Merge pull request #1277 from RosettaCommons/vmullig/parisa_bug
Trying to fix a bug identified by Parisa
Cyclic geometry with multiple chains seems not to be calculating mainchain torsions at the breakpoint properly. This was due to an overly-lax check for cutpoints that wasn't actually looking for a cutpoint variant. This has been corrected now; some integration tests involving unconventional connections will show trajectory changes. Others show cosmetic changes due to certain DOFs not being found.