Merge pull request #4970 from RosettaCommons/RFeehan-KU/EZpotential R feehan ku/e zpotential

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Merge pull request #5660 from RosettaCommons/vmullig/citation_info_for_approx_buried_unsat_penalty Updating citation for approximate buried unsatisfied penalty to list Coventry and Baker PlosCompBio 2021. (Small update to the citation database.)

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Merge pull request #5657 from RosettaCommons/vmullig/another_minor_clang_tidy_fix Remove redundant "virtual" keywords from function prototypes already marked as "override". This is another stylistic thing flagged by clang-tidy.

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Merge pull request #5656 from RosettaCommons/vmullig/suppress_thread_index_in_tracers_if_single_threaded Suppress output of thread index in tracer lines if the RosettaThreadManager has been instructed to launch only one thread. Requested by @ajasja.

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Merge pull request #5620 from RosettaCommons/vmullig/pdb_names_in_cluster_output Ensure that the energy_based_clustering app writes out the filenames or other descriptors of poses that it clusters.

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Merge pull request #5654 from RosettaCommons/vmullig/minor_clang_tidy_fix Minor fix to something that I introduced that clang tidy doesn't like. Clang tidy complains about using string::compare() instead of string::operator==. Fixing.

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Merge pull request #5633 from RosettaCommons/tjbrunette/loop_closure_python_fix Tjbrunette/loop closure python fix

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Merge pull request #5226 from RosettaCommons/jadolfbr/fix_total_energy_metric Fix bug in TotalEnergyMetric that was missing non-pairwise-decomposable terms

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Merge pull request #5641 from RosettaCommons/brownbp1/bcl_submodule_updates_10-2021 Brownbp1/bcl submodule updates 10 2021

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Merge pull request #5572 from RosettaCommons/vmullig/simple_threading_mover_changes Add better support for noncanonicals to the SimpleThreadingMover This PR: - [x] Switches the SimpleThreadingMover to use the MutateResidue mover rather than the packer (allowing more diverse mutations to be introduced). - [x] Adds support for sequences provided as oneletter codes, three letter codes, base names, full names, _etc._ - [x] Adds a series of unit tests for using the SimpleThreadingMover to thread sequences that include non-canonical amino acids, provided as oneletter codes, threeletter codes, base names, or full names. - [x] Updates the SeqeunceMetric to use enum classes for its modes rather than ordinary enums. - [x] Restore support for indicating a space (no mutation) with a dash. - [x] Confirm that `GraftSwitchMoverTests:test_graft_switch_mover_setup`, which was flagging this, now passes. - [x] Updates documentation for SimpleThreadingMover.

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Merge pull request #5635 from RosettaCommons/cmaes_minimizer Fixing Cmaes minimizer integration test, adding lambda option

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Merge pull request #5352 from RosettaCommons/bcl_integration_submodule Bcl integration submodule

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dummy commit to trigger test run

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Merge pull request #5628 from RosettaCommons/ssm_update_9-30-21 minor tweaks to ROSIE stabilize-pm script

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Merge pull request #5618 from RosettaCommons/cmaes_minimizer Adding "blackbox" covariance matrix adaptation evolution strategy (Cmaes) minimizer.

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Merge pull request #5626 from RosettaCommons/jadolfbr/public_apps Make rosetta_scripts_jd3 public. Documentation: https://new.rosettacommons.org/docs/latest/RosettaScripts-JD3

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