ost.mol.alg.structure_analysis Namespace Reference

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

---

Detailed Description

Some functions for analyzing trajectories

Author: Niklaus Johner

---

Function Documentation

def ost.mol.alg.structure_analysis.CalculateBestFitLine

(

sele1

)

This function calculates the best fit line to the atoms in sele1.
Input:
  sele1 : EntityView
It returns a geom::Line3

Definition at line 88 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.
Input:
  sele1 : EntityView
It returns a geom::Plane

Definition at line 102 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 as a Line3.  residues should be ordered correctly
in the EntityView.
Input:
  sele1 : EntityView
It returns a geom::Line3

Definition at line 116 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)
Input:
  sele1 : EntityView

Definition at line 73 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.
Input:
  sele1 : EntityView
  sele2 : EntityView

Definition at line 18 of file structure_analysis.py.

def ost.mol.alg.structure_analysis.GetFrameFromEntity

(

eh

)

This function returns a CoordFrame from an EntityHandle
Input:
  eh : EntityHandle

Definition at line 10 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.
Input:
  sele1 : EntityView
  sele2 : EntityView

Definition at line 36 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.
Input:
  sele1 : EntityView from which the center of mass is taken
  sele2 : EntityView

Definition at line 54 of file structure_analysis.py.