Merge pull request #297 from RosettaCommons/vmullig/layerdesign_ncaas
Tweak LayerDesign so that it can work with noncanonical residue types
This alters the LayerDesign TaskOperation so that it can work with noncanonical residue types. In addition, it removes highly counter-intuitive behaviour in LayerDesign that breaks TaskOperation commutativity (while adding an option to turn that behaviour back on if that's what the user really wants).
I'm also turning off "DCYD.params" and "DCYS.params" in residue_types.txt. These D-amino acid residues should not be loaded by default, and can be specified with the -extra_res_fa flag.
Tasks:
- Stop having LayerDesign skip residues that were set with PIKAA or NATRO in a resfile as the default behaviour. This is counter-intuitive behaviour for this TaskOperation because the skip ONLY occurs if the resfile was applied before LayerDesign -- i.e. resfile,LayerDesign is different than LayerDesign,resfile, which violates the rule that TaskOperations are commutative.
- Add an option to restore the old, non-commutative behaviour if an advanced user so desires (while keeping it off by default for users who need to be able to assume that TaskOperations follow consistent rules).
- Stop automatically restricting non-protein residues to repacking. If the user wants to do this, he or she can do so with another TaskOperation. TaskOperations should be atomistic; they shouldn't do several unrelated things that limit their usefulness.
- Add code to LayerDesign to parse NCAA options.
- Add code to LayerDesign to actually add NCAAs to the PackerTask.
- Alter the use_residue_neighbors code so that it uses the (first sidechain atom)-(first sidechain atom parent) vector rather than the CB-CA vector.
- Add integration tests for NCAA design with LayerDesign.
- Update the documentation wiki.
Expected unit test failures: NONE.
Expected integration test changes:
- LayerDesign (trivial, cosmetic change to output).
- LayerDesign_ncaa (newly-added test).
- fibre_diffraction_fad (cosmetic changes to output since the DCYD and DCYS params files are no longer being loaded).
- mm_params (cosmetic changes to output since the DCYD and DCYS params files are no longer being loaded).
- fold_and_dock (cosmetic changes to output since the DCYD and DCYS params files are no longer being loaded).
- number_of_residuetypes (since the number of residue types is changing, since DCYD and DCYS are no longer being loaded).