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In rf/utils.py, around line 78, should the 3 lines be added, in case the residue numbering in the original PDB file has a gap? Thanks!
if L > 0:
new_contig.append(f"{L}-{L}")
unseen = []
### in case residue numbering jumps
elif len(seen)>0 and seen[-1][1]!=i-1:
new_contig.append(f"{seen[0][0]}{seen[0][1]}-{seen[-1][1]}")
seen = []
###
seen.append([c,i])
The text was updated successfully, but these errors were encountered:
Using the following toy example, the output from fix_partial_contigs becomes A1-44, and this then leads to incorrect output for fix_pdb, (chain E should have been renamed to B, but it is renamed to chain A by mistake).
If you change fix_partial_contigs to fix_contigs, the behavior is correct.
['A1-44', 'E45-46']
ATOM 323 CB ASN A 44 12.266 4.769 13.501 1.00 7.27 A C
ATOM 324 CG ASN A 44 12.538 4.304 14.922 1.00 7.98 A C
ATOM 325 ND2 ASN A 44 13.407 3.298 15.015 1.00 10.32 A N
ATOM 326 OD1 ASN A 44 11.982 4.849 15.886 1.00 11.00 A O
ATOM 327 OXT ASN A 44 12.703 4.973 10.746 1.00 7.86 A O1-
TER
In rf/utils.py, around line 78, should the 3 lines be added, in case the residue numbering in the original PDB file has a gap? Thanks!
The text was updated successfully, but these errors were encountered: