trajectory_analysis – DRMSD, Pairwise Distances and More¶

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)

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

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

Parameters:

• t (CoordGroupHandle) – the trajectory

• sele (EntityView) – the selection used to determine the atom pairs

• first (int) – the first frame of t to be used

• last (int) – the last frame of t to be used

Returns:

a numpy N_pairsxN_pairs matrix, where N_pairs is the number of atom pairs in sele.

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.

Parameters:

• t (CoordGroupHandle) – the trajectory

• sele (EntityView) – the selection used to calculate the distance RMSD

• ref_sele (EntityView) – the reference selection used to determine the atom pairs and reference distances

• radius (float) – the upper limit of distances in ref_sele considered for the calculation

• seq_sep (int) – the minimal sequence separation between atom pairs considered for the calculation

• average (bool) – use the average distance in the trajectory as reference instead of the distance obtained from ref_sele

• first (int) – the first frame of t to be used

• last (int) – the last frame of t to be used

Returns:

a numpy vecor dist_rmsd(N_frames).

DistanceMatrixFromPairwiseDistances(distances, p=2)¶

This function calculates an distance matrix M(N_framesxN_frames) from the pairwise distances matrix D(N_pairsxN_frames), where N_frames is the number of frames in the trajectory and N_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).

Parameters:

• distances – a pairwise distance matrix as obtained from PairwiseDistancesFromTraj()

• p – exponent used for the p-norm.

Returns:

a numpy N_framesxN_frames matrix, where N_frames is the number of frames.

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_frames columns, where N_frames is the number of frames in the trajectory.

Parameters:

• t (CoordGroupHandle) – the trajectory

• sele (EntityView) – the selection used to determine the atom pairs

• first (int) – the first frame of t to be used

• last (int) – the last frame of t to be used

• seq_sep (int) – The minimal sequence separation between atom pairs

Returns:

a numpy N_pairsxN_frames matrix.

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.

Parameters:

• t (CoordGroupHandle) – the trajectory

• sele (EntityView) – the selection used for alignment and RMSD calculation

• first (int) – the first frame of t to be used

• last (int) – the last frame of t to be used

Returns:

Returns a numpy N_framesxN_frames matrix, where N_frames is the number of frames.