Migrate from PDB to PDBx/mmcif

[ijpulidos]

Since the RCSB is officially dropping support for PDB files in favor of using PDBx/mmcif formatted files, I think we should consider making sure we support this format.

I suspect we could still use PDB formats for our own serializations and internal representation of objects (topologies, positions, etc.), but we should expect the source/input files to be in the new PDBx/mmcif format, at the very least.