Hi,

I worked on issue #3988. The idea was to extend the obsolete file handling in update_pdb so it works with mmCIF and XML formats (not just PDB), and to move assembly files when a structure becomes obsolete.

Changes made:

1. Correct filenames for each format – The old code used pdb{pdb_code}.{file_format} for all formats, which was wrong. mmCIF files are {pdb_code}.cif, XML are {pdb_code}.xml, PDB are pdb{pdb_code}.ent. I added a _get_obsolete_filename helper that returns the right name for each format.

2. mmtf and bundle – Obsolete structures are not available in mmtf (as noted in the docstring). For these formats we skip the obsolete move step.

3. Assembly files – When with_assemblies=True and a structure becomes obsolete, we now also move the corresponding assembly files (e.g. {pdb_code}-assembly1.cif or {pdb_code}.pdb1) to the obsolete folder.

4. Bug fix – Replaced pl.retrieve_assembly_file with self.retrieve_assembly_file in the new/modified download loop.

5. Assert replacement – Replaced the asserts on local_pdb and obsolete_pdb with explicit if/raise ValueError (consistent with Do not use assert outside of testing code #3600).

Closes #3988