ost.mol.alg.trajectory_analysis Namespace Reference

Functions
def	smooth
def	RMSD_Matrix_From_Traj
def	PairwiseDistancesFromTraj
def	DistanceMatrixFromPairwiseDistances
def	DistRMSDFromTraj

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Detailed Description

Some functions for analyzing trajectories

Author: Niklaus Johner

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Function Documentation

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

This function calculates an distance matrix M(NxN) from
the pairwise distances matrix D(MxN), where N is the number
of frames in the trajectory and M 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).
Inputs:
  distances : a pairwise distance matrix as obtained from PairwiseDistancesFromTraj()
Returns a numpy NxN matrix, where N is the number of frames.

Definition at line 123 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 that 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.
Its inputs are:
  t       : the trajectory (CoordGroupHandle)
  sele    : the EntityView used to determine the distances from t
  radius=7  : the upper limit of distances in ref_sele considered for the calculation
  seq_sep=4 : The minimal sequence separation between atom pairs considered for the calculation 
  average=false : use the average distance in the trajectory as reference instead of the distance obtained from ref_sele
  first=0 : the first frame of t to be used
  last=-1 : the last frame of t to be used
Returns a numpy vecor dist_rmsd(Nframes).  

Definition at line 151 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 the
EntityView 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 columns, where
N is the length of the trajectory.
Its inputs are:
  t       : the trajectory (CoordGroupHandle)
  sele    : the EntityView used to determine the atom pairs
  first=0 : the first frame of t to be used
  last=-1 : the last frame of t to be used
  seq_sep=1 : The minimal sequence separation between
Returns a numpy NpairsxNframes matrix.

Definition at line 86 of file trajectory_analysis.py.

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

This function calculates a matrix M such that M[i,j] is the
RMSD of the EntityView sele between frames i and j of the trajectory t
aligned on sele.
Its inputs are:
  t       : the trajectory (CoordGroupHandle)
  sele    : the EntityView used for alignment and RMSD calculation
  first=0 : the first frame of t to be used
  last=-1 : the last frame of t to be used
Returns a numpy NxN matrix, where n is the number of frames.

Definition at line 55 of file trajectory_analysis.py.

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

Definition at line 12 of file trajectory_analysis.py.