CLI Reference#
This section documents the command line interface (CLI) of PyJess.
Usage#
usage: pyjess [-h] [-V] [-j JOBS] -T TEMPLATES -Q QUERIES -R RMSD -D
DISTANCE_CUTOFF -M MAXIMUM_DISTANCE [-n] [-f] [-i]
[--ignore-res-chain] [-q] [-e] [-c MAX_CANDIDATES]
[--no-reorder] [-b]
Named Arguments#
- -V, --version
Show the version number and exit.
- -j, --jobs
The number of jobs to use for multithreading.
Default:
2
Mandatory Parameters#
- -T, --templates
The path to the template list file.
- -Q, --queries
The path to the query list file.
- -R, --rmsd
The RMSD threshold.
- -D, --distance-cutoff
The distance-cutoff.
- -M, --maximum-distance
The maximum allowed template/query atom distance after adding the global distance cutoff and the individual atom distance cutoff defined in the temperature field of the ATOM record in the template file.
Flags#
- -n, --no-transform
Do not transform coordinates of hit into the template coordinate frame
Default:
True- -f, --filenames
Show PDB filenames in progress on stderr
Default:
False- -i, --ignore-chain
Include matches composed of residues belonging to multiple chains (if template is single-chain) or matches with residues from a single chain (if template has residues from multiple chains).
Default:
False- --ignore-res-chain
Include matches composed of residues belonging to multiple chains but still enforce all atoms of a residue to be part of the same chain.
Default:
False- -q, --query-filename
Write filename of query instead of PDB ID from HEADER
Default:
False- -e, --ignore-endmdl
Parse atoms from all models separated by ENDMDL (use with care).
Default:
False- -c, --max-candidates
Set a maximum number of candidates to return by template.
- --no-reorder
Disable template atom reordering in the matching process, useful to enforce results to be returned exactly in the same order as the original Jess, at the cost of longer runtimes.
Default:
True- -b, --best-match
Return only the best match for each template/query pair.
Default:
False