Merge pull request #3371 from RosettaCommons/guangfeng/cryst_dock Several bugfixes in 3D-lattice docking. Addresses issue #3363. Minor outputting changes expected in small_molecule_lattice_dock integration test.

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Merge pull request #3370 from RosettaCommons/everyday847/never_stop_fighting_pdb_input Continued PDB input fixes

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Merge pull request #3372 from RosettaCommons/roccomoretti/fix_integration_output Fix integration test run output redirection. Some integration tests were dumping output to stdout, rather than redirecting to a file. Fix this.

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Merge pull request #3369 from RosettaCommons/roccmoretti/backrubdd_options Fix XML parsing for BackrubDD. The documentation and reality of BackrubDD were at odds. Attempt to fix/coordinate them.

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Merge pull request #3134 from RosettaCommons/roccomoretti/ResourceManager_unit_fix Fix the ResourceManagerTests with CMake. The CMake builds contain the full path to source files in error messages. Adjust unit tests to ignore the file path.

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beautifying

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Merge pull request #3315 from RosettaCommons/hdanderson/protac_stuff Hdanderson/protac stuff Converted UBQ_Gp_LYX-Cterm application into a mover compatible with RosettaScripts. Made some modifications to the mover code so that it supported a ResidueSelector for choosing the lysine to which the ubiquitin would bind. Also updated the application so that it calls UBQ_GTPaseMover from protocols. The output of UBQ_GP_LYX-Cterm is expected to change as part of this merge. There were also some changes in the integration test for cycpep, but I expect that this is just noise. I am open to reverting if the cycpep change turns out to be real.

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Merge pull request #3362 from RosettaCommons/weitzner/clang_conda_cpp Enable C++ conda builds (for Mac)

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Merge pull request #3361 from RosettaCommons/sergey/binder Refactoring PyRosetta, adding Pybind11 as git submodule

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Merge pull request #3350 from RosettaCommons/roccomoretti/fix_san_tests Fixes for some of the ubsan/addsan/valgrind errors.

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Merge pull request #3317 from RosettaCommons/sergey/f2 Adding workaround for serialization test. Disabling serialization to `JSON` and `XML` archives

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Merge pull request #3348 from RosettaCommons/aleaverfay/jd3_fix_score_file_in_jobdef jd3 fix score file in jobdef I discovered that a few things concerning how score file output is controlled in the job definition file for JD3 were not working correctly. 1. If a (non default) filename were provided inside the ScoreFile tag, it was not getting used. 2. If multiple ScoreFiles were listed in a single SecondaryOutput tag for a job (say you want to record the job's scores in two locations), then the schema validator would throw an error. 3. (related to 2.) The StandardJobQueen didn't really support the idea of allowing multiple SecondaryOutputters, so even when you fix the schema definition bug, there are other things lying in wait. I've fixed these issues. Now you can say for job 1 that the outputs will go to directory1/ and for job 2 that the outputs will go to directory2/.

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Merge pull request #3355 from RosettaCommons/JackMaguire/FastDesignScriptsInDatabase Creating Database Directory For RelaxScripts Currently, the only way to run FastRelax/FastDesign is to either provide your own relax script or use one of the defaults hard-coded in the c++. This PR creates the directory main/database/sampling/relax_scripts where anyone can add scripts that are non-default but general enough to be used by other people. Now, FastRelax parses the optional relaxscript tag and looks for the script in database/sampling/relax_scripts if it otherwise does not exist (i.e., if the file is not local to the working directory). For example, you might develop a relaxscript that works well for carbohydrates and write database/sampling/relax_scripts/carbohydrates.txt. Anyone could use it by adding the tag <FastDesign relaxscript="carbohydrates"/>. I think it's worth noting that I have not changed any of the previously defined behavior; nobody's rosetta_scripts will behave differently if this PR is accepted. All I have done is added a set of additional cases for the relaxscript option and rearranged how some information is stored.

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Merge pull request #3364 from RosettaCommons/vmullig/fix_carbohydrate_issue Fixing the PyRosetta build

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Merge pull request #3359 from RosettaCommons/MelanieAprahamian/per_residue_solvent_exposure pilot app to calculate per residue solvent exposure in a variety of ways

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Merge pull request #3360 from RosettaCommons/everyday847/hotfix_stochastic_failures Set UPPER to NONE in 3prime_deoxy

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