Merge pull request #951 from RosettaCommons/vmullig/disulf_pep
Add support for disulfides to the simple_cycpep_predict app
This will add simple support for disulfides to the simple_cycpep_predict app. If the -require_disulfides flag is used, then the app will require that solutions have disulfide bonds between all residues of types that can form disulfide bonds. Every set of pairwise disulfide combinations will be tried.
Tasks:
- Add flags to the options system for requiring disulfides, and for cutoff energies.
- Have these flags actually do something in the app.
- Add a mover for disulfide construction and checking (trying all permutations or just a user-defined connectivity).
- apply() function.
- parse_my_tag() function.
- Support for ResidueSelectors.
- Support for odd numbers of disulfide-forming residues + integration test.
- Integration test.
- Documentation.
- Handle the special case of an odd number of disulfide-forming residues OR throw an error (for now).
- Add disulfide construction and checking to the parsed protocol called for every closure solution.
- Add a post-relaxation check for disulfide energy.
- The depermute() function needs to preserve disulfide linkages.
- Test with Gaurav's test cases.
- Update documentation.
Put off to another pull request:
x Add a unit test for symmetric glycine scoring when the -symmetric_gly_tables flag is used.
x Debug asymmetries in gly scoring that currently persist.
x Add a way for users to specify a desired disulfide connectivity.
@gbhardwaj