Improvements:

- The identification of protonation states when creating molecules from a
  PDB file now takes into account the common situation of crystallographic
  PDB files that contain no hydrogens at all. In that case, the most frequent
  protonation is used for each individual residue.

- Ewald summation works for non-orthogonal universes.

Bug fixes:

- Universe.distanceVector raised an exception when called with the optional
  configuration argument and for an InfiniteUniverse.

- MMTK.Universe.contiguousObjectOffset could crash when input arrays
  do not use contiguous storage (very unlikely in normal MMTK usage)

- NumPy compatibility problem: indexing trajectory variables did not
  work with indices coming from a NumPy array.

- Removal of objects from a universe (e.g. by calling replaceResidue()
  on a biopolymer chain) could cause incorrect atom indices in the
  universe.

- A force field containing more than one restraint term did not permit
  the retrieval of the evaluator parameters.