We need to clean up what happens when multiple molecules are loaded
from a PDB. My current favorite is to
- make the current read_pdb only support loading a single protein
(chain) from the first model of a PDB file and return it as a
Hierarchy with the root being a PROTEIN. It can spit out warnings if
there are other molecules in there.
- add a read_model_from_pdb which loads all molecules from a given
model in the PDB (defaulting to the first) and which returns an array
of Hierarchy decorators each of which has a root of either a PROTEIN
or a MOLECULE (or some other name to specify a molecule that is not a
protein or nucleic acid).