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Revisions №59970

branch: master 「№59970」
Commited by: Vikram K. Mulligan
GitHub commit link: 「464272a25dbde507」 「№2705」
Difference from previous tested commit:  code diff
Commit date: 2018-01-09 21:07:35

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

Rocco Moretti 3 years
Looks like the oligourea_design test is now reporting a backtrace, though for some reason it doesn't look like it's being flagged as a magenta failure.
Vikram K. Mulligan 3 years
Weird -- something's up. Will fix.