Merge pull request #2617 from RosettaCommons/darwinyfu/minor-ligand
Basic constraints can now be used with ligand docking low resolution Transform mover sampling.
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Merge pull request #2862 from RosettaCommons/roccomoretti/header_using_as_typedef_fix
Fix the `header_using_check` integration test to allow new using syntax.
The new syntax (with a = in the line) is a replacement for typedef, rather than a questionable/objectionable use of using, so don't raise a warning/error on it.
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Merge pull request #2857 from RosettaCommons/vmullig/voidspenalty_fix
Correct a silly mistake in the scorefunction setup options for the voids_penalty energy.
I was calling the wrong setters. Whoops.
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Merge pull request #2705 from RosettaCommons/vmullig/polar_oligourea
Adding a few polar oligoureas to the database (and a few hydrophobics)
I want to be able to design surfaces with oligoureas, too. In addition to adding these oligoureas, this pull request resolves some NCAA issues.
Tasks:
- [x] Add OU3_THR.params.
- [x] Add rotamer library to Git LFS repository.
- [x] Add OU3_ASN.params.
- [x] Add rotamer library to Git LFS repository.
- [x] Add OU3_GLN.params.
- [x] Add rotamer library to Git LFS repository.
- [x] Add OU3_TRP.params.
- [x] Add rotamer library to Git LFS repository.
- [x] Add OU3_TYR.params.
- [x] Add rotamer library to Git LFS repository.
- [x] Update residue_types.txt.
- [x] Fix bug in `pro_close` energy that was affecting OU3_PRO and DOU3_PRO.
- [x] Test all oligoureas (_not_ as a unit test, though, since this would require adding all oligourea rotlibs to the database).
- All work well EXCEPT OU3_PRO, which seems to have a problem with `pro_close` --> fixed.
- [x] I will add a unit test for the OU3_PRO case, just to be on the safe side.
- [x] Figure out rotamer-building problem --> fixed.
- [x] Figure out OU3_PRO geometry problem. This seems to be a fundamental issue with `fa_dun` derivatives and scoring.
- [x] Adding a scoring test.
- [x] Fix beta-amino acid problem.
- [x] Small tweak to the cis-peptide bond GeneralizedKICperturber to make it work with oligoureas.
- [x] Check integration tests.
- Most integration test changes are cosmetic (caused by additional residue types or noisy tracer now made into a Debug tracer).
- `cyclization` is due to slightly different peptoid rotamers since a Dunbrack bug was fixed. Qualitatively the same.
- `disulfidize_beta_cys` finds more and better beta-cysteine disulfides due to Dunbrack bugfix.
- `ncaa_fixbb` finds new and slightly better rotamers at peptoid positions due to Dunbrack bugfix.
- `oligourea_design` and `oligourea_predict` show expected trajectory changes due to Dunbrack bugfix and GenKIC cis-peptide bugfix.
- `unfolded_state_energy_calc` changes expected due to Dunbrack bugfix affecting peptoids.
@twcraven
Rocco Moretti 7 years Looks like the oligourea_design test is now reporting a backtrace, though for some reason it doesn't look like it's being flagged as a magenta failure.
Merge pull request #2859 from RosettaCommons/dougrenfrew/fix_permissions
Change permissions on cc, hh, and some other files so that they are not executable
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Merge pull request #2849 from RosettaCommons/vmullig/dun02_ncaa_unit_test
Add unit test for Dun02 canonical-noncanonical equivalence.
In pull request #2773, I added a unit test for equivalent canonical/noncanonical rotamers, derivatives, and scoring, but I only did it for Dun10-style libraries. Adam might have identified a bug specific to Dun02-style libraries, so I need a unit test for this, too.
Update -- I think Adam has identified the problem, now, and I'll open another pull request to fix it. I'd like these unit tests in master, though, so that I know that I don't break anything while fixing the problem.
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Merge pull request #2816 from RosettaCommons/jadolfbr/glycan_mm_factory
Glycans in MoveMapFactory
The `MoveMapFactory` now deals with glycans properly in that it uses IUPAC definitions for chi/bb. Since Rosetta does not understand what a BB torsion is for glycans very well. This includes setting proper 'branch' torsions as well and differentiating from a proper 'chi' that we think of vs a proper 'bb' in glycan nomenclature.
This change allows us to use the MMFactory to properly select and minimize glycans. In combination with the GlycanResidueSelector, we now have full control of sane glycan torsional selection.
This PR separates out the core glycan MM code we had previously (and is covered with proper unit tests) so that it can be called independently of the`get_movemap_for_glycans` function.
@raemisch
@BrandonFrenz
@JWLabonte
Example Use in a script to do FastRelax on an H3 loop in addition to minimizing the neighboring glycan tree after threading a sequence:
```
<ROSETTASCRIPTS>
<SCOREFXNS>
</SCOREFXNS>
<RESIDUE_SELECTORS>
<Neighborhood name="nbrhood" resnums="%%start%%-132H"/>
<Not name="others" selector="nbrhood" />
<Index name="cst_residues" resnums="%%start%%-132H"/>
<Glycan name="glycan_tree" include_root="1" branch="1332A"/>
</RESIDUE_SELECTORS>
<TASKOPERATIONS>
<OperateOnResidueSubset name="turn_off_others" selector="others">
<PreventRepackingRLT/>
</OperateOnResidueSubset>
<RestrictToRepacking name="rtrp"/>
</TASKOPERATIONS>
<MOVE_MAP_FACTORIES>
<MoveMapFactory name="fr_mm_factory" bb="0" chi="0">
<Backbone residue_selector="cst_residues" />
<Chi residue_selector="nbrhood" />
<Backbone residue_selector="glycan_tree" />
</MoveMapFactory>
</MOVE_MAP_FACTORIES>
<FILTERS>
</FILTERS>
<MOVERS>
<SimpleThreadingMover name="threader" start_position="%%thread_start%%" thread_sequence="%%sequence%%" pack_neighbors="1" />
<FoldTreeFromLoops name="loopFT" loops="%%ft_start%%:133H:115H" add_cp_variants="1"/>
<FastRelax name="fast_relax" task_operations="rtrp,turn_off_others" movemap_factory="fr_mm_factory"/>
<AddConstraints name="add_dih_csts">
<DihedralConstraintGenerator name="dih_cst_phi" dihedral="phi" residue_selector="cst_residues" />
<DihedralConstraintGenerator name="dih_cst_psi" dihedral="psi" residue_selector="cst_residues" />
</AddConstraints>
<RemoveConstraints name="rm_csts" constraint_generators="dih_cst_phi,dih_cst_psi" />
</MOVERS>
<APPLY_TO_POSE>
</APPLY_TO_POSE>
<PROTOCOLS>
<Add mover_name="threader"/>
<Add mover_name="add_dih_csts"/>
<Add mover_name="loopFT" />
<Add mover_name="fast_relax"/>
<Add mover_name="rm_csts" />
</PROTOCOLS>
<OUTPUT />
</ROSETTASCRIPTS>
```
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Merge pull request #2805 from RosettaCommons/jadolfbr/improve_glycan_error_handling
Improve Glycan Error Handling
This PR fixes map access in GlycanTreeSet so that we actually check if the residues are there before accessing them. This allows us to cleanly exit with helpful error messages.
This also adds more helpful XSD text for GlycanTreeRelax and GlycanRelax use of the Residue Selector. We also now check to make sure we only have glycans selected from the ResidueSelector in GlycanTreeRelax - instead of cryptic crashes.
Cosmetic integration changes expected in all tests that load glycan poses.
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Merge pull request #2820 from RosettaCommons/roccomoretti/switch_residue_type_set_fix
Fix issue with crashing SwitchResidueTypeSet
The make_centroid() utility function, which is applied when SwitchResidueTypeSetMover can't find a corresponding type, had a bug where resetting the ResidueType's atom type assumed that it was operating with the same type set with the current and replacement type - which wasn't the case for make_centroid().
Change things such that switching the atom type set on a ResidueType appropriately swaps out the atom types, as much as possible.
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