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fix(numbering): avoid NoneType errors for PDBs with non-Fv chains #1

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fix(numbering): avoid NoneType errors for PDBs with non-Fv chains #1

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6 changes: 3 additions & 3 deletions abangle/number.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,19 +76,19 @@ def number_sequences(sequences: Dict[str, SeqRecord], scheme: str = 'chothia') -

numbering, details, _ = anarci(formatted_input, scheme = scheme)

numbering = [
numbering_fv = [
[(' ', res_id[0][0], res_id[0][1]) for res_id in num[0][0] #(hetcode, seqid, icode)
if res_id[1] != '-'] # remove gapped elements
for num in numbering
if num # drop numbering where no Fv could be found
]

details = dict2obj([det[0] for num, det in zip(numbering, details) if num]) # extract details from list wrapper
details_fv = dict2obj([det[0] for num, det in zip(numbering, details) if num]) # extract details from list wrapper

return dict2obj({
det.query_name:
{'chain': parse_chain_type(det),'span': slice(det.query_start, det.query_end), 'numbering': num}
for num, det in zip(numbering, details)
for num, det in zip(numbering_fv, details_fv)
})

def contains_single_model(structure: Structure) -> bool:
Expand Down