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