「view this page in B3 βῆτα server」

Revisions №61493

branch: master 「№61493」
Commited by: Vikram K. Mulligan
GitHub commit link: 「8ea92071489cad58」 「№5019」
Difference from previous tested commit:  code diff
Commit date: 2020-11-23 19:33:58

Merge pull request #5019 from RosettaCommons/vmullig/c2_crosslinkers Add full support for 1,4-bis(bromomethyl)benzene to CrosslinkerMover and simple_cycpep_predict This pull request adds full support for 1,4-bis(bromomethyl)benzene to the `CrosslinkerMover` and to `simple_cycpep_predict`. When used with the `CrosslinkerMover`, this crosslinker can be used to link two L- or D-cysteine residues in either an asymmetric or C2-symmetric pose, or an L- and a D-cysteine residue in an S2-symmetric pose (all of which are symmetries matching the crosslinker itself). Tasks: - [x] Add symmetric params file. - [x] Add `CrosslinkerHelper` subclass for 1,4-bis(bromomethyl)benzene - [x] Copy from 1,3,5-tris(bromomethyl)benzene case. - [x] Update asymmetric case. - [x] Update symmetric case. - [x] Switch to using `CYS:SIDECHAIN_CONJUGATION` patch instead of `CYX`. `CYX` should eventually be deprecated. - [x] For 1,3,5-tris(bromomethyl)benzene, too. - [x] Check TBMB tests. - [x] `CrosslinkerMover` integration tests: - [x] C2 symmetry. - [x] S2 symmetry. - [x] No symmetry. - [x] Add to `simple_cycpep_predict`. - [x] Integration test. - [x] Check integration test. - [x] Beauty. - [x] Documentation. - [x] For `CrosslinkerMover`. - [x] For `simple_cycpep_predict`. - [x] Update to point at latest master for documentation submodule. Tests pass. Integration test changes are all expected: - simple_cycpep_predict_1_4_bbmb, crosslinkermover_1_4_bbmb_asymm, crosslinkermover_1_4_bbmb_c2_symmetry, and crosslinkermover_1_4_bbmb_s2_symm fail since they're newly added with this PR. - database_md5 is picking up the new params file. - simple_cycpep_predict_tbmb and threefoldlinkermover_tbmb_symmetric have small but expected trajectory changes resulting from the switch from CYX to CYS:Sidechain_Conjugation. Qualitatively, the output is the same. ![BBMB_render1](https://user-images.githubusercontent.com/4205776/95399812-0af8cb00-08d7-11eb-8b34-9953383ab1d7.png)

...