Merge pull request #1846 from RosettaCommons/vmullig/symm_predict
Adding options to simple_cycpep_predict app for only sampling symmetric conformations. Integration test changes to simple_cycpep_predict integration tests are expected.
Tasks:
- [x] Add the options.
- [x] Have them do something.
- [x] Integration test.
- [x] Add mirroring integration test.
- [x] Mute unnecessary output in integration test.
- [x] Find and fix bug in CycpepSymmetryFilter.
- Added a unit test for this, but can't really reproduce the bug, if it exists. It could be that it was a problem with where the filter was applied, and that the asymmetry was introduced in the final relaxation...
- [x] Add GenKIC perturber for copying DoFs (addresses issue #1877).
- [x] Integration test
- [x] Allow perturber to steal DoFs from non-loop residues, too.
- [x] Ensure that anchor_res DoFs are properly grabbed in simple_cycpep_predict.
- [x] Add mirroring option.
- [x] Add mirroring option to integration test.
- [x] Hook this in to the simple_cycpep_predict app in symmetry mode.
- [x] Document GenKIC perturber.
- [x] Document new flags for simple_cycpep_predict.
- [x] Have simple_cycpep_predict ignore linkers when doing RMSD calculation (addresses issue #1879).
- [x] Add option to simple_cycpep_predict to connect ALL cysteines with TBMB (addresses issue #1879).
- [x] Document this.
- [x] Fix issue with output structure numbering in simple_cycpep_predict, so that every output structure in MPI mode has a unique name and number.
- [x] Beauty.
- [x] Documentation.
Put off to a future pull request:
- Add support for multiple natives to simple_cycpep_predict.