Merge pull request #2828 from RosettaCommons/vmullig/fix_rama_sampling_issue
Fix a bug in RamaPrePro that was preventing sampling/scoring for residues with BACKBONE_AA.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #2817 from RosettaCommons/jadolfbr/fix_ff_from_loops
Fix DihedralConstraintGenerator XSD and add option to FoldTreeFromLoopsWrapper to add cutpoint variants for the proper use of the chain break term.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #2792 from CyrusBiotechnology/smlewis/commons/json_utils_sqtest_2
nlohmann::json extraction utilities
From Steven Lewis:
This is a set of functions with type-checking and bounds-checking for getting values out of nlohmann::json (the one added to the external libs). This gives us Rosetta-style error behavior in error cases instead of either nlohmann-style or uninterpretable-style. This addresses #2763 for Commons, and lets me reduce a lot of boilerplate on the Cyrus side. (Replying to @asford 's comment in #2763 : json-schema is absolutely a good way to address this, but it doesn't work for initial writing/debugging stages of the code - plus we're already using it, and I want a second layer of checking for a comfy security blanket!)
I chose to make all the functions have the same signature - return by reference - for consistency. It's inconvenient for bool/Real.
This PR will also give us a "real test" for @lyskov 's tweaks to see if we can test cross-fork merges properly.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #2818 from RosettaCommons/egurapha/remodel_stable
Egurapha/remodel stable Fixing errors in two_chain_tree, and insert_segment_from_pdb flags in remodel.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #2773 from RosettaCommons/vmullig/fix_ncaa_rotlibs
Fix major bug in noncanonical rotamer library scoring.
Currently, non-canonical rotamer libraries do not score or minimize properly with `fa_dun`. This pull request aims to find and fix the problem.
Tasks:
- [x] Add unit test for scoring (comparing Leu loaded as a canonical rotamer library _vs._ Leu loaded as a non-canonical rotamer library).
- [x] Correct path to canonical library.
- [x] Add unit test for minimizing (comparing Leu loaded as a canonical rotamer library _vs._ Leu loaded as a non-canonical rotamer library).
- [x] Find the problem. (Nice work, Andy and Adam!)
- [x] Fix it. (Nice work, Andy!)
- [x] Beauty.
@atom-moyer @everyday847 @twcraven
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #2411 from RosettaCommons/sboyken/buns4
Updating BuriedUnsatHbondsFilter; details can be found here: https://www.rosettacommons.org/docs/wiki/scripting_documentation/RosettaScripts/Filters/filter_pages/BuriedUnsatHbondsFilter
Vikram K. Mulligan 7 years This revision broke a few integration tests (i.e. they no longer successfully run in release_debug or release modes). These include homodimer_fnd_ref2015_memb, ppi_v3_suiteA, and thread_local_tracers_check. Scott, can you fix these?[list]
notify author
notify list [rosetta-logs@googlegroups.com]