「view this page in B3 βῆτα server」

Revisions №60131

branch: master 「№60131」
Commited by: Vikram K. Mulligan
GitHub commit link: 「2b4b9485da60c209」 「№3000」
Difference from previous tested commit:  code diff
Commit date: 2018-03-31 17:05:24

Merge pull request #3000 from RosettaCommons/vmullig/lariats_for_kris Add support for isopeptide-bonded lariats to simple_cycpep_predict This pull request adds support to `simple_cycpep_predict` for peptides in which a D/L-aspartate or D/L-glutamate side-chain is connected to the N-terminus. Requested by @deiblerk. Tasks: - [x] Add sidechain conjugation patch for D/L-aspartate. - [x] Add sidechain conjugation patch for D/L-glutamate. - [x] Add `SET_NET_FORMAL_CHARGE` patch operation. - [x] Add flags to `simple_cycpep_predict` for specifying lariat closure. - [x] Have them do something internally. - [x] Add flags to `simple_cycpep_predict` for specifying sidechain isopeptide closure. - [x] Have them do something internally. - [x] Integration tests: - [x] N-terminal lariat. - [x] Debug alignment code. - [x] C-terminal lariat. - [x] Sidechain isopeptide bond. - [x] Sidechain isopeptide bond - reverse direction. - [x] Documentation. - [x] Include note about ASX and GLX not being used in `simple_cycpep_predict`. - [x] Beauty. Also: - [x] Deprecate the old carboxy sidechain-conjugation patch. - [x] ~~Update code that called it~~ --> I don't think there was any. - [x] Add unit tests for isopeptide bonded peptide scoring. - [x] ~~Fix `rama`~~. --> Not necessary. Not fully compatible with NCAAs in any case, and `rama_prepro` is its replacement. - [x] Fix `rama_prepro`. - [x] Note: I found a little bug in rama_prepro that's also fixed in this pull request. This creates a number of minor trajectory changes in integration tests. - [x] Remove debug output from unit test. - [x] Update `ResidueType` and `Conformation` to allow easy, efficient updating of coordinates that depend on nonpolymeric connections (or on other atoms that depend on non polymeric connections).