CDPL.Shape Package Reference

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

Classes
class	AlignedColorTverskyScore
class	AlignedShapeTverskyScore
class	AlignedTotalOverlapTverskyScore
class	AlignedTverskyComboScore
class	AlignmentResult
class	AlignmentResultSelectionMode
class	BoolAlignmentResult2Functor
class	BoolSizeType2Functor
class	BoolSizeTypeFunctor
class	ColorTanimotoScore
class	ColorTverskyScore
class	DoubleAlignmentResultFunctor
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	ReferenceColorTverskyScore
class	ReferenceShapeTverskyScore
class	ReferenceTotalOverlapTverskyScore
class	ReferenceTverskyComboScore
class	ScreeningProcessor
class	ScreeningSettings
class	ShapeTanimotoScore
class	ShapeTverskyScore
class	SymmetryClass
class	TanimotoComboScore
class	TotalOverlapTanimotoScore
class	TotalOverlapTverskyScore
class	TverskyComboScore
class	Vector7D
class	VoidMolecularGraph2AlignmentResultFunctor

Functions
float	calcTanimotoComboScore (AlignmentResult res)
float	calcTverskyComboScore (AlignmentResult res, float alpha=0.95, float beta=0.05)
float	calcAlignedTverskyComboScore (AlignmentResult res, float beta=0.95)
float	calcReferenceTverskyComboScore (AlignmentResult res, float alpha=0.95)
float	calcShapeTanimotoScore (AlignmentResult res)
float	calcTotalOverlapTanimotoScore (AlignmentResult res)
float	calcColorTanimotoScore (AlignmentResult res)
float	calcShapeTverskyScore (AlignmentResult res, float alpha=0.95, float beta=0.05)
float	calcAlignedShapeTverskyScore (AlignmentResult res, float beta=0.95)
float	calcReferenceShapeTverskyScore (AlignmentResult res, float alpha=0.95)
float	calcTotalOverlapTverskyScore (AlignmentResult res, float alpha=0.95, float beta=0.05)
float	calcAlignedTotalOverlapTverskyScore (AlignmentResult res, float beta=0.95)
float	calcReferenceTotalOverlapTverskyScore (AlignmentResult res, float alpha=0.95)
float	calcColorTverskyScore (AlignmentResult res, float alpha=0.95, float beta=0.05)
float	calcAlignedColorTverskyScore (AlignmentResult res, float beta=0.95)
float	calcReferenceColorTverskyScore (AlignmentResult res, float alpha=0.95)
None	generateGaussianShape (Chem.AtomContainer atoms, GaussianShape shape, bool append=False, float radius=-1.0, bool inc_h=False, float p=2.7)
None	generateGaussianShape (Chem.AtomContainer atoms, GaussianShape shape, Chem.Atom3DCoordinatesFunction coords_func, bool append=False, float radius=-1.0, bool inc_h=False, float p=2.7)
None	generateGaussianShape (Pharm.FeatureContainer features, GaussianShape shape, bool append=False, float radius=-1.0, bool inc_xv=False, float p=5.0)
int	calcCenterAlignmentTransforms (GaussianShapeFunction func, Math.Matrix4D to_ctr_xform, Math.Matrix4D from_ctr_xform, float mom_eq_thresh=0.15)
None	transform (GaussianShape shape, Math.Matrix4D xform)
int	centerAndAlignPrincipalAxes (GaussianShape shape, GaussianShapeFunction func, Math.Matrix4D back_xform, float mom_eq_thresh=0.15)
None	calcQuadrupoleTensorEigenDecomposition (Math.Matrix3D quad_tensor, Math.Matrix3D eigen_vecs, Math.Vector3D eigen_vals)
None	calcPrincipalAxes (Math.Matrix3D quad_tensor, Math.Vector3D x_axis, Math.Vector3D y_axis, Math.Vector3D z_axis, Math.Vector3D moments)
None	matrixToQuaternion (Math.Matrix4D mtx, Math.Vector7D quat)
int	perceiveSymmetryClass (Math.Vector3D moments, float eq_thresh=0.15)
None	quaternionToMatrix (Math.Vector7D quat, Math.Matrix4D mtx)

Detailed Description

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

Function Documentation

calcTanimotoComboScore()

float CDPL.Shape.calcTanimotoComboScore

(

AlignmentResult

res

)

Parameters

res

Returns

calcTverskyComboScore()

float CDPL.Shape.calcTverskyComboScore	(	AlignmentResult	res,
		float	alpha = 0.95,
		float	beta = 0.05
	)

Parameters

res
alpha
beta

Returns

calcAlignedTverskyComboScore()

float CDPL.Shape.calcAlignedTverskyComboScore	(	AlignmentResult	res,
		float	beta = 0.95
	)

Parameters

res
beta

Returns

calcReferenceTverskyComboScore()

float CDPL.Shape.calcReferenceTverskyComboScore	(	AlignmentResult	res,
		float	alpha = 0.95
	)

Parameters

res
alpha

Returns

calcShapeTanimotoScore()

float CDPL.Shape.calcShapeTanimotoScore

(

AlignmentResult

res

)

Parameters

res

Returns

calcTotalOverlapTanimotoScore()

float CDPL.Shape.calcTotalOverlapTanimotoScore

(

AlignmentResult

res

)

Parameters

res

Returns

calcColorTanimotoScore()

float CDPL.Shape.calcColorTanimotoScore

(

AlignmentResult

res

)

Parameters

res

Returns

calcShapeTverskyScore()

float CDPL.Shape.calcShapeTverskyScore	(	AlignmentResult	res,
		float	alpha = 0.95,
		float	beta = 0.05
	)

Parameters

res
alpha
beta

Returns

calcAlignedShapeTverskyScore()

float CDPL.Shape.calcAlignedShapeTverskyScore	(	AlignmentResult	res,
		float	beta = 0.95
	)

Parameters

res
beta

Returns

calcReferenceShapeTverskyScore()

float CDPL.Shape.calcReferenceShapeTverskyScore	(	AlignmentResult	res,
		float	alpha = 0.95
	)

Parameters

res
alpha

Returns

calcTotalOverlapTverskyScore()

float CDPL.Shape.calcTotalOverlapTverskyScore	(	AlignmentResult	res,
		float	alpha = 0.95,
		float	beta = 0.05
	)

Parameters

res
alpha
beta

Returns

calcAlignedTotalOverlapTverskyScore()

float CDPL.Shape.calcAlignedTotalOverlapTverskyScore	(	AlignmentResult	res,
		float	beta = 0.95
	)

Parameters

res
beta

Returns

calcReferenceTotalOverlapTverskyScore()

float CDPL.Shape.calcReferenceTotalOverlapTverskyScore	(	AlignmentResult	res,
		float	alpha = 0.95
	)

Parameters

res
alpha

Returns

calcColorTverskyScore()

float CDPL.Shape.calcColorTverskyScore	(	AlignmentResult	res,
		float	alpha = 0.95,
		float	beta = 0.05
	)

Parameters

res
alpha
beta

Returns

calcAlignedColorTverskyScore()

float CDPL.Shape.calcAlignedColorTverskyScore	(	AlignmentResult	res,
		float	beta = 0.95
	)

Parameters

res
beta

Returns

calcReferenceColorTverskyScore()

float CDPL.Shape.calcReferenceColorTverskyScore	(	AlignmentResult	res,
		float	alpha = 0.95
	)

Parameters

res
alpha

Returns

generateGaussianShape() [1/3]

None CDPL.Shape.generateGaussianShape	(	Chem.AtomContainer	atoms,
		GaussianShape	shape,
		bool	append = False,
		float	radius = -1.0,
		bool	inc_h = False,
		float	p = 2.7
	)

Parameters

atoms
shape
append
radius
inc_h
p

generateGaussianShape() [2/3]

None CDPL.Shape.generateGaussianShape	(	Chem.AtomContainer	atoms,
		GaussianShape	shape,
		Chem.Atom3DCoordinatesFunction	coords_func,
		bool	append = False,
		float	radius = -1.0,
		bool	inc_h = False,
		float	p = 2.7
	)

Parameters

atoms
shape
coords_func
append
radius
inc_h
p

generateGaussianShape() [3/3]

None CDPL.Shape.generateGaussianShape	(	Pharm.FeatureContainer	features,
		GaussianShape	shape,
		bool	append = False,
		float	radius = -1.0,
		bool	inc_xv = False,
		float	p = 5.0
	)

Parameters

features
shape
append
radius
inc_xv
p

calcCenterAlignmentTransforms()

int CDPL.Shape.calcCenterAlignmentTransforms	(	GaussianShapeFunction	func,
		Math.Matrix4D	to_ctr_xform,
		Math.Matrix4D	from_ctr_xform,
		float	mom_eq_thresh = 0.15
	)

Parameters

func
to_ctr_xform
from_ctr_xform
mom_eq_thresh

Returns

transform()

None CDPL.Shape.transform	(	GaussianShape	shape,
		Math.Matrix4D	xform
	)

Parameters

shape
xform

centerAndAlignPrincipalAxes()

int CDPL.Shape.centerAndAlignPrincipalAxes	(	GaussianShape	shape,
		GaussianShapeFunction	func,
		Math.Matrix4D	back_xform,
		float	mom_eq_thresh = 0.15
	)

Parameters

shape
func
back_xform
mom_eq_thresh

Returns

calcQuadrupoleTensorEigenDecomposition()

None CDPL.Shape.calcQuadrupoleTensorEigenDecomposition	(	Math.Matrix3D	quad_tensor,
		Math.Matrix3D	eigen_vecs,
		Math.Vector3D	eigen_vals
	)

Parameters

quad_tensor
eigen_vecs
eigen_vals

calcPrincipalAxes()

None CDPL.Shape.calcPrincipalAxes	(	Math.Matrix3D	quad_tensor,
		Math.Vector3D	x_axis,
		Math.Vector3D	y_axis,
		Math.Vector3D	z_axis,
		Math.Vector3D	moments
	)

Parameters

quad_tensor
x_axis
y_axis
z_axis
moments

matrixToQuaternion()

None CDPL.Shape.matrixToQuaternion	(	Math.Matrix4D	mtx,
		Math.Vector7D	quat
	)

Parameters

mtx
quat

perceiveSymmetryClass()

int CDPL.Shape.perceiveSymmetryClass	(	Math.Vector3D	moments,
		float	eq_thresh = 0.15
	)

Parameters

moments
eq_thresh

Returns

quaternionToMatrix()

None CDPL.Shape.quaternionToMatrix	(	Math.Vector7D	quat,
		Math.Matrix4D	mtx
	)

Parameters

quat
mtx