Merge pull request #3659 from RosettaCommons/JackMaguire/HBondState_part1
This PR is just the result of a bunch of sed commands to change AtomLevelHBondGraph to HBondGraph and MCHBNetInteractionGraph to HBondGraphInitializerIG (now that it's used in more than just MC HBNet). I also sprinkled in a few make_shared's but there's nothing exciting.
Thanks to Andy for the review!