Merge pull request #515 from RosettaCommons/vmullig/gamma_aas
Vmullig/gamma_aas
This should get the BackboneGridSampler working with repeating units of more than one residue. This also adds a number of gamma-amino acids to the database.
Tasks:
-- Add several gamma-amino acids to the database.
-- Tweak NtermProteinFull patch for gamma-amino acids.
-- Adds a TRIAZOLEMER class of residues (a new type of unnatural backbone).
-- Adds support to the BackboneGridSampler for repeating units of more than one residue (to allow sampling of secondary structures that are possible with, for example, D-L-D-L or L-L-D-L-L-D patterns, or with alpha-beta-alpha-beta or whatnot).
-- Add RosettaScripts parsing for setting the number of residues per repeating unit.
-- Update the residue type list in the BackboneGridSampler.
-- Update the fixed torsions list in the BackboneGridSampler, and add RosettaScripts parsing.
-- Update the varying torsions list in the BackboneGridSampler, and add RosettaScripts parsing.
-- Update text output.
-- Update the BackboneGridSamplerHelper, and make sure that it samples all residues properly.
-- Add integration tests.
-- Ensure backward compatibility.
-- Check existing integration tests for changes (cosmetic changes only are expected, since the default behaviour is still one residue per repeating unit).
-- Add documentation for new features to the Gollum wiki.
All unit tests pass. Integration tests pass with expected cosmetic changes to the backbonegridsampler test's output log (though full backward compatibility is maintained). Small stochastic changes to the backbonegridsamper_nstruct_mode test since this uses a nonmonotone minimizer, but no major or unexpected changes. The backbonegridsampler_multiresidue test produces appropriate output, but fails because it's new.