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.