Merge pull request #5826 from RosettaCommons/everyday847/new_metrics RDKit metrics can apply to whole chains

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Merge pull request #5693 from RosettaCommons/roccomoretti/update_submodules Update various submodules The assorted submodules have accumulated additional commits in their master branches versus their state in the main repo. Update the various submodules to their most recent master branch status. (Submodules for build & PyRosetta build weren't touched -- it's assumed that they're at the state they're supposed to be.)

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Merge pull request #5802 from RosettaCommons/roccomoretti/fix_master Fix master tests *Beautification for PR #5800 * Fix uninitialized variable detected by Valgrind for PR #5683

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Merge pull request #5800 from RosettaCommons/nrbennet/samplerotamersfix Added "db_file_name" flag to parse_xml_schema of SampleRotamersFromPDB

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Merge pull request #5796 from RosettaCommons/roccomoretti/pyrosetta_atomid Enable wrapping of nested AtomID datastructures for PyRosetta. PyRosetta apparently needs some additional help to know that it needs to wrap nested templated types. The standard way of doing this is apparently to make a dummy function for PyRosetta only.

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Merge pull request #5776 from RosettaCommons/roccomoretti/pyrosetta_Vector1_fix Fix pyrosetta.Vector1 for AtomID lists

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Merge pull request #5790 from RosettaCommons/weitzner/fix-macos-bitness Updating Rosetta for Apple Silicon (M1) Macs

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Merge pull request #5786 from RosettaCommons/vmullig/fix_rama_prepro_edge_case Fix an edge case for bad input files for the rama_prepro scoreterm Andy Watkins found a bug that produces very hard-to-diagnose errors in scoring: if a rama_prepro map has 0 for any probability entry, it creates NaNs that appear far downstream. This PR adds an error message if a rama_prepro map has 0 for any probability entry. It also switches a few more instances of `new` to use `utility::pointer::make_shared`.

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Merge pull request #5779 from RosettaCommons/vmullig/fix_mpi_build_issue_on_ubuntu Fix MPI build on newer Ubuntu Disabling C++ MPI bindings in MPI builds. This is to correct a known issue with newer GCC building against older (e.g. v. 1.10.7) OpenMPI. This is safe to do since (a) we don't use the C++ bindings (only the C bindings), (b) the C++ bindings were redundant and useless anyways, and (c) the C++ bindings have been removed in OpenMPI 4.

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beautifying

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Merge pull request #5778 from RosettaCommons/brownbp1/bcl_submodule_update_12-02-2021 Brownbp1/bcl submodule update 12 02 2021

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Merge pull request #5699 from RosettaCommons/everyday847/peptidream_prediction Thioether lariat structure prediction

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Merge pull request #5720 from RosettaCommons/vmullig/cycpep_permutation_mover Add a mover to superimpose a cyclic peptide on itself with cyclic permutation Requested by @skudlacek. Tasks: - [x] Add the mover. - [x] Configuration: - [x] Allow user-specified cyclic permutation or reverse permutation. - [x] Allow random cyclic permutation or reverse permutation. - [x] Additional random displacement and/or roll. - [x] parse_my_tag() - [x] provide_xml_schema() - [x] C++ getters and setters. - [x] apply() - [x] Check that pose or selection is a cyclic peptide. - [x] Set_permutaion mode. - [x] Set_permutaion mode with inversion. - [x] Randomized_permutaion mode. - [x] Randomized_permutaion mode with inversion allowed. - [x] Align peptide to original. - [x] Add random offset. - [x] Add random orientation perturbation. - [x] CitationManager functions. - [x] Unit test for set_permutation mode. - [x] Fix errors revealed by unit test. - [x] Integration test for randomized_permutation mode. - [x] Fix errors revealed by integration test. - [x] Documentation. --> See pull request RosettaCommons/documentation#49 - [x] Beauty.

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Update slurm.py explicitly specifying the correct SLURM partition

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Merge pull request #5769 from RosettaCommons/vmullig/generalize_virtual_residue Generalize the virtual residue patch. Currently, the protein virtual residue patch is special-cased for each amino acid type, and doesn't support terminal types. This is silly. We have a `VIRTUALIZE_ALL` `PatchOperation` (which is used for RNA); we might as well use it for everything. Tasks: - [x] Switch patch to use `VIRTUALIZE_ALL`. - [x] Rename patch from `VirtualProteinResidue` to `VirtualResidue`. - [x] Ensure the `VIRTUALIZE_ALL` `PatchOperation` also zeros the net formal charge. - [x] Unit test to confirm that this lets us virtualize all residues in a pose.

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hot-fixing release scripts

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