[WIP] Modifications to acceptance ratio from Moves

[sgill2]

This PR allows the Move class the option to directly impact the acceptance ratio of a move by the Move.acceptance_ratio attribute. This can potentially come into effect in a variety of circumstances for example, due to dart overlap in Smart Darting. The log of the Move.acceptance_ratio is added to the protocol work to get the overall acceptance ratio during the acceptRejectNCMC() portion of the simulation.

Also in the case when Move.acceptance_ratio == 0 at either the beginning of the NCMC iteration, or after the Move.move() method takes place, the entire NCMC portion is automatically rejected. This can come up in numerous places as well, like @khburley's dihedral rotational moves within specific regions where you wouldn't want to continue calculations if the dihedral ends up outside those regions.

[stevenayoub]

@davidlmobley
This can be closed if we decide to merge the side chain bias pull request (#160: #160), as it introduces acceptance_ratio as a per-move parameter to optionally skip NCMC integration when a move is known to be unproductive (e.g., rotamer rejection in SideChainMove).