Merge pull request #5720 from RosettaCommons/vmullig/cycpep_permutation_mover
Add a mover to superimpose a cyclic peptide on itself with cyclic permutation
Requested by @skudlacek.
Tasks:
- [x] Add the mover.
- [x] Configuration:
- [x] Allow user-specified cyclic permutation or reverse permutation.
- [x] Allow random cyclic permutation or reverse permutation.
- [x] Additional random displacement and/or roll.
- [x] parse_my_tag()
- [x] provide_xml_schema()
- [x] C++ getters and setters.
- [x] apply()
- [x] Check that pose or selection is a cyclic peptide.
- [x] Set_permutaion mode.
- [x] Set_permutaion mode with inversion.
- [x] Randomized_permutaion mode.
- [x] Randomized_permutaion mode with inversion allowed.
- [x] Align peptide to original.
- [x] Add random offset.
- [x] Add random orientation perturbation.
- [x] CitationManager functions.
- [x] Unit test for set_permutation mode.
- [x] Fix errors revealed by unit test.
- [x] Integration test for randomized_permutation mode.
- [x] Fix errors revealed by integration test.
- [x] Documentation. --> See pull request RosettaCommons/documentation#49
- [x] Beauty.