Pull Request №619 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/rac_pyrosetta_notebook_edits Merge: 70d16afc3112608e6c9218151616659589b7d46e←12682579581d705e0a5d355798fdc1f5509cea43 Update PyRosetta.notebooks submodule ---------------- Merge commit message: Built the student notebooks and fixed issue with notebook 02.01-Pose-Basics (see Sergey L.'s comment in the PR).

• Summary
• PyRosetta.notebook 「1」

Pull Request №619 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/rac_pyrosetta_notebook_edits Merge: 70d16afc3112608e6c9218151616659589b7d46e←4dcf4ac91b8e8c7692aa02f0fe1add0d02cb1c24 Update PyRosetta.notebooks submodule ---------------- Merge commit message: Point PyRosetta.notebooks submodule at rac_edits, this branch has edits to the pyrosettacolabsetup options, an updated guide for installing PyRosetta locally, and a Markdown version of the PyMOL workshop.

• Summary
• PyRosetta.notebook 「1」

Pull Request №612 RosettaCommons/rosetta/main ← klimaj/rosetta/secure_packages Merge: e5a76a2dbd7e42e1271d0af460926c86e29e59d1←66c0d9146fd390668bf2924b24822457d00eceaa Minor change to PackedPose.scores dictionary construction ---------------- Merge commit message: dummy commit to trigger test run

• Summary

Pull Request №617 RosettaCommons/rosetta/main ← lyskov/rosetta/pyrosetta-release-links Merge: e5a76a2dbd7e42e1271d0af460926c86e29e59d1←df5ee44cc896759318b07101d4f3a7e06ba90726 update PyRosetta release links ---------------- Merge commit message: update symlink name

• Summary

Pull Request №612 RosettaCommons/rosetta/main ← klimaj/rosetta/secure_packages Merge: e5a76a2dbd7e42e1271d0af460926c86e29e59d1←a51271c2af0747198e6ef3f6c42e3a6c19a14b8e Minor change to PackedPose.scores dictionary construction ---------------- Merge commit message: Skip dtype conversion; add documentation that PyArrow-backed dtypes may be used by default, depending on pandas version

• Summary

Pull Request №612 RosettaCommons/rosetta/main ← klimaj/rosetta/secure_packages Merge: e5a76a2dbd7e42e1271d0af460926c86e29e59d1←9e58cfdc48123249e0aa0079ec921c2489d3b2c2 Minor change to PackedPose.scores dictionary construction ---------------- Merge commit message: Test re-enabling test_smoke.ScoresTest.test_secure_packages_billiard unit test

• Summary
• ubuntu-20.04.clang.cxx11thread.serialization.python313.PyRosetta.unit.pixi 「1」
• ubuntu-20.04.clang.cxx11thread.serialization.python314.PyRosetta.unit.pixi 「1」
• ubuntu-20.04.clang.cxx11thread.serialization.python310.PyRosetta.unit 「1」
• ubuntu-20.04.clang.cxx11thread.serialization.python39.PyRosetta.unit 「1」
• ubuntu-20.04.gcc.cxx11thread.serialization.python310.PyRosetta.unit 「1」
• ubuntu-20.04.gcc.cxx11thread.serialization.python39.PyRosetta.unit 「1」
• ubuntu-22.04.clang.cxx11thread.serialization.python310.PyRosetta.unit 「1」
• ubuntu-22.04.clang.cxx11thread.serialization.python39.PyRosetta.unit 「1」
• ubuntu-22.04.gcc.cxx11thread.serialization.python310.PyRosetta.unit 「1」
• ubuntu-22.04.gcc.cxx11thread.serialization.python39.PyRosetta.unit 「1」
• ubuntu-24.04.clang.cxx11thread.serialization.python310.PyRosetta.unit 「1」
• ubuntu-24.04.clang.cxx11thread.serialization.python39.PyRosetta.unit 「1」
• ubuntu-24.04.gcc.cxx11thread.serialization.python310.PyRosetta.unit 「1」
• ubuntu-24.04.gcc.cxx11thread.serialization.python39.PyRosetta.unit 「1」

Pull Request №612 RosettaCommons/rosetta/main ← klimaj/rosetta/secure_packages Merge: e5a76a2dbd7e42e1271d0af460926c86e29e59d1←01c3cc0f6938f98955716a5957f93b68800e253d Minor change to PackedPose.scores dictionary construction ---------------- Merge commit message: Debugging Benchmark server error: 'self-test.py scripts failed to delete files: outputs'

• Summary
• ubuntu-20.04.clang.cxx11thread.serialization.python313.PyRosetta.unit.pixi 「1」
• ubuntu-20.04.clang.cxx11thread.serialization.python314.PyRosetta.unit.pixi 「1」

Pull Request №612 RosettaCommons/rosetta/main ← klimaj/rosetta/secure_packages Merge: e5a76a2dbd7e42e1271d0af460926c86e29e59d1←32b3137b756878e68a73d97295f9c7b27697df20 Minor change to PackedPose.scores dictionary construction ---------------- Merge commit message: git pull origin main

• Summary
• ubuntu-20.04.clang.cxx11thread.serialization.python310.PyRosetta.unit 「1」
• ubuntu-20.04.clang.cxx11thread.serialization.python312.PyRosetta.unit 「1」
• ubuntu-20.04.clang.cxx11thread.serialization.python313.PyRosetta.unit 「1」
• ubuntu-20.04.clang.cxx11thread.serialization.python39.PyRosetta.unit 「1」
• ubuntu-20.04.gcc.cxx11thread.serialization.python310.PyRosetta.unit 「1」
• ubuntu-20.04.gcc.cxx11thread.serialization.python39.PyRosetta.unit 「1」

Updated PARCS applications and IMMS_CCS score function (#609) This application builds on the existing PARCS (parcs_ccs_calc.cc) application and the IMMS_CCS energy term originally developed by smturzo. I extended PARCS to support multimeric protein complexes, enabling simulation of PARCS CCS data for input structures containing multiple chains. In addition, the existing IMMS_CCS energy term, which was previously limited to monomers, was generalized for complexes through the introduction of a new IMMS_ComplexCCS_Energy term. I also implemented a new CCS_IMMS_with_CryoEMEnergy score term that integrates experimental CCS data with cryo-EM information. Method: For PARCS multimer support, I introduced a boolean flag (-multimer) to the existing PARCS application. When enabled, the algorithm predicts CCS values for multimeric assemblies by reparameterizing the original CCS calculation. For the IMMS-based energy terms, I developed on the existing CCS_IMMSEnergy implementation (source/src/core/energy_methods/CCS_IMMSEnergy.cc/.hh) by adding new energy classes: * CCS_IMMSComplexEnergy, which enables CCS-based scoring for protein complexes * CCS_IMMS_with_CryoEMEnergy, which incorporates cryo-EM restraints alongside experimental CCS data Integration test: I did integration just like how it was done for monomers with additional flag. for multimer The test passed.

• Summary

Pull Request №608 RosettaCommons/rosetta/main ← klimaj/rosetta/uv_project Merge: 1a56185c2592611dec4c9c75ddc9468cd2227c1f←7c22c2482bdde0c764fd815e3dd14e3b4257d087 Minor updates to uv project export machinery in PyRosettaCluster ---------------- Merge commit message: Use uv.lock file instead of exported requirements.txt

• Summary

Pull Request №611 RosettaCommons/rosetta/main ← klimaj/rosetta/disallowed_packages Merge: 1a56185c2592611dec4c9c75ddc9468cd2227c1f←50be604361f57befadb3487787bdfcd626ffe5f3 Update SecureUnpickler disallowed packages ---------------- Merge commit message: Merge branch 'main' of github.com:klimaj/rosetta into disallowed_packages

• Summary

Pull Request №612 RosettaCommons/rosetta/main ← klimaj/rosetta/secure_packages Merge: 1a56185c2592611dec4c9c75ddc9468cd2227c1f←3c508bc5e2d89fdff22125c3efeb4ad0733330a6 Minor change to PackedPose.scores dictionary construction ---------------- Merge commit message: Merge branch 'main' of github.com:klimaj/rosetta into secure_packages

• Summary
• ubuntu-20.04.clang.cxx11thread.serialization.python312.PyRosetta.unit 「1」
• ubuntu-20.04.clang.cxx11thread.serialization.python314.PyRosetta.unit 「1」
• ubuntu-20.04.clang.cxx11thread.serialization.python39.PyRosetta.unit 「1」
• ubuntu-20.04.gcc.cxx11thread.serialization.python310.PyRosetta.unit 「1」
• ubuntu-20.04.gcc.cxx11thread.serialization.python313.PyRosetta.unit 「1」
• ubuntu-20.04.gcc.cxx11thread.serialization.python314.PyRosetta.unit 「1」

Pull Request №609 RosettaCommons/rosetta/main ← akshayansamy/rosetta/app_score_imms Merge: 307045a3f7fe7488f28b6c4422425c60f04a78cd←94372e897bdacd8c409a52609951a64609805675 Updated PARCS applications and IMMS_CCS score function ---------------- Merge commit message: beautification 2

• Summary
• code_quality.merge_size
• integration.mpi 「2」
• integration.release_debug 「7」
• integration.tensorflow 「1」
• integration.thread 「1」
• integration 「7」
• windows.build.release

Pull Request №609 RosettaCommons/rosetta/main ← akshayansamy/rosetta/app_score_imms Merge: 307045a3f7fe7488f28b6c4422425c60f04a78cd←9c46025304ecc8a8784e1a0f4fd9d1ea89aeb0c9 Updated PARCS applications and IMMS_CCS score function ---------------- Merge commit message: Beautified

• Summary
• beautification
• code_quality.merge_size
• integration.mpi 「2」
• integration.release_debug 「7」
• integration.tensorflow 「1」
• integration.thread 「1」
• integration 「7」

Pull Request №612 RosettaCommons/rosetta/main ← klimaj/rosetta/secure_packages Merge: 307045a3f7fe7488f28b6c4422425c60f04a78cd←7325ee730f01491ddf29d83201d343e7026f70cb Minor change to PackedPose.scores dictionary construction ---------------- Merge commit message: Add deprecation warning and helpful KeyError message

• Summary
• ubuntu-20.04.gcc.cxx11thread.serialization.python312.PyRosetta.unit 「1」

Pull Request №612 RosettaCommons/rosetta/main ← klimaj/rosetta/secure_packages Merge: 307045a3f7fe7488f28b6c4422425c60f04a78cd←3b46aec5160fc1fe1ed1bef0b5a02ca0b4f29aa2 Minor change to PackedPose.scores dictionary construction ---------------- Merge commit message: Fix TestReproducibilityMulti and use Pose.cache._reserved

• Summary
• ubuntu-20.04.clang.cxx11thread.serialization.python310.PyRosetta.unit 「2」
• ubuntu-20.04.clang.cxx11thread.serialization.python311.PyRosetta.unit 「1」
• ubuntu-20.04.clang.cxx11thread.serialization.python312.PyRosetta.unit 「1」
• ubuntu-20.04.clang.cxx11thread.serialization.python313.PyRosetta.unit 「1」
• ubuntu-20.04.clang.cxx11thread.serialization.python39.PyRosetta.unit 「2」
• ubuntu-20.04.gcc.cxx11thread.serialization.python312.PyRosetta.unit 「1」
• ubuntu-20.04.gcc.cxx11thread.serialization.python313.PyRosetta.unit 「1」
• ubuntu-20.04.gcc.cxx11thread.serialization.python314.PyRosetta.unit 「1」
• ubuntu-20.04.gcc.cxx11thread.serialization.python39.PyRosetta.unit 「1」

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