Client Plane Angular Oscillations

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A command-line interface for Molecular Dynamics Analysis routines.

version: 0.11.2

Calculate angular oscillation of a plane along the trajectory.

A plane is defined by the centers of geometry of three atom selection groups. The angle between that plane in each frame and itself in the reference frame is computed. Angle can be reported in degrees (default) or radians.

Algorithm

Plane equation is computed by libcalc.calc_plane_eq. Angle between planes is computed by libcalc.calc_planes_angle. Refer to our documentation page for more details.

Examples

Given a protein of 3 subunits (chains or segids) calculate the angle variation of a plane that crosses the protein longitudinally:

taurenmd pangle top.pdb traj.xtc -z 'segid A' 'segid B' 'segid C' -x

-x exports the data to a CSV file. You can also plot the data with the -v option:

[...] -v title=my-plot-title xlabel=frames ylabel=degrees ...

where [...] is the previous command example.

pangle can be run directly as main command instead of subroutine:

tmdpangle

References

usage: tmdpangle [-h] [-v] [-i] -z PLANE_SELECTION PLANE_SELECTION
                 PLANE_SELECTION [-a {degrees,radians}] [-r REF_FRAME]
                 [-s START] [-e STOP] [-p STEP] [-x [EXPORT]]
                 [--plot [PLOT [PLOT ...]]]
                 topology trajectories [trajectories ...]

Positional Arguments

topology

Path to the topology file.

trajectories

Path to the trajectory files. If multiple files are given, trajectories will be concatenated by input order.

Named Arguments

-v, --version

show program’s version number and exit

-i, --insort

Sorts input trajectories paths according to their tail numbers, if paths are formatted as follows: my_trajectory_#.dcd, where # is a number. Defaults to False.

Default: False

-z, --plane-selection

Three selection strings representing three atom regions. The plane is defined by the three centres of geometry of the three selections. For example: -z ‘segid A’ ‘segid B’ ‘segid C’.

-a, --aunit

Possible choices: degrees, radians

Angular unit, either degrees or radians.

Default: “degrees”

-r, --ref-frame

The frame in the trajectory that serves as reference to compute against.Defaults to 0.

Default: 0

-s, --start

The starting index for the frame slicing. Frames are 0-indexed, so the first frame is -s 0. The starting index is inclusive. Defaults to None, considers from the beginning.

-e, --stop

The ending index for the frame slicing. Frames are 0-indexed, so the last frame of a 500 frame trajectory is index 499, but because the ending index is exclusive, -e 500 is required. Defaults to None, considers to the end.

-p, --step

The periodicity step value for the frame slicing, -p 10 means every 10 frames. Defaults to None, considers every 1 frame.

-x, --export

Export calculated values to a CSV file. Defaults to ‘results.csv’, alternatively, you can give a specific file name.

Default: False

--plot

Plot results. Additional arguments can be given to configure the plot style. Example: –plot xlabel=frames ylabel=RMSD color=red.Accepted plot arguments are defined by the function used to plot the result. The main description of this client which plotting function is used. Defaults to None, no plot is produced.

Default: False