Several updates for new data layout

I also added in some minor style cleanups...should have kept them
separate ideally but they are fairly trivial.

Change-Id: I4db9a5c594edd4ec2c162b2e6f52f268729c9de2
Updates for the new layout in quantum collections

The computational results model always issues an empty query, which
resulted in the construction fetching all QM documents in the
collections! This easily led to memory exhaustion on big collections,
and was very slow. After that found made some small changes to account
for the updates layout, and to query on the molecule id which serves
as the primary link to the molecule collection.

Change-Id: I0883b4423ad1b2e69d4e4d4f7d96a860e17b4189
Added a databaseName method to MongoDatabase

This is very useful, and should be cleaned up in the code where this
is done manually.

Change-Id: I0800598d4ac1751074c5df873afca0d800b3a32e
Adapted the 3D structure code to the new layout

The 3d structure is in a linked collection, with base information
taken from the parent molecule.

Change-Id: I8d5340a641434d6a00188b4776b66bc62a81a8df
Merge branch 'updates-to-new-layout'

Change-Id: Ifa7eb2bd2b7cfa18b8cb48fe387378b9537eb859