Pull Request №698 RosettaCommons/rosetta/main ← roccomoretti/rosetta/change_chirality_loading Merge: 8f55d1556a33b9d485bc33f6e788ddf6f5216669←3dcd35ef3b290a2461db2f870b1048350163baef Rework chirality detection in restype determination for PDB loading ---------------- Merge commit message: Merge remote-tracking branch 'origin/main' into change_chirality_loading

• Summary
• integration.mpi 「3」
• integration.release_debug 「6」

Pull Request №714 RosettaCommons/rosetta/main ← roccomoretti/rosetta/molfile_gzip Merge: a31d9d50e217e874c57db71bf169052467a8e3d8←24e07ced73aa6046ef5f68ba193608b63a1a06fe molfile_to_params: fix support for gzipped files. ---------------- Merge commit message: molfile_to_params: fix support for gzipped files. In Python3, gzip returns a bytes-based object, rather than a string one (which is what open() returns), which results in errors later. We can use TextIOWrapper to fix the issue.

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

Pull Request №150 RosettaCommons/rosetta/main ← roccomoretti/rosetta/fix_cycle_chain_settings Merge: 957f89124e90fb02e8795d195b994b0af005603f←b622887b2d38b50ce508486bbc77a14ce078abde Fix issue with chain endings in cyclic peptide PDB reading. ---------------- Merge commit message: Fix issue with cutpoints (shouldn't be separate chains)

• Summary
• integration.mpi 「1」
• integration.release_debug 「1」
• integration.tensorflow 「0」
• integration.thread 「0」
• integration.torch
• integration 「3」
• performance 「0」
• profile 「0」
• linux.clang.score 「0」
• linux.gcc.score 「0」
• mac.clang.score 「0」
• scripts.pyrosetta

Pull Request №687 RosettaCommons/rosetta/main ← roccomoretti/rosetta/pdb_cif_diagnostic_fixes Merge: 91e8dceb14197d722d77bbb2030a7a0240653d86←247be7b9ccd50de43b5f8239bd1210a8729f65dc Update handling of CCD residue types. ---------------- Merge commit message: Adjust how we handle component naming, so error messages work a bit better.

• Summary
• beautification
• code_quality.merge_size
• integration.mpi 「1」
• integration.release_debug 「33」
• integration.tensorflow 「1」
• integration.thread 「1」
• integration 「31」
• performance 「1」

Pull Request №708 RosettaCommons/rosetta/main ← klimaj/rosetta/test_builds Merge: 91e8dceb14197d722d77bbb2030a7a0240653d86←0cf5cafd81bb20dcb70d1c230245bbd8ad71d0e1 Testing Pose bindings/numeric unit tests with standard PyRosetta builds ---------------- Merge commit message: Remove duplicate tests; exit if numpy is not installed

• Summary

Pull Request №708 RosettaCommons/rosetta/main ← klimaj/rosetta/test_builds Merge: 91e8dceb14197d722d77bbb2030a7a0240653d86←737977f45d4fa5e478aa5ddb78e6a64c0a400468 Testing Pose bindings/numeric unit tests with standard PyRosetta builds ---------------- Merge commit message: Initial commit

• Summary
• gcc-9.gcc.python37.PyRosetta.unit 「2」
• m1.clang.python310.PyRosetta.unit 「2」
• m1.clang.python311.PyRosetta.unit 「2」
• m1.clang.python312.PyRosetta.unit 「2」
• m1.clang.python313.PyRosetta.unit 「2」
• m1.clang.python314.PyRosetta.unit 「2」
• m1.clang.python38.PyRosetta.unit 「2」
• m1.clang.python39.PyRosetta.unit 「2」
• mac.clang.python310.PyRosetta.unit 「2」
• mac.clang.python311.PyRosetta.unit 「2」
• mac.clang.python312.PyRosetta.unit 「2」
• mac.clang.python313.PyRosetta.unit 「2」
• mac.clang.python314.PyRosetta.unit 「2」
• mac.clang.python38.PyRosetta.unit 「2」
• mac.clang.python39.PyRosetta.unit 「2」
• ubuntu-20.04.clang.python39.PyRosetta.unit 「2」
• ubuntu-22.04.clang.python39.PyRosetta.unit 「2」
• ubuntu.clang.python310.PyRosetta.unit 「2」
• ubuntu.clang.python311.PyRosetta.unit 「2」
• ubuntu.clang.python39.PyRosetta.unit 「2」
• ubuntu.gcc.python310.PyRosetta.unit 「2」
• ubuntu.gcc.python312.PyRosetta.unit 「2」
• ubuntu.gcc.python39.PyRosetta.unit 「2」

Pull Request №658 RosettaCommons/rosetta/main ← klimaj/rosetta/cache_efficiency Merge: 91e8dceb14197d722d77bbb2030a7a0240653d86←877c2c50ce1d50313e23621b314be31652282a96 Improving `Pose.cache` dictionary getter and setter performance ---------------- Merge commit message: Enhance robustness of unit tests for fast accessor methods

• Summary

Pull Request №707 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/fix/off-by-one-1-indexed-loops-batch Merge: 91e8dceb14197d722d77bbb2030a7a0240653d86←9f26b0468d3e771e44a89a18f0aeee8e42457326 Fix off-by-one loops over 1-indexed residue/atom/element ranges ---------------- Merge commit message: Fix off-by-one loops over 1-indexed residue/atom/element ranges Replace `i < container.size()` with `i <= container.size()` (or the matching `i < pose.size()` -> `i <= pose.size()`) across 35 loops where the body uses `i` as a direct 1-indexed element accessor (`pose.residue(i)`, `vec[i]`, etc.) — so the last residue/atom/element was silently being skipped. Also fixes two related copy-paste bugs in pose_sewing that surfaced during the audit: the distance check `pose.residue(upstream_res).xyz(2) .distance(pose.residue(upstream_res).xyz(2))` was self-distance (always zero, condition always satisfied) — should compare upstream vs downstream residue xyz. Affects helix_pair detection in BlockwiseAnalysisMover and OmnibusDisulfideAnalysisLabelerMover. Skipped candidates: loops with pair access `[i+1]` (correct stop at size-1), cutpoint-style "between residues" loops, MEM-chain-skipping loops in protocols/membrane, separator-style "all-but-last + last raw" patterns, suite/connection enumerations (N-1 connections for N segments), and commented-out code.

• Summary
• integration.mpi 「1」
• integration.release_debug 「5」
• integration 「6」
• performance 「1」
• linux.clang.unit 「3」
• linux.gcc.cxx11thread.serialization.unit 「3」
• linux.gcc.unit 「3」
• mac.clang.unit 「3」

Pull Request №692 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/utility-iterator-rule-of-zero Merge: 80efd178b93d19b7cb76d9a0b34788104381afaa←44a614b5bac4fa3cef17fcdfc514da8e1240e8da Apply Rule of Zero across utility/ helpers ---------------- Merge commit message: Suppress cppcheck false positive on UpperEdgeGraph private helpers UpperEdgeGraph::get_vertex_ptr and ::note_edge_deleted are called from the friend class UEEdge (constructors at lines 314/315/325/326 and delete_edge at line 342), but cppcheck does not trace template friend usage and flags them as unusedPrivateFunction.

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

Pull Request №687 RosettaCommons/rosetta/main ← roccomoretti/rosetta/pdb_cif_diagnostic_fixes Merge: 91e8dceb14197d722d77bbb2030a7a0240653d86←d24b7fa41008082e821d5edce593766c3513e596 Update handling of CCD residue types. ---------------- Merge commit message: Merge remote-tracking branch 'origin/main' into pdb_cif_diagnostic_fixes

• Summary
• code_quality.merge_size
• integration.mpi 「1」
• integration.release_debug 「29」
• integration.thread 「1」
• integration 「28」
• performance 「1」

Pull Request №551 RosettaCommons/rosetta/main ← roccomoretti/rosetta/multiletter_chain Merge: 91e8dceb14197d722d77bbb2030a7a0240653d86←2314bf971b9d8a71e0107f7fa75719c8efef0ce3 Support chain designations of multiple letters. ---------------- Merge commit message: Merge remote-tracking branch 'origin/main' into multiletter_chain

• Summary
• code_quality.merge_size
• integration.mpi 「1」
• integration.release_debug 「41」
• integration 「40」
• linux.clang.score 「1」
• linux.gcc.score 「1」
• mac.clang.score 「1」

Pull Request №706 RosettaCommons/rosetta/main ← lyskov-ai/rosetta/refactor/core-empty-dtors-rule-of-zero Merge: b2a0ff32f3ee01822f6f18b9d21ea27357a5f6bc←b9ffb8f38f6f8ae2fd2a072786cb3c81bfd4901f Apply Rule of Zero to empty destructors across core/ ---------------- Merge commit message: Apply Rule of Zero to empty destructors across core/ Move trivially empty or `= default;`-bodied destructors from .cc files to header declarations using `= default`, then remove the now-redundant .cc implementations. Where a destructor was declared `~X() {}` inline in a header, switch it to `~X() = default;` for the same reason. Affected sibling groups: - core/conformation/membrane/* and membrane_geometry/* (8 classes) - core/conformation/parametric/*ValuedParameter (5 classes) - core/io/silent/SilentFileData iterator and const_iterator - core/pack/interaction_graph/RotamerDots family (4 classes) - core/scoring/etable/EtableEvaluator hierarchy (3 classes) - core/scoring/hbonds/graph/HBondInfo (2 classes) - core/scoring/nmr/NMRDummySpinlabelVoxelGrid family (4 classes) - core/scoring/sc/MolecularSurfaceCalculator::Atom - core/energy_methods/SAXSEnergy

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

Pull Request №698 RosettaCommons/rosetta/main ← roccomoretti/rosetta/change_chirality_loading Merge: d10f3af574b60550f256856d5a9742600ce1128b←7deac7bddc1a96697703edf4e0062907772168ad Rework chirality detection in restype determination for PDB loading ---------------- Merge commit message: Missing file

• Summary
• integration.mpi 「1」
• integration.release_debug 「6」
• integration 「6」

Pull Request №687 RosettaCommons/rosetta/main ← roccomoretti/rosetta/pdb_cif_diagnostic_fixes Merge: b8e64ecdc0338b77c231760f7f9bdcd4d500a240←0c77d823e0d5cf0427766fa33cfd34104bc5a260 Update handling of CCD residue types. ---------------- Merge commit message: Merge remote-tracking branch 'origin/change_chirality_loading' into pdb_cif_diagnostic_fixes

• Summary
• windows.build.debug
• windows.build.release

Pull Request №698 RosettaCommons/rosetta/main ← roccomoretti/rosetta/change_chirality_loading Merge: d10f3af574b60550f256856d5a9742600ce1128b←f8f08cc7c79a2b63cfcc5182c19ddfa19d4bc0ea Rework chirality detection in restype determination for PDB loading ---------------- Merge commit message: Fix issues surrounding DNA typing.

• Summary
• build.ninja_debug
• integration.mpi 「1」
• integration.release_debug 「6」
• integration 「6」
• linux.clang.unit
• linux.gcc.cxx11thread.serialization.unit
• linux.gcc.unit
• mac.clang.unit
• windows.build.debug
• windows.build.release

Pull Request №551 RosettaCommons/rosetta/main ← roccomoretti/rosetta/multiletter_chain Merge: 068bd85322153b1ddc5a354f8cf0633a5631e9fa←2d42b3dd49d7432dbdf983a5de00f5aefa938d75 Support chain designations of multiple letters. ---------------- Merge commit message: Fix PyRosetta docking tests.

• Summary
• ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit 「2」
• code_quality.merge_size
• integration.mpi 「2」
• integration.release_debug 「41」
• integration.tensorflow 「1」
• integration 「40」
• linux.clang.score 「1」
• linux.gcc.score 「1」
• mac.clang.score 「1」

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