ost.mol.alg.structure_analysis Namespace Reference

Functions
def	GetFrameFromEntity
def	GetDistanceBetwCenterOfMass
def	GetMinDistanceBetweenViews
def	GetMinDistBetwCenterOfMassAndView
def	GetAlphaHelixContent
def	CalculateBestFitLine
def	CalculateBestFitPlane
def	CalculateHelixAxis
def	CalculateDistanceDifferenceMatrix

Detailed Description

Some functions for analyzing structures

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

Function Documentation

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.

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.

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.

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.

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.

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.

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.

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.

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.