Chemical Data Processing Library Python API - Version 1.1.1
Classes | Functions
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