ost.mol.alg.trajectory_analysis Namespace Reference

Functions
def	smooth
def	RMSD_Matrix_From_Traj
def	PairwiseDistancesFromTraj
def	DistanceMatrixFromPairwiseDistances
def	DistRMSDFromTraj
def	AverageDistanceMatrixFromTraj
def	AnalyzeDistanceFluctuationMatrix
def	IterativeSuperposition

Detailed Description

**This Module requires numpy**

This module contains functions to analyze trajectories, mainly 
similiraty measures baed on RMSDS and pairwise distances.

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

Function Documentation

def ost.mol.alg.trajectory_analysis.AnalyzeDistanceFluctuationMatrix	(		t,
			sele,
			first = 0,
			last = -1
	)

Definition at line 264 of file trajectory_analysis.py.

def ost.mol.alg.trajectory_analysis.AverageDistanceMatrixFromTraj	(		t,
			sele,
			first = 0,
			last = -1
	)

This function calcultes the distance between each pair of atoms
in **sele**, averaged over the trajectory **t**.

:param t: the trajectory
:param sele: the selection used to determine the atom pairs
:param first: the first frame of t to be used
:param last: the last frame of t to be used
:type t: :class:`~ost.mol.CoordGroupHandle`
:type sele: :class:`~ost.mol.EntityView`
:type first: :class:`int`
:type last: :class:`int`

:return: a numpy N\ :subscript:`pairs`\ xN\ :subscript:`pairs` matrix, where N\ :subscript:`pairs`
 is the number of atom pairs in **sele**.

Definition at line 232 of file trajectory_analysis.py.

def ost.mol.alg.trajectory_analysis.DistanceMatrixFromPairwiseDistances	(		distances,
			p = 2
	)

This function calculates an distance matrix M(N\ :subscript:`frames`\ xN\ :subscript:`frames`\ ) from
the pairwise distances matrix D(N\ :subscript:`pairs`\ xN\ :subscript:`frames`\ ), where 
N\ :subscript:`frames` is the number of frames in the trajectory
and N\ :subscript:`pairs` the number of atom pairs.
M[i,j] is the distance between frame i and frame j
calculated as a p-norm of the differences in distances
from the two frames (distance-RMSD for p=2).

:param distances: a pairwise distance matrix as obtained from 
 :py:func:`~mol.alg.trajectory_analysis.PairwiseDistancesFromTraj`
:param p: exponent used for the p-norm.

:return: a numpy N\ :subscript:`frames`\ xN\ :subscript:`frames` matrix, where N\ :subscript:`frames`
 is the number of frames.

Definition at line 140 of file trajectory_analysis.py.

def ost.mol.alg.trajectory_analysis.DistRMSDFromTraj	(		t,
			sele,
			ref_sele,
			radius = 7.0,
			average = False,
			seq_sep = 4,
			first = 0,
			last = -1
	)

This function calculates the distance RMSD from a trajectory.
The distances selected for the calculation are all the distances
between pair of atoms from residues that are at least **seq_sep** apart
in the sequence and that are smaller than **radius** in **ref_sel**.
The number and order of atoms in **ref_sele** and **sele** should be the same.

:param t: the trajectory
:param sele: the selection used to calculate the distance RMSD
:param ref_sele: the reference selection used to determine the atom pairs and reference distances
:param radius: the upper limit of distances in ref_sele considered for the calculation
:param seq_sep: the minimal sequence separation between atom pairs considered for the calculation 
:param average: use the average distance in the trajectory as reference instead of the distance obtained from ref_sele
:param first: the first frame of t to be used
:param last: the last frame of t to be used

:type t: :class:`~ost.mol.CoordGroupHandle`
:type sele: :class:`~ost.mol.EntityView`
:type ref_sele: :class:`~ost.mol.EntityView`
:type radius: :class:`float`
:type average: :class:`bool`
:type first: :class:`int`
:type last: :class:`int`
:type seq_sep: :class:`int`

:return: a numpy vecor dist_rmsd(N\ :subscript:`frames`).  

Definition at line 173 of file trajectory_analysis.py.

def ost.mol.alg.trajectory_analysis.IterativeSuperposition	(		t,
			sele,
			threshold = 1.0,
			initial_sele = None,
			iterations = 5,
			ref_frame = 0
	)

Definition at line 280 of file trajectory_analysis.py.

def ost.mol.alg.trajectory_analysis.PairwiseDistancesFromTraj	(		t,
			sele,
			first = 0,
			last = -1,
			seq_sep = 1
	)

This function calculates the distances between any pair of atoms in **sele**  
with sequence separation larger than **seq_sep** from a trajectory **t**.
It return a matrix containing one line for each atom pair and N\ :subscript:`frames` columns, where
N\ :subscript:`frames` is the number of frames in the trajectory.

:param t: the trajectory
:param sele: the selection used to determine the atom pairs
:param first: the first frame of t to be used
:param last: the last frame of t to be used
:param seq_sep: The minimal sequence separation between atom pairs
:type t: :class:`~ost.mol.CoordGroupHandle`
:type sele: :class:`~ost.mol.EntityView`
:type first: :class:`int`
:type last: :class:`int`
:type seq_sep: :class:`int`

:return: a numpy N\ :subscript:`pairs`\ xN\ :subscript:`frames` matrix.

Definition at line 97 of file trajectory_analysis.py.

def ost.mol.alg.trajectory_analysis.RMSD_Matrix_From_Traj	(		t,
			sele,
			first = 0,
			last = -1,
			align = True,
			align_sele = None
	)

This function calculates a matrix M such that M[i,j] is the
RMSD (calculated on **sele**) between frames i and j of the trajectory **t**
aligned on sele.

:param t: the trajectory
:param sele: the selection used for alignment and RMSD calculation
:param first: the first frame of t to be used
:param last: the last frame of t to be used
:type t: :class:`~ost.mol.CoordGroupHandle`
:type sele: :class:`~ost.mol.EntityView`
:type first: :class:`int`
:type last: :class:`int`

:return: Returns a numpy N\ :subscript:`frames`\ xN\ :subscript:`frames` matrix, 
 where N\ :subscript:`frames` is the number of frames.

Definition at line 58 of file trajectory_analysis.py.

def ost.mol.alg.trajectory_analysis.smooth	(		vec,
			n
	)

Definition at line 15 of file trajectory_analysis.py.