Merge pull request #192 from RosettaCommons/vmullig/parametric
vmullig/parametric
This creates a new PerturbBundle mover, which permits sampling of Crick parameter space during a design or structure prediction protocol.
Done:
Created the PerturbBundle mover
Created the PerturbBundleHelix mover that's called by the PerturbBundle mover.
Moved utility functions from MakeBundleHelix.cc to util.cc to permit re-use by PerturbBundle.cc.
Fixed a serious mistake in the MakeBundle mover that was resulting in improper placement of secondary structure elements.
Added a symmetry_copies option to the MakeBundle mover to allow creation of partial bundles or beta-barrels.
Implemented the PerturbBundle mover's parse_my_tags() and apply() functions.
Tweaked the helical_bundle and helical_bundle_nonideal integration tests. (Changes expected.)
Added additional unit tests to confirm proper copying of Paramters and ParamtersSet objects when Conformations or Poses are copied, cloned, or assigned (operator=).
Added slightly more verbose output (including a summary of the perturbed Crick parameters).
Added an integration test for the PerturbBundle mover.
Fixed the case in which a helix copies a DOF from another helix, where the DOF is never perturbed. (Or, at least, added a suitable error message.)
This merge also brings in the following changes:
Added sidechain-conjugation variants of D-asp/asn, D-glu/gln, and D-lys as params files in the database.
Tweaked some params files.