Allows for non-polymer atoms in Entity declaration

[mtrellet]

Allows for non-polymer atoms in Entity declaration

[benmwebb]

If you like, you could certainly make your own Alphabet subclass for ligands. But you're supposed to pass ChemComp objects for each ligand directly to the Entity constructor. That being said, you'll run into problems later on (since the dumpers assume all entities are polymeric) but I'll work on that and update this issue accordingly.

[benmwebb]

The library should now have basic support for writing out structures containing nonpolymers, although there are still a few loose ends. See the ligands_water.py example, and open issues for any further problems you run into.