Improvements:

- Allow a Collection to be constructed from a generator

- Make Amber file parser more tolerant to accept more mod_files

- More pdb_alternative atom names: GROMACS-style OC1/OC2 in
  C-terminal peptide group

- Compile C versions of extension modules if Cython is not installed

Bug fixes:

- Remove long delays when deallocating thread-based
  energy evaluators