Merge pull request #383 from RosettaCommons/kwikwag/peptiderive-talaris
Peptiderive: merge second round of fixes to the PeptiDerive protocol and adjacent logic. Note that this includes some fixes to pose::util and to unit testing infrastructure. Detailed change list below.
DisulfideInsertionMover
- unit tests
- RosettaScripts support
PeptideDeriverFilter unit tests
- use -in:missing_density_to_jump 1
- change input PDB to check more edge cases: discontinuous chains, short segments, and zero-isc segments.
Bug fixes in basic Rosetta code
- fix `return_nearest_residue()` and `addVirtualResAsRoot()` in pose::util
- fix test core files to reuse `get_commandline_with_additional_options()` and always use `initialize_rng()`
Logic fixes
- anchor residue in the receptor for receptor-peptide jump is now nearest residue to the peptide
- make jump id is returned from `build_receptor_peptide_pose()` (as it changes when using `-in:missing_density_to_jump 1`)
- fix #371 : remove truncated terminus variant type before adding full terminus variant type
- use iterators for the `next_cutpoint` logic; this fixed some logic flaws
- fix incorrect pose PDB being output as best linear
- change translation magnitude to 2e6
Option tune-ups
- compressed report output (`report_gzip` option)
- output PDBs by default