Merge pull request #484 from RosettaCommons/vmullig/ncaa_residue_counter
Updating ResidueCountFilter.cc to work if the input pose has a different residue type set from the pose at apply time.
This can happen if, for example, the parse-time pose is a centroid pose (e.g. the product of the -in:file:fasta flag) while the apply-time pose is full atom. The current hacky fix is to try first with the residue type set of the parse-time pose, then with the fa_standard residue type set.
Note that mpi tests have been failing intermittently depending on which test server node runs the test. Aside from this, no integration or unit test failures are anticipated.
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Merge pull request #480 from RosettaCommons/vmullig/demo_fix_1
Fixing a "bug" for the Rosetta 201 training session.
This is intended to demo the GitHub pull request workflow for Bakerites during the Rosetta 201 lecture on Thursday. The "bug" is a typo in an output message in GeneralizedKIC that I introduced deliberately a few days ago. Fixing this should result in cosmetic integration test changes in the GeneralizedKIC tests.
(This is the "Martha Stewart" pull request that I'm setting up the day before so that it will be all tested and ready to go during the actual session, so that I can push the big green button there. "So put that in the oven and let it bake. Now here's one we made earlier.")
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Merge pull request #479 from RosettaCommons/vmullig/z_is_for_zibo_that_good_enough_for_me
Adding Crick parameters for an alpha helix with a turn per residue of exactly 100 degrees
The new Crick parameters file was generated by fitting an alpha helix with phi=-62.648, psi=-41.0, omega=180.0. No test changes expected (database-only change).
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Merge pull request #471 from RosettaCommons/vmullig/z_is_for_zibo_that_good_enough_for_me
Adjusting z1_offset parameter in helical bundle code to match Grigoryan paper's convention.
This adds a correction factor so that z1_offset is measured as the offset along the global z-axis, in Angstroms, rather than as the offset along the local helix axis. This is intended to match Grigoryan and DeGrado (2011) J. Mol. Biol. 405(4):1079-1100.
Tasks:
-- Add correction factor.
-- Double-check that this does, indeed, produce the correct offsets.
-- Update documentation.
-- Also, switch convention for inverted helices. (They now move in the opposite direction to right-side-up helices).
Expect integration test changes to z0_offset and z1_offset integration tests for the BundleGridSampler and PerturbBundle movers.
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Merge pull request #465 from RosettaCommons/justinrporter/env_release
Error reporting for RigidChunkCM & SlidingWindowLoopClosure. Performance and integration test changes are being shown for other branches as well--will revert if they persist.
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