Merge pull request #590 from RosettaCommons/vmullig/layerdesign_ligand Adding support for ligands to LayerDesign in use_sidechain_neighbours mode This allows ligands in use_sidechain_neighbours mode. Instead of the CA atom, it uses the nbr_atom for ligands.

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Two small bugfixes for density

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Merge pull request #585 from RosettaCommons/rhiju/resleveltask_in_separate_file Rhiju/resleveltask in separate file This may cause headaches to folks doing future merges to/from master who have changed the class ResidueLevelTask_ . Unfortunately, while git does track movement of functions within files, it generally fails to check movement across files. If you run into an issue with a conflict in your branch involving PackerLevelTask_.cc when trying to merge master, the best thing to do is: git diff <commit at head of your branch> core/pack/task/PackerTask_.cc Record changes that you made in the ResidueLevelTask_ class functions. Then make sure they go into the new ResidueLevelTask_.cc file, and remove your conflicting code block in PackerLevelTask_.cc.

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Merge pull request #588 from RosettaCommons/JWLabonte/PyMOL_Mover PyMOL_Mover/PyMOLMover: Squashing rare class definition bugs This merge removes a class definition notation in the PyMOLPyRosettaServer that some versions of Python and/or versions of PyMOL cannot seem to handle. PyRosetta unit tests passed.

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Merge pull request #84 from RosettaCommons/roccomoretti/rotamer_refactor Rotamer Generation Refactor This is a project I've been working on to clean up the way rotamer libraries get generated. Currently, there's an ad-hoc system based on various bits of data in the ResidueType, along with various if/else statements in RotamerLibrary as well as RotamerSet. This pull request implements a scheme to replace that with a more unified and extendable system. * The various loose bits of rotamer specification data in the ResidueType are replaced with a single OP to a RotamerLibrarySpecification object. (in src/core/chemical/rotamers/) Generally, each various type of SingleResidueRotamerLibrary will have it's own RotamerLibrarySpecification subtype, each with it's own set of data. * RotamerLibrarySpecification objects are created either based on the current rotamer lines in .params files, or with a new ROTAMERS line, which has the format ROTAMERS <tag> <data> where <tag> is a string which specifies which RotamerSpecification class to instantiate and <data> is in a class-specific, newline terminated format. * To facilitate adding new rotamer library types, RotamerLibrarySpecifications have a (RosettaScripts-like) factory system. This not only allows "easy" addition of new rotamer types, but also allows you to place the implementation anywhere in the library hierarchy. * SingleResidueRotamerLibraries are now instantiated based on the type of RotamerLibrarySpecification that's in the ResidueType. * This is also a factory based system, based off of the same tag from the RotamerLibrarySpecification class - each RotamerLibrarySpecification class has a corresponding SingleResidueRotamerLibrary, more or less. It's flexible enough that you can do one to many or many to one if you want to. * The SingleResidueRotamerLibrary factory functionality has been excised from the RotamerLibrary class into a new SingleResidueRotamerLibraryFactory class. This makes core::pack::dunbrack::RotamerLibrary strictly a class for handling the Dunbrack rotamer libraries. * This also entailed splitting off the CenRot library functionality - the upshot of which is that it is no longer necessary to have a separate flag to enable CenRot rotamers - it will do auto lazy loading. * Functionality in core/pack/dunbrack/ was also split between core/pack/dunbrack/ and core/pack/rotamers/ - core/pack/dunbrack should contain the functionality which is specific for handling Dunbrack-based rotamer libraries, and core/pack/rotamers/ hold code which is more generic and not necessarily related to the Dunbrack rotamer libraries. * The previous SingleResidueRotamerLibrary caching scheme used has been replaced by a new write-once/software transactional memory inspired one which should be more threadsafe than the previous one. * The way SingleLigandRotamerLibrary's data are stored has changed. Previously the library was read and stored as Residue objects. This introduces an implicit cross dependency between the RotamerLibraries and ResiudeTypes/ResidueTypeSets, which breaks down if the underlying ResidueType is deleted, or if there are multiple ResidueTypeSets with different ResidueTypes with the same name. Now, instead of storing Residues the SingleLigandRotamer now represents the input pdb as an atom name/coordinate map, and the vector of Rotamer objects is recreated each time it's needed, just as it is for the Dunbrack libraries. As a benefit, this simplifies the enzdes/metal ion covalent residue patching code a bit. I (started to) remove the implicit dependence of Rotamer library on the AA enum. Instead, canonical amino acids now have an explicit ROTAMER_AA line which specifies the Dunbrack rotamer library to use. This removes the "magic" that previously happened based on the ResidueTypeSet identity, so that AA LYS in fa_standard magically got Dunbrack rotamers, but AA LYS in centroid didn't. Now AA LYS in fa_standard gets Dunbrack rotamers because the params file says that it should, and AA LYS in centroid doesn't because the params file says that it doesn't. Certain types (RNA, DNA, etc.) still base rotamers off of AA type in an ugly if/else clause in RotamerSet - changing this is a TODO future goal. (Preferably one which lands on someone else's plate) Cosmetic tracer changes expected on the following 25 integration tests: Enzrevert_xml coupled_moves cstfile_to_theozyme_pdb enzdes extract_atomtree_diffs hybridization inverse_rotamer_remodel kinemage_grid_output ligand_database_io ligand_dock_7cpa ligand_dock_grid ligand_dock_script ligand_motif_design ligand_water_docking match_1n9l mp_relax_w_ligand orbitals relax_w_allatom_cst residue_data_resource sdf_reader startfrom_file validate_database write_mol_file -- fiber_diffraction_fad fold_and_dock The last two look worse than they are due to extra debugging output. I'm also seeing a ~10% slowdown on the fa_dun* scoreterm performance tests, though not really on the full-scale scoring/minimization tests. It's slightly concerning, but I don't think it's worth putting off the merge for.

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Merge pull request #577 from RosettaCommons/roccomoretti/tilt_mover Add an option to tilt (nutate) the docking partners in DockingInitialPerturbation, in addition to the spin possibility. By default the tilt will happen perpendicular to the axis connecting the center of masses of the two binding partners. The center and the magnitude of the random tilt can be varied. This is code that I'm committing on behalf of Joerg Schaarschmidt. (Though bugs have a good possibility to be from my code cleanup efforts.)

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Merge pull request #563 from RosettaCommons/everyday847/make_rot_lib_with_tripeptide MakeRotLIb now can use acetylated, N-methylamidated poses with three residues (-make_rot_lib: use_terminal_residues) and can use k-medoids instead of k-means clustering (-make_rot_lib:k_medoids).

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Merge pull request #578 from RosettaCommons/everyday847/awatkins_pilot_apps2 Some of my pilot apps that might be useful for general consumption

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Update split_unfolded_one_body_mm_std I believe these missing peptoid parameters are the remaining source of the instability of ncaa_fixbb. (Really just adding 001 and 601 ought to fix it.)

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Merge pull request #579 from RosettaCommons/vmullig/mpitests2 Tweaking MPI-mode integration tests to try to improve stability I'm temporarily dropping one test down to 3 processes instead of 4, to see whether this improves stability. Ultimately, I need to find the source of the instability, though. Expect changes to MPI-mode integration tests. Merging without testing.

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Merge pull request #530 from RosettaCommons/everyday847/disulfide_atom_tree_solution No hard coded atom names in disulfide code

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Fixing benchmark release.py script indentation

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Merge pull request #575 from RosettaCommons/kimdn/sw_unit_fix [minor modification] Initialize 2 uninitialized variables since http://benchmark.graylab.jhu.edu/sub_test/17264163 http://benchmark.graylab.jhu.edu/sub_test/17264479

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Update release.py Inexplicable typo from my recent merge... My apologies, Sergey!

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Merge pull request #574 from RosettaCommons/dougrenfrew/fix_tcre_tests Adding a missing param tot he TCRE methods. Changing oop_dock design to only to a single run. This should fix the instability in the ncaa_fixbb and oop_dock_design integration tests and the mm_std_fa_elec_dslf_fa13_split_unfolded score function finger print test

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Branching: Various updates to branching/chemical conjugation: Part A This is a merging in of Part A of Pull Request #459 NEWS: This merge... * Adds a new TorsionType for branch connection torsions, which are located at CHEMICAL EDGEs of the FoldTree. * Adds a new BRANCH TorsionType to MoveMap. * Adds the ability to get or set a torsion angle in the AtomTree by TorsionID containing a BRANCH TorsionType. * Allows the minimizer functionality to minimize TorsionIDs containing BRANCH TorsionTypes if permitted by MoveMap. * Has Rosetta automatically set up a FoldTree in the reverse direction for ubiquitin on load-in from a PDB file without resorting to Movers by using LINK records (as wanted by @hajosep). * Has Rosetta ignore LINK records defining sugar main chains that Rosetta could figure out on its own anyway (as wanted by @fdimaio for easier loading of glycoproteins for crystal refinement). * Automatically sets angle and bond constraints for chemical conjugation based on LINK records. @everyday847 also contributed to this branch. I am keeping the pull request open, as not all desired/related tasks are completed. ---------------------------------------- Unit test status: Pass Integration test status: 20 changed tests carbohydrates: expected c_term_conjugation: new 18 other tests: output modifications regarding branches or the MoveMap

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