Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←ddd55ceca94f37874358fb7f5c19a82b1ff4f9f1 Updated Ligand Motifs Code ---------------- Merge commit message: I forgot to include working_position in the function to apply constraints

• Summary
• linux.clang.build.debug
• linux.gcc.build.debug
• linux.gcc.cxx11thread.serialization.build.debug
• mpi
• mac.clang.build.debug
• build.ninja_debug
• graphics
• linux.clang.build.release
• linux.gcc.build.release
• static
• mac.clang.build.release
• beautification
• serialization 「1」
• integration.release_debug
• integration.thread
• performance
• profile
• linux.clang.score
• linux.gcc.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←55d1d46f4d932feb99da1b76e858194380a225ce Updated Ligand Motifs Code ---------------- Merge commit message: compartmentalizing creation of working pose constraint set into separate function to make code cleaner # Please enter the commit message for your changes. Lines starting

• Summary
• mac.clang.python38.PyRosetta.unit
• linux.clang.build.debug
• linux.gcc.build.debug
• linux.gcc.cxx11thread.serialization.build.debug
• mac.clang.build.debug
• build.ninja_debug
• graphics
• linux.clang.build.release
• linux.gcc.build.release
• static
• mac.clang.build.release
• integration
• performance
• profile
• mac.clang.score
• linux.clang.unit
• mac.clang.unit

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←d9c4000ca8a8e80f98868a3dd7ba36d8c5476329 Updated Ligand Motifs Code ---------------- Merge commit message: fixing syntax of score_minipose call for minipose poseOP object (and missing semicolon in hh)

• Summary
• beautification
• 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←8eb232ed003d9035754b73501611b1d7399509da Updated Ligand Motifs Code ---------------- Merge commit message: implementing score_minipose function to excise scoring of the minipose into its own function. Cases of resetting the minipose on the current placement have also been simplified so that it is always reset after calling this function. I also found a small bug where working_pose_ was not properly reset in a condition where the whole score on working_pose was bad

• Summary
• mac.clang.python38.PyRosetta.unit
• linux.clang.build.debug
• linux.gcc.build.debug
• linux.gcc.cxx11thread.serialization.build.debug
• mac.clang.build.debug
• build.header
• build.ninja_debug
• linux.clang.build.release
• mac.clang.build.release
• serialization 「2」
• integration.release_debug
• integration
• performance
• profile
• linux.clang.score
• mac.clang.score
• linux.clang.unit
• linux.gcc.cxx11thread.serialization.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←956f6fba6692f7bca16250a8e1589a980bcbed81 Updated Ligand Motifs Code ---------------- Merge commit message: removing seed function from hh

• Summary
• beautification
• integration.release_debug 「3」
• integration.thread 「0」
• performance 「0」
• linux.clang.score 「0」
• mac.clang.score 「0」

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←b41625ef6174afb664efcacb32f0f65473af65d7 Updated Ligand Motifs Code ---------------- Merge commit message: implementing change of cutoff class variables into their proper locations. Also fixing syntax error in seed cutoffs function

• Summary
• performance 「0」

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←836a0c40a4d53b950d40bb7b0fd101946ada4732 Updated Ligand Motifs Code ---------------- Merge commit message: removing angl_threshold and distance_threshold variables, which were pretty redundant in discover() function and using class variables would be more efficient

• Summary
• beautification
• code_quality.merge_size
• integration.mpi 「23」
• integration.release_debug 「3」
• integration.thread 「0」
• integration.torch
• 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←67e7791def29880a54374893ce7f40e307e95c9c Updated Ligand Motifs Code ---------------- Merge commit message: reverting changes back to before trying to move scoring into its own function. There are over 10 variables that go into that block that probably should not be made as class varaibles, so it does not make sense to turn that entire chunk into one function. I can try to break it up into a few functions, and that may be more manageable

• Summary
• beautification
• 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←b4cd9605b23ed80a4eb8720a3249bb08d7f0ef59 Updated Ligand Motifs Code ---------------- Merge commit message: handling delta_score and clashing_counter, which are variables that are used in and out of the scoring function, but probably shouldn't be class variables

• Summary
• linux.clang.cxx11thread.serialization.python37.PyRosetta.unit
• linux.clang.build.debug
• linux.gcc.build.debug
• linux.gcc.cxx11thread.serialization.build.debug
• mpi
• mpi.serialization
• mac.clang.build.debug
• build.ninja_debug
• linux.clang.build.release
• linux.gcc.build.release
• static
• mac.clang.build.release
• beautification
• code_quality.merge_size
• serialization 「1」
• integration.mpi
• integration.release_debug
• integration.thread
• performance
• profile
• linux.clang.score
• linux.gcc.score
• scripts.pyrosetta
• scripts.rosetta.parse
• 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←41fcf791fb0d5706b8f7387683fc9b14573160ec Updated Ligand Motifs Code ---------------- Merge commit message: fixed typo

• Summary
• linux.clang.build.debug
• linux.gcc.build.debug
• linux.gcc.cxx11thread.serialization.build.debug
• mpi
• mpi.serialization
• build.ninja_debug
• linux.clang.build.release
• linux.gcc.build.release
• static
• beautification
• serialization 「1」
• integration.release_debug
• integration.thread
• integration.torch
• 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←886ef0643ede1ab44705f03e05545da27f550842 Updated Ligand Motifs Code ---------------- Merge commit message: I forgot to define the function in the hh file. I also updated the function so that it could successfully handle the pdb name and pdb internal comment data variables (which are used within this function and need to be passed to later functions)

• Summary
• linux.clang.build.debug
• linux.gcc.build.debug
• build.ninja_debug
• linux.clang.build.release
• linux.gcc.build.release
• static

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←54e452375f36602198245667b225ab8aa65ecb45 Updated Ligand Motifs Code ---------------- Merge commit message: large overhaul, moving the placement scoring into its own function as score_placed_ligands(). The function reads in the minipose and a copt of the original pose to help revert the working_pose pointer (to avoid movers affecting future placements). Turned score cutoff variables into class variables so that they don't have to be passed into the scoring function.

• 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
• beautification
• serialization 「1」
• integration.release_debug
• 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←5b9801ae8dbc644be8a91334d2bdc2570e7203ec Updated Ligand Motifs Code ---------------- Merge commit message: I forgot to include ligresOP in the make_minipose function

• Summary
• beautification
• 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←91cefde8067a59d64934500c41fe8cd3f6d09a1d Updated Ligand Motifs Code ---------------- Merge commit message: condensing minipose generation code into a function to help shorten/compartmentalize discover()

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

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←937b9e49a2963a2844b51cfda7c2512aaae07ed0 Updated Ligand Motifs Code ---------------- Merge commit message: adjusting named of tracers in code to put a period between LigandDiscoverySearch and the function that the tracer appears in (better for parsing)

• Summary
• integration.release_debug 「3」
• performance 「0」
• linux.clang.score 「0」

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←23f69d87795a7ed91e90ea5c359ffa9882850be4 Updated Ligand Motifs Code ---------------- Merge commit message: getting rid of the print of discovery_positions_int in app because the debug compile does not like the ambiguity, and this print isn't critical, so it's best to just leave it out

• Summary
• beautification
• 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」

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