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Merge pull request #1913 from RosettaCommons/vmullig/cycpep_align
Add a mover to align a quasi-symmetric peptide to the origin and Z-axis, for true symmetry setup
Currently I do this with some manual editing of PDB files, a script, and the minimizer, but a specialized mover could do this more easily and more efficiently. This will be a needed part of the symmetric cyclic peptide design pipeline.
Tasks:
- [x] Create the mover with Jared's code template scripts.
- [x] Register it.
- [x] Add options to parse_my_tag() for specifying symmetry.
- [x] XSD information for these.
- [x] Add length check and symmetry check (with the CycpepSymmetryFilter) to apply() function.
- [x] Add origin alignment to apply() function.
- [x] Add Z-axis alignment to apply() function.
- [x] Ensure above handles non-protein residues properly (ignores them).
- [x] Allow auto-detection of symmetry.
- [x] In parse_my_tag().
- [x] XSD information.
- [x] In apply() function.
- [x] Add option to delete all but a selected repeat:
- [x] To parse_my_tag().
- [x] XSD information.
- [x] To apply() function.
- [x] Ensure this deletes non-protein residues like TBMB. (Symmetric versions can be added back after symmetry is set up, using the ThreefoldCrosslinkerMover.)
- [x] Document this deletion of non-protein residues.
- [x] Unit tests.
- [x] Integration test.
- [x] Beauty.
- [x] Documentation.