Merge pull request #1640 from RosettaCommons/vmullig/cyclic_cart2
Splitting cyclic Cartesian pull request so that I can merge in the stuff that IS working now.
I'm still having trouble with symmetric glycine minimization, for reasons to be determined. This pull request will merge in fixes to the following:
- Using cart_bonded with cyclic geometry.
- Using cart_bonded with D-amino acids.
- Unit test coverage for cart_bonded with cyclic geometry and D-amino acids.
Tests of symmetric glycine minimization are temporarily commented out.