,
		const Chem::Atom3DCoordinatesFunction &	coords_func,
		bool	append = false,
		double	radius = -1.0,
		bool	inc_h = false,
		double	p = 2.7
	)

generateGaussianShape() [3/3]

CDPL_SHAPE_API void CDPL::Shape::generateGaussianShape	(	const Pharm::FeatureContainer &	features,
		GaussianShape &	shape,
		bool	append = false,
		double	radius = -1.0,
		bool	inc_xv = false,
		double	p = 5.0
	)

transform()

CDPL_SHAPE_API void CDPL::Shape::transform	(	GaussianShape &	shape,
		const Math::Matrix4D &	xform
	)

centerAndAlignPrincipalAxes()

CDPL_SHAPE_API unsigned int CDPL::Shape::centerAndAlignPrincipalAxes	(	GaussianShape &	shape,
		const GaussianShapeFunction &	func,
		Math::Matrix4D &	back_xform,
		double	mom_eq_thresh = 0.15
	)

calcTotalOverlapTanimotoScore()

CDPL_SHAPE_API double CDPL::Shape::calcTotalOverlapTanimotoScore

(

const AlignmentResult &

res

)

calcShapeTanimotoScore()

CDPL_SHAPE_API double CDPL::Shape::calcShapeTanimotoScore

(

const AlignmentResult &

res

)

calcColorTanimotoScore()

CDPL_SHAPE_API double CDPL::Shape::calcColorTanimotoScore

(

const AlignmentResult &

res

)

calcTanimotoComboScore()

CDPL_SHAPE_API double CDPL::Shape::calcTanimotoComboScore

(

const AlignmentResult &

res

)

calcTotalOverlapTverskyScore()

CDPL_SHAPE_API double CDPL::Shape::calcTotalOverlapTverskyScore	(	const AlignmentResult &	res,
		double	alpha = 0.95,
		double	beta = 0.05
	)

calcShapeTverskyScore()

CDPL_SHAPE_API double CDPL::Shape::calcShapeTverskyScore	(	const AlignmentResult &	res,
		double	alpha = 0.95,
		double	beta = 0.05
	)

calcColorTverskyScore()

CDPL_SHAPE_API double CDPL::Shape::calcColorTverskyScore	(	const AlignmentResult &	res,
		double	alpha = 0.95,
		double	beta = 0.05
	)

calcTverskyComboScore()

CDPL_SHAPE_API double CDPL::Shape::calcTverskyComboScore	(	const AlignmentResult &	res,
		double	alpha = 0.95,
		double	beta = 0.05
	)

calcReferenceTotalOverlapTverskyScore()

CDPL_SHAPE_API double CDPL::Shape::calcReferenceTotalOverlapTverskyScore	(	const AlignmentResult &	res,
		double	alpha = 0.95
	)

calcReferenceShapeTverskyScore()

CDPL_SHAPE_API double CDPL::Shape::calcReferenceShapeTverskyScore	(	const AlignmentResult &	res,
		double	alpha = 0.95
	)

calcReferenceColorTverskyScore()

CDPL_SHAPE_API double CDPL::Shape::calcReferenceColorTverskyScore	(	const AlignmentResult &	res,
		double	alpha = 0.95
	)

calcReferenceTverskyComboScore()

CDPL_SHAPE_API double CDPL::Shape::calcReferenceTverskyComboScore	(	const AlignmentResult &	res,
		double	alpha = 0.95
	)

calcAlignedTotalOverlapTverskyScore()

CDPL_SHAPE_API double CDPL::Shape::calcAlignedTotalOverlapTverskyScore	(	const AlignmentResult &	res,
		double	beta = 0.95
	)

calcAlignedShapeTverskyScore()

CDPL_SHAPE_API double CDPL::Shape::calcAlignedShapeTverskyScore	(	const AlignmentResult &	res,
		double	beta = 0.95
	)

calcAlignedColorTverskyScore()

CDPL_SHAPE_API double CDPL::Shape::calcAlignedColorTverskyScore	(	const AlignmentResult &	res,
		double	beta = 0.95
	)

calcAlignedTverskyComboScore()

CDPL_SHAPE_API double CDPL::Shape::calcAlignedTverskyComboScore	(	const AlignmentResult &	res,
		double	beta = 0.95
	)

calcQuadrupoleTensorEigenDecomposition()

CDPL_SHAPE_API void CDPL::Shape::calcQuadrupoleTensorEigenDecomposition	(	const Math::Matrix3D &	quad_tensor,
		Math::Matrix3D &	eigen_vecs,
		Math::Vector3D &	eigen_vals
	)

calcPrincipalAxes()

CDPL_SHAPE_API void CDPL::Shape::calcPrincipalAxes	(	const Math::Matrix3D &	quad_tensor,
		Math::Vector3D &	x_axis,
		Math::Vector3D &	y_axis,
		Math::Vector3D &	z_axis,
		Math::Vector3D &	moments
	)

perceiveSymmetryClass()

CDPL_SHAPE_API unsigned int CDPL::Shape::perceiveSymmetryClass	(	const Math::Vector3D &	moments,
		double	eq_thresh = 0.15
	)

calcCenterAlignmentTransforms()

CDPL_SHAPE_API unsigned int CDPL::Shape::calcCenterAlignmentTransforms	(	const Shape::GaussianShapeFunction &	func,
		Math::Matrix4D &	to_ctr_xform,
		Math::Matrix4D &	from_ctr_xform,
		double	mom_eq_thresh = 0.15
	)

matrixToQuaternion()

CDPL_SHAPE_API void CDPL::Shape::matrixToQuaternion	(	const Math::Matrix4D &	mtx,
		QuaternionTransformation &	quat
	)

quaternionToMatrix()

CDPL_SHAPE_API void CDPL::Shape::quaternionToMatrix	(	const QuaternionTransformation &	quat,
		Math::Matrix4D &	mtx
	)