usage: python -m tcr_pmhc_interface_analysis.apps.colour_tcr_on_mhc
[-h] --output OUTPUT --contacts-path CONTACTS_PATH --mhc-chain-id
MHC_CHAIN_ID --antigen-chain-id ANTIGEN_CHAIN_ID
[--num-contacts-cutoff NUM_CONTACTS_CUTOFF]
[--percentage-contacts-cutoff PERCENTAGE_CONTACTS_CUTOFF]
[--dominant-peptide-contacts DOMINANT_PEPTIDE_CONTACTS [DOMINANT_PEPTIDE_CONTACTS ...]]
[--log-level {debug,info,warning,error}]
mhc_path
positional arguments:
mhc_path path to the template MHC PDB file to colour with the
contact information
options:
-h, --help show this help message and exit
--output OUTPUT, -o OUTPUT
name of output pymol session
--contacts-path CONTACTS_PATH
path to the CSV file containg contacts information
--mhc-chain-id MHC_CHAIN_ID
chain id of the main MHC chain
--antigen-chain-id ANTIGEN_CHAIN_ID
chain id of the antigen
--num-contacts-cutoff NUM_CONTACTS_CUTOFF
number of contacts needed to highlight the MHC residue
with contact information (Default: 100)
--percentage-contacts-cutoff PERCENTAGE_CONTACTS_CUTOFF
A percentage cutoff instead of the raw count numbers,
will override `--num-contacts-cutoff` (Default: None)
--dominant-peptide-contacts DOMINANT_PEPTIDE_CONTACTS [DOMINANT_PEPTIDE_CONTACTS ...]
list of dominat CDRs for each peptide contact postion
(CDR-A3, CDR-A3, ..., CDR-B3)
Logging:
Options for logging
--log-level {debug,info,warning,error}
Level to log messages at (Default: 'warning')