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Functions
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.