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

   usage: python -m tcr_pmhc_interface_analysis.apps.align_tcr_pmhcs
          [-h] [--output OUTPUT] [--only-holo]
          [--log-level {debug,info,warning,error}]
          structures
   
   Align TCR, pMHC, and TCR:pMHC on the TCR framework region or the floor of the MHC antigen binding groove.
   
   Requirements:
       - PyMOL: https://www.pymol.org/
   
   positional arguments:
     structures            path to the structures to align
   
   options:
     -h, --help            show this help message and exit
     --output OUTPUT, -o OUTPUT
                           path to output the aligned files
     --only-holo           only align the holo structures based on either TCR CDR
                           sequences or mhc allele and peptide sequence.
   
   Logging:
     Options for logging
   
     --log-level {debug,info,warning,error}
                           Level to log messages at (Default: 'warning')