RESNAME selector does not accept 5-character ligand IDs (e.g., A1D51 in 8y42)

[sgvallve]

Summary
pdbe-arpeggio fails to accept 5-character ligand IDs in the RESNAME: selector.
Example: PDB entry 8y42 contains ligand A1D51. Running:

pdbe-arpeggio -s RESNAME:A1D51 -o out 8y42.cif -m

returns:

ERROR//Invalid selector: RESNAME:A1D51

Selecting the same ligand by chain/residue works:

pdbe-arpeggio -s /A/401/ -o out 8y42.cif -m

Expected behavior
RESNAME: should accept wwPDB’s extended 5-character chemical component IDs (introduced in 2023 and distributed only in PDBx/mmCIF).

Actual behavior
RESNAME: appears to reject IDs longer than three characters, producing Invalid selector.

Environment

• OS: Linux (Ubuntu 22.04)
• Python: 3.10
• Installation: pip install pdbe-arpeggio
• Input: PDBx/mmCIF file (8y42.cif with added hydrogens downloaded from PDBe)
• Command: as above

Workarounds

1. Select by chain/residue number, e.g. /A/401/, which works.
2. Run without -s, then filter the JSON output by label_comp_id == "A1D51" and/or label_comp_type == "B" (bound ligand). This is feasible since PDBe Arpeggio outputs label_comp_id/label_comp_type in the JSON.

Additional context / references

• wwPDB announcement on extended 5-character ligand IDs (mmCIF/PDBML only): see RCSB/PDBe news posts (2023–2024).

Feature request / question

• Could the CLI parser be updated so that RESNAME: accepts 1–5 character label_comp_id values from mmCIF?

Many thanks for maintaining pdbe-arpeggio!

[sgvallve]

Suggested fix for 5-character ligand codes

I have tested this issue and identified the cause.
In the file arpeggio/core/utils.py, within the function selection_parser, the code currently restricts RESNAME: selectors to three-character residue/ligand codes.

Proposed modification at line 437

- if len(selection) > 3:
+ if len(selection) > 5:

This change allows pdbe-arpeggio to correctly process ligands with 5-character identifiers such as A1D51 (e.g. PDB entry 8Y42).