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

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←dbc2c3253d708de4cc9caca102d04833b9439285 Updated Ligand Motifs Code ---------------- Merge commit message: I forgot to fix the function call

• Summary
• beautification
• integration.mpi 「23」
• integration.release_debug 「3」
• integration.tensorflow 「0」
• integration.thread 「0」
• linux.clang.score 「0」
• windows.build.debug

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←6f78ba39a5f1e32ee652dd96d5b096460aef9a6e Updated Ligand Motifs Code ---------------- Merge commit message: adjusting create_protein_representation_matrix_space_fill function to have working_position passed into it, since working_positino_ is now removed from being a class variable

• 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

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←06ce990d437c6ff8a988a68d049ba45109a328c7 Updated Ligand Motifs Code ---------------- Merge commit message: Removing working_position_ class variable is it is now replaced by working_positions_ vector. Added additional support to working_positions_ by allowing to write with a single non-vector value as well as ability to append new values to end of vector (append vector or single value)

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

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←d2af695de06e5df30235cf0301b8f61d69bebec5 Updated Ligand Motifs Code ---------------- Merge commit message: adjusted another for loop and revered loop that used binding_pocket_dimensions vector as that may be a tricky fix

• Summary
• integration.release_debug 「3」
• linux.clang.score 「0」
• windows.build.debug

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←5dd8ff7d317ee1992b00014f35d28a9f29b12ce9 Updated Ligand Motifs Code ---------------- Merge commit message: converting some for loops that iterate over .size() indexing to beign range based. Making a checkpoint here to make sure I didn't break anything, and will convert more

• Summary
• linux.clang.build.debug
• linux.gcc.build.debug
• mac.clang.build.debug
• build.ninja_debug
• graphics
• linux.clang.build.release
• linux.gcc.build.release
• static
• mac.clang.build.release
• windows.build.debug
• windows.build.release

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←c748cec9d3781a8cb2c3d88c8c9f078360f9201e Updated Ligand Motifs Code ---------------- Merge commit message: changing working_positinos iteration loop to be range based instead of iterative by index

• Summary
• beautification
• integration.mpi 「23」
• integration.thread 「0」
• performance 「0」
• profile 「0」
• linux.clang.score 「0」
• linux.gcc.score 「0」
• windows.build.debug

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←aa64dd54254a6b2c0d5731aa4f2a2036760b2bda Updated Ligand Motifs Code ---------------- Merge commit message: fixing syntax for calling SpaceFillMatrix as return type in space_fill_analysis()

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

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: ec708a4c40449ea419c8fcac0d507440400bf75f←832b19f11f6105111ad9b3a1204aceedb71b01b1 Updated Ligand Motifs Code ---------------- Merge commit message: using typedef to create simplified shorthand for space fill matrices and clash matrices. Made sure to change all instances of these matrix declarations to the new typedef types. Opting to not make a new class, as I am not sure how useful these will be beyond the scope of this script (especially space fill, due to specificities with int values)

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

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