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.