Fix bug #196 - setLimit takes a molecule reference

Passing the pointer resulted in a reference that had zero atoms, and so
the default of the origin with padding was being used. Verified for
larger molecules too, the cube dimensions are now being calculated for
the atoms in the molecule.

Change-Id: Ib975d148ed54b67d2ad70dee7123bde8fe28637c
Merge topic 'fix-cube-limit' into master

ce8a7733 Fix bug #196 - setLimit takes a molecule reference