Merge pull request #5482 from RosettaCommons/j0kaso/sci_benchmark_sfxn_mpcart j0kaso/sci_benchmark_sfxn_mpcart: new scientific benchmark test for cartesian ddG protocol for mp sfxn comparison

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Merge pull request #5513 from RosettaCommons/ajasja/fix_find_hbnet Fix error in hbnet if find_only_native_networks does not find networks

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• integration.tutorials 「1」
• scientific.sb_score12_loop_modeling_ngk_12res

Merge pull request #5512 from RosettaCommons/vmullig/fix_randomize_bb_by_rama_prepro_if_no_selector_is_used Minor fix for RandomizeBBByRamaPrePro mover. This PR adds a little fix to RandomizeBBByRamaPrePro mover: previously, if a residue selector wasn't used, a cryptic error message would result. Now it should work.

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• integration.tutorials 「1」
• scientific.FlexPepDock

Merge pull request #5508 from RosettaCommons/ajasja/nc_metric_fix Fixed truncation/rounding of values in SidechainNeighborCountMetric

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• scientific.glycan_dock.debug

updating PyRosetta.notebooks to its latests master to fix notebooks tests

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Merge pull request #4801 from RosettaCommons/JWLabonte/PDB_IO/splittable_residues PDB IO: Adding a way for .pdb residues to be "split" into multiple Rosetta residues upon import Sometimes the PDB has a 3-letter code for a ligand that Rosetta represents as an oligomer of smaller residues. For example, the small molecule maltose exists in the PDB both as the single ligand MAL and as a dimer of GLC (→4)-α-D-Glcp in Rosetta) residues. This merge provides a way in the database to provide instructions to Rosetta to be able to split such residues properly automatically.

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Merge pull request #5498 from RosettaCommons/BYachnin/silent_struct_type_bug Fix in reading silent files with multiple remarks When reading a silent file, Rosetta attempts to determine the silent file type using the first remark line. Previously, we did this check on ALL remark lines, which is usually fine, since only one type is indicated. An obscure/entertaining bug occurs if a subsequent remark line added elsewhere contains one of the string keywords. Most likely, you store some sequence info in a REMARK, and that info contains the one-letter code for Arg-Asn-Ala (RNA), triggering the "rna" silent_structure_type_. This PR fixes that behaviour, and adds unit tests to ensure it doesn't get reintroduced.

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Merge pull request #5487 from RosettaCommons/Rituparnasamanta/squashed_commits_membrane_benchmark Rituparnasamanta/squashed commits membrane benchmark

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DockIntoDensityMover refactor 02 (#5497) In anticipation of releasing some other code that uses this machinery I'm refactoring some parts of the DockIntoDensityMover to be functions rather than a class member functions so that other classes can use them. This is strictly a refactor and shouldn't change anything except the accessibility of some functions. This refactor specifically moves to another file as functions: get_radius get_spectrum apply_transform select_points -> select_density_points RBfitResult RefinementResult RBfitResultComparitor RefinementResultComparitor PointScoreComparator ResultDB RBfitResultDB RefinementResultDB DensitySymmInfo::mask_asu -> becomes a const function

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Merge pull request #5464 from RosettaCommons/jkleman/sciben_june2021_fixes sciben fixes for paper revisions: fixes to various scientific tests and adding ab initio RosettaNMR tests for RDCs and PCS

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DockIntoDensityMover refactor 01 (#5495) Refactor poseSphericalSamples into DockIntoDensityUtils This refactor will allow outside classes to access the density searching capabilities of the DockIntoDensity code In anticipation of releasing some other code that uses this machinery I'm refactoring some parts of the DockIntoDensityMover to be functions rather than a class member functions so that other classes can use them. This is strictly a refactor and shouldn't change anything except the accessibility of some functions.

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Merge pull request #5493 from RosettaCommons/sergey/f fixing LLVM tool install

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Merge pull request #5492 from RosettaCommons/mlnance/GlycanDock_sci_test_no_history GlycanDock Scientific Benchmark

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Merge pull request #5350 from RosettaCommons/Rituparnasamanta/updating_scientific_benchmark Rituparnasamanta/updating scientific benchmark

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Merge pull request #5424 from RosettaCommons/Rituparnasamanta/Rituparnasamanta/scientific_benchmark_mp_sequence-recovery Rituparnasamanta/rituparnasamanta/scientific benchmark mp sequence recovery

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Merge pull request #5484 from RosettaCommons/roccomoretti/less_python_verify Reduce the number of times Python verification happens in integration tests. The changes in PR #5399 exposed the fact that generateIntegrationTestGlobalSubstitutionParameters() was being called multiple times per test suite. This is unneeded, as we've already generated the parameters and have stored them in a variable we could be re-using.

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