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')