Merge pull request #5565 from RosettaCommons/vmullig/helical_bundle_predict_scipred_file_input
Allow helical_bundle_predict to take a PsiPred file as an alternative to a helix definition file, for canonical amino acid prediction
This PR adds the option of providing a PsiPred file as input to the helical_bundle_predict application instead of a helix definition file. This is convenient for predicting canonical amino acid helical bundles (but obviously cannot be used for exotic noncanonicals).
I'll expand the tasks below as I go along.
Tasks:
- [x] Add the option.
- [x] Add alpha helix and beta strand cutoffs.
- [x] Have it do something.
- [x] Add means of setting file.
- [x] Add means of reading file contents.
- [x] ~~Use existing PsiPred reader code; don't reinvent the wheel.~~ --> In this case, it really was simpler to write my own parser.
- [x] Use file contents to set up helix definitions.
- [x] ~~Check that _either_ a helix definition file _or_ a PsiPred file was provided (but not both).~~ Global settings can only be set with a helix definition file. Allow both to be used together.
- [x] Integration test.
- [x] Check that this works.
- [x] MPI mode too.
- [x] Check that this works in MPI mode.
- [x] Update documentation.
- [x] Run beautifier.
@jameseastwood