Merge pull request #5376 from RosettaCommons/JackMaguire/ddgjumpsele Adding Jump Selector XML attribute for Ddg and ShapeComp filters

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Merge pull request #5377 from RosettaCommons/roccomoretti/fix_tensorflow Fix tensorflow build. I mixed up namespaces with my PR, and didn't catch it because it was behind #ifdefs.

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Merge pull request #4268 from RosettaCommons/roccomoretti/option_include_removal_rebase Reduce transitive inclusion of option system in headers. It looks like option system headers contribute a not insignificant amount to compilation time of just the headers. Generally speaking, though, there really should be very few reasons for an hh file to include an options system header. Go through and clear out as many of them as possible. (By rearranging code in some cases.)

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Merge pull request #4255 from RosettaCommons/roccomoretti/orbital_include Reduce transitive inclusions of orbital headers. Certain Orbital-related headers were contributing more than they likely should to the amount of included header lines. We can adjust the Residue and ResidueTypeBase classes such that these headers are only in the cc files, and aren't included for everything that needs Residue.hh or ResidueType.hh. To aid in this conversion (and to keep the deep copy semantics of the vector-of-Orbital objects), I've added a deep_copy_vector1 class, which subclasses vector1, but provides deep copy semantics for vectors-of-OPs.

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Merge pull request #5299 from RosettaCommons/JackMaguire/OptOutFilterReport Adding more filter report options

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Merge pull request #5368 from RosettaCommons/vmullig/galiganddock_ring_conformers (Replaces #4541) Ensure that GALigandDock's sample_ring_conformers option is actually obeyed This replaces pull request #4541. It ensures that the sample_ring_conformers option actually behaves as expected, and also adds an integration test for docking a single amino acid residue. The previous PR had been based atop changes that are now redundant (and which were part of a PR that has now been closed); this one is based off of master. Thanks to Frank for the review!

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Merge pull request #5203 from RosettaCommons/vmullig/add_more_citatoins Add more citations Now that we have the script, it's easy to add lots of citations to the database... This may be a longstanding PR, but I'll use it to add a bunch. Tasks: - [x] Add a bunch of citations to the database. - [x] Add citations to a bunch of Rosetta modules. - [x] Check that Rosetta still compiles and runs (i.e. run tests). - [x] Beauty. - [x] Pull request #5202 must be merged before this one.

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Merge pull request #5363 from RosettaCommons/vmullig/fix_rmsd_zero_error Ensure that numeric::model_quality::rmsfitca2() doesn't fail silently Currently, this function (which is called by `superimpose_pose()`) returns an RMSD of 0.0 on failure. This is reported as the RMSD by other code. This PR aims to fix this. Tasks: - [x] Have this function return its failure status. - [x] Have `core::scoring::superimpose_pose()` do something with this information. Option to throw on error, default true. - [x] Have simple_cycpep_predict pay attention to whether RMSD was calculated correctly.

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Merge pull request #5190 from RosettaCommons/teunhoevenaars/jacobi_loop_closure_update Performance improvements and generalization to Jacobi loop closure algorithm (loop closure based on linearised kinematics), including an addition to HomogeneousTransform to handle ZYX Euler angles. Thanks Mads and Vikram for the reviews!

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Merge pull request #5296 from RosettaCommons/JackMaguire/JumpSele New Jump Selector that calls FoldTree::get_jump_that_builds_residue from a residue selector User can pass a residue selector to a jump selector, the jump selector will select the jump(s) that build those residues. Uses tree-traversal recursion just in case users pass residues that aren't built directly by jumps. Thanks Vikram for the review!

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Merge pull request #5357 from RosettaCommons/klimaj/logging Minor fixes to PyRosetta logging

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Merge pull request #5358 from RosettaCommons/klimaj/molfile_to_params Broaden the allowed root atoms in molfile_to_params.py

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Merge pull request #5355 from RosettaCommons/guangfeng/galiganddock_update2 Bugfixes and updates in GALigandDock and GenericBondedPotential

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Merge pull request #5353 from RosettaCommons/roccomoretti/ignore_big_files Add .gitignore entries for some potentially big files From my quick run of my large file detection script (RosettaCommons/tools#99), I identified a number of filetypes that can be quite large which were likely added to the repo accidentally. Add these files to the .gitignore such that future people will be less likely to accidentally commit them.

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Merge pull request #5354 from RosettaCommons/jkleman/SciBen_more_small_fixes Jkleman/sci ben more small fixes: various small fixes to scientific benchmarks

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Merge pull request #5279 from RosettaCommons/AmeyaHarmalkar/flexible_dock_sci_tests Adds flexible docking Scientific Tests

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