Use WholeMoleculeTransform for orires and epsilon-surface

Use WholeMoleculeTransform for orires and epsilon-surface

Remove direct use of the graph from the orientation restraint
and Ewald epsilon-surface term code by passing in whole molecules
created by the WholeMolecules class.
Since this was the only remaining use of graph in do_force(),
it can now be removed.

Also enabled the epsilon-surface mdrun-test.

Fixes #3441

Change-Id: Idfec6508c6dfd9e1a656cf23613ede3793794901