Support new MDTraj mmCIF/PDBx reader

[mjo22]

mdtraj will release a mmCIF/PDBx loader not dependent on openMM in version 1.11.0, via mdtraj/mdtraj#1998

[mjo22]

Looking into this, a straightforward implementation from mdtraj with the current AtomicModelFile object is non-trivial. For now we should encourage people to just use mdtraj to load mmCIF, but in the long-term this is important for cryoJAX as loading b-factors using mdtraj is not built in. We can make a plan for how to generalize the mdtraj PDBx functionality to our AtomicModelFile object.

[mjo22]

@DSilva27 teamtomo has developed a nice package for loading PDB+mmCIF using gemmi: https://github.com/teamtomo/mmdf.

It looks like this suffices for our needs… for example, mdtraj selection string filtering would be replaced by operations on pandas dataframes.

It sounds like a road to mmCIF support would be much simpler if we use mmdf instead of mdtraj? We should see if this comes with the same gemmi bugs as we were experiencing.

EDIT: for context, mmdf uses gemmi for their backend