tcr_pmhc_interface_analysis.apps.cluster_cdr_loop_structures

usage: python -m tcr_pmhc_interface_analysis.apps.cluster_cdr_loop_structures
       [-h] [--output OUTPUT] [--assign-cluster-types]
       [--stcrdab-path STCRDAB_PATH] [--log-level {debug,info,warning,error}]
       structure_names distance_matrices [distance_matrices ...]

Cluster TCR CDR Loop structures and assign them as canonical or pseudo clusters.

Adding cannonical conformation information to clusters
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Based on the definition from Comparative Analysis of the CDR Loops of Antigen Receptors
(https://doi.org/10.3389/fimmu.2019.02454), canonical clusters are any cluster where there are more than two unique
sequences within the density clusters. The other clusters will be refered to as pseudo-clusters, as these may just be
the effect of the same loop finding the same conformation.

positional arguments:
  structure_names       path to the structure names file
  distance_matrices     paths to the distance matrices

options:
  -h, --help            show this help message and exit
  --output OUTPUT, -o OUTPUT
                        output path
  --assign-cluster-types
                        assign cluster types (requires --stcrdab-path input)
  --stcrdab-path STCRDAB_PATH
                        path to the STCRDab

Logging:
  Options for logging

  --log-level {debug,info,warning,error}
                        Level to log messages at (Default: 'warning')