ost::mol::alg::trajectory_analysis Namespace Reference
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 |
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t, |
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sele, |
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first = 0 , |
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last = -1 | |
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def ost::mol::alg::trajectory_analysis::AverageDistanceMatrixFromTraj |
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t, |
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sele, |
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first = 0 , |
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last = -1 | |
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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 |
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distances, |
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p = 2 | |
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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 |
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t, |
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sele, |
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ref_sele, |
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radius = 7.0 , |
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average = False , |
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seq_sep = 4 , |
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first = 0 , |
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last = -1 | |
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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 |
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t, |
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sele, |
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threshold = 1.0 , |
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initial_sele = None , |
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iterations = 5 , |
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ref_frame = 0 | |
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def ost::mol::alg::trajectory_analysis::PairwiseDistancesFromTraj |
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t, |
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sele, |
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first = 0 , |
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last = -1 , |
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seq_sep = 1 | |
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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 |
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t, |
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sele, |
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first = 0 , |
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last = -1 , |
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align = True , |
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align_sele = None | |
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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 |
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vec, |
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n | |
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