Merge pull request #313 from RosettaCommons/vmullig/genkic_sampling
Create a bin transition probability-based backbone sampling method.
This allows sampling based on the probability of residue i being in mainchain torsion bin X, given the mainchain torsion bin of one or both adjacent residues.
Organization/Tasks:
In database/protocol_data/generalizedKIC/bin_params/, added data files for bin transition probabilities.
In core.3 (core/scoring/bin_transitions/) created a new BinTransitionCalculator class with methods for calculating bin transition probabilities, and a new BinTransitionData class for storing bin transition probability matrices and derived data. These classes also have methods for reading in bin transition probability data files. (Note that this has to be in core.3 because it draws on functions from the Ramachandran class, and it will be used by energy methods among other things.)
Added a unit test for some of the core functionality of the above.
In protocols/generalized_kinematic_closure/perturber/GeneralizedKICperturber class, added a new "randomize_backbone_by_bins" perturber.
In protocols/generalized_kinematic_closure/perturber/GeneralizedKICperturber class, added a new "perturb_backbone_by_bins" perturber.
Adding an integration test for GenKIC with bin-based initialization.
Adding an integration test for GenKIC with bin-based perturbations.
Adding a stand-alone randomize mover.
Adding a stand-alone perturb mover.
Adding integration tests for the stand-alone randomize mover.
Adding integration tests for the stand-alone perturb mover.
Documentation.
Put off to a future pull request:
Figure out how to do the stats for D-amino acids, and add D-amino acids probability matrices to the database.