Merge pull request #1077 from RosettaCommons/rfalford12/transmembrane_selections
Residue Selector for Transmembrane Spanning Regions
This pull request includes residue selectors specific for transmembrane proteins. To use them, the pose must be membrane-aware (i.e. `AddMembraneMover` has already been applied to your pose). The following residue selectors are included here:
New Residue Selectors in `src/core/select/residue_selector`
* **TMSpanSelector**: Select all or a subset of transmembrane spans in the pose
* **MembraneResidueSelector**: Select only the membrane residue (the special virtual that stores the membrane coordinate)
* **ByMembraneDepth**: Select all residues located at a certain depth in the membrane
Each residue selector includes a corresponding unit test in `test/core/select/residue_selector`
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Merge pull request #1197 from RosettaCommons/JWLabonte/sugars/input
Carbohydrates: Allowing glycans with sialic acids to be created by sequence
This merge will fix a bug preventing sialic acids from being read into Rosetta by IUPAC sequence. This was caused by the fact that the handedness designation is inherent to the 3-letter code for some codes, such as Neu.
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Merge pull request #1194 from RosettaCommons/roccomoretti/public_template_features
Promote the template_features application to public.
This application has been used in a published protocol, and external users are hoping to use it.
A new template_features integration test has been added, and will "fail" the first time.
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Merge pull request #1193 from RosettaCommons/mlnance/glycam_codes
Expanding list of GLYCAM 3-letter codes. This merge will introduce a list of all the 3-letter GLYCAM codes and their corresponding Rosetta name.
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Merge pull request #1191 from RosettaCommons/revert-1190-revert-1176-vmullig/genkic_tweaks2
Re-merge "Add a low-memory mode option to GenKIC"
This reverts RosettaCommons/main#1190 (reverting the reversion, bringing back the original merge).
This adds a low-memory option to GenKIC (minus the bug that I had inadvertently created the first time I tried to merge this).
Tasks:
- [x] Debug integration tests that fail to run.
- [x] Fix vector element erasure issue that was causing the problem.
- [x] Re-beautify.
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Merge pull request #1192 from RosettaCommons/dimaio/fix_centroid_symm_silent
Small bugfix for reading symmetric centroid silent files inadvertantly introduced in mirrorsymm checkin
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Merge pull request #1190 from RosettaCommons/revert-1176-vmullig/genkic_tweaks2
Revert "Add a low-memory mode option to GenKIC"
Whoops! Merged too soon -- there were some integration test failures.
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Merge pull request #1176 from RosettaCommons/vmullig/genkic_tweaks2
Add a low-memory mode option to GenKIC
I modified GenKIC a while back to store full solution poses rather than just solution DoF vectors. This was to accommodate the pre-selection mover, which could modify the pose in complicated ways that would not be captured by just storing DoFs. However, this can create problems for users who want to do a lot of sampling: memory becomes an issue. This adds an option to restore the old behaviour.
Tasks:
-- Add the option.
-- Modify GeneralizedKIC::add_solution() to store either a vector of solution poses (default mode) or a vector of loop DoFs (low-memory mode).
-- Modify final selection to use either the vector of solution poses (default mode) or the vector of loop DoFs (low-memory mode).
-- Modify selection logic.
-- Add warning if low-memory mode is used with a preselection mover.
-- Debug.
-- Integration test.
-- Unit test.
-- Documentation.
-- Beauty.
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Merge pull request #327 from RosettaCommons/aleaverfay/lbfgs_as_default
Unit test failures have been rectified. Integration test failures are expected, seeing as they each use minimization that is now lbfgs.
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Merge pull request #1187 from RosettaCommons/vmullig/add_talaris2014_tests
Adding sfxn_fingerprint tests for talaris2014.
Our default scorefunction should have a regression test to ensure that it doesn't change beneath us. (Granted, all but one of the terms are shared with talaris2013 -- but still, we should test it.)
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