Merge pull request #4928 from RosettaCommons/vmullig/tidy_up_clang_tidy_warnings
Removing unused values flagged by clang-tidy.
Note that the operator() called here has no side-effects; its ONLY effect is to return a value that's never used, so it's safe to delete it.
Additional notes added by Rocco:
Looking at the code and #4890, it looks like the removal is fine. The computation that was previously done with these variables has been moved to the output_interface_deltas().
Presuming the component energies sum to the total scores, then the transformation should be valid. (As the difference of the sums of the components should be equal to the sums of the differences in components.)
... Well, with the caveat that you're either not using the normalization function, or that the normalization function is a linear (not affine) scaling, and the sum of normalized components is equal to the normalized sum of components. -- But looking through the current options for normalization factors, that's the case. (And the normalization option isn't used much, anyway.)
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Merge pull request #4926 from RosettaCommons/revert-4897-dpaoliello/noreturn
Revert "Use the C++11 `[[ noreturn ]]` attribute"
Reverts #4897
This merge broke compilation. Reverting temporarily until this can be fixed.
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Merge pull request #4859 from RosettaCommons/vmullig/handle_disulfides_in_mutate_residue
Allow the MutateResidue mover to break disulfide bonds automatically.
It's a bit silly to have the MutateResidue mover leave a pose in an unstable, un-scorable state with a "dangling" disulfide partner (which still expects to be bonded to something) if you try to mutate a disulfide-bonded cysteine. This PR ensures that the mover automatically removes the disulfide partner's DISULFIDE variant type when it makes the mutation. There is an option to restore the old behaviour in the rare cases in which a user might want that, but it's clearly marked as not recommended.
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Merge pull request #4592 from RosettaCommons/vmullig/add_cys_sidechain_conjugation_patch
Adding CYS:SidechainConjugation patch.
It's a bit silly that we still have CYX for sidechain conjugation to cysteine. This adds a CYS:SidechainConjugation patch. For now, I won't remove CYX, since it's probably needed for backwards-compatibility with a lot of things.
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Merge pull request #4915 from RosettaCommons/JackMaguire/SingleResSelect
Adding residue selector interface for DeclareBond mover
This PR:
- Allows DeclareBond to take a residue selector instead of a raw resid
- asserts that the residue selector accounts for exactly one residue
- Inserts this new usage into some integration tests
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Merge pull request #4786 from RosettaCommons/vmullig/cycpep_predict_hbonds_update
Switch simple_cycpep_predict to use the PeptideInternalHbondsFilter
This is a simple PR to switch the simple_cycpep_predict application over to using the PeptideInternalHbondsFilter, which should reduce computational cost a bit.
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Merge pull request #4914 from RosettaCommons/jadolfbr/timing_profile_bug
Fix bug in TimingProfileMetric copy constructor.
This makes the copy constructor not copy over the construction time. This was a major bug identified by @francesc45 where the time would be additive and not per-nstruct due to the use of copy constructors in RS.
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