Merge pull request #355 from RosettaCommons/vmullig/genkic_binfilter
Adds a new GeneralizedKICfilter based on whether pivot residues are in desired mainchain torsion bins
This creates a new GeneralizedKICfilter called "backbone_bin". It rejects solutions in which a particular residue (presumably a pivot residue) is in an undesired mainchain torsion bin.
Tasks completed:
-- Clean up GenKIC clone and copy functionality a bit.
-- Create the backbone_bin GeneralizedKICfilter.
-- Add an apply() function for the filter.
-- Add suitable hooks in the BinTransitionCalculator object for the check that we want to do.
-- Add RosettaScripts parsing for the unique filter options.
-- Add integration test.
-- Documentation.
Expected test changes:
-- set_backbone_bin integration test should change considerably, since it now tests this filter in addition to the set_backbone_bin perturber. (This filter is intended to be used with this perturber, so it makes sense for the integration test to test both.)
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Merge pull request #351 from RosettaCommons/vmullig/genkic_sampling
Adding some new features to GenKIC
Tasks:
-- Add a set_backbone_bin GeneralizedKICPerturber.
-- Add integration test for set_backbone_bin GeneralizedKICPerturber.
-- Have GenKIC use and respect mover status.
-- Update documentation.
Cosmetic integration test changes expected for the genkic_bin_perturbing integration test. Failure expected for the new genkic_bin_setting integration test, since it is new.
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Merge pull request #290 from RosettaCommons/justinrporter/env_release
ParsedProtocol MoverStatus handling. Merge a bugfix for MoverStatus handling by EnvMover. A few scattered integration test differences on the test server, but I don't think they're real. Will revert if they persist.
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Merge pull request #350 from RosettaCommons/vmullig/ssshapecomp_threshold
Add min_sc option to SSShapeComplementarityFilter
Updating SSShapeComplementarityFilter with a threshold option ("min_sc" in RosettaScripts), so that it may be used to filter designs. Also, updating the tracer for the ShapeComplementarityFilter to properly reflect its namespace. (This also fixes a trivial typo in LayerDesign).
Tasks completed:
- Write code.
- Write documentation.
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Bugfix: B3P.params
Beta-3-proline had a problem! It only listed two chi angles and didn't have a virtual nitrogen shadowing its nitrogen, so it wouldn't work with cart-bonded either
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Merge pull request #339 from RosettaCommons/tjbrunette/repeatExtract
Tjbrunette/repeat extract mostly updates apps. But in the main code there was a fix to the linkRes command. For some reason a residue needed to be linked to itself or the code seg-faults
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Merge pull request #341 from RosettaCommons/jkleman/mp_updates
Jkleman/mp updates:
small updates for membrane proteins:
= changed the scorefunction names to match the one in the supplement for the paper (also changed that in demos)
= changed default thickness for both membrane viewers from 12.5 to 15A (in options file)
integration test changes: expected
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Merge pull request #349 from RosettaCommons/vmullig/fix_unfolded_e_calc_instability
Trying to fix instability that I introduced in the unfolded state energy calculator integration test
I think this is due to a couple of uninitialized variables in some of the constructors for the MutateResidue mover. Fixed now.
Integration test changes are possible in the msd_mover, unfolded_state_energy_calc, and remodel_disulfides_rosettascripts integration tests, all of which were potentially affected by this uninitialized variable.
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