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')