Changed Amber Atom comparison to use mass, name and then index.
Previously just used index.
Added pint package to amber/measure.py for managing units. Not sure we
want to add it to a list of dependencies yet.
Updated amber.read_amber to read coordinates from inpcrd files into
Molecule objects. Also added a new file for converting to and from
internal coordinates.
Merge remote-tracking branch 'origin/master' into hs_wca_interface
comparisions to None, formatting
use array_wrap_np for boxvector
move wrapping of reference coords
move wrapping of frozen dof array, duplicate wrapping function for size_t
move wrapping of radii
move more wrapping
formatting
fix array declaration
fix None check of frozen atoms dof
formatting