Clean up available PDB stuctures and add CIF

[khuddzu]

The current state of the structure data should be refined.

For PDB:

• Currently processing the PDB requires you to rename the ligand chain ID as LIG. This was originally for compatibility with MTENN within anvil, but has proven over time to be a nuisance. I won't take this away in the code, in case it is every needed, but I will make it optional and the data available for pdb will still contain the original chain IDs. (I also need to make it optional in toolkit)

PDB is a deprecated file format. We should predominately be using CIF files, so I will add these as well, and make them the default download. (@PatWalters has code for this that I will add to the repo)