Merge pull request #3133 from RosettaCommons/jadolfbr/simple_metrics Bug fixes: SequenceMetric and sequence motif split - Fix major bug in SequenceMetric where the unit test was also wrong. - Fix minor bug in splitting of sequence motif that made the CreateSequenceMotifMover/SequenceMotifTaskOp to incorrectly design motifs which had no inner brackets. So this - `N-T` would fail, but `N[-]T` would be designed correctly. Expand unit tests for this specific motif type. - Fix `simple_metric_features` integration test through dumping the db. Thanks @roccomoretti ! - Condense splitting sequence motif function into a single function. - Add cluster and distance info to scorefile for antibody design as a stop gap until we have a full SimpleMetric.

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Merge pull request #3135 from RosettaCommons/vmullig/buried_unsat_score_incremental_merge_1 Incremental merge of buried unsatisfied penalty scoreterm. (This currently lacks symmetry support.) This is an incremental merge of pull request #2597. This pull request adds basic support for asymmetric poses, but no support yet for symmetric poses. This scoreterm guides the packer to solutions with no buried unsatisfied hydrogen bond donors or acceptors. It is intended for use with the rest of the scorefunction, and possibly for use with the `voids_penalty`, `aa_composition`, and `hbnet` scoreterms. Tasks: - [x] Basic support for asymmetric poses. - [x] (Temporary) error if used on a symmetric pose. - [x] Unit tests. - [x] Integration tests. - [x] Documentation. - [x] Beauty.

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Merge pull request #3118 from RosettaCommons/fordas/cmake_extern_extras Update cmake build configuration to disable extras-enabled-externals.

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RosettaAI: Setting pyrosetta_scripts submodule to latest origin/master version.

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Merge pull request #3129 from RosettaCommons/sergey/binder PyRosetta update: porting Binder PR44 to `build.py` so LLVM is now installed from source-download instead of Git-clone (this should save ~3Gb of disk space). Thanks to @asford for prototyping this!

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Merge pull request #3124 from RosettaCommons/kkappel1/benchmark_RNP RNA-protein ddG calculations. All integration test changes are expected due to new score terms and a new energy method option.

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Merge pull request #3119 from RosettaCommons/jadolfbr/simple_metrics Fix SimpleMetric integration tests Fix the simple_metric_filter and simple_metric_features integration tests. Remove the IntegerMetric code after Rocco's excellent points.

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updating mpi_fraction_outputters default

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Merge pull request #3111 from RosettaCommons/MelanieAprahamian/HRFMSLabeling burial_measure_centroid Integration Test fix

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RosettaAI: Setting rosetta_scripts_scripts submodule to latest origin/master version.

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Merge pull request #3123 from RosettaCommons/benchmark Fixing Python-3.* local install issues in Benchmark scripts

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Merge pull request #3122 from RosettaCommons/everyday847/reduce_default_outputter_fraction Reduce default on -jd3:mpi_fraction_outputters. @vmullig i am tagging you in case you used this option default during Blue Gene runs.

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Merge pull request #3117 from RosettaCommons/everyday847/noncanonical_bp_constraints Base pair constraints for noncanonical residues

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Merge pull request #2950 from RosettaCommons/everyday847/erraser2_wip More erraser2 stuff

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Merge pull request #3108 from RosettaCommons/danpf/static_fix Danpf/static fix

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Merge pull request #3091 from RosettaCommons/JackMaguire/MCHBNetCorrection Removed overkill utility_exit_with_message() from MC HBNet When writing MC HBNet, I apparently thought that the reasonable way to handle the lack of results from a single instance of the mover is to kill the user's entire rosetta_script run. This PR changes this so that the mover just prints a message and returns 0 results, letting the other trajectories continue. Thanks to Vikram for reviewing!

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