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

   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')