Switch from MMTF to BinaryCIF

[ghutchis]

As of July 2024 the PDB file archive will not be offered in MMTF format anymore. Users are strongly encouraged to switch to the BinaryCIF format, which has been available since 2020.

The new BinaryCIF format: https://github.com/molstar/BinaryCIF/blob/master/encoding.md
For example: https://models.rcsb.org/4hhb.bcif.gz

Or .. while it's not as efficient:
https://files.rcsb.org/download/4hhb.pdb

[ghutchis]

The easiest way to handle this for now might be with a Python reader:
https://github.com/rcsb/py-mmcif

There do seem to be some useful C++ versions though:

• https://github.com/RBVI/readcif
• https://github.com/PDB-REDO/libcifpp

These would also offer us some general utility for handling CIF files directly (i.e., not through Open Babel).