Lots of comments
add documentation, add layout
add wrapping
fix typo
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
change comment scheme

use comments rather than strings to comment.  It's cleaner and shorter
remove other hs_wca wrappings