Merge pull request #4465 from RosettaCommons/vmullig/fix_james_helical_bundle_predict_issues_2
Fix an issue with, and add some features to, helical_bundle_predict.
This PR:
- [x] Fixes a silly bug in parsing FASTA files in helical_bundle_predict.
- [x] Adds an option to skip residues in the native structure in alignments.
- [x] Adds an option to skip residues in the generated structure in alignments.
- [x] Adds integration tests for the new options.
- [x] Adds documentation for the new options.