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

   usage: python -m tcr_pmhc_interface_analysis.apps.compute_apo_holo_differences
          [-h] [--output OUTPUT] [--select-entities {tcr,pmhc}]
          [--pmhc-tcr-contact-residues PMHC_TCR_CONTACT_RESIDUES [PMHC_TCR_CONTACT_RESIDUES ...]]
          [--align-entities] [--per-residue] [--crop-to-abd]
          [--num-anchors NUM_ANCHORS]
          [--per-residue-measurements {rmsd,ca_distance,chi_angle_change,com_distance,d_score,all} [{rmsd,ca_distance,chi_angle_change,com_distance,d_score,all} ...]]
          [--log-level {debug,info,warning,error}]
          input
   
   Compute the differences between the apo and holo forms of TCR, pMHC, and TCR:pMHCs.
   
   positional arguments:
     input                 path to data directory
   
   options:
     -h, --help            show this help message and exit
     --output OUTPUT, -o OUTPUT
                           path to output file
     --select-entities {tcr,pmhc}
     --pmhc-tcr-contact-residues PMHC_TCR_CONTACT_RESIDUES [PMHC_TCR_CONTACT_RESIDUES ...]
                           if selecting pmhc, separate rmsds by tcr contact
                           positions and not. The input here is a list of residue
                           codes that are contact positions on the MHC.
     --align-entities      perform an alignment on the selected entities before
                           computing RMSD.
     --per-residue         Perform measurements on each residue individually as
                           oppose to the entity as a whole.
     --crop-to-abd         Crop MHC entities to the antigen binding domain when
                           performing comparisons
     --num-anchors NUM_ANCHORS
                           number of anchor residues for CDR loops to include
                           (Default: 0)
     --per-residue-measurements {rmsd,ca_distance,chi_angle_change,com_distance,d_score,all} [{rmsd,ca_distance,chi_angle_change,com_distance,d_score,all} ...]
                           Measurments to take between residues if `--per-
                           residue` is selected.
   
   Logging:
     Options for logging
   
     --log-level {debug,info,warning,error}
                           Level to log messages at (Default: 'warning')