Modifications

This pull request effectively eliminates ModernaResidue.py. All functionality goes to moderna.modifications. The package has a few convenience functions:

modifications.exchange_base(resi, new_name)
modifications.add_modification(resi, abbrev)
modifications.remove_modification(resi)

The most difficult part was dealing with the methods in RNAModel. This module got a bit smaller, but might require further thought.

Almost 2000 LOC changed. Curious about your opinion.