Update PDB id handling so that it uses the new PDB id structure

[marcuscollins]

See https://www.rcsb.org/news/feature/69ebcdca1103c56d3f444159

Due July 21, 2027 (we have lots of time)

There are several places where this could come up:

1. Our own internal naming for PDB files should be updated to use the standard format and avoid confusion. For instance, we have regex for PDB ids that are of the form r"some_file_path/(.{4})".
2. We use other packages like biotite to download PDB data files using the RCSB APIs. This API will now require the new IDs starting July 21, 2027.

We should catalog all of the places where we use these IDs and make sure our systems are fully compatible before the cutover. We should be able to point to the beta database (see URL at top) before then for testing.