Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: 74f819c4dd58142810833fb8e63211f2974ee342←5cc64a5558f31e8bd3c605c36aa5752e575c9771 Updated Ligand Motifs Code ---------------- Merge commit message: adding substantial progress on writing the functions for the space fill and clash check analyses, along with setting up functionality for the output of matrices. Also adjusted the initialization of member variables to be performed in an initialization function that is called at the start of constructors (besides the copy constructor). Also preparing a new options space for protein_grid, and preparing to move the options for defining how to print the matrix to pdb in this new space

• Summary
• linux.clang.build.debug
• linux.gcc.build.debug
• linux.gcc.cxx11thread.serialization.build.debug
• mpi
• mac.clang.build.debug
• build.header
• build.ninja_debug
• linux.clang.build.release
• linux.gcc.build.release
• static
• mac.clang.build.release
• beautification
• serialization 「2」
• integration.release_debug
• integration.thread
• performance
• profile
• 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: 74f819c4dd58142810833fb8e63211f2974ee342←a01ad6942b744cd92a9539b162c7194bfa9e1b14 Updated Ligand Motifs Code ---------------- Merge commit message: wrote initial version of the project lj function. Also added additional variables functions that better support the sub area, and set up functions for clash check and matrix print

• Summary
• mac.clang.python38.PyRosetta.unit
• ubuntu.clang.cxx11thread.serialization.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.ninja_debug
• graphics
• 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.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
• windows.build.debug
• windows.build.release

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: 74f819c4dd58142810833fb8e63211f2974ee342←fb0e2b95ee5a308dca2cf983eb63ecba80b4fc86 Updated Ligand Motifs Code ---------------- Merge commit message: adding functions that turn off the lj radius usage

• Summary
• beautification
• code_quality.merge_size
• integration.mpi 「23」
• integration.release_debug 「5」
• integration 「5」

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: 74f819c4dd58142810833fb8e63211f2974ee342←865c55715b6e3db6bcecf81089c2dda0fb84e95a Updated Ligand Motifs Code ---------------- Merge commit message: modifying warning print of vectors recognized as too small

• Summary
• beautification
• code_quality.merge_size
• integration.mpi 「23」
• integration.release_debug 「5」
• integration 「6」

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: 74f819c4dd58142810833fb8e63211f2974ee342←7dadd412d814467e5ac4e4891dde6613223fc900 Updated Ligand Motifs Code ---------------- Merge commit message: adding additional logic for turning the sub areas on and off, as well as determining if a coordinate in the proteinmatrix is within the sub area

• Summary
• linux.clang.build.debug
• windows.build.debug

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: 74f819c4dd58142810833fb8e63211f2974ee342←34d918bae93043b95ba240e0e79ab7542e92c3f0 Updated Ligand Motifs Code ---------------- Merge commit message: debugging and removing old code

• Summary
• mac.clang.build.debug
• integration 「6」
• mac.clang.unit
• windows.build.debug

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: 74f819c4dd58142810833fb8e63211f2974ee342←65245891bb435e2182ac2614ef815b5c484f14df Updated Ligand Motifs Code ---------------- Merge commit message: fixing issue where wrong (old) variables were used in defining xyz_bound_

• Summary
• code_quality.merge_size
• integration.mpi 「24」

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: 74f819c4dd58142810833fb8e63211f2974ee342←9c879e239dfa84153dcde0a7611e7778aa27a1ed Updated Ligand Motifs Code ---------------- Merge commit message: adding the protein grid to the protocols src settings

• Summary

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: 74f819c4dd58142810833fb8e63211f2974ee342←80eff2f37a026af30207661351c018793e6bea58 Updated Ligand Motifs Code ---------------- Merge commit message: additional path fixing

• Summary
• windows.build.debug

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: 74f819c4dd58142810833fb8e63211f2974ee342←10d69fbf8dc044fff2a5633ef9ebfc116333176a Updated Ligand Motifs Code ---------------- Merge commit message: moving ProteinGrid to protocols, so the library levels are better, and maybe this shouldn't be in core code anyway

• Summary
• linux.clang.build.debug
• build.levels
• linux.clang.build.release
• linux.clang.unit

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: 74f819c4dd58142810833fb8e63211f2974ee342←75b83212956c775d2446ee107cde86542e612ad4 Updated Ligand Motifs Code ---------------- Merge commit message: creating setter functions for the sub regions as well as cleaning the code for initializing the vectors

• Summary
• build.levels
• integration.release_debug 「6」

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: 74f819c4dd58142810833fb8e63211f2974ee342←ed45089911fe07b26cce99db5ab102009adab267 Updated Ligand Motifs Code ---------------- Merge commit message: had accidentally mixed up the cc and hh files, flipping those now

• Summary
• mac.clang.python38.PyRosetta.unit
• ubuntu.clang.cxx11thread.serialization.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.levels
• build.ninja_debug
• linux.clang.build.release
• linux.gcc.build.release
• mac.clang.build.release
• beautification
• code_quality.cppcheck 「1」
• code_quality.merge_size
• serialization 「1」
• integration.mpi
• integration.release_debug
• integration.tensorflow
• integration.thread
• 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: 74f819c4dd58142810833fb8e63211f2974ee342←f323c18e5bf717097315da280b00efbca2ce4fbe Updated Ligand Motifs Code ---------------- Merge commit message: dividing proteingrid into cc and hh file so that the files can be compiled properly

• Summary
• mac.clang.python38.PyRosetta.unit
• ubuntu.clang.cxx11thread.serialization.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.levels
• build.ninja_debug
• linux.clang.build.release
• linux.gcc.build.release
• mac.clang.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
• windows.build.debug
• windows.build.release

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: 74f819c4dd58142810833fb8e63211f2974ee342←9c7d4a69681917bc18c999e6edb3ff88bde872f7 Updated Ligand Motifs Code ---------------- Merge commit message: adding consructors, = overload, and clone function to class to start to give it bones. Also removing the template line since I think we want rigidity here

• Summary
• build.header
• build.levels
• integration.release_debug 「7」

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: 74f819c4dd58142810833fb8e63211f2974ee342←dc20285c6b6e5275f9a389cf1d0421126f3d35ec Updated Ligand Motifs Code ---------------- Merge commit message: commiting initial incomplete build of ProteinGrid class for initial compile to make sure this first bit of code is ok

• Summary
• build.header
• build.levels
• integration.release_debug 「7」
• integration 「6」
• windows.build.release

Pull Request №375 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/roccomoretti-load_ligand_patch Merge: 695b0f21aed8ace84a900449ce857ab632f8e4d1←9a0fe5812f1f459942c02083096face1b7f5ad83 Fix import of load_ligand.py ---------------- Merge commit message: Update load_ligand.py Fix issues with `import pyrosetta.toolbox.load_ligand` -- This won't fix things for people who use the functions in question, but it will allow for use of the other functions in this module.

• Summary

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