Deal with residue features in protein-ligand graphs

[DaniBodor]

If not all chains contain residue atoms, then some features will not parse properly.

For each such feature decide and implement one of the following:

• Do not allow the feature in these graph types.
• Only add the feature to the residue-containing chain and find a proper entry type in the non-residue chain (e.g., nan or 0).

Blocked by #544