Merge pull request #565 from RosettaCommons/vmullig/multirepeat_bundle
Permit helical bundles to have repeating units that are more than one residue.
Currently, our parametric design code assumes that the repeating unit in a helix is a single residue. This changes that to permit the repeating unit to be more than one residue. This allows interesting secondary structures like alpha-sheets (made from alternating D- and L- amino acids in the left- and right-handed helix regions of Ramachandran space, respectively) to be generated parametrically. It also allows things like the collagen triple helix to be created parametrically.
Tasks:
-- Update the write function for Crick params files.
-- Update the minor helix fitting app.
-- Update the minimizer called by the minor helix fitting app.
-- Add an integration test for fitting a helix with a multi-residue repeating unit.
-- Update and test the MakeBundle mover.
-- Update the read function for Crick params files.
-- Update and test the MakeBundleHelix mover called by the MakeBundle mover.
-- Add an integration test for the MakeBundle mover + more than one residue in the repeating unit.
-- Update and test the PerturbBundle mover.
-- Add an integration test for the PerturbBundle mover + more than one residue in the repeating unit.
-- Update and test the BundleGridSampler mover.
-- Add an integration test for the BundleGridSampler mover + more than one residue in the repeating unit.
-- UPDATE DOCUMENTATION.
Also:
- Adding a symmetrically split TBMB to the database, for symmetric linker design.
Integration test changes observed for all parametric generation/design integration tests; these are all cosmetic and expected. Slight numerical changes to the fitter are possible since the fit algorithm has been tweaked. Two new integration tests have been added, and will fail because they're new.