Merge pull request #2272 from RosettaCommons/vmullig/ui/bundle_gui Add a GUI pilot app that permits interactive, realtime parametric design MOTIVATION AND DESCRIPTION This is primarily intended to be a fun demonstration of the power of a graphical user interface for Rosetta design. There are many tasks that we currently do in a very time-consuming and painful manner. One such task is the selection of parameter ranges for parametric design. Typically, a helical bundle designer must arbitrarily pick some parameter values, write a RosettaScripts XML file that calls the MakeBundle mover or the BundleGridSampler mover to generate geometry from those values, write the geometry out to disk as a PDB file, read the PDB file into a program like PyMOL, examine the output, and make decisions about how to vary the parameter values. One iteration might take a minute or so, a few milliseconds of which are spent actually computing the geometry. Wouldn't it be better if we could make that an interactive process? This application does just that, making it easy to select parameter values that one might then sample around in a large-scale, non-interactive sampling session. I've also added some extra bells and whistles that let you call the packer and the minimizer (to get a crude idea of the packed geometry possible with a given backbone), or to import additional non-parametric geometry (e.g. for small-molecule binder design) that you can drag and rotate independently from the parametric geometry. INTERNALS This pull request adds: - The app (which internally is calling the MakeBundle mover, PerturbBundle mover, PackRotamersMover, and MinMover). - New UI directories (note that these are not currently separate libraries, but could be made into separate libraries should the need arise) for: - Code that only links up to Rosetta's utility library. - Code that only links up to Rosetta's core.5 library. - Code that links up to Rosetta's protocols.7 library. - A new base class for a basic OpenGL pose-drawing widget. This is NOT meant to replace the work being done by @jadolfbr to create pose-drawing widgets. This is just a temporary standin. Its current features include: - Van der Waals sphere representations of a pose (but no sticks, ribbons, or anything else that's fancy). - Colouring by selection or by per-residue score. - Dragging to rotate, and right-dragging to zoom. - Tens of millisecond refresh on moderately-sized poses (i.e. realtime interactivity). - A derived OpenGL pose-drawing widget class specific for this app, which adds the ability to drag the nonparametric geometry separately from the parametric. I think that we can handle a lot of the specialization of the visualization widget by subclassing, and this demonstrates that idea. - Some specialized widgets built for Crick parameter manipulation. ADDITIONAL STUFF (done now): - Figure out what copyright text needs to go at the top of Rosetta ui files. It oughtn't be identical to the Rosetta copyright, I think, since this isn't strictly part of the Rosetta software suite. It should convey that it's covered by the same type of licence and all that, though. --> Update: Dennis at CoMotion has confirmed that we can just use the regular Rosetta copyright text, so I shall do that. - Figure out how to cover this with unit tests. --> Put off to a future pull request. - Fix bug when helix 1 is deleted and other helices copy from it.

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Merge pull request #2348 from RosettaCommons/jadolfbr/rs_jd3 RosettaScripts - JD3 Port and PyRosetta Support Overview ====== This PR brings RosettaScripts into the modern era of JD3 and PyRosetta. The implementation is version 1 - with support for different protocols and script_vars being passed to the job_definition file. This should enable fairly robust benchmarking of protocols through RosettaScripts. Thanks to @aleaverfay for his guidance, debugging, and code added to the branch! PyRosetta support is here through a slew of new functions in RosettaScriptsParser to easily take an XML/Pose and return a ParsedProtocol. @basantab ``` ///@brief /// Main, Basic XML to Mover Function. /// ParsedProtocolOP generate_mover_and_apply_to_pose(core::pose::Pose & pose, std::string const & xml_fname); ``` This PR also removes the JD2 integrated code in the RosettaScriptsParser and removes the 'Parser' class as it was unused. An example JD3 job_definition file for RosettaScripts: ``` <JobDefinitionFile> <Job nstruct="2"> <Input> <PDB filename="five_glycans.pdb"/> </Input> <Output> <PDB filename_pattern="default_$"/> </Output> <Options> <parser__protocol value="glycan_relax.xml"/> <parser__script_vars value="cartmin=0"/> </Options> </Job> <Job nstruct="1"> <Input> <PDB filename="five_glycans.pdb"/> </Input> <Output> <PDB filename_pattern="cartmin_$"/> </Output> <Options> <parser__protocol value="glycan_relax.xml"/> <parser__script_vars value="cartmin=1"/> </Options> </Job> <Job nstruct="1"> <Input> <PDB filename="pareto_4JAN_CH103_GP120_renum_0001.pdb"/> </Input> <Output> <PDB filename_pattern="glycosylated_$"/> </Output> <Options> <parser__protocol value="glycosylate.xml"/> <parser__script_vars value="positions=463G,460G glycosylation=man5 cartmin=1"/> </Options> </Job> </JobDefinitionFile> ``` Command to run this: ``` rosetta_scripts_jd3.macosclangrelease -include_sugars -write_pdb_link_records -in:file:job_definition_file jd3_rs_definition.xml ``` Other Changes ========== - Add Overwrite support to JD3 (Thanks @aleaverfay ) - Fix a few JD3 bugs ( @aleaverfay ) - Add support for prefix/suffix - Move ```protocols/jd2/parser``` to ```protocols/parser``` - Add Integration test - @vmullig Port -info and -output_schema options to the JD3 implementation, moved functions to rosetta_scripts/util.hh Integration tests: =========== All changes are cosmetic and have been gone over manually.

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Merge pull request #2306 from RosettaCommons/roccomoretti/add_residuetype_reporting Better reporting of double-addition of ResidueTypes to an RTS Change a runtime_assert to an if + tracer output + utility_exit.

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Merge pull request #2311 from RosettaCommons/roccomoretti/fix_atom_alias_delete Fix issue with delete_atom and atom_aliases. If you had a patch which deleted an atom which has an atom alias, there's a good possibility that it wouldn't work, as it would crash when you're attempting to delete the alias and the stripped alias name.

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Merge pull request #2205 from RosettaCommons/guffysl/setup_metals_mover Added SetupMetalsMover, which provides auto_setup_metals functionality in mover form. In addition to the normal command line options for auto_setup_metals (which default to the command line values), this mover takes as attributes an optional selector or resnum list to specify which metal(s) should be set up and an option to only add constraints and not chemical bonds/patches (useful for reapplying constraints if they are removed during a protocol).

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Merge pull request #2351 from RosettaCommons/roccomoretti/erraser_fix Add missing dot to ERRASER linuxgccrelease test Make it look like the other platform settings. Should address an issue mentioned on the forums: https://www.rosettacommons.org/node/9955

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Merge pull request #2347 from RosettaCommons/JWLabonte/sugars/database Carbohydrates: Adding a few more sugars to the database for the GlycanRelax benchmark All tests pass (except the broken ones).

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Merge pull request #2265 from RosettaCommons/roccomoretti/grid_global_fix Fix global state usage in ScoringGrids The protocols::qsar::scoring_grids::GridManager was a strange mix of a global cache and modifiable global state. That wasn't great because the implementation resulted in a lot of cross-dependencies between grid usage. This pull request should hopefully decouple the global grid caching (still held by GridManager) from the modifiable state (now held in local variables as a GridSet object). An upshot of this change is now you can have multiple GridSet objects in a single RosettaScripts run. Previously, all grids you were working with were . The multiple-grid approach is being done in a backwards-compatible way, so existing XMLs should be able to work as-is.

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Merge pull request #2332 from RosettaCommons/jadolfbr/jd3_template Add JD3 Code Template - Note that this will change the app from generate_app_templates_jd2 to generate_app_templates and you will need to specify the --type option to either jd2 or jd3_standard.

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Revert "Update pyrosetta distro to bootstrap minimum setuptools." This reverts commit 7b4b4e0db91e111c9c5898287c02368820f7fad3.

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Update pyrosetta distro to bootstrap minimum setuptools. Update pyrosetta distribution to include ez_setup.py and bootstrap a minimum setuptools version if setuptools is not present in the install environment. Specify a minimum setuptools version needed to support setup.py.

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Removing unneeded include key-arg from find_packages

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Merge pull request #2342 from RosettaCommons/sergey/f Merging parts of #2285 related to adding new JSON library to add json.hpp into external lib files

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Beautifying unbeautified file in master.

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Merge pull request #2337 from RosettaCommons/bcov/fixes/NeighborhoodDontIncludeFocus NeighborhoodResidueSelector include_focus_in_subset=false fixes

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Merge pull request #2336 from RosettaCommons/dimaio/cartsymmmin_fix Bugfix for cartesian symmetric minimization with new min scheme

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