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Revisions №57794

branch: master 「№57794」
Commited by: Vikram K. Mulligan
GitHub commit link: 「031e04ef528e2114」 「№457」
Difference from previous tested commit:  code diff
Commit date: 2015-04-16 18:27:11

Merge pull request #457 from RosettaCommons/vmullig/z_is_for_zibo_that_good_enough_for_me Adding some features to the MakeBundle, BundleGridSampler, and PerturbBundle movers Zibo requested a z-offset option, so I'm adding that. I also wanted to change the default behaviour to set all backbone DOFs (not just dihedral values), and to add a constant helix pitch option. Tasks: Change default behaviour so that mainchain bond lengths, bond angles, and dihedral angles are set by the MakeBundle and BundleGridSampler movers, not just the mainchain dihedral angles. The user can turn off the bond length and bond angle options to preserve ideal bond geometry, at the expense of sacrificing ideal helix-of-helices geometry. Add z1_offset (offset along the minor helix axis) and z0_offset (offset along the major helix axis) options: Add these to the BundleParameters class, with getters and setters. Update the MakeBundle mover's parse functions to set these. Update the BundleGridSampler mover to allow sampling of z1_offset and z0_offset. Update the PerturbBundle mover to allow sampling of z1_offset and z0_offset. Update the MakeBundle mover to use these in its apply() function. Update the numeric libraries to do something with these values. Update the PerturbBundle mover to connect properly with the updated functions in util.cc. Update the parameters data storage unit test to test for proper storage and copying of z1_offset and z0_offset parameters. Add an integration test for sampling over these parameters. Add an integration test for perturbing these parameters. Add a BundleGridSampler option to let one helix copy the pitch angle (rather than omega0 value) of another helix. Fix the math! It's not quite right. Add an integration test for pitch angle copying with the BundleGridSampler. Add a PerturbBundle option to let one helix copy the pitch angle (rather than omega0 value) of another helix. Add an integration test for pitch angle copying with PerturbBundle. Update documentation. Expected test changes: -- No unit test failures (though one new unit test is introduced). -- Existing BundleGridSampler and PerturbBundle integration tests will show a cosmetic change (z0_offset and z1_offset values are now reported). -- New BundleGridSampler and PerturbBundle integration tests have been introduced, and will fail once because they're new. -- Some unrelated integration tests are already failing.

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