Merge pull request #1636 from RosettaCommons/vmullig/cyclic_cart
Making cart_bonded compatible with cyclic geometry, D-amino acids, and symmetric gly tables.
Most of this pull request was already merged. This corrects symmetric glycine scoring and minimization with cart_bonded, and should also fix a bug with cyclic geometry and cart_bonded minimization. Tiny cart_bonded scoring changes are expected, and changes to cart_bonded minimization trajectories in several integration tests are likely.