Merge pull request #792 from RosettaCommons/vmullig/better_error
Adding a more explicit error message to replace the seqpos <= size error, which didn't mean much to users.
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Merge pull request #790 from RosettaCommons/vmullig/layerdes_defaults
Making use_symmetry=true the default LayerDesign behaviour.
Previously, the default behaviour was to extract the asymmetric unit and only use this when setting up layers. Now, the whole, symmetric pose is used by default. The user can override this by setting use_symmetry=false in RosettaScripts.
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Merge pull request #779 from RosettaCommons/axial_equatorial/main
ÆRIS-Project
All unit tests pass.
carbohydrate, fiber_diffraction, and fold_and_dock integration test changes expected because of output changes.
code_duplication is because of moving code.
dna_interface, mm_params, pna, inverse_rotamer_remodel, and match tests are broken and/or unstable.
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Merge pull request #785 from RosettaCommons/vmullig/symm_layerdes
Allow LayerDesign to use symmetry
Currently, LayerDesign extracts the asymmetric unit of a symmetric pose, and uses that to define core, boundary, and surface layers. This adds an option to use the whole symmetric pose.
Tasks:
- [x] Add "use_symmetry" option.
- [x] Have the option alter LayerDesign's behaviour.
- [x] Integration test.
- [x] Documentation.
- [x] Beauty.
- [x] Also, pulling in a minor change to core::conformation::parameters::ParametersSet.hh. (It's something that will have to be tweaked when I fix the ResidueOP issue, and I want it in master so that I remember to do this, rather than in the branch where I added the functions, where the functions will be broken by a fix in master.)
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Merge pull request #782 from RosettaCommons/dimaio/denovo_density_fixes
This pull requests add the de novo cryoEM model-building tools described from Wang et al. 2015 to public apps.
It introduces the new public app, 'denovo_density'. Additionally, it makes a few bugfixes to the spherical harmonic code, and introduces a new mover, electron_density/DockIntoDensity, a general mover for matching proteins structures to density maps through fast 6D search.
Additionally, several other miscellaneous fixes for modelling into cryoEM density are added in this checkin. This includes a number of accumulated bugfixes and new features to RosettaCM.
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Merge pull request #735 from RosettaCommons/roccomoretti/gasteiger_SO4
Gasteiger atom typing updates
We weren't appropriately handling some of the "stranger" ways of specifying certain functional groups. Add fixes and unit tests, and add an "allow_unknown" option for Gasteiger atom typing, so it doesn't crash on difficult typing.
Integration test changes in "carbohydrates" expected, as we're now special-casing the N-terminus of amino acids to get the correct typing.
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Merge pull request #780 from RosettaCommons/vmullig/fix_restype
Fix the uninitialized variable issue in ResidueType identified by Valgrind
Tasks:
-- Revert Andy's pull request 777 temporarily.
-- Valgrind with --track-origins to identify where the uninitialized variable is.
-- Initialize the uninitialized variable.
-- Reinstate Andy's 777 pull request.
-- Full unit tests with a few rounds of commits.
-- Full tests.
-- Beauty.
-- Also, merges in Rocco's branch 743.
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Merge pull request #774 from RosettaCommons/vmullig/genkic_feature
Adds an option to GenKIC to stop after at least N solutions have been found.
Previously, users only had the option to stop when a solution was found. I want to be able to stop after 5 are found, or 10 are found, or whatnot.
Tasks:
-- Add stop_when_n_solutions_found=int option.
-- Remove stop_when_solution_found option, and add error message if the user tries to use this directing him/her to use stop_when_n_solutions_found option instead.
-- Update unit tests.
-- Update integration tests.
-- Also, refactoring a bit so that solution poses are stored after applying pre-selection mover, and the selector just picks from pre-generated poses. (This allows the choice of when to stop to be made after applying pre-selection movers, so I can pull out 20 solutions that pass the pre-selection movers).
-- Documentation.
-- Beauty.
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