tcr_pmhc_interface_analysis.apps.colour_tcr_on_mhc

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')