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_protein_peptide_pass mis-assigns antigens for structures with >26 chains (list(cpx.id) splits two-character chain ids) #90

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_protein_peptide_pass mis-assigns antigens for structures with >26 chains (list(cpx.id) splits two-character chain ids) #90

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10 changes: 9 additions & 1 deletion stcrpy/tcr_processing/TCRParser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1192,7 +1192,15 @@ def _protein_peptide_pass(
# all_cpx_chains is a dictionary that has a TCR/MHC chain as a key and the ID of the TCR/MHC as value
all_cpx_chains = dict()
for cpx in complexes:
cpx_ch = list(cpx.id)
# cpx.id is the CONCATENATION of the complex's chain ids, so list() only
# decomposes it correctly while every chain id is a single character. Chain ids
# are two characters once a structure exceeds 26 chains, and then e.g. "AAZ"
# becomes ['A','A','Z'] instead of ['AA','Z'] -- so the real chain never
# registers and is later mistaken for antigen. Take the chain objects instead.
try:
cpx_ch = [c.id for c in cpx.get_chains()]
except AttributeError: # a bare TCRchain/MHCchain, not a paired complex
cpx_ch = [cpx.id]
for c in cpx_ch:
all_cpx_chains[c] = cpx.id

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