Merge pull request #3697 from RosettaCommons/roccomoretti/promote_create_clash-based_repack_shell Promote create_clash-based_repack_shell to public @rpache had a pilot app that was useful, and is missing it now that he's in industry. At his request, I'm promoting the application to public.

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Merge pull request #3699 from RosettaCommons/roccomoretti/reduce_hotspot_runtime Reduce the runtime of the hotspot_hashing integration test. A quick profiling of the runtime pointed toward a loop which may have been doing more cycles than strictly necessary. Add a new option which allows us to cut down on those cycles (for the integration test, at least.)

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Merge pull request #3702 from RosettaCommons/everyday847/reimplement_fixed_res fixed_res for rebuilds

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Merge pull request #3667 from RosettaCommons/aloshbau/CM BoltzmannRotamerMover bug fix

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Merge pull request #3695 from RosettaCommons/jadolfbr/fix_sm_test Fix Per-residue SimpleMetric int test Include ignore list in second command.

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Merge pull request #3696 from RosettaCommons/jadolfbr/score_snugdock Fix bug in SnugDock where the pose looses its energies Pose energies were being lost from an energies clear after deleting virts. This simply scores the pose afterwards. Addresses: https://www.rosettacommons.org/node/10403

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Merge pull request #3691 from RosettaCommons/everyday847/new_metrics Calculate dihedral RMS or gdt in rna_score

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Merge pull request #3689 from RosettaCommons/jadolfbr/fix_xcode_build Fix Xcode build

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Merge pull request #3673 from RosettaCommons/everyday847/header_strategy Remove some common header transclusions

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Merge pull request #3690 from RosettaCommons/sergey/binder Updating PyRosetta. Fixing build on GCC-7, fixing build on Mojave.

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Merge pull request #3687 from RosettaCommons/vmullig/relax_ddg_a_bit Add some options to the DDG mover and filter Adding explicit options to the DDG mover and filter to control packing or custom relax mover application for both the bound and unbound states. (This is useful, for example, when I have a relax mover that only repacks and relaxes a binding site in a giant pose that would otherwise be extremely expensive to repack.) Tasks: - [x] Make the change. - [x] Update documentation. - [x] Beauty.

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Merge pull request #3620 from RosettaCommons/klimaj/worker_extra Allowing facile dask_jobqueue module usage with pyrosetta.distributed

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Merge pull request #3683 from RosettaCommons/gideonla/add_xsd_descriptors Gideonla/add xsd descriptors

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Merge pull request #3685 from RosettaCommons/JackMaguire/Ofast Added "mode=release_native" build option This might be deemed trivial, but I have measured that building with -Ofast instead of -O3 results in a 2.5% speedup in Rosetta runtime (i.e., the new runtime is 97.5% of the default runtime). mode=release_native also adds the -mtune="native" flag which allows the compiler to optimize for the specific processor being used to compile. This means that you would not want to build on one computer and run it on a different computer (though you could get away with it if the CPUs are similar enough). I'm not submitting all tests for this because this change wouldn't affect any of them. I'll add the build test just to make sure that the build process still works though. Thanks to Sergey for the review!

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Merge pull request #3676 from RosettaCommons/jkleman/input_for_mutate Jkleman/input for mutate

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Merge pull request #3672 from RosettaCommons/jadolfbr/new_simple_metrics Add 3 new SimpleMetrics with associated unit and integration tests. Documentation has been updated for this incoming PR. ResidueSummaryMetric ================= The `ResidueSummaryMetric` takes a `PerResidueRealMetric` and summarizes the data in various ways, such as the mean, sum, or the number of residues above, below, or equal to a certain value. This Metric is itself a `RealMetric` and can be used as such in filters, features reporters, etc. Can use cached metric data. InteractionEnergyMetric ================= A metric for measuring the interaction energy between residues using two sets of residue selectors. If residue_selector2 is unset, will use TrueResidueSelector to compare 1 with all other residues. `Rama_prepro` and `pro_close` are ignored by default. Options are included for only including a subset of score types or skipping a set of score types. Uses the EnergyMap to find edges and calculates the energy in that way. PerResidueClashMetric ================= A SimpleMetric that calculates the number of atomic clashes per residue using the LJ radius (at 0) using two residue selectors. Default is to use a soft radius, which reduces it by 33% (the dampening of which can be set.). Does not calculate intra-residue clashes. Other ==== Fix serialization of the SimpleMetric custom_type option. Add an `is_bonded` function to Conformation and associated unit test. Change to print out full name of SimpleMetric during RunSimpleMetric's apply function.

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