Client Distances¶

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A command-line interface for Molecular Dynamics Analysis routines.

version: 0.11.2

Calculates distances between centers of geometry of two selections.¶

Distance is given in 3D XYZ coordinate space units.

Algorithm¶

Distance between centers of geometry is calculated by::

np.linalg.norm(np.subtract(coord1, coord2))

Where, coord* are the centers of geometry of each atom selection -l1 and -l2, respectively. Read further on np.linalg.norm and np.subtract.

Examples¶

Calculate the distances between two carbon alphas:

taurenmd dist top.pdb traj.dcd -l1 'resnum 10 and name CA' -l2 'resnum 20 and name CA'

Calculate the distances between two chains:

taurenmd dist top.pdb traj.dcd -l1 'segid A' -l2 'segid B'

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

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

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

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

tmddist

References¶

MD data accessed using MDAnalysis.
selection commands follow MDAnalysis selection nomenclature.

usage: tmddist [-h] [-v] [-i] [-l1 SEL1] [-l2 [SEL2 [SEL2 ...]]] [-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

-l1, --sel1

First selection (a single selection).

Default: “all”

-l2, --sel2

Second selections. As many as desired. For example: –sel2 “segid A” “segid B and name CA”.

Default: “all”

-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