Functions
	smooth (vec, n)

	RMSD_Matrix_From_Traj (t, sele, first=0, last=-1, align=True, align_sele=None)

	PairwiseDistancesFromTraj (t, sele, first=0, last=-1, seq_sep=1)

	DistanceMatrixFromPairwiseDistances (distances, p=2)

	DistRMSDFromTraj (t, sele, ref_sele, radius=7.0, average=False, seq_sep=4, first=0, last=-1)

	AverageDistanceMatrixFromTraj (t, sele, first=0, last=-1)

	AnalyzeDistanceFluctuationMatrix (t, sele, first=0, last=-1)

	IterativeSuperposition (t, sele, threshold=1.0, initial_sele=None, iterations=5, ref_frame=0)

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

◆ AnalyzeDistanceFluctuationMatrix()

AnalyzeDistanceFluctuationMatrix	(	t,
		sele,
		first = `0`,
		last = `-1`
	)

Definition at line 264 of file trajectory_analysis.py.

◆ AverageDistanceMatrixFromTraj()

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.

◆ DistanceMatrixFromPairwiseDistances()

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.

◆ DistRMSDFromTraj()

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.

◆ IterativeSuperposition()

IterativeSuperposition	(	t,
		sele,
		threshold = `1.0`,
		initial_sele = `None`,
		iterations = `5`,
		ref_frame = `0`
	)

Definition at line 280 of file trajectory_analysis.py.

◆ PairwiseDistancesFromTraj()

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.

◆ RMSD_Matrix_From_Traj()

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.

◆ smooth()

smooth	(	vec,
		n
	)

Definition at line 15 of file trajectory_analysis.py.

Functions