Merge pull request #1695 from RosettaCommons/vmullig/eccentricity2
Add a parameter to the Crick parameters to allow lateral sqash of bundles or beta-barrels
The old pull request branch was branched off of master with the toxic commit. I've re-pulled (removing the toxic commit), created a new branch, and cherry-picked all of my changes from the old.
Tasks:
- Add the parameter to functions in numeric.
- Add arclength correction factor (t->t' s.t. int(0->t')(|f'(x,epsilon)|dx) = int(0->t)(|f'(x,epsilon=1)|dx)) This is very hard to compute, but as it turns out, the correction factor is negligibly small.
- Add correction factor in numeric to normalize the path tangent vector.
- Update protocols/helical_bundle/util.cc/hh.
- Update MakeBundleHelix mover.
- Update PerturbBundleHelix mover.
- Update MakeBundle mover.
- Update PerturbBundle mover.
- Update BundleGridSampler mover.
- Update BundleGridSamplerHelper class.
- Update BundleParameters class.
- Update BundleParametersSet class. Nothing to update.
- Update PerturbBundleOptions class. Nothing to update.
- Update test_makebundle_mover pilot app.
- Integration test.
- Documentation.
- Beauty.
(Note: at some point, I'll properly set things up so that the parametric movers don't need to be updated whenever a new parameter is added to the generating equations. When I initially implemented this, I failed to anticipate the need for this.)