Support mmCIF files

[RagnarB83]

Support reading of pdbx/mmCIF files. Fragment class: add support for parsing coordinates and elements See: https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/beginner’s-guide-to-pdb-structures-and-the-pdbx-mmcif-format

Topology parsing: handled by OpenMM but need to extend OpenMMTheory to support reading and writing. See: http://docs.openmm.org/latest/api-python/generated/openmm.app.pdbxfile.PDBxFile.html