Client Frame Extract

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A command-line interface for Molecular Dynamics Analysis routines.

version: 0.11.2

Extract trajectory frames to individual files.

Normally used to extract frames to PDB topology files so those can be inspected independently.

Note

Frame number is 0-indexed.

Examples:

Extract frames 11 to 49 (inclusive), remember frames index start at 0:

taurenmd fext topology.pdb trajectory.dcd -s 10 -e 50

Extract the first frame:

taurenmd fext topology.pdb trajectory.dcd -flist 0

Extract a selection of frames:

taurenmd fext topology.pdb trajectory.dcd -flist 0,10,23,345

Frame file types can be specified:

taurenmd fext topology.pdb trajectory.dcd -p 10 -x .dcd

Atom selection can be specified as well, the following extracts only the ‘segid A’ atom region of the first frame. Selection rules are as decribed for MDAnalysis selection.

taurenmd fext topology.pdb trajectory.xtc -flist 0 -l 'segid A'

Multiple trajectories can be given, they will be contatenated:

taurenmd fext top.pdb traj1.xtc traj2.xtc traj3.xtc -p 10

Can also be used as main command:

tmdfext topology.pdb ...

References:

usage: tmdfext [-h] [-v] [-i] [-l SELECTION] [-t FLIST [FLIST ...]] [-s START]
               [-e STOP] [-p STEP] [-f PREFIX] [-x EXT] [--odir ODIR]
               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

-l, --selection

Atom selection for the output trajectory. Selection rules are as defined by the MD analysis library used by the client interface. For instructions read the main command-line client description. Defaults to ‘all’.

Default: “all”

-t, --flist

List of frames (time steps) to consider.If applicable, this can used instead of the start, stop and step slicing arguments.

Default: False

-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.

-f, --prefix

String prefix for each file. Defaults to frame_.

Default: “frame_”

-x, --ext

Extension of frame files. Defaulst to .pdb

Default: “.pdb”

--odir

Save output to directory. Creates directory if doesn’t exist. Defaults to the current working directory.

Default: /home/docs/checkouts/readthedocs.org/user_builds/taurenmd/checkouts/latest/docs