Merge pull request #182 from RosettaCommons/vmullig/parametric
vmullig/parametric into master
This creates classes for storing parameters for parametric backbone generation. These classes are intended as general base classes for parameter storage for many different types of parametric backbone generation protocols, and to facilitate storing parameters inside Conformation objects so that different Movers can use stored parameters. Derived classes for the specific case of helical bundles generated using the Crick parameters are also implemented with ths pull request.
- Created core::conformation::parametric::Parameters base class. This is intended to store a set of parameters for generating one (likely-contiguous) piece of a conformation (e.g. one piece of secondary structure).
- Created core::conformation::parametric::ParametersSet base class. This stores a collection of Parameters objects for generating an assemblage of discontinuous pieces of a conformation (e.g. a helical bundle, a beta-barrel, etc.).
- Modified the Conformation object to contain a vector of ParametersSet owning pointers. This change is intended to be lightweight in terms of memory use. In most cases, one isn't working with parametrically-generated backbones, so the Conformation object won't store any additional data. In cases where one is working with parametrically-generated backbones, the Conformation object will link to the ParametersSet objects, which link to the Parameters objects.
- Created protocols::helical_bundle::parameters::BundleParameters and protocols::helical_bundle::parameters::BundleParametersSet classes, derived from Parameters and ParametersSet respectively. The former is meant to store the Crick parameters for a SINGLE helix in a bundle, and the latter, to store several BundleParameters objects to define a bundle (with some additional data for a bundle).
- Defined the variables that the BundleParameters class will hold.
- Rewrote the MakeBundleHelix mover's setters and getters so that now the MakeBundleHelix mover does not directly store the Crick parameters for the helix that it is generating, but instead holds an owning pointer to a BundleParameters object.
- This merge also brings in a small tweak to the bettercluster.cc pilot app to make it work with the new owning pointers.
- Had the MakeBundleHelix mover pass the BundleParameters object into the Conformation of the Pose that it operates on, so that the Crick parameters are stored for use by subsequent Movers (e.g. to perturb the conformation, to minimize in Crick parameter space, to report the current values of the Crick parameters, etc.).
- Had the MakeBundleHelix mover properly initialize the residue list in its BundleParameters object.
- Checked BundleParameters and Parameters copy constructors.
- Checked BundleParametersSet and ParametersSet copy constructors.
- Added a unit test to make sure that Conformation objects properly pass their Parameters objects into a unified ParametersSet when they are merged, and properly update links to Residue objects.
- Had the MakeBundle mover properly store a BundleParametersSet object, just as the MakeBundleHelix mover currently stores a BundleParameters object.
- Had the BundleParametersSet object store additional information associated with bundle symmetry.
- Added helix parameters for a D-amino acid alpha helix and beta strand, and for a "neutral" beta strand that could be composed of D- or L-amino acids (with perfect 180,180 phi/psi values).
Relegated to a future pull request:
X Add delta_z and curvature parameters to BundleParameters for Zibo.
X Write a sampling Mover that permits perturbation of the Crick parameters (and corresponding alteration of the backbone conformation) given a Pose that has parametrically-generated elements.