fixing Binder submodule (got broken by https://benchmark.graylab.jhu.edu/revision?branch=master&id=60598)

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Merge pull request #3779 from RosettaCommons/roccomoretti/change_position_of_atom_on_ring Fix for position_of_atom_on_ring() There was some confusion on the behavior of position_of_atom_on_ring() in the case when an atom is part of the ring. The documentation was unclear, and the actual implementation was highly dependent on the atom ordering of get_adjacent_heavy_atoms(). This PR changes things such that atoms on the ring get a return value of 0, just like atoms which aren't directly connected to the ring.

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Merge pull request #2999 from RosettaCommons/sergey/f enabling STL debug mode We've done it! Let me know if you'd like to put in some effort to make your favorite integration/unit test faster, either for its own sake or so that it can be reactivated in release_debug mode. (There are only a handful affected.)

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Merge pull request #3776 from RosettaCommons/roccomoretti/upper_atom_selector Convert UPPER_POSITION patch selector to UPPER_ATOM selector. The UPPER_POSITION patch selector currently has a dependency on the CarbohydrateInfo object. This makes the selector not as general as it could be. I've changed this to an UPPER_ATOM selector, which cues based on the atom name of the atom connected to the UPPER connection, rather than the mainchain position setting in the CarbohydrateInfo object.

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Merge pull request #3771 from RosettaCommons/vmullig/fix_xcode_yet_again Fixing a few more xcode build errors. (Same thing: missing ampersands.)

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Merge pull request #3773 from RosettaCommons/vmullig/debug_mode_mathvector_overruns Correct bounds-checking on MathVectors MathVectors are zero-based, not one-based, but the bounds checking on the class assumes that indices 0 through (size) are valid. This corrects that. This turns out to be exactly what was wrong with my PolycubicSpline unit tests, too. This pull request corrects the indexing in the MathVector that I use in that test, so that I don't write past the end of an array. Finally, the bounds check was being performed in release and debug modes. This adds an #ifdef to ensure that the bounds check only happens in debug mode, for speed.

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Merge pull request #3769 from RosettaCommons/aleaverfay/slim_lkball2 ifndef-wrap a unit test which relies on a debug-mode assertion failure This PR fixes a currently-failing release-mode unit test that I added in the last PR (#3729)

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Merge pull request #3767 from RosettaCommons/vmullig/fix_spline_tests Trying to fix PolycubicSplineTest intermittent failure on Mac/clang build

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Merge pull request #3768 from RosettaCommons/vmullig/fix_xcode_build_after_jd3 Trying to fix xcode build after JD3 refactor. Xcode flags cases in which `auto` is misused, causing objects to be copied inadvertently. For example: `for ( auto const larvaljob: larvaljobs_ ) { ... }` This should be `auto const & larvaljob`.

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Merge pull request #3761 from RosettaCommons/dougrenfrew/restore_oop_design This PR adds back a mc->recover_low( pose ) that was accidentally removed in 67479d1. The removal resulted in identical poses being output for each nstruct. It was found by an external user who contacted the original author @ksdrew .

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Merge pull request #3759 from RosettaCommons/JackMaguire/FastDesignScriptsInDatabase Fixing Tests That I Broke Rocco noticed that the changes I made to FastRelax broke integration tests that used custom scorefxn weight files. This PR adds a patch that handles that case. Sorry for not noticing the failed tests! Not sure why it gave me a green checkmark.

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Merge pull request #3709 from RosettaCommons/jadolfbr/jd3_updates JD3 Simplification/Refactor Code Changes: ===== - Code templates have been added for common JD3 classes. - Transferred `StandardInnerLarvalJob`s use of `prelim_job_node` as` job_node` into the `InnerLarvalJob`. Since the ILJ is passed with the LarvalJob, this makes every function in the SJQ easier to use as you know which job_node you have - and this is not limited to `PreliminaryLarvalJobs`. - - This makes the StandardInnerLarvalJob obsolete as that was the only extra thing about it. It has been removed and classes refactored to call the InnerLarvalJob. - Moved `PreliminaryLarvalJob` to its own file in `jd3/standard`, changed it to a struct as per conventions, as everything was public. - Added the `PreliminaryLarvalJobTracker`, which the SJQ now uses to track the progress of the PJNs. This is a full class, with private data and initialization methods and is in `jd3/standard` - Added the `JobTracker` class. This class tracks completed and assigned jobs in the SJQ. This JobTracker is now updated by the JQ base class - through a wrapper/decorator function that is called by the JD. This means that SJQ developers can be ensured that the `JobTracker` is up to date and they are not responsible for updating it. Protected accessor methods have been added. - The JQ now holds an OP to the `JobDigraph`. This OP is stored during the JQs version of `initial_job_digraph`, which is a wrapper/decorator to derived class functions - ensuring that the SJQ developer is not responsible for setting it, and protected accessor methods have been added. - `JobNode `now has an optional variable, job_label - this is to better delineate how jobs are constructed. We can now ask the `JobDigraph` which job_label a particular job_node is for - IE this is useful for multiple stages, such as if all Prelim jobs undergo some stage 1, and all jobs from global index i -> j undergo job_type "2". This reduces the amount of logging needed so we do not have to track all the global index ranges to simply start a job of some type. - `EnergyJobSummary` is now in its own file, and the **4?** places where it was copied have been removed! - Add a new `StandardPoseJobSummary`, which is a JobSummary that extracts the Energy and SimpleMetricData from a pose. This should cover Most data needed for a summary ;) - `MoverAndPoseJob` has now been changed to `MoverJob`. The `pose` part of the job is inferred - no need to add that to the name. The `MoverJob` has been expanded to use the `StandardPoseJobSummary` and run a set of optional simple metrics on the final pose before returning the `PoseJobResult` and `StandardPoseJobSummary` pair. MoverJob is now aware of a SequenceMover to make it easier to either set a mover or add movers (which is extremely common). - `InputSource` pose_id variable and function are now source_id to go with the more generalized interface. General SJQ Edits ============= - The SJQ header interface is completely re-organized to have typical derived functions at the top, and mainly unused/specialized functions at the bottom. - Move some SJQ function bulk out of the SJQ and into JD3 util files. - **The number of SJQ private variables has been reduced from 50 members to 32 members** !! - All function briefs in the SJQ have been updated to separate briefs from details (almost all of it was details before). The descriptions have been updated/simplified where possible, and instructions for override behavior or gotchas have been added. Tests ==== A full suite of unit tests have been added for the new main classes, the SJQ tests have been updated to fully test the `JobTracker` and the `PreliminaryLarvalJobTracker`.

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Merge pull request #3737 from CyrusBiotechnology/bfrenz/fix_pro_terminal_ddg fix to prolines near an internal breakpoint

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Merge pull request #3754 from RosettaCommons/vmullig/splinetests Add unit test to determine whether polycubic interpolation of symmetric points is symmetric for N>2

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Merge pull request #3755 from CyrusBiotechnology/bfrenz/hybrid_add_hetatm_setter Bfrenz/hybrid add hetatm setter

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Merge pull request #3662 from RosettaCommons/JackMaguire/FastDesignScriptsInDatabase Adding new non-default FastDesign scripts. Update to the docs wiki coming soon to describe them. Thanks to Vikram for the review.

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