Merge pull request #3292 from RosettaCommons/JWLabonte/sugars/database Carbohydrates: Database additions and .pdb input (and output) bug fixes This merge attempts to increase the percentage of sugar-containing .pdb files that can be read in to Rosetta without modification. I have a current benchmark of 104 .pdb files containing (free) glycan ligands. Before these changes, 78/104 files could load. Files that do not load have 5 separate problems, 3 of which I address with this merge. After this merge 92/104 files should load. As an extra bonus, this merge expands on @BrandonFrenz's work and completes the database such that all sugars can be output with the PDB 3-letter codes, if that is what is desired, not only the limited subset. It also integrates (effectively) the bug fix made in PR #3289 and negates the need for PR #3175. All unit tests pass. c-term_conjugation test is simply the centroid ResidueTypeSet reporting on its larger size. carbohydrates integration test expanded. glycan_anomers test is currently unstable and it is hoped that this merge corrects that. Note that master was already broken when I made this merge.

• Summary

Merge pull request #3305 from RosettaCommons/jaumebonet/fflchem allow FFL to work with chemical binders

• Summary

Merge pull request #3303 from RosettaCommons/everyday847/revive_cif_io Hotfix 2: unit tests are ok now

• Summary

Merge pull request #3301 from RosettaCommons/sergey/binder PyRosetta, updating Binder submodule and putting `Pybind11` into system includes

• Summary

Merge pull request #3302 from RosettaCommons/everyday847/revive_cif_io Master unit test hotfix -- adding new centroid-rot params that I didn't commit earlier.

• Summary

Merge pull request #2845 from RosettaCommons/everyday847/revive_cif_io Revive CIF I/O and fix some big bug classes At final tally, this branch fixes about 8K new PDBs (~1/2 of broken PDBs) and 1K cifs (and thousands of others it moves to a more 'chemically realistic' bug class'). Massive bugfix to `metalloprotein_abrelax` which had been loading in the CCD type `pdb_CYZ` for its centroid_rot phase, and to various enumerative_sampling and related tests that had been loading in `pdb_VRT`. A couple trajectory changes are observed due to floating point issues. Some logfiles change due to spacing alterations in atom names. (Use stripped names in more places -- the RT will always have them in addition to the with-spaces alias, while the CCD residue will ONLY have the stripped version.) Also prevented `PartitionContactScreener` from wiping out protein trajectories -- residues often won't make adjacent-residue contacts in typical (say) cyclic peptides.

• Summary

Merge pull request #2984 from RosettaCommons/kalekundert/cbrss Improvements to CoupledMoves and ClashBasedRepackShell

• Summary

beautifying

• Summary

Merge pull request #3298 from RosettaCommons/sergey/f2 Fixing an inclusion-order related problem and removing `/usr/include` and `/usr/local/include` from our default include paths

• Summary

Merge pull request #3177 from RosettaCommons/darwinyfu/ProtEnsemble Adding of protein ensembles to small molecule docking. Can now pass in multiple receptor files to dock ligands against when using the Transform and TransformEnsemble movers. Expected integration test changes: hash signature of ligand docking applications. hts_io will change since it runs Transform with repeat option and transform conformation update has been moved outside of the repeat loop so it only updates the final pose once.

• Summary

Merge pull request #3213 from RosettaCommons/hssnzdh2/unsatsel2 Updating UnsatSel to be better

• Summary

Merge pull request #3286 from RosettaCommons/roccomoretti/scientific_test_update Update the PDB diagnostic scientific test reference results, in light of the recent fixes. In addition, I've added a few extra failure categories, which will further separate out the unknown category into manageable chunks to fix.

• Summary

Merge pull request #3293 from RosettaCommons/fix_SpliceOut_bug In SpliceOut, Splice_filter() did not use the scorefunction defined i…

• Summary

Merge pull request #3294 from RosettaCommons/jadolfbr/iam_ft Make InterfaceAnalyzerMover FT independant This PR makes the explicit constructors independent of the FoldTree (those other than the Jump Number specification). It does this through moving chains in cartesian space instead of dihedral space for ignored chains and interface chains to create the separated pose needed. This makes IAM crash a lot less on general structures and enables its broad use for ligands (of different chains). Consequently, `InterfaceMonteCarlo`, which is used in `RosettaAntibodyDesign`, is much more robust. Thanks to Joel Karpiak from GSK for identifying this issue and testing. A new integration test is added that would segfault fail before this PR.

• Summary

Merge pull request #2850 from RosettaCommons/roccomoretti/clang_SA_fixes Knock out most of the Clang Static Analysis issues There's still about 12 files with issues. As I've knocked out all of the "easy" ones, all of these are pointing to potential bugs (perhaps). It will take expert eyes to figure out what should be going on here. See https://github.com/RosettaCommons/main/pull/2850 for a list of remaining issues.

• Summary

Merge pull request #3288 from CyrusBiotechnology/196_BASE_cm_ligand_mode resolves #3275, #3276. CoupledMovesProtocol now exits with more interpretable errors when misconfigured (ligands present but not flagged as on) instead of segfaulting. It also takes ligand-related settings via getter/setter instead of command line flag.

• Summary

Legend: