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.