tcr_pmhc_interface_analysis.apps.colour_tcr_on_mhc
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.. code-block:: text

   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')