Merge pull request #1801 from RosettaCommons/vmullig/tbmb_predict
Add support for sampling threefold-symmetric crosslinkers during peptide structure prediction
Tasks:
- [x] Add a mover to place 1,3,5-tris(bromomethyl)benzene and other three-way crosslinkers.
- [x] It should take a ResidueSelector to pick three residues.
- [x] It should add and place the linker.
- [x] It should set up constraints.
- [x] Distance.
- [x] Torsion.
- [x] It should have an option to pack and minimize the linker and the side-chains to which it's connected.
- [x] It should have an option to do a final relaxation of the structure.
- [x] It needs a parse_my_tag().
- [x] It needs a way to set different crosslinkers.
- [x] Optional distance filters.
- [x] Optional filters for pre- and post-minimization energy.
- [x] More controls for stringency of filters.
- [x] Integration tests.
- [x] Documentation.
- [x] Add support for symmetry.
- [x] Integration test.
- [x] Documentation.
- [x] Add options and code to call the above in simple_cycpep_predict.
- [x] Debug RMSD steps.
- [x] Debug de-permutation steps.
- [x] More controls for stringency of filters.
- [x] Integration test.
- [x] Re-enable filters in integration test.
- [x] Documentation.
- [x] Aw, crap -- I'll need to write XML schema for the new mover.
- [x] Beauty.
Put off to a future pull request:
- Add options to call the above in classic <i>ab initio</i>.
- Add other threefold-symmetric crosslinkers (<i>e.g.</i> Kathy's case).
- Maybe generalize this for Nfold-symmetric crosslinkers?