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Improve error message and consistency of ordering

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PiperOrigin-RevId: 820694312
Change-Id: I6b04514b1f838c49bf5dca1e138e1d6b2ff81139
This commit is contained in:
Augustin Zidek
2025-10-17 08:05:29 -07:00
committed by Copybara-Service
parent 142e4bc6e5
commit 3c89cc7b89
1 changed files with 6 additions and 5 deletions
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11
src/alphafold3/structure/parsing.py
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@ -1209,11 +1209,11 @@ def _maybe_add_missing_scheme_tables(
inplace=False, inplace=False,
) )
update['_pdbx_poly_seq_scheme.asym_id'] = res_asym_ids update['_pdbx_poly_seq_scheme.asym_id'] = res_asym_ids
update['_pdbx_poly_seq_scheme.pdb_strand_id'] = res_strand_ids
update['_pdbx_poly_seq_scheme.pdb_seq_num'] = auth_seq_ids[res_mask] update['_pdbx_poly_seq_scheme.pdb_seq_num'] = auth_seq_ids[res_mask]
update['_pdbx_poly_seq_scheme.pdb_ins_code'] = pdb_ins_codes[res_mask] update['_pdbx_poly_seq_scheme.pdb_ins_code'] = pdb_ins_codes[res_mask]
update['_pdbx_poly_seq_scheme.seq_id'] = label_seq_ids[res_mask] update['_pdbx_poly_seq_scheme.seq_id'] = label_seq_ids[res_mask]
update['_pdbx_poly_seq_scheme.mon_id'] = label_comp_ids[res_mask] update['_pdbx_poly_seq_scheme.mon_id'] = label_comp_ids[res_mask]
update['_pdbx_poly_seq_scheme.pdb_strand_id'] = res_strand_ids
required_nonpoly_scheme_cols = ( required_nonpoly_scheme_cols = (
'_pdbx_nonpoly_scheme.mon_id', '_pdbx_nonpoly_scheme.mon_id',
@ -1612,10 +1612,11 @@ def get_tables(
except KeyError as e: except KeyError as e:
raise ValueError( raise ValueError(
'Lookup for the following atom from the _atom_site table failed: ' 'Lookup for the following atom from the _atom_site table failed: '
f'(atom_id, auth_seq_id, res_name, ins_code)={e}. This is ' f'(label_asym_id, auth_seq_id, res_name, ins_code)={e}. This typically '
'likely due to a known issue with some multi-model mmCIFs that only ' 'indicates that the _pdbx_poly_seq_scheme, _pdbx_nonpoly_scheme, or '
'match the first model in _atom_site table to the _pdbx_poly_scheme, ' '_pdbx_branch_scheme tables do not have data for all residues present '
'_pdbx_nonpoly_scheme, or _pdbx_branch_scheme tables.' 'in the _atom_site table. It could also be due to a known issue with '
'a small number of multi-model mmCIFs.'
) from e ) from e
# The residue ID will be shared for all atoms within that residue. # The residue ID will be shared for all atoms within that residue.