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.
