tcr_pmhc_interface_analysis.apps.compute_apo_holo_differences

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]
       [--per-residue-measurements {rmsd,ca_distance,chi_angle_change,com_distance,all} [{rmsd,ca_distance,chi_angle_change,com_distance,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
  --per-residue-measurements {rmsd,ca_distance,chi_angle_change,com_distance,all} [{rmsd,ca_distance,chi_angle_change,com_distance,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')