Merge pull request #700 from RosettaCommons/vmullig/gellman_helix
The main purpose of this merge is to fix packing when mainchain chiral centres switch their chirality (e.g. design with both D- and L-amino acids). This also introduces a subset of the L-gamma-4 amino acids with canonical side-chains. The following integration test changes are expected:
- flexpepdock (There really was an HA atom in a wonky place in this integration test, which this change fixes.)
- dcys_disulfidize (Expected changes to HA placement when designing with D and L residues -- the major bugfix that this merge introduces.)
- cyclization (Very small changes to post-relaxation geometry with peptoid residues. Tracked this down to the swapping of 1HA and 2HA atoms that were in the incorrect relative arrangement. So that's good.)
- oop_design (No changes to structure, but minor changes to some output information. Also not surprising.)
- d_workflow (HA atoms are now in the correct positions after design. Yay!)
- cluster_alns (Very minor changes to side-chain rotamers. Curious.)
- oop_dock_design (No structural changes; minor changes to output information.)
- ncaa_fixbb (Different non-canonical side-chain no longer chosen after fixing HLU. The only difference is that 1HA2 and 2HA2 in the "601" residue, which were staring out in swapped positions, are now correctly swapped back by the packer. So that's good.)