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

Classes
class	AlignedColorTverskyScore
	Functor wrapping Shape.calcAlignedColorTverskyScore(). More...

class	AlignedShapeTverskyScore
	Functor wrapping Shape.calcAlignedShapeTverskyScore(). More...

class	AlignedTotalOverlapTverskyScore
	Functor wrapping Shape.calcAlignedTotalOverlapTverskyScore(). More...

class	AlignedTverskyComboScore
	Functor wrapping Shape.calcAlignedTverskyComboScore(). More...

class	AlignmentResult
	Result of a Gaussian-shape alignment between a reference and an aligned shape. More...

class	AlignmentResultSelectionMode
	Provides constants for selecting which alignment results are kept by alignment routines. More...

class	BoolAlignmentResult2Functor

class	BoolSizeType2Functor

class	BoolSizeTypeFunctor

class	ColorTanimotoScore
	Functor wrapping Shape.calcColorTanimotoScore(). More...

class	ColorTverskyScore
	Functor wrapping Shape.calcColorTverskyScore(). More...

class	DoubleAlignmentResultFunctor

class	ExactGaussianShapeOverlapFunction
	Shape.GaussianShapeOverlapFunction implementation that evaluates the overlap analytically using the full Gaussian-product expansion (no approximations). More...

class	FastGaussianShapeAlignment
	High-level driver for the fast alignment of Gaussian shapes against a set of reference shapes. More...

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

class	GaussianShape
	Data type for the descripton of arbitrary shapes composed of spheres approximated by gaussian functions. More...

class	GaussianShapeAlignment
	High-level driver for the alignment of Gaussian shapes against a set of reference shapes. More...

class	GaussianShapeAlignmentStartGenerator
	Abstract base class for generators of starting transformations used to seed Gaussian-shape overlap optimization. More...

class	GaussianShapeFunction
	Function representation of a Gaussian shape, used to evaluate the shape's density, volume, surface area and related quantities at arbitrary 3D positions. More...

class	GaussianShapeFunctionAlignment
	Driver for the alignment of one Shape.GaussianShapeFunction (the aligned shape) against a fixed reference Shape.GaussianShapeFunction. More...

class	GaussianShapeGenerator
	Generates Shape.GaussianShape instances from molecular graphs. More...

class	GaussianShapeOverlapFunction
	Abstract base class for functions evaluating the overlap between two Gaussian shape functions. More...

class	GaussianShapeSet
	Data structure storing a set of (shared) Gaussian shapes. More...

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

class	ReferenceColorTverskyScore
	Functor wrapping Shape.calcReferenceColorTverskyScore(). More...

class	ReferenceShapeTverskyScore
	Functor wrapping Shape.calcReferenceShapeTverskyScore(). More...

class	ReferenceTotalOverlapTverskyScore
	Functor wrapping Shape.calcReferenceTotalOverlapTverskyScore(). More...

class	ReferenceTverskyComboScore
	Functor wrapping Shape.calcReferenceTverskyComboScore(). More...

class	ScreeningProcessor
	High-level driver for shape-based virtual screening of molecular databases. More...

class	ScreeningSettings
	Bundle of configuration parameters for Shape.ScreeningProcessor. More...

class	ShapeTanimotoScore
	Functor wrapping Shape.calcShapeTanimotoScore(). More...

class	ShapeTverskyScore
	Functor wrapping Shape.calcShapeTverskyScore(). More...

class	SymmetryClass
	Provides constants for the rotational symmetry class of a Gaussian shape. More...

class	TanimotoComboScore
	Functor wrapping Shape.calcTanimotoComboScore(). More...

class	TotalOverlapTanimotoScore
	Functor wrapping Shape.calcTotalOverlapTanimotoScore(). More...

class	TotalOverlapTverskyScore
	Functor wrapping Shape.calcTotalOverlapTverskyScore(). More...

class	TverskyComboScore
	Functor wrapping Shape.calcTverskyComboScore(). More...

class	Vector7D

class	VoidMolecularGraph2AlignmentResultFunctor

Functions
float	calcAlignedColorTverskyScore (AlignmentResult res, float beta=0.95)
	Returns the color (pharmacophore) aligned-normalized Tversky similarity score of res. More...

float	calcAlignedShapeTverskyScore (AlignmentResult res, float beta=0.95)
	Returns the shape-only aligned-normalized Tversky similarity score of res. More...

float	calcAlignedTotalOverlapTverskyScore (AlignmentResult res, float beta=0.95)
	Returns the (shape + color) total-overlap aligned-normalized Tversky similarity score of res. More...

float	calcAlignedTverskyComboScore (AlignmentResult res, float beta=0.95)
	Returns the combined shape + color aligned-normalized Tversky score of res. More...

int	calcCenterAlignmentTransforms (GaussianShapeFunction func, Math.Matrix4D to_ctr_xform, Math.Matrix4D from_ctr_xform, float mom_eq_thresh=0.15)
	Calculates the affine transformations that align a Gaussian shape to its center of mass and back. More...

float	calcColorTanimotoScore (AlignmentResult res)
	Returns the color (pharmacophore) Tanimoto similarity score of res. More...

float	calcColorTverskyScore (AlignmentResult res, float alpha=0.95, float beta=0.05)
	Returns the color (pharmacophore) symmetric Tversky similarity score of res. More...

None	calcPrincipalAxes (Math.Matrix3D quad_tensor, Math.Vector3D x_axis, Math.Vector3D y_axis, Math.Vector3D z_axis, Math.Vector3D moments)
	Calculates the principal axes and principal moments of a quadrupole tensor. More...

None	calcQuadrupoleTensorEigenDecomposition (Math.Matrix3D quad_tensor, Math.Matrix3D eigen_vecs, Math.Vector3D eigen_vals)
	Calculates the eigen-decomposition of a 3x3 quadrupole tensor. More...

float	calcReferenceColorTverskyScore (AlignmentResult res, float alpha=0.95)
	Returns the color (pharmacophore) reference-normalized Tversky similarity score of res. More...

float	calcReferenceShapeTverskyScore (AlignmentResult res, float alpha=0.95)
	Returns the shape-only reference-normalized Tversky similarity score of res. More...

float	calcReferenceTotalOverlapTverskyScore (AlignmentResult res, float alpha=0.95)
	Returns the (shape + color) total-overlap reference-normalized Tversky similarity score of res. More...

float	calcReferenceTverskyComboScore (AlignmentResult res, float alpha=0.95)
	Returns the combined shape + color reference-normalized Tversky score of res. More...

float	calcShapeTanimotoScore (AlignmentResult res)
	Returns the shape-only Tanimoto similarity score of res. More...

float	calcShapeTverskyScore (AlignmentResult res, float alpha=0.95, float beta=0.05)
	Returns the shape-only symmetric Tversky similarity score of res. More...

float	calcTanimotoComboScore (AlignmentResult res)
	Returns the combined shape + color Tanimoto score of res. More...

float	calcTotalOverlapTanimotoScore (AlignmentResult res)
	Returns the (shape + color) total-overlap Tanimoto similarity score of res. More...

float	calcTotalOverlapTverskyScore (AlignmentResult res, float alpha=0.95, float beta=0.05)
	Returns the (shape + color) total-overlap symmetric Tversky similarity score of res. More...

float	calcTverskyComboScore (AlignmentResult res, float alpha=0.95, float beta=0.05)
	Returns the combined shape + color symmetric Tversky score of res. More...

int	centerAndAlignPrincipalAxes (GaussianShape shape, GaussianShapeFunction func, Math.Matrix4D back_xform, float mom_eq_thresh=0.15)
	Centers shape at its centroid and aligns its principal axes with the coordinate axes. More...

None	generateGaussianShape (Chem.AtomContainer atoms, GaussianShape shape, bool append=False, float radius=-1.0, bool inc_h=False, float p=2.7)
	Builds a Gaussian shape from the atoms of atoms (using the default atom 3D coordinates accessor). More...

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)
	Builds a Gaussian shape from the atoms of atoms using coords_func to retrieve atom positions. More...

None	generateGaussianShape (Pharm.FeatureContainer features, GaussianShape shape, bool append=False, float radius=-1.0, bool inc_xv=False, float p=5.0)
	Builds a Gaussian shape from the pharmacophore features of features. More...

None	matrixToQuaternion (Math.Matrix4D mtx, Math.Vector7D quat)
	Converts an affine 4x4 transformation matrix to a quaternion-plus-translation representation. More...

int	perceiveSymmetryClass (Math.Vector3D moments, float eq_thresh=0.15)
	Classifies the rotational symmetry of a shape from its principal moments (see namespace Shape.SymmetryClass). More...

None	quaternionToMatrix (Math.Vector7D quat, Math.Matrix4D mtx)
	Converts a quaternion-plus-translation representation back to an affine 4x4 transformation matrix. More...

None	transform (GaussianShape shape, Math.Matrix4D xform)
	Applies an affine transformation to the element positions of shape. More...

Detailed Description

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

Function Documentation

◆ calcAlignedColorTverskyScore()

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

Returns the color (pharmacophore) aligned-normalized Tversky similarity score of res.

Parameters

res	The alignment result.
beta	The aligned-side Tversky weighting factor.

Returns: The color aligned-normalized Tversky similarity score.

◆ calcAlignedShapeTverskyScore()

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

Returns the shape-only aligned-normalized Tversky similarity score of res.

Parameters

res	The alignment result.
beta	The aligned-side Tversky weighting factor.

Returns: The shape-only aligned-normalized Tversky similarity score.

◆ calcAlignedTotalOverlapTverskyScore()

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

Returns the (shape + color) total-overlap aligned-normalized Tversky similarity score of res.

Parameters

res	The alignment result.
beta	The aligned-side Tversky weighting factor.

Returns: The total-overlap aligned-normalized Tversky similarity score.

◆ calcAlignedTverskyComboScore()

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

Returns the combined shape + color aligned-normalized Tversky score of res.

Parameters

res	The alignment result.
beta	The aligned-side Tversky weighting factor.

Returns: The aligned-normalized Tversky combo score (sum of shape and color aligned-Tversky scores).

◆ calcCenterAlignmentTransforms()

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

Calculates the affine transformations that align a Gaussian shape to its center of mass and back.

Parameters

func	The Gaussian shape function.
to_ctr_xform	The output transformation that places the shape at its center of mass with principal axes aligned to the coordinate axes.
from_ctr_xform	The output inverse transformation.
mom_eq_thresh	The relative threshold below which two principal moments are considered equal.

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

◆ calcColorTanimotoScore()

float CDPL.Shape.calcColorTanimotoScore ( AlignmentResult res )

Returns the color (pharmacophore) Tanimoto similarity score of res.

Parameters

res	The alignment result.

Returns: The color Tanimoto similarity score.

◆ calcColorTverskyScore()

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

Returns the color (pharmacophore) symmetric Tversky similarity score of res.

Parameters

res	The alignment result.
alpha	The weight of the reference self-overlap contribution.
beta	The weight of the aligned self-overlap contribution.

Returns: The color symmetric Tversky similarity score.

◆ calcPrincipalAxes()

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

Calculates the principal axes and principal moments of a quadrupole tensor.

Parameters

quad_tensor	The input symmetric quadrupole tensor.
x_axis	The output principal x-axis.
y_axis	The output principal y-axis.
z_axis	The output principal z-axis.
moments	The output principal moments.

◆ calcQuadrupoleTensorEigenDecomposition()

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

Calculates the eigen-decomposition of a 3x3 quadrupole tensor.

Parameters

quad_tensor	The input symmetric quadrupole tensor.
eigen_vecs	The output eigenvector matrix (columns are eigenvectors).
eigen_vals	The output eigenvalues.

◆ calcReferenceColorTverskyScore()

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

Returns the color (pharmacophore) reference-normalized Tversky similarity score of res.

Parameters

res	The alignment result.
alpha	The reference-side Tversky weighting factor.

Returns: The color reference-normalized Tversky similarity score.

◆ calcReferenceShapeTverskyScore()

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

Returns the shape-only reference-normalized Tversky similarity score of res.

Parameters

res	The alignment result.
alpha	The reference-side Tversky weighting factor.

Returns: The shape-only reference-normalized Tversky similarity score.

◆ calcReferenceTotalOverlapTverskyScore()

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

Returns the (shape + color) total-overlap reference-normalized Tversky similarity score of res.

Parameters

res	The alignment result.
alpha	The reference-side Tversky weighting factor.

Returns: The total-overlap reference-normalized Tversky similarity score.

◆ calcReferenceTverskyComboScore()

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

Returns the combined shape + color reference-normalized Tversky score of res.

Parameters

res	The alignment result.
alpha	The reference-side Tversky weighting factor.

Returns: The reference-normalized Tversky combo score (sum of shape and color reference-Tversky scores).

◆ calcShapeTanimotoScore()

float CDPL.Shape.calcShapeTanimotoScore ( AlignmentResult res )

Returns the shape-only Tanimoto similarity score of res.

Parameters

res	The alignment result.

Returns: The shape-only Tanimoto similarity score.

◆ calcShapeTverskyScore()

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

Returns the shape-only symmetric Tversky similarity score of res.

Parameters

res	The alignment result.
alpha	The weight of the reference self-overlap contribution.
beta	The weight of the aligned self-overlap contribution.

Returns: The shape-only symmetric Tversky similarity score.

◆ calcTanimotoComboScore()

float CDPL.Shape.calcTanimotoComboScore ( AlignmentResult res )

Returns the combined shape + color Tanimoto score of res.

Parameters

res	The alignment result.

Returns: The Tanimoto combo score (sum of shape and color Tanimoto scores).

◆ calcTotalOverlapTanimotoScore()

float CDPL.Shape.calcTotalOverlapTanimotoScore ( AlignmentResult res )

Returns the (shape + color) total-overlap Tanimoto similarity score of res.

Parameters

res	The alignment result.

Returns: The total-overlap Tanimoto similarity score.

◆ calcTotalOverlapTverskyScore()

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

Returns the (shape + color) total-overlap symmetric Tversky similarity score of res.

Parameters

res	The alignment result.
alpha	The weight of the reference self-overlap contribution.
beta	The weight of the aligned self-overlap contribution.

Returns: The total-overlap symmetric Tversky similarity score.

◆ calcTverskyComboScore()

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

Returns the combined shape + color symmetric Tversky score of res.

Parameters

res	The alignment result.
alpha	The weight of the reference self-overlap contribution.
beta	The weight of the aligned self-overlap contribution.

Returns: The symmetric Tversky combo score (sum of shape and color Tversky scores).

◆ centerAndAlignPrincipalAxes()

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

Centers shape at its centroid and aligns its principal axes with the coordinate axes.

Parameters

shape	The Gaussian shape to align (modified in place).
func	The associated Shape.GaussianShapeFunction used to compute the principal axes.
back_xform	The output transformation that maps the aligned shape back to its original frame.
mom_eq_thresh	The relative threshold below which two principal moments are considered equal.

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

◆ 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`
	)

Builds a Gaussian shape from the atoms of atoms (using the default atom 3D coordinates accessor).

Parameters

atoms	The atom container.
shape	The output Gaussian shape.
append	If `True`, the new elements are appended to shape. Otherwise, shape is cleared first.
radius	The sphere radius to use for all atoms, or a negative value to use atom-specific Van der Waals radii.
inc_h	If `True`, hydrogen atoms are also included in the shape.
p	The Gaussian hardness used for all generated spheres.

◆ 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`
	)

Builds a Gaussian shape from the atoms of atoms using coords_func to retrieve atom positions.

Parameters

atoms	The atom container.
shape	The output Gaussian shape.
coords_func	The function used to retrieve atom 3D-coordinates.
append	If `True`, the new elements are appended to shape. Otherwise, shape is cleared first.
radius	The sphere radius to use for all atoms, or a negative value to use atom-specific Van der Waals radii.
inc_h	If `True`, hydrogen atoms are also included in the shape.
p	The Gaussian hardness used for all generated spheres.

◆ 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`
	)

Builds a Gaussian shape from the pharmacophore features of features.

Parameters

features	The feature container.
shape	The output Gaussian shape.
append	If `True`, the new elements are appended to shape. Otherwise, shape is cleared first.
radius	The sphere radius to use for all features, or a negative value to use feature-specific tolerances.
inc_xv	If `True`, exclusion-volume features are also included in the shape.
p	The Gaussian hardness used for all generated spheres.

◆ matrixToQuaternion()

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

Converts an affine 4x4 transformation matrix to a quaternion-plus-translation representation.

Parameters

mtx	The input transformation matrix.
quat	The output Shape.QuaternionTransformation (4 quaternion + 3 translation components).

◆ perceiveSymmetryClass()

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

Classifies the rotational symmetry of a shape from its principal moments (see namespace Shape.SymmetryClass).

Parameters

moments	The principal moments.
eq_thresh	The relative threshold below which two moments are considered equal.

Returns: The perceived symmetry class.

◆ quaternionToMatrix()

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

Converts a quaternion-plus-translation representation back to an affine 4x4 transformation matrix.

Parameters

quat	The input Shape.QuaternionTransformation (4 quaternion + 3 translation components).
mtx	The output transformation matrix.

◆ transform()

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

Applies an affine transformation to the element positions of shape.

Parameters

shape	The Gaussian shape to transform (modified in place).
xform	The 4x4 transformation matrix.

Classes

Functions

Detailed Description

Function Documentation

◆ calcAlignedColorTverskyScore()

◆ calcAlignedShapeTverskyScore()

◆ calcAlignedTotalOverlapTverskyScore()

◆ calcAlignedTverskyComboScore()

◆ calcCenterAlignmentTransforms()

◆ calcColorTanimotoScore()

◆ calcColorTverskyScore()

◆ calcPrincipalAxes()

◆ calcQuadrupoleTensorEigenDecomposition()

◆ calcReferenceColorTverskyScore()

◆ calcReferenceShapeTverskyScore()

◆ calcReferenceTotalOverlapTverskyScore()

◆ calcReferenceTverskyComboScore()

◆ calcShapeTanimotoScore()

◆ calcShapeTverskyScore()

◆ calcTanimotoComboScore()

◆ calcTotalOverlapTanimotoScore()

◆ calcTotalOverlapTverskyScore()

◆ calcTverskyComboScore()

◆ centerAndAlignPrincipalAxes()

◆ generateGaussianShape() [1/3]

◆ generateGaussianShape() [2/3]

◆ generateGaussianShape() [3/3]

◆ matrixToQuaternion()

◆ perceiveSymmetryClass()

◆ quaternionToMatrix()

◆ transform()