Merge pull request #3277 from RosettaCommons/roccomoretti/PDB_xyzvector_fix
Fixes for xyzVector normalization in PDB loading
There's two main issues here, both related to Stub::from_four_points().
* With the PDB components, there's a number of (perfectly) colinear residues. These fail in Icoor assignment, as we attempt to grab a cross-product of two colinear vectors
* I fixed this by tweaking Stub::from_four_points() itself. The docs just guarantee that the second stub coordinate is within the a/b/c plane. When a/b/c are colinear, any arbitrary orthogonal vector will satisfy this requirement, so I pull out an arbitrary one.
* When there are co-incident adjacent atoms, fill_missing_atoms can choke when it tries to build based on a zero length vector.
* I fixed this by altering AtomICoor::build() -- we're already tweaking things slightly here, and I'm of the opinion that an arbitrarily build atom is better than a hard crash.
Note that in both cases I've taken the approach of applying arbitrary (small) tweaks to the vectors, rather than crashing with a zero-length error.
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Merge pull request #3279 from RosettaCommons/JWLabonte/sugars/branching
Glycosylation: Allowing glycosylation of lipids and nucleotide diphosphates
This merge will allow one to glycosylate an appropriate lipid or nucleotide diphosphate (e.g., UDP) using the glycosylate_pose() functions.
For example:
make_pose_from_sequence( pose, "Z[UDP:non-conjugated]", *residue_set );
pose::carbohydrates::glycosylate_pose( pose, 1, "a-D-Glcp-" );
carbohydrates integration test changes expected.
rosetta_scripts_jd3 and simple_glycosylation test changes are cosmetic.
All unit tests pass.
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Merge pull request #3247 from RosettaCommons/everyday847/odd_error
Add functionality to rna_minimizer plus fix a patching bug
This branch cannot be beautified, so we'll just have to beautify master.
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Merge pull request #3270 from RosettaCommons/smlewis/pdb_diagnostic_test_language
New language for the PDB diagnostic test, to make its results more interpretable to the community. Example run here: http://benchmark.graylab.jhu.edu/test/418571.
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Merge pull request #3269 from RosettaCommons/vmullig/fix_clang6_werror
Fix a couple of unused variable warnings-as-errors preventing compilation with clang 6 on Ubuntu 18.04.
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Merge pull request #3266 from RosettaCommons/dimaio/cryst_gen_mirrorsyms
Updating a pilot app. Making one small change in numeric (changing absolute float check to a tolerance check).
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Merge pull request #3190 from RosettaCommons/vmullig/fix_peptidestubmover
The PeptideStubMover is kinda crappy. Fix it.
This pull request adds proper unit tests for the PeptideStubMover, and fixes the currently super-twitchy behaviour of the mover. (The problem was diagnosed by Andrew Leaver-Fay, and fixed by Brian Wetizner, so thanks to both of those fellows!)
@weitzner @aleaverfay
Tasks:
- [x] Add unit test for Append.
- [x] With repeat.
- [x] Add unit test for Prepend.
- [x] With repeat.
- [x] Fix aberrant behaviour in all of the above.
Not in this pull request, but possibly in future:
- Add unit test for Insert.
- With repeat.
- Add unit test for sidechain conjugation.
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Merge pull request #3258 from RosettaCommons/JWLabonte/sugars/output
Pose IO: Providing option to force Rosetta to assign ligands unique .pdb chainIDs
This merge will provide an option, `-output_ligands_as_separate_chains`, that will cause Rosetta to reassign the `.pdb` `chainID` of a ligand when it shares the same `chainID` as one of the peptide chains.
Very often in `.pdb` structures, there might be, for example, a homodimeric protein with chains A and B in addition to a cofactors or product molecules, _etc.,_ that are also labeled as chains A and B. Using this option forces Rosetta to output them instead as belonging to separate chains, for example, C, D, _etc._ This new option will _not_ reassign a chain to a PTM, such as glycosylation; that is, saccharide or other residues that are attached covalently to a peptide chain will maintain the same `chainID` as the peptide chain to which they are attached.
All tests pass.
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Merge pull request #3259 from RosettaCommons/revert-3242-revert-3240-smlewis_for_gideonla/add_additional_protocol_data_submodule
adding `additional_protocol_data` as a submodule, on Gideon's behalf
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Merge pull request #2480 from RosettaCommons/JWLabonte/sugars/database
Carbohydrates: Ensuring that all sugars in the database have their anomeric forms also
This merge adds about 20 new .params files to the database, such that all current sugars have their anomeric forms present.
All unit tests pass; integration test changes expected in a few carbohydrate-related tests. Output change in c-term-conjugation test because of additional residue types being added.
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