Merge pull request #3090 from RosettaCommons/vmullig/fix_sidechain_conjugation
Just fix SIDECHAIN_CONJUGATION patch.
Since pull request #3089 generated controversy, I'm cherry-picking out the changes that actually seem to fix the problem that I'm seeing and leaving the others for later. This pull request corrects the SIDECHAIN_CONJUGATION patch, and fixes a few little things in the Patch and PatchOperation classes. It does not alter the Conformation class in any way. Cosmetic integration test changes are expected from the Patch tracer name correction, and some trajectory changes in those integration tests involving sidechain-conjugated ASP or GLU are expected too (e.g. the simple_cycpep_predict isopeptide tests).