Updated open in editor handler for new layout

The main molecule reference simply contains a pointer to the 3D
structure now, and this class had not been updated to reflect that
change. Also made some minor documentation and style updates.

Change-Id: I1a84923c0b495a0eb64e97d760ebd419198a7cc8
Merge branch 'fix-open-in-editor'

Change-Id: I47f7e3e83aa38662ab0d044e61cecd13dced4517