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Revisions №59788

branch: master 「№59788」
Commited by: Vikram K. Mulligan
GitHub commit link: 「57ab09b04ac7a81a」 「№2528」
Difference from previous tested commit:  code diff
Commit date: 2017-10-18 14:10:52

Merge pull request #2528 from RosettaCommons/vmullig/oligourea Add support for oligoureas in Rosetta peptide design and structure prediction These resemble beta-amino acids, but with a urea linkage to the next amino acid instead of a simple amide bond. @twcraven Tasks: - [x] Add `OLIGOUREA` property. - [x] Convenience functions in `ResidueType` class. - [x] Torsion specifications in `Pose` class. - [x] Add to the horrible `Conformation::backbone_torsion_angle_atoms()` function... ugh. (At least I'll have it call another function for oligoureas, so that it's not more mess in that function.) - [x] Some new unit tests for `Conformation`. - [x] Update relevant patches: - [x] NtermProteinFull. - [x] CtermProteinFull. - [x] N-terminal acetylation. - [x] C-terminal methylation. - [x] Cutpoint variants. - [x] Update `SmallMover` to support oligoureas. - [x] Unit test. - [x] Document this. - [x] Update `pro_close` energy to support OU3_PRO. - [x] Unit test. - [x] Document this. - [x] Update `OmegaTetherEnergy` to support oligoureas. - [x] Unit test. - [x] Unit test: minimization. - [x] Document this. - [x] Update CycpepSymmetryFilter to support oligoureas. - [x] Document this. - [x] Add oligourea mainchain potentials. - [x] Update mainchain potential class so that it can be applied to a subset of mainchain torsions. - [x] Unit test. - [x] Add oligourea params files. - [x] OU3_ALA. - [x] Update peptide bond geometry. - [x] OU3_PHE. - [x] OU3_ILE. - [x] OU3_LEU. - [x] OU3_PRO. - [x] OU3_VAL. - [x] Update peptide bond geometry in all of the above. - [x] Add oligourea mainchain potentials. - [x] For OU3_ALA. - [x] Unit tests for mainchain potential with 3 mainchain torsions. - [x] For OU3_PRO. - [x] Add oligourea rotamer libraries to Git LFS repository. - [x] Update `simple_cycpep_predict` to allow oligourea prediction. - [x] Integration test: `simple_cycpep_predict`. - [x] Integration test: oligourea design. - [x] Address points in comments below: make it possible for rotamer libraries to be dependent on a subset of mainchain torsions. - [x] Documentation: `simple_cycpep_predict`. - [x] Beauty. Put off to a future pull request: - Unit test: cyclic geometry. - Unit test: mirroring. - Add additional oligourea params files. - OU3_AIB. - OU3_CYS. - OU3_ASP. - OU3_GLU. - OU3_GLY. - OU3_HIS. - OU3_LYS. - OU3_MET. - OU3_ASN. - OU3_ORN. - OU3_DAB. - OU3_DAP. - OU3_GLN. - OU3_ARG. - OU3_SER. - OU3_THR. - OU3_TRP. - OU3_TYR. - Update peptide bond geometry in all of the above. - Add additional oligourea mainchain potentials. - For OU3_AIB. - For OU3_GLY. - Symmetry unit tests for OU3_GLY, OU3_AIB.