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Chemical Data Processing Library C++ API - Version 1.1.1
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CDPL::Shape Namespace Reference

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

Namespaces

 AlignmentResultSelectionMode
 
 SymmetryClass
 

Classes

class  AlignedColorTverskyScore
 
class  AlignedShapeTverskyScore
 
class  AlignedTotalOverlapTverskyScore
 
class  AlignedTverskyComboScore
 
class  AlignmentResult
 
class  ColorTanimotoScore
 
class  ColorTverskyScore
 
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  TanimotoComboScore
 
class  TotalOverlapTanimotoScore
 
class  TotalOverlapTverskyScore
 
class  TverskyComboScore
 

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 
)
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