Fix the restart file parser/writer
Add a BeemanRestart class to parse out restart files printed by the Beeman
integrator in pmemd.amoeba

Also fix the mask parser so that you can escape the * character (this allows you
to select N* atom types with the mask string @%N\* rather than having * act as a
wildcard).
Enable writeOFF in ChamberParm (but warn about the dangers of using the
resulting OFF file in LEaP).

Improve Python3 compatibility (only override __delslice__ in Python 2)
Fix parameter set parser to work with the carbohydrate parameter file (it has an
END card at the end... unlike every other parameter file I've seen).
Extend the PDB parser to extract more metadata from the header (if present).
Generalize boxLengths to handle non-orthogonal unit cells.
Make Charmm PSF parameter loader more robust wrt dihedral parameters -- have
separate lists for the parameters and for the atoms involved in dihedrals (for
multiterm torsions).
Fix dihedral equality detection and improve the logic in that part of the code
in general. Should be robust now. This also eliminates some duplicate parameters
that are dumped to an frcmod file from ParmEd. Update the saved frcmod file with
the new output (I verified that all terms that were deleted appeared in their
reordered form elsewhere in the frcmod and were equal).

Thanks to Jeff Thompson from UT Austin for the report and diagnosis!
When name-mangling for the sake of looking for unique atom types, make sure to
add two indexes to ensure that the atom type will not accidentally match a
different atom type that is not name-mangled.

Also simplify the same_atoms function call by eliminating the 'improper'
argument and simply determining whether an improper torsion should be tested for
by looking at the nature of the torsion being compared.
Fix indentation error in '# Put together the title' section of _amberparm.py
Fix indentation error... Thanks to Jeff Thompson for finding it.
Merge branch 'master' of https://github.com/jpthompson17/ParmEd
Add subscript 0 to oparam.same_atoms() return value in DihedralParamList.add_param(). We want the firt value (same_atoms) in the tuple.
Merge pull request #1 from jpthompson17/master

Fix check for same atoms in DihedralParamList.add_param() function
Tentatively add NBFIX support to ParmEd.
Fix atom type compression.
Add a test for chemistry/system.py
Have PDB files with 1 model report models=1 rather than 0
Add more tests.
More tests and fix the package names in chemistry/tinker
Add a test for Tinker .dyn files.