Pull Request №299 RosettaCommons/rosetta/main ← roccomoretti/rosetta/master_fix Merge: 1f5080a079a5261122c0e532c46f61a4f7e20df8←e3950ef0f6e22f1874b013d3400b454212f3d496 Attempt to fix failing tests in main. ---------------- Merge commit message: Remove unneeded (for the scientific test) repacking stage.

• Summary
• code_quality.clang_tidy
• integration.mpi
• integration
• unit.valgrind

Merge branch 'main' into benchmark

• Summary

Pull Request №295 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/roccomoretti-patch-2 Merge: 1f5080a079a5261122c0e532c46f61a4f7e20df8←f14cfde15403352a976dafc427f084304c5fc5b9 Attempt to fix simple_cycpep_predict ---------------- Merge commit message: Fix spacing, address similar issue in other script.

• Summary
• scientific.peptide_pnear_vs_ic50

Pull Request №295 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/roccomoretti-patch-2 Merge: 1f5080a079a5261122c0e532c46f61a4f7e20df8←90ea6fad7b4f251891e3c0561e616c5e3372d641 Attempt to fix simple_cycpep_predict ---------------- Merge commit message: Attempt to fix simple_cycpep_predict

• Summary
• scientific.simple_cycpep_predict.debug

Pull Request №243 RosettaCommons/rosetta/main ← lyskov/rosetta/pyrosetta Merge: 4e95d564dc8b93fbe830018d2f295f3f69a70dfd←259ea7e252a19d4012e421d8052343b66f4fff50 Update Conda setup ---------------- Merge commit message: mitigate error if no `defaults` channel was set

• Summary
• mac.clang.cxx11thread.serialization.python310.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python310.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python311.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python312.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python313.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python38.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python39.release.PyRosetta.conda.Release
• release.rosetta.conda.release

Pull Request №243 RosettaCommons/rosetta/main ← lyskov/rosetta/pyrosetta Merge: 4e95d564dc8b93fbe830018d2f295f3f69a70dfd←d8c6c48f0b7bb42fcb33bc7b497c0e26ddd0783f Update Conda setup ---------------- Merge commit message: remove `defaults` channel

• Summary
• m1.clang.cxx11thread.serialization.python310.release.PyRosetta.conda.Release
• m1.clang.cxx11thread.serialization.python311.release.PyRosetta.conda.Release
• m1.clang.cxx11thread.serialization.python312.release.PyRosetta.conda.Release
• m1.clang.cxx11thread.serialization.python313.release.PyRosetta.conda.Release
• m1.clang.cxx11thread.serialization.python39.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python310.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python311.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python310.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python311.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python312.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python313.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python38.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python39.release.PyRosetta.conda.Release
• release.rosetta.conda.release

remove conda `defaults` and add `conda-forge` channel

• Summary
• ubuntu.clang.cxx11thread.serialization.python311.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python312.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python313.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python38.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python39.release.PyRosetta.conda.Release
• release.rosetta.conda.release

Fix issue related to PackerTask usage in homodimer_design. (#115) With a -pack_min_runs of 2 or greater, there's a chance that the sequence of the structure changes. This is a problem for a fixed PackerTask run, as `task_is_valid( pose )` fails if the base residue types don't match up properly. This is an issue found in Discussion #112 The fix is simple -- just use the TaskFactory which we already have lying around instead of manually generating the packer task. (The PackRotamersMover will properly re-apply the TaskFactory.) We can also make the interface of PackRotamersMover a bit nicer.

• Summary

Pull Request №241 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/lyskov-patch-1 Merge: 4e95d564dc8b93fbe830018d2f295f3f69a70dfd←d9908863413d639c6fbbaf44422111eaa442fa01 removing "defaults" Conda channel in favor of "conda-forge" ---------------- Merge commit message: removing "defaults" Conda channel in favor of "conda-forge" Conda recently changed the licensing terms for they "defaults" channel so let use conda-forge instead.

• Summary

Pull Request №282 RosettaCommons/rosetta/main ← roccomoretti/rosetta/drug_design Merge: 26484dedf0f1404f3b8d60dcc4163af48455e793←d0e78e8f31a5db70d7aed115ba898eb01aa9a83d Monte Carlo Drug Design, base code. ---------------- Merge commit message: Merge remote-tracking branch 'origin/main' into drug_design

• Summary
• mac.clang.python38.PyRosetta.unit
• ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit
• code_quality.cppcheck 「1」
• code_quality.merge_size
• integration.mpi 「1」
• integration.release_debug 「3」
• integration 「2」
• scripts.pyrosetta

Pull Request №172 RosettaCommons/rosetta/main ← folmilsch/rosetta/main Merge: 59628fbc5bc09f1221e1642f1f8d157ce49b1410←dba98c0cdaec9a8d9e1f7f6f3248342116595d91 Building PHENIX interface - add missing imports ---------------- Merge commit message: Update PhenixInterface.cc Put extra includes into #ifdef blocks

• Summary
• beautification
• integration.mpi 「1」
• integration.release_debug 「1」
• integration.tensorflow 「0」
• integration.thread 「0」
• integration.torch
• performance 「0」
• profile 「0」
• linux.clang.score 「0」
• linux.gcc.score 「0」

Pull Request №277 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/roccomoretti-cmath-patch Merge: 4e95d564dc8b93fbe830018d2f295f3f69a70dfd←71277403334c9b421f9f8022d15888fd11b5a7bf Add cmath includes ---------------- Merge commit message: Update MC_RNA_KIC_Sampler.cc

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

fixing function def for vector of vector of strings(resi base name) and unit test

• Summary

Pull Request №263 RosettaCommons/rosetta/main ← tydingcw/rosetta/methyllanthionine_params_update Merge: 4e95d564dc8b93fbe830018d2f295f3f69a70dfd←266cb2d3b7d88da3698a1e42ec28dba7b6b74506 Lanthipeptide and recon multistate design update ---------------- Merge commit message: fixing function def for vector of vector of strings(resi base name) and unit test

• Summary
• beautification
• integration.mpi 「4」
• integration.release_debug 「5」
• integration.tensorflow 「1」
• integration.thread 「1」
• integration 「5」

Ligand identification in cryoEM maps with GALigandDock (#227) This PR contains updates to density tools and GALigandDock to detect unmodeled regions of cryoEM maps and evaluate docked ligands based on their dG and density fit. Changes include: * Adding ligand identity evaluation in multiple_ligands_ mode in GALigandDock if a density map is present * Adding find_unassigned_density to density_tools.cc * Adding the sim_cryo.cc app to simulate cryoEM data * Improvements to docking large ligands, including an alternative density erosion algorithm and alternative crossover and mutations in GALigandDock

• Summary

Pull Request №243 RosettaCommons/rosetta/main ← lyskov/rosetta/pyrosetta Merge: 4e95d564dc8b93fbe830018d2f295f3f69a70dfd←b4505e50fec4806065b35bf471998147365ec513 Update Conda setup ---------------- Merge commit message: fix Conda install

• Summary
• ubuntu.clang.cxx11thread.serialization.python313.release.PyRosetta.conda.Release
• release.rosetta.conda.release

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