Merge pull request #5093 from RosettaCommons/ninabozhanova/chromophore
Adding ReadResidueCoordinatesFromPDB class, which reads and saves xyz coordinates for the specified residue(s) from a PDB file, and a unit test for it.
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Merge pull request #5139 from RosettaCommons/vmullig/BuriedUnsatHbonds2_to_protocols
Move BuriedUnsatHbonds2 filter from devel to protocols
This was requested by a user. @aleaverfay reports that this can be moved to protocols.
Tasks:
- [x] Move files.
- [x] Update namespaces.
- [x] Update `.src.settings` files.
- [x] Check compilation.
- [x] Check unit test compilation.
- [x] Check that there exists a unit or integration test. --> Yes, several integration tests.
- [x] Check that XSD functions exist.
- [x] Add a description to the XSD function.
- [x] Check that parse_my_tag function exists.
- [x] Documentation.
- [x] Beauty.
Integration test changes are all cosmetic and expected.
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Merge pull request #5135 from RosettaCommons/vmullig/update_docs1
Update documentation so that main repo points to current master of docs.
This is to add the page on using VSCode with RosettaScripts (https://www.rosettacommons.org/docs/wiki/scripting_documentation/RosettaScripts/Using-RosettaScripts-with-VSCode).
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Merge pull request #5122 from RosettaCommons/roccomoretti/fix_PoseRTS_get_variants
Fix issue with PoseResidueTypeSet::get_all_types_with_variants_aa()
It looks like that due to caching behavior, PoseResidueTypeSet::get_all_types_with_variants_aa() will "double up" the underlying residue types.
It turns out that special casing this function isn't necessary, as the base class implementation effectively only uses the public interface which is properly overloaded.
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Make addVirtualResAsRoot add a residue to its own chain (#5116)
I think that this is a reasonable change since it doesn't make sense to have the virtual root in the same chain grouping as the last residue of the pose that you are adding it too.
the current implementation is annoying because if you're trying to make sure the pdb_info is is line with experimental data I use pose.chain_sequence(i) to get the polymeric entities, then each are aligned. Adding an X at the end can make this annoying. If this PR breaks a lot -- then I will figure out the corner case in my own code.
* Make vrt residue on its own chain
* update ssa test
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Merge pull request #5110: aleaverfay/bugfix_pepspec_anchor_at_term
pepspec: copy coords instead of overwriting anchor
This fixes a bug brought to me by Astghik Tsokolakyan who was
getting a segfault from the count_pair code and saw that I had
written count_pair. Astghik was using the pepspec application
setting the pep_anchor to be the first residue in the peptide,
but also extending the peptide 3 residues off both the N-
and C-termini. The extension code works nicely building off
the termini, but after the extension completes, it does some
centroid modeling and switches back to fullatom where it
calls "replace_residue" on the anchor residue to restore
its rotamer. This is a problem when the anchor residue in
the original pose was a termini residue and its a middle-of-
the-chain residue after the extensions have been added.
One solution is to not anchor from either termini, but
that can't be the right solution as the app in its
documentation says that you should be able to use a
single residue for the anchor.
The bug fix is to copy the coordinates that can be copied
from the original residue into the new residue.
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Merge pull request #5108 from RosettaCommons/vmullig/update_energy_method_tracers
Update tracer names for classes in core/energy_methods
This is a follow-up PR to #5103 . That PR corrected the namespaces for files in `core/energy_methods`, but was not intended to alter output (so that I could confirm that there were no integration test changes). This replaces the tracer names with ones reflecting the new namespaces, which _will_ change a lot of integration tests (but trivially in each case).
<b>Note:</b> The initial diff includes all the changes from PR #5103, since this is branched off of that branch. Once #5103 is merged, I will merge the latest master into this branch to make it clearer that the only changes are from commit d6df11b, only updating tracer names.
- [x] PR #5103 must be merged before this PR.
- [x] Update integration tests that selectively unmute tracers.
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Merge pull request #5103 from RosettaCommons/vmullig/clean_up_namespaces_a_wee_bit
Clean up the namespaces a bit.
When energy methods were moved from core/scoring to core/energy_methods in order to split core.3 and create the current core.4, there was a need to finish the split quickly: linking the enormous core.3 library was taking too long and using too much memory for some people's systems, and the change needed to be in master before additional energy methods were added. Unfortunately, this meant that the energy methods retained their old namespace, breaking the convention of ensuring that directory structure and namespace match in Rosetta. This PR aims to clean this up, and to change the namespace for the energy methods that are in core/energy_methods from core::scoring to core::energy_methods.
Note: in the interests of keeping the integration tests interpretable, this PR does not change tracer names. Pull request #5108 will subsequently update the tracer names. This PR must be merged before that one.
For reviewers: Although this is a huge PR, it should only change namespaces. (The only other cases are a few places where I switched new to make_shared, and one or two places where I switched MyClass myobject = MyClass( params ) to MyClass myobject( params ).) Nothing in this PR should alter Rosetta function or output (but for possible trajectory changes that are hard to anticipate from mysterious things that the compiler does differently).
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