Merge pull request #6072 from RosettaCommons/vmullig/fix_cycpep_bug_identified_by_jared
Fix a simple_cycpep_predict bug in cis-trans sampling with lariats, identified by Jared
The bug is actually in N-terminal N-methylated thioether-cyclized variants, which are introduced in the `jadolfbr/cycpep` branch. This branch has `jadolfbr/cycpep` merged into it. @jadolfbr, is it okay to merge the contents of `jadolfbr/cycpep` into `master`, or do you want to keep that private for now?
Tasks:
- [x] Add integration test that should trigger the bug.
- [x] Track down the bug.
- [x] Check whether `jadolfbr/cycpep` can be merged into master.
- [x] Fix the bug.
- [x] Beauty.
From `jadolfbr/cycpep`:
- [x] This adds support to the AcetylatedProteinNterm for N-methylation.
- [x] This adds support for the `out::path::pdb`, `out::path::all`, `out::path::path`, `out::suffix`, and `out::prefix` commandline flags to the `simple_cycpep_predict` application.