fixing source and Conda releases

• Summary
• integration.mpi 「5」
• integration.release_debug 「2」
• integration.tutorials 「1」
• integration 「1」
• scientific.make_fragments.debug
• scientific.make_fragments
• scientific.mp_f19_decoy_discrimination.debug
• scientific.mp_f19_decoy_discrimination
• scientific.mp_f19_tilt_angle
• scientific.peptide_pnear_vs_ic50.debug

Merge pull request #6046 from RosettaCommons/AJVincelli-UpdateReferenceResults Update Reference Results

• Summary
• integration.addsan 「2」
• integration.mpi 「5」
• integration.release_debug 「3」
• integration 「1」

Merge pull request #6061 from RosettaCommons/oanhvu/molfile_to_params_polymer_test_fix Oanhvu/molfile to params polymer test fix

• Summary
• integration.mpi 「11」
• integration.release_debug 「3」
• integration 「2」

Merge pull request #6056 from RosettaCommons/AmeyaHarmalkar/replica_docking_tests Fixes issues in replica_docking evaluation metrics and adds new integration test

• Summary
• integration.addsan 「2」
• integration.mpi 「11」
• integration.release_debug 「4」
• integration 「3」
• scientific.mp_f19_ddG_of_mutation.debug
• scientific.mp_f19_tilt_angle
• gcc-11.gcc.python39.unit 「17」

Merge pull request #6057 from CyrusBiotechnology/smlewis/bfrenz_ref_fix_second_attempt From @BrandonFrenz : fixed a bug Chris Moth [unsure how to @] found where cartesian ddg was not exiting on convergence because the data storage object was not passed by reference

• Summary
• integration.addsan 「1」
• integration.mpi 「4」
• integration.release_debug 「3」
• integration 「2」

Merge pull request #5680 from RosettaCommons/vuoanh/molfile_polymer_updates Updating script for non-canonical amino acid parameter generation

• Summary
• linux.clang.cxx11thread.serialization.python37.PyRosetta.unit 「1」
• integration.addsan 「1」
• integration.mpi 「4」
• integration.release_debug 「3」
• integration 「2」

Merge pull request #5835 from RosettaCommons/sherilynlim03/butyryl_sugars This code will add an acylation patch (butyryl) to the database for carbohydrates, which will allow for further expansion with other small-chain acylations in the future. All unit tests pass; integration test changes are as expected.

• Summary
• integration.mpi 「5」
• integration.release_debug 「6」
• integration.tensorflow 「1」
• integration.thread 「1」
• integration 「4」
• gcc-11.gcc.python39.unit 「5」

Merge pull request #6050 from RosettaCommons/yhsia/slice_selector_bugfix bugfix for SliceResidueSelector (oob_mode option variable)

• Summary
• integration.mpi 「4」
• integration.release_debug 「2」
• integration 「1」

Merge pull request #6044 from RosettaCommons/AJVincelli-update_CCD Update the CCD files as of June 4th 2022

• Summary
• integration.mpi 「11」
• integration.release_debug 「3」
• integration.tensorflow 「1」
• integration.thread 「1」
• integration 「2」
• scientific.mp_f19_decoy_discrimination.debug
• scientific.mp_f19_decoy_discrimination
• gcc-11.gcc.python39.unit 「5」

Merge pull request #6033 from RosettaCommons/ajasja/fix_antibody use_epitope_constraints_ was not properly set

• Summary
• integration.mpi 「10」
• integration.release_debug 「1」
• integration 「1」
• scientific.make_fragments.debug
• scientific.make_fragments

Merge pull request #5947 from RosettaCommons/odaunc/sixdofsampler Odaunc/sixdofsampler

• Summary
• integration.mpi 「4」
• integration.release_debug 「7」
• integration.tensorflow 「1」
• integration 「7」

removing conda-forge channel when building PyRosetta

• Summary
• integration.mpi 「4」
• integration.release_debug 「2」
• integration.tensorflow 「1」
• integration 「1」
• scientific.ddg_ala_scan
• scientific.docking
• scientific.glycan_dock

updating `PyRosetta,notebook` test and notebooks

• Summary
• integration.addsan 「1」
• integration.mpi 「4」
• integration.release_debug 「2」
• integration.tutorials 「1」
• integration.ubsan 「1」
• integration 「1」
• scientific.docking
• scientific.ligand_scoring_ranking
• gcc-10.gcc.unit 「3」

Merge pull request #6032 from RosettaCommons/benchmark updating release.PyRosetta.conda build procedure

• Summary
• integration.addsan 「2」
• integration.mpi 「3」
• integration.release_debug 「1」
• integration.tutorials 「1」
• integration.ubsan 「1」
• integration 「2」
• scientific.make_fragments.debug
• scientific.make_fragments
• scientific.mp_f19_tilt_angle

Merge pull request #6019 from RosettaCommons/ajasja/fixviewer Bug in the the way the py3dmol size is initiated

• Summary
• integration.addsan 「1」
• integration.mpi 「3」
• integration.release_debug 「2」
• integration.tutorials 「1」
• integration.ubsan 「1」
• integration 「1」
• release.PyRosetta.conda.Release
• scientific.mp_f19_decoy_discrimination.debug
• scientific.mp_f19_decoy_discrimination
• scientific.peptide_pnear_vs_ic50.debug

Merge pull request #6013 from RosettaCommons/vmullig/thioether_crosslink Bugfixes and feature enhancements for thioether lariats. This pull request does four things: - It adds code templates to make it easy to add new crosslink types to the CrosslinkerMover. - It adds support for thioether lariat crosslinks to the CrosslinkerMover. - It fixes a number of thioether bugs affecting placement of hydrogen atoms near the thioether. (This should improve thioether-cyclized peptide structure prediction with simple_cycpep_predict.) - It adds CitationManager citations to the CrosslinkerMover. Tasks: - [x] Add code template files for new CrosslinkerMoverHelpers. - [x] Update code template scripts (to indicate where CrosslinkerMoverHelpers must be registered). - [x] Add new thioether cyclization helper. - [x] Register it. - [x] Add citations to CrosslinkerMover while I'm at it. - [x] Means of indicating that a particular helper is unpublished. - [x] Citations for the metal setup helpers. - [x] Citations for other helpers. - [x] Citations for the Thioether_Helper. - [x] Pull geometry setup functions out of simple_cycpep_predict into a utility function. - [x] Call this in Thioether_Helper. - [x] Pull bond setup functions out of simple_cycpep_predict into a utility function. - [x] Call this in Thioether_Helper. - [x] Pull constraint setup functions out of simple_cycpep_predict into a utility function. - [x] Call this in Thioether_Helper. - [x] Asymmetric functions. - [x] Symmetry support? - [x] Fix bug in placement of thioether N hydrogen. - [x] Fix bug in placement of thioether aliphatic hydrogens --> need virtual atom and to redo constraints. - [x] Figure out why I can't set cys sidechain angle and length dofs. - [x] Figure out why I'm getting wonky bond angles with GenKIC. - [x] Integration tests. - [x] Fix integration test failure `simple_cycpep_predict_beta_thioether_lariat`. - [x] Fix integration test failure `simple_cycpep_predict_thioether_lariat`. - [x] Add integration test for code template with CrosslinkerMover_Helper. - [x] Add bond geometry unit test. - [x] Documentation: - [x] simple_cycpep_predict documentation. - [x] CrosslinkerMover documentation. - [x] Beauty. I have checked that integration test changes are all either: - Failures that are happening in master - Cosmetic (due to changes to a patch file) - Expected due to new citations added (various CrosslinkerMover tests) - Expected due to changes to simple_cycpep_predict's output with thioethers (simple_cycpep_predict_thioether_lariat and simple_cycpep_predict_beta_thioether_lariat tests) - Expected since the test is new (crosslinkermover_thioether test) @everyday847 @jadolfbr @skudlacek