Since no one had any good reasons to keep the non-sphere version of
the nonbonded lists around, I removed them while I was making various
changes. The other change I made is a added slightly more clever than
before quadratic nonbonded lists (I think we want these at least for
testing purposes). In addition, the constructors have been rearranged
so that various things are optional since I often want to construct
the states without knowing the full set of particles.
API changes:
AllSphereNonbondedListScoreState is now AllNonbondedListScoreState and
the radius key is first, if used.
BipartiteNonbondedListScoreState now uses a dumber algorithm, but
supports radii. I can move it back to a grid based implementation later.