Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←01b7b1388bbd4d1c8a205bdee79936cfb156f771 Updated Ligand Motifs Code ---------------- Merge commit message: fixing declaration of hash motif library function in hh

• Summary
• linux.clang.build.debug
• linux.gcc.build.debug
• linux.gcc.cxx11thread.serialization.build.debug
• mac.clang.build.debug
• build.ninja_debug

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←adce85f822bdd838f004f4b26b11f222164233aa Updated Ligand Motifs Code ---------------- Merge commit message: specifying source of atom_trios to be LigandDiscoverySearch::atom_trios. I also seem to have accidentally removed hash_motif_library_into_map from the hh file...

• Summary
• linux.clang.build.debug
• linux.gcc.build.debug
• linux.gcc.cxx11thread.serialization.build.debug
• mac.clang.build.debug
• build.header
• build.ninja_debug
• graphics
• linux.clang.build.release
• linux.gcc.build.release
• static
• mac.clang.build.release
• serialization 「2」
• integration.release_debug
• performance
• profile
• linux.clang.score
• linux.clang.unit
• linux.gcc.cxx11thread.serialization.unit
• linux.gcc.unit
• mac.clang.unit
• windows.build.debug

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←b29fa7b474cb6dc09635976fddd51059dfa46d2a Updated Ligand Motifs Code ---------------- Merge commit message: fixing new function by having atom type set get passed in that it needs (better to pass the same one in once, than make a new one each time the function is called, because the function could be called a lot

• Summary
• linux.clang.build.debug
• linux.gcc.build.debug
• linux.gcc.cxx11thread.serialization.build.debug
• mac.clang.build.debug
• build.ninja_debug
• linux.clang.build.release
• linux.gcc.build.release
• static
• beautification
• serialization 「1」
• integration.release_debug
• integration.thread
• performance
• profile
• linux.clang.score
• linux.clang.unit
• linux.gcc.cxx11thread.serialization.unit
• linux.gcc.unit

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←487dfb6bd18a691a0a090e8e650d8f2e7647f239 Updated Ligand Motifs Code ---------------- Merge commit message: Cleaning definition of ligand_atom_trios. Data type is now cleaned in a typedef (atom_trios), and derivation of trios is now moved to private function derive_adjacent_atoms_of_ligandy

• Summary
• linux.clang.build.debug
• linux.gcc.build.debug
• linux.gcc.cxx11thread.serialization.build.debug
• mac.clang.build.debug
• build.header
• build.ninja_debug
• graphics
• linux.clang.build.release
• linux.gcc.build.release
• static
• mac.clang.build.release
• beautification
• serialization 「2」
• integration.release_debug
• linux.clang.score
• linux.clang.unit
• linux.gcc.cxx11thread.serialization.unit
• linux.gcc.unit
• windows.build.debug

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←07ad0db00d02ec9dd6810e8f55a60c6dd42d22f0 Updated Ligand Motifs Code ---------------- Merge commit message: adjusting usage of protein_discovery_locus input option to try to get it to pass correctly into ligand discovery search

• Summary
• linux.clang.build.debug
• linux.gcc.build.debug
• linux.gcc.cxx11thread.serialization.build.debug
• mpi
• mpi.serialization
• mac.clang.build.debug
• build.ninja_debug
• beautification
• integration.release_debug
• integration.thread
• integration.torch
• integration 「2」
• performance 「0」
• linux.clang.score 「0」
• mac.clang.score 「0」
• linux.clang.unit
• linux.gcc.cxx11thread.serialization.unit
• linux.gcc.unit
• mac.clang.unit
• windows.build.debug

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←65c1a58b6cb3ad2533c41a37ad9dfa3a3a0bffdd Updated Ligand Motifs Code ---------------- Merge commit message: adding debug statement to help troubleshoot working_positions_ size

• Summary
• linux.clang.build.debug
• linux.gcc.build.debug
• linux.gcc.cxx11thread.serialization.build.debug
• mpi
• mpi.serialization
• mac.clang.build.debug
• build.ninja_debug
• beautification
• code_quality.merge_size
• integration.mpi
• integration.release_debug
• integration.thread
• integration 「2」
• performance 「0」
• linux.clang.score 「0」
• linux.gcc.score 「0」
• mac.clang.score 「0」
• linux.clang.unit
• linux.gcc.cxx11thread.serialization.unit
• linux.gcc.unit
• mac.clang.unit
• windows.build.debug

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←9687a3877496ebc11f4b71e0e1fcae4f48ee97b8 Updated Ligand Motifs Code ---------------- Merge commit message: tryingto fix syntax for score function creation

• Summary
• beautification
• integration.mpi 「23」
• integration.release_debug 「3」
• integration.tensorflow 「0」
• integration.thread 「0」
• performance 「0」
• profile 「0」
• linux.clang.score 「0」
• linux.gcc.score 「0」

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←bd4619871a985b2df6dfd53b709b4df068bab89a Updated Ligand Motifs Code ---------------- Merge commit message: moving initial seeding of class score functions to constructors. I also forgot to actually put in the call to setup_score_functions() in discover()

• Summary
• linux.clang.cxx11thread.serialization.python37.PyRosetta.unit
• mac.clang.python38.PyRosetta.unit
• linux.clang.build.debug
• linux.gcc.build.debug
• mpi
• mpi.serialization
• build.header
• build.ninja_debug
• linux.clang.build.release
• linux.gcc.build.release
• beautification
• code_quality.merge_size
• serialization 「1」
• integration.mpi
• integration.release_debug
• integration.tensorflow
• integration.thread
• integration.torch
• integration
• performance
• profile
• linux.clang.score
• linux.gcc.score
• mac.clang.score
• scripts.pyrosetta
• scripts.rosetta.parse
• scripts.rosetta.validate
• scripts.rosetta.verify
• linux.clang.unit
• linux.gcc.cxx11thread.serialization.unit
• linux.gcc.unit
• mac.clang.unit

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←c0245ff6b062591652cc92af85f6a5f21e29a4b1 Updated Ligand Motifs Code ---------------- Merge commit message: fixing namespace syntax

• Summary
• mac.clang.python38.PyRosetta.unit
• linux.clang.build.debug
• linux.gcc.build.debug
• linux.gcc.cxx11thread.serialization.build.debug
• mpi
• mpi.serialization
• mac.clang.build.debug
• build.header
• build.ninja_debug
• graphics
• linux.clang.build.release
• linux.gcc.build.release
• static
• mac.clang.build.release
• beautification
• serialization 「2」
• integration.release_debug
• integration.tensorflow
• integration.thread
• integration.torch
• integration
• performance
• profile
• linux.clang.score
• mac.clang.score
• linux.clang.unit
• linux.gcc.cxx11thread.serialization.unit
• linux.gcc.unit
• mac.clang.unit
• windows.build.debug

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←8af9af21be9243024ff5ffff7db503ce256189ea Updated Ligand Motifs Code ---------------- Merge commit message: adding scorefunctionfactory hh (not .fwd.hh, which is already present) so that score function class variables can be initialized without the constructor

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

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←0fd0f0a18cd9610957b3f570e2a1bb594397af78 Updated Ligand Motifs Code ---------------- Merge commit message: Migrating code used to set up score functions used in discover() into new function called setup_score_functions. Converting used score functions into class variables as well (this may be handy as I try to excise code from discover() into other functions)

• Summary
• linux.clang.cxx11thread.serialization.python37.PyRosetta.unit
• mac.clang.python38.PyRosetta.unit
• linux.clang.build.debug
• linux.gcc.build.debug
• linux.gcc.cxx11thread.serialization.build.debug
• mpi
• mpi.serialization
• mac.clang.build.debug
• build.header
• build.ninja_debug
• graphics
• linux.clang.build.release
• linux.gcc.build.release
• static
• mac.clang.build.release
• beautification
• code_quality.merge_size
• serialization 「2」
• integration.mpi
• integration.release_debug
• integration.thread
• integration.torch
• integration
• performance
• profile
• linux.clang.score
• linux.gcc.score
• mac.clang.score
• scripts.pyrosetta
• scripts.rosetta.parse
• scripts.rosetta.validate
• scripts.rosetta.verify
• linux.clang.unit
• linux.gcc.cxx11thread.serialization.unit
• linux.gcc.unit
• mac.clang.unit
• windows.build.debug
• windows.build.release

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←7ae64301c4e4cba6c1464e3dd87beefb56c4f835 Updated Ligand Motifs Code ---------------- Merge commit message: Overhauling tracer verbosity. Removing verbose option and its usage from LigandDiscoverySearch. Using recommended extensions (Warning, Trace, Debug) from natural tracer usage.

• Summary
• beautification
• code_quality.beautify
• code_quality.merge_size
• integration.mpi 「23」
• integration.release_debug 「3」
• integration.tensorflow 「0」
• integration.thread 「0」
• integration.torch
• integration 「2」
• performance 「0」
• profile 「0」
• linux.clang.score 「0」
• linux.gcc.score 「0」
• mac.clang.score 「0」

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←0d095368e728c273a250ea29327451209153ad00 Updated Ligand Motifs Code ---------------- Merge commit message: Fixing how Real is called in hh

• Summary
• beautification
• code_quality.merge_size
• integration.mpi 「23」
• integration.release_debug 「3」
• integration.tensorflow 「0」
• integration.thread 「0」
• integration.torch
• performance 「0」
• profile 「0」
• linux.clang.score 「0」
• linux.gcc.score 「0」

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←25be92f119198a5eeb428b246553c03e5f3fcf02 Updated Ligand Motifs Code ---------------- Merge commit message: addressing how dist_threshold and angl_threshold were used in discover function. Values have not been converted to class variables (dist_threshold_ and angl_threshold_), and those values are used to assign to dist_threshold and angl_threshold in their original locations. The original parameterized constructor now seeds values to the class variables from the relevant flags, and a new parameterized constructor was made to seed the class variables. Setter functions were also made.

• Summary
• linux.clang.build.debug
• linux.gcc.build.debug
• build.ninja_debug
• linux.clang.build.release
• performance
• windows.build.debug

Pull Request №170 RosettaCommons/rosetta/main ← lyskov/rosetta/torch Merge: 200d5f9a7d8cdd7afdd078f156da6b5a7d97543f←b3b354275e2a62ac15db0de79e04089168a082c4 rename pytorch → torch extras and defines ---------------- Merge commit message: rename pytorch → torch extras and defines

• Summary
• integration.tensorflow 「1」

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←e7f69386318de312f57f10c40f706b322c20ef52 Updated Ligand Motifs Code ---------------- Merge commit message: improving handling of kill_bad_init where working_pose_ could call a bad residue and crash Rosetta. The call attempt is now wrapped in an else statement that requires the residue position to be valid

• Summary
• beautification
• code_quality.merge_size
• integration.mpi 「24」
• integration.release_debug 「3」
• integration.tensorflow 「0」
• integration.thread 「0」
• integration.torch
• integration 「1」
• performance 「0」
• profile 「0」
• linux.clang.score 「0」
• linux.gcc.score 「0」
• mac.clang.score 「0」
• windows.build.debug

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