4.3. curp conv-trj
curp conv-trj [-h] [-crd | -vel] -i TRJ_FILENAME [TRJ_FILENAME ...]
-if FORMAT [--irange FIRST LAST INTER] [-o TRJ_FILENAME]
[-of FORMAT] [--orange FIRST LAST INTER] -pf FORMAT
-p TPL_FILENAME [-nf DIST_FORMAT]
{convert-only, dry-run, adjust-vel, mask, dist} ...
Various scripts to process and analyze trajectories.
4.3.1. Positional arguments
convert-only
Convert the trajectory intoother format.
dry-run
Do dry-run mode.
adjust-vel
Adjust time of the velocity trajectory to t from t-dt/2.
mask
Remove solvent from trajectory.
dist
Calculate inter-residue distances.
4.3.2. Common options
- -h, –help
Show this help message and exit.
- -crd
Specify the format of the trajectory. This argument allows you specify multiple formats.
- -vel
Specify the format of the trajectory. This argument allows you specify multiple formats.
-i TRJ_FILENAME [TRJ_FILENAME …], –input-filenames TRJ_FILENAME [TRJ_FILENAME …]
The trajectory file names.
- -if FORMAT, –input-formats FORMAT
Specify the format of the trajectory. This argument allows you specify multiple formats.
–irange FIRST LAST INTER (type: int, default: none)
The trajectory range to process over all trajectory file.
-o TRJ_FILENAME, –output-filename TRJ_FILENAME
The trajectory file name.
-of FORMAT, –output-format FORMAT
The trajectory file format for output.
–orange FIRST LAST INTER (type: int, default: 0, -1, 1)
The trajectory range for output.
-pf FORMAT, –topology-format FORMAT
Specify the format of the topology file.
-p TPL_FILENAME, –topology-file TPL_FILENAME
Specify the topology file.
-nf DIST_FORMAT, –name-format DIST_FORMAT (default: {rid:05}_{rname})
Specify the format for representing residue identify.
4.3.3. Additional options
convert-only options
-h, –help
Show this help message and exit
dry-run options
-h, –help
Show this help message and exit
adjust-vel options
-h, –help
Show this help message and exit
mask options
-h, –help
Show this help message and exit
dist options
-m DISTANCE_METHOD, –method DISTANCE_METHOD {cog|nearest|farthest}
The method used in calculating the inter-residue distances.
-c CUTOFF_LENGTH, –cutoff-length CUTOFF_LENGTH (type: float, default: 5.0)
The distance cutoff in angstrom.