Functions
def	GetFrameFromEntity (eh)

def	GetDistanceBetwCenterOfMass (sele1, sele2)

def	GetMinDistanceBetweenViews (sele1, sele2)

def	GetMinDistBetwCenterOfMassAndView (sele1, sele2)

def	GetAlphaHelixContent (sele1)

def	CalculateBestFitLine (sele1)

def	CalculateBestFitPlane (sele1)

def	CalculateHelixAxis (sele1)

def	CalculateDistanceDifferenceMatrix (sele1, sele2)

Detailed Description

Some functions for analyzing structures

Author: Niklaus Johner (Niklaus.Johner@unibas.ch)

Function Documentation

◆ CalculateBestFitLine()

def ost.mol.alg.structure_analysis.CalculateBestFitLine ( sele1 )

This function calculates the best fit line to the atoms in **sele1**.

:param sele1:
:type sele1: :class:`~ost.mol.EntityView`

:return: :class:`~ost.geom.Line3`

Definition at line 105 of file structure_analysis.py.

◆ CalculateBestFitPlane()

def ost.mol.alg.structure_analysis.CalculateBestFitPlane ( sele1 )

This function calculates the best fit plane to the atoms in **sele1**.

:param sele1:
:type sele1: :class:`~ost.mol.EntityView`

:return: :class:`~ost.geom.Plane`

Definition at line 121 of file structure_analysis.py.

◆ CalculateDistanceDifferenceMatrix()

def ost.mol.alg.structure_analysis.CalculateDistanceDifferenceMatrix	(	sele1,
		sele2
	)

This function calculates the pairwise distance differences between two selections (\\ :class:`~ost.mol.EntityView`\\ ).
The two selections should have the same number of atoms
It returns an NxN DistanceDifferenceMatrix M (where N is the number of atoms in sele1)
where M[i,j]=||(sele2.atoms[i].pos-sele2.atoms[j].pos)||-||(sele1.atoms[i].pos-sele1.atoms[j].pos)||

:param sele1:
:param sele2:
:type sele1: :class:`~ost.mol.EntityView`
:type sele2: :class:`~ost.mol.EntityView`

:return: NxN numpy matrix

Definition at line 156 of file structure_analysis.py.

◆ CalculateHelixAxis()

def ost.mol.alg.structure_analysis.CalculateHelixAxis ( sele1 )

This function calculates the best fit cylinder to the CA atoms in **sele1**,
and returns its axis.  Residues should be ordered correctly
in **sele1**.

:param sele1:
:type sele1: :class:`~ost.mol.EntityView`

:return: :class:`~ost.geom.Line3`

Definition at line 137 of file structure_analysis.py.

◆ GetAlphaHelixContent()

def ost.mol.alg.structure_analysis.GetAlphaHelixContent ( sele1 )

This function calculates the content of alpha helix in a view.
All residues in the view have to ordered and adjacent (no gaps allowed)

:param sele1:
:type sele1: :class:`~ost.mol.EntityView`

:return: :class:`float`

Definition at line 87 of file structure_analysis.py.

◆ GetDistanceBetwCenterOfMass()

def ost.mol.alg.structure_analysis.GetDistanceBetwCenterOfMass	(	sele1,
		sele2
	)

This function calculates the distance between the centers of mass
of **sele1** and **sele2**, two selections from the same Entity.

:param sele1:
:param sele2:
:type sele1: :class:`~ost.mol.EntityView`
:type sele2: :class:`~ost.mol.EntityView`

:return: :class:`float`

Definition at line 20 of file structure_analysis.py.

◆ GetFrameFromEntity()

def ost.mol.alg.structure_analysis.GetFrameFromEntity ( eh )

This function returns a CoordFrame from an EntityHandle

:param eh: 
:type eh: :class:`~ost.mol.EntityHandle`

:return: :class:`ost.mol.CoordFrame`

Definition at line 9 of file structure_analysis.py.

◆ GetMinDistanceBetweenViews()

def ost.mol.alg.structure_analysis.GetMinDistanceBetweenViews	(	sele1,
		sele2
	)

This function calculates the minimal distance between
**sele1** and **sele2**, two selections from the same Entity.

:param sele1:
:param sele2:
:type sele1: :class:`~ost.mol.EntityView`
:type sele2: :class:`~ost.mol.EntityView`

:return: :class:`float`

Definition at line 42 of file structure_analysis.py.

◆ GetMinDistBetwCenterOfMassAndView()

def ost.mol.alg.structure_analysis.GetMinDistBetwCenterOfMassAndView	(	sele1,
		sele2
	)

This function calculates the minimal distance between **sele2** and
the center of mass of **sele1**, two selections from the same Entity.

:param sele1: The selection from which the center of mass is taken
:param sele2:
:type sele1: :class:`~ost.mol.EntityView`
:type sele2: :class:`~ost.mol.EntityView`

:return: distance (\\ :class:`float`\\ )

Definition at line 64 of file structure_analysis.py.

Functions