Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←1292c75d3d666ff18a21a1f5c0a356a92de36785 Updated Ligand Motifs Code ---------------- Merge commit message: Ran beautify on these scripts

• Summary
• code_quality.merge_size
• integration.mpi 「1」
• integration.release_debug 「4」
• integration 「3」

Crosslinker Mover lanthionine (#24) This is the code to enable lanthipeptide modeling in Rosetta. Crosslinker updated to include lanthionine and methyllanthionine connections. -This includes D/L ALA steriochem for lanthionine and D/L and 3 R/S steriochem for methylanthionine (B(L/D)(R/S)) Dehydrated amino acid patches for DBU and DHU were updated/added The AmbiguouosNMRDistanceConstraints were updated to work for NCAA (hardcoding was generalized) Additionally, I noticed that the thioether lariat in simple cyc pep predict only samples cis omega bonds for the N terminal residue. I changed this to trans, which should be energetically preferred.

• Summary
• integration.mpi 「2」

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←77ec594e31ba88e6257ebee1465fa3d34189be84 Updated Ligand Motifs Code ---------------- Merge commit message: Adding integration test for remove_duplicate_motifs app

• Summary
• beautification
• code_quality.merge_size
• integration.mpi 「1」
• integration.release_debug 「4」
• integration 「3」

Adding integration test for remove_duplicate_motifs app

• Summary
• beautification
• code_quality.merge_size
• integration.mpi 「2」
• integration.release_debug 「13」

changing score function used in ddg calculation to whole

• Summary
• beautification
• integration.mpi 「2」
• integration.release_debug 「12」
• linux.gcc.cxx11thread.serialization.unit 「3」
• linux.gcc.unit 「3」

additional fixes for function calls that need to have excess parameters reduced

• Summary
• beautification
• integration.mpi 「1」
• integration.release_debug 「5」

adjusting space fill analysis and print space fill matrix functions to remove usage of unused parameters

• Summary
• linux.gcc.build.debug
• linux.gcc.cxx11thread.serialization.build.debug
• build.ninja_debug
• linux.gcc.build.release
• static

adjusting input of protein discovery loci (anchor residues) to be a vector of indices instead of a single value

• Summary
• linux.clang.build.debug
• linux.gcc.build.debug
• linux.gcc.cxx11thread.serialization.build.debug
• mpi
• mpi.serialization
• build.ninja_debug
• beautification
• integration.mpi
• integration.release_debug
• linux.clang.unit
• linux.gcc.cxx11thread.serialization.unit
• linux.gcc.unit

Adding motif_ligand_discovery/remove_duplicate_motifs

• Summary
• linux.clang.build.debug
• linux.gcc.build.debug
• linux.gcc.cxx11thread.serialization.build.debug
• build.ninja_debug
• linux.clang.build.release
• linux.gcc.build.release
• static
• performance
• profile

Pull Request №24 RosettaCommons/rosetta/main ← tydingcw/rosetta/crosslinkmover_lanthionine Merge: a34b73c40fe9c61558d566d6a63f803cfb15a4fc←350705af73de0b6632a804a121748dc22ca1ee27 Crosslinker Mover lanthionine ---------------- Merge commit message: merging windows build fix

• Summary
• integration.mpi 「3」
• integration.release_debug 「15」
• integration.tensorflow 「1」
• integration.thread 「1」
• integration 「13」

Fix pre-compile script calls on Windows build (#58) The windows build test on the test server doesn't seem to be updating options appropriately. It looks like the issue is that the *.sh files aren't being properly called -- adding "bash" to the front of them allows them to run properly.

• Summary

Pull Request №58 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/roccomoretti/windows_cmake_test Merge: baad48240e60f121d84dc6443bd8745c8d8becdc←c60f6252800dba1efd5feb0d7dbebf0bdb8f3a3a Additional annotations to debug the windows build test. ---------------- Merge commit message: Cleanup

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

Pull Request №58 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/roccomoretti/windows_cmake_test Merge: baad48240e60f121d84dc6443bd8745c8d8becdc←0d6a250bacd0da9f48ae8fe344a42395dcea4f46 Additional annotations to debug the windows build test. ---------------- Merge commit message: Re-enable shell

• Summary

Pull Request №58 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/roccomoretti/windows_cmake_test Merge: baad48240e60f121d84dc6443bd8745c8d8becdc←2dc125e948f6fac2147a549e95e58dc2da3a837f Additional annotations to debug the windows build test. ---------------- Merge commit message: Adjust to better run on Linux.

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

Pull Request №58 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/roccomoretti/windows_cmake_test Merge: baad48240e60f121d84dc6443bd8745c8d8becdc←8b831716474b8df4fcea799392b22ce064b4dc8f Additional annotations to debug the windows build test. ---------------- Merge commit message: Be explicit about the parser used.

• Summary

Pull Request №58 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/roccomoretti/windows_cmake_test Merge: baad48240e60f121d84dc6443bd8745c8d8becdc←7a4eff08b1e8299193cc4bc1cf8ac031e336e6e4 Additional annotations to debug the windows build test. ---------------- Merge commit message: Fix windows path finding issues.

• Summary

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