Merge pull request #2705 from RosettaCommons/vmullig/polar_oligourea
Adding a few polar oligoureas to the database (and a few hydrophobics)
I want to be able to design surfaces with oligoureas, too. In addition to adding these oligoureas, this pull request resolves some NCAA issues.
Tasks:
- [x] Add OU3_THR.params.
- [x] Add rotamer library to Git LFS repository.
- [x] Add OU3_ASN.params.
- [x] Add rotamer library to Git LFS repository.
- [x] Add OU3_GLN.params.
- [x] Add rotamer library to Git LFS repository.
- [x] Add OU3_TRP.params.
- [x] Add rotamer library to Git LFS repository.
- [x] Add OU3_TYR.params.
- [x] Add rotamer library to Git LFS repository.
- [x] Update residue_types.txt.
- [x] Fix bug in `pro_close` energy that was affecting OU3_PRO and DOU3_PRO.
- [x] Test all oligoureas (_not_ as a unit test, though, since this would require adding all oligourea rotlibs to the database).
- All work well EXCEPT OU3_PRO, which seems to have a problem with `pro_close` --> fixed.
- [x] I will add a unit test for the OU3_PRO case, just to be on the safe side.
- [x] Figure out rotamer-building problem --> fixed.
- [x] Figure out OU3_PRO geometry problem. This seems to be a fundamental issue with `fa_dun` derivatives and scoring.
- [x] Adding a scoring test.
- [x] Fix beta-amino acid problem.
- [x] Small tweak to the cis-peptide bond GeneralizedKICperturber to make it work with oligoureas.
- [x] Check integration tests.
- Most integration test changes are cosmetic (caused by additional residue types or noisy tracer now made into a Debug tracer).
- `cyclization` is due to slightly different peptoid rotamers since a Dunbrack bug was fixed. Qualitatively the same.
- `disulfidize_beta_cys` finds more and better beta-cysteine disulfides due to Dunbrack bugfix.
- `ncaa_fixbb` finds new and slightly better rotamers at peptoid positions due to Dunbrack bugfix.
- `oligourea_design` and `oligourea_predict` show expected trajectory changes due to Dunbrack bugfix and GenKIC cis-peptide bugfix.
- `unfolded_state_energy_calc` changes expected due to Dunbrack bugfix affecting peptoids.
@twcraven