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branch: master 「№61912」
Commited by: Vikram K. Mulligan
GitHub commit link: 「28c0a2c167ac7098」 「№6110」
Difference from previous tested commit:  code diff
Commit date: 2022-07-26 17:08:48
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta.notebook gcc-9.gcc.python37.PyRosetta.unit linux.clang.cxx11thread.serialization.python37.PyRosetta.unit linux.clang.python310.PyRosetta.unit linux.gcc.python36.PyRosetta.unit m1.clang.python310.PyRosetta.unit m1.clang.python38.PyRosetta.unit m1.clang.python39.PyRosetta.unit mac.clang.python310.PyRosetta.unit mac.clang.python38.PyRosetta.unit mac.clang.python39.PyRosetta.unit ubuntu-20.04.clang.python39.PyRosetta.unit ubuntu-22.04.clang.python39.PyRosetta.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.python39.build.debug gcc-9.gcc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization linux.icc.build.debug mac.clang.bcl.build.debug OpenCL ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics static beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression linux.gcc.mpi.serialization.integration.mpi linux.gcc.mpi.serialization.python310.integration.mpi linux.gcc.mpi.serialization.python36.integration.mpi linux.gcc.mpi.serialization.python38.integration.mpi linux.gcc.mpi.serialization.python39.integration.mpi integration.release_debug integration.tensorflow integration.thread integration performance profile release.PyRosetta.Debug m1.clang.python310.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel mac.clang.python310.release.PyRosetta.MinSizeRel m1.clang.python310.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release mac.clang.python310.release.PyRosetta.Release mac.clang.python38.release.PyRosetta.Release release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release mac.clang.unit.release gcc-10.gcc.unit gcc-11.gcc.python39.unit gcc-9.gcc.unit m1.clang.python39.unit ubuntu-20.04.clang.python39.unit ubuntu-20.04.gcc.python39.unit ubuntu-22.04.clang.python39.unit ubuntu-22.04.gcc.python39.unit util.apps windows.build.debug windows.build.release

Merge pull request #6110 from RosettaCommons/vmullig/b2ec4c93907 Fix a bug with thioether lariat structure prediction. This fixes a bug in simple_cycpep_predict with thioether lariats with tails and a native structure. (There was a spot in the code where I was assuming that the last residue was the cysteine residue.)

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Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
match_xml
Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
match_xml
Test: linux.clang.profile

Failed sub-tests (click for more details):
jd2test


branch: master 「№61911」
Commited by: John Wang
GitHub commit link: 「fc0fea1e324ec999」 「№6082」
Difference from previous tested commit:  code diff
Commit date: 2022-07-21 20:06:57
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta.notebook gcc-9.gcc.python37.PyRosetta.unit linux.clang.cxx11thread.serialization.python37.PyRosetta.unit linux.clang.python310.PyRosetta.unit linux.gcc.python36.PyRosetta.unit m1.clang.python310.PyRosetta.unit m1.clang.python38.PyRosetta.unit m1.clang.python39.PyRosetta.unit mac.clang.python310.PyRosetta.unit mac.clang.python38.PyRosetta.unit mac.clang.python39.PyRosetta.unit ubuntu-20.04.clang.python39.PyRosetta.unit ubuntu-22.04.clang.python39.PyRosetta.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.python39.build.debug gcc-9.gcc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization linux.icc.build.debug mac.clang.bcl.build.debug OpenCL ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics static mac.clang.static.build.release beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.addsan integration.mpi integration.release_debug integration.tensorflow integration.thread integration.tutorials integration.ubsan integration.valgrind integration maintenance.documentation performance profile linux.clang.python310.release.PyRosetta.Debug linux.clang.python36.release.PyRosetta.Debug linux.clang.python37.release.PyRosetta.Debug linux.clang.python38.release.PyRosetta.Debug linux.clang.python39.release.PyRosetta.Debug mac.clang.python310.release.PyRosetta.Debug mac.clang.python36.release.PyRosetta.Debug mac.clang.python38.release.PyRosetta.Debug mac.clang.python39.release.PyRosetta.Debug linux.clang.python310.release.PyRosetta.MinSizeRel linux.clang.python36.release.PyRosetta.MinSizeRel linux.clang.python37.release.PyRosetta.MinSizeRel linux.clang.python38.release.PyRosetta.MinSizeRel linux.clang.python39.release.PyRosetta.MinSizeRel m1.clang.python310.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel mac.clang.python310.release.PyRosetta.MinSizeRel mac.clang.python38.release.PyRosetta.MinSizeRel mac.clang.python39.release.PyRosetta.MinSizeRel ubuntu.clang.python310.release.PyRosetta.MinSizeRel ubuntu.clang.python36.release.PyRosetta.MinSizeRel ubuntu.clang.python37.release.PyRosetta.MinSizeRel ubuntu.clang.python38.release.PyRosetta.MinSizeRel ubuntu.clang.python39.release.PyRosetta.MinSizeRel linux.clang.python310.release.PyRosetta.Release linux.clang.python36.release.PyRosetta.Release linux.clang.python37.release.PyRosetta.Release linux.clang.python38.release.PyRosetta.Release linux.clang.python39.release.PyRosetta.Release m1.clang.python310.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release mac.clang.python310.release.PyRosetta.Release mac.clang.python36.release.PyRosetta.Release mac.clang.python38.release.PyRosetta.Release mac.clang.python39.release.PyRosetta.Release ubuntu.clang.python310.release.PyRosetta.Release ubuntu.clang.python36.release.PyRosetta.Release ubuntu.clang.python37.release.PyRosetta.Release ubuntu.clang.python38.release.PyRosetta.Release ubuntu.clang.python39.release.PyRosetta.Release release.PyRosetta.conda.Release release.source scientific.FlexPepDock.debug scientific.FlexPepDock scientific.RosettaCM.debug scientific.RosettaCM scientific.abinitio_RosettaNMR_pcs.debug scientific.abinitio_RosettaNMR_pcs scientific.abinitio_RosettaNMR_rdc.debug scientific.abinitio_RosettaNMR_rdc scientific.antibody_grafting.debug scientific.antibody_grafting scientific.antibody_h3_modeling.debug scientific.antibody_h3_modeling scientific.antibody_snugdock.debug scientific.antibody_snugdock scientific.cofactor_binding_sites.debug scientific.cofactor_binding_sites scientific.ddg_ala_scan.debug scientific.ddg_ala_scan scientific.design_fast.debug scientific.design_fast scientific.docking.debug scientific.docking_ensemble.debug scientific.docking_ensemble scientific.docking scientific.enzyme_design.debug scientific.enzyme_design scientific.fragments_picking.debug scientific.fragments_picking scientific.glycan_dock.debug scientific.glycan_dock scientific.ligand_docking.debug scientific.ligand_docking scientific.ligand_scoring_ranking.debug scientific.ligand_scoring_ranking scientific.loop_modeling_ccd_12res.debug scientific.loop_modeling_ccd_12res scientific.loop_modeling_kic_12res.debug scientific.loop_modeling_kic_12res scientific.loop_modeling_kic_fragments_12res.debug scientific.loop_modeling_kic_fragments_12res scientific.loop_modeling_ngk_12res.debug scientific.loop_modeling_ngk_12res scientific.make_fragments.debug scientific.make_fragments scientific.mhc_epitope_energy.debug scientific.mhc_epitope_energy scientific.mp_dock.debug scientific.mp_dock scientific.mp_domain_assembly.debug scientific.mp_domain_assembly scientific.mp_f19_ddG_of_mutation.debug scientific.mp_f19_ddG_of_mutation scientific.mp_f19_decoy_discrimination.debug scientific.mp_f19_decoy_discrimination scientific.mp_f19_sequence_recovery.debug scientific.mp_f19_sequence_recovery scientific.mp_f19_tilt_angle.debug scientific.mp_f19_tilt_angle scientific.mp_lipid_acc.debug scientific.mp_lipid_acc scientific.mp_relax.debug scientific.mp_relax scientific.mp_symdock.debug scientific.mp_symdock scientific.peptide_pnear_vs_ic50.debug scientific.peptide_pnear_vs_ic50 scientific.protein_data_bank_diagnostic.cif scientific.protein_data_bank_diagnostic.full scientific.relax_cartesian.debug scientific.relax_cartesian scientific.relax_fast.debug scientific.relax_fast_5iter.debug scientific.relax_fast_5iter scientific.relax_fast scientific.rna_denovo_favorites.debug scientific.rna_denovo_favorites scientific.sb_franklin2019_mpddg_cartesian.debug scientific.sb_franklin2019_mpddg_cartesian scientific.sb_ref2015_docking.debug scientific.sb_ref2015_docking scientific.sb_ref2015_fast_design.debug scientific.sb_ref2015_fast_design scientific.sb_ref2015_loop_modeling_ccd_12res.debug scientific.sb_ref2015_loop_modeling_ccd_12res scientific.sb_ref2015_loop_modeling_kic_12res.debug scientific.sb_ref2015_loop_modeling_kic_12res scientific.sb_ref2015_loop_modeling_kic_fragments_12res.debug scientific.sb_ref2015_loop_modeling_kic_fragments_12res scientific.sb_ref2015_loop_modeling_ngk_12res.debug scientific.sb_ref2015_loop_modeling_ngk_12res scientific.sb_ref2015_relax_cartesian.debug scientific.sb_ref2015_relax_cartesian scientific.sb_ref2015_relax_fast.debug scientific.sb_ref2015_relax_fast_5iter.debug scientific.sb_ref2015_relax_fast_5iter scientific.sb_ref2015_relax_fast scientific.sb_score12_fast_design.debug scientific.sb_talaris13_docking.debug scientific.sb_talaris13_docking scientific.sb_talaris13_fast_design.debug scientific.sb_talaris13_fast_design scientific.sb_talaris13_loop_modeling_ccd_12res.debug scientific.sb_talaris13_loop_modeling_ccd_12res scientific.sb_talaris13_loop_modeling_kic_12res.debug scientific.sb_talaris13_loop_modeling_kic_12res scientific.sb_talaris13_loop_modeling_kic_fragments_12res.debug scientific.sb_talaris13_loop_modeling_kic_fragments_12res scientific.sb_talaris13_loop_modeling_ngk_12res.debug scientific.sb_talaris13_loop_modeling_ngk_12res scientific.sb_talaris13_relax_cartesian.debug scientific.sb_talaris13_relax_cartesian scientific.sb_talaris13_relax_fast.debug scientific.sb_talaris13_relax_fast_5iter.debug scientific.sb_talaris13_relax_fast_5iter scientific.sb_talaris13_relax_fast scientific.sb_talaris14_docking.debug scientific.sb_talaris14_docking scientific.sb_talaris14_fast_design.debug scientific.sb_talaris14_fast_design scientific.sb_talaris14_loop_modeling_kic_12res.debug scientific.sb_talaris14_loop_modeling_kic_12res scientific.sb_talaris14_loop_modeling_kic_fragments_12res.debug scientific.sb_talaris14_loop_modeling_kic_fragments_12res scientific.sb_talaris14_loop_modeling_ngk_12res.debug scientific.sb_talaris14_loop_modeling_ngk_12res scientific.sewing.debug scientific.sewing scientific.simple_cycpep_predict.debug scientific.simple_cycpep_predict scientific.stepwise_rna_favorites.debug scientific.stepwise_rna_favorites linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release mac.clang.unit.release unit.ubsan unit.valgrind gcc-10.gcc.unit gcc-11.gcc.python39.unit gcc-9.gcc.unit m1.clang.python39.unit ubuntu-20.04.clang.python39.unit ubuntu-20.04.gcc.python39.unit ubuntu-22.04.clang.python39.unit ubuntu-22.04.gcc.python39.unit util.apps windows.build.debug windows.build.release

Merge pull request #6082 from RosettaCommons/revert-6081-revert-5520-jyjwang/degreaser-fresh fixed things so that the tests that were broken passed. main culprits: unused variables / functions. annoying fix: indexing with Size instead of SSize. Thanks Sergey for checking in on the original PR ! Revert "Revert "Degreaser v 1.0""

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Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
Protein-Protein-Docking
Test: ubuntu.gcc.integration.ubsan

Failed sub-tests (click for more details):
simple_cycpep_predict_square_pyramidal_metal
Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
match_xml output_schema test_degreaser
Test: linux.clang.profile

Failed sub-tests (click for more details):
AnchoredDesign monte_carlo_hbnet
Test: linux.clang.python36.scientific.make_fragments.debug

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Test: linux.clang.python36.scientific.make_fragments

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Test: linux.clang.python36.scientific.mp_lipid_acc

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Test: linux.clang.python36.scientific.sb_talaris13_relax_fast

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Test: linux.clang.python36.scientific.sb_talaris14_fast_design

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branch: master 「№61910」
Commited by: Sergey Lyskov
GitHub commit link: 「6d8bd5373da1dfd4」
Difference from previous tested commit:  code diff
Commit date: 2022-07-21 16:51:14
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta.notebook gcc-9.gcc.python37.PyRosetta.unit linux.clang.cxx11thread.serialization.python37.PyRosetta.unit linux.clang.python310.PyRosetta.unit linux.gcc.python36.PyRosetta.unit m1.clang.python310.PyRosetta.unit m1.clang.python38.PyRosetta.unit m1.clang.python39.PyRosetta.unit mac.clang.python310.PyRosetta.unit mac.clang.python38.PyRosetta.unit mac.clang.python39.PyRosetta.unit ubuntu-20.04.clang.python39.PyRosetta.unit ubuntu-22.04.clang.python39.PyRosetta.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.python39.build.debug gcc-9.gcc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization linux.icc.build.debug mac.clang.bcl.build.debug OpenCL ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics static beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.mpi integration.release_debug integration.tensorflow integration.thread integration performance profile release.PyRosetta.Debug mac.clang.python38.release.PyRosetta.MinSizeRel mac.clang.python39.release.PyRosetta.MinSizeRel release.PyRosetta.Release release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release mac.clang.unit.release gcc-10.gcc.unit gcc-11.gcc.python39.unit gcc-9.gcc.unit m1.clang.python39.unit ubuntu-20.04.clang.python39.unit ubuntu-20.04.gcc.python39.unit ubuntu-22.04.clang.python39.unit ubuntu-22.04.gcc.python39.unit util.apps windows.build.debug windows.build.release

increasing _merge_size_failure_threshold_bytes_ to 128KB

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Test: linux.clang.tensorflow.integration.tensorflow

Failed sub-tests (click for more details):
tensorflow_manager
Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
match_xml
Test: linux.clang.profile

Failed sub-tests (click for more details):
AnchoredDesign monte_carlo_hbnet relax_native


branch: master 「№61909」
Commited by: Sergey Lyskov
GitHub commit link: 「6521f2d82b6d1576」 「№6083」
Difference from previous tested commit:  code diff
Commit date: 2022-07-20 21:52:45
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta.notebook gcc-9.gcc.python37.PyRosetta.unit linux.clang.cxx11thread.serialization.python37.PyRosetta.unit linux.clang.python310.PyRosetta.unit linux.gcc.python36.PyRosetta.unit m1.clang.python310.PyRosetta.unit m1.clang.python38.PyRosetta.unit m1.clang.python39.PyRosetta.unit mac.clang.python310.PyRosetta.unit mac.clang.python38.PyRosetta.unit mac.clang.python39.PyRosetta.unit ubuntu-20.04.clang.python39.PyRosetta.unit ubuntu-22.04.clang.python39.PyRosetta.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.python39.build.debug gcc-9.gcc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization linux.icc.build.debug mac.clang.bcl.build.debug OpenCL ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics static mac.clang.static.build.release beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.addsan integration.mpi integration.release_debug integration.tensorflow integration.thread integration.tutorials integration maintenance.documentation performance profile linux.clang.python36.release.PyRosetta.Debug linux.clang.python38.release.PyRosetta.Debug mac.clang.python310.release.PyRosetta.Debug mac.clang.python38.release.PyRosetta.Debug mac.clang.python39.release.PyRosetta.Debug linux.clang.python310.release.PyRosetta.MinSizeRel linux.clang.python36.release.PyRosetta.MinSizeRel linux.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python310.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel mac.clang.python310.release.PyRosetta.MinSizeRel mac.clang.python38.release.PyRosetta.MinSizeRel mac.clang.python39.release.PyRosetta.MinSizeRel ubuntu.clang.python310.release.PyRosetta.MinSizeRel ubuntu.clang.python38.release.PyRosetta.MinSizeRel linux.clang.python36.release.PyRosetta.Release linux.clang.python37.release.PyRosetta.Release linux.clang.python38.release.PyRosetta.Release linux.clang.python39.release.PyRosetta.Release m1.clang.python310.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release mac.clang.python310.release.PyRosetta.Release mac.clang.python38.release.PyRosetta.Release ubuntu.clang.python310.release.PyRosetta.Release ubuntu.clang.python37.release.PyRosetta.Release ubuntu.clang.python39.release.PyRosetta.Release release.source scientific.FlexPepDock.debug scientific.abinitio_RosettaNMR_rdc scientific.docking.debug scientific.loop_modeling_kic_12res scientific.mp_domain_assembly scientific.mp_symdock.debug scientific.peptide_pnear_vs_ic50 linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release mac.clang.unit.release unit.ubsan gcc-10.gcc.unit gcc-11.gcc.python39.unit gcc-9.gcc.unit m1.clang.python39.unit ubuntu-20.04.clang.python39.unit ubuntu-20.04.gcc.python39.unit ubuntu-22.04.clang.python39.unit ubuntu-22.04.gcc.python39.unit util.apps windows.build.debug windows.build.release

Merge pull request #6083 from RosettaCommons/sergey/binder fixing Rosetta and PyRosetta builds on Ubuntu-22.04

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Test: linux.clang.tensorflow.integration.tensorflow

Failed sub-tests (click for more details):
tensorflow_manager
Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
Protein-Protein-Docking
Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
match_xml
Test: linux.clang.performance

Failed sub-tests (click for more details):
instantiate_modules_packer_palettes
Test: linux.clang.scientific.FlexPepDock.debug

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Test: linux.clang.scientific.abinitio_RosettaNMR_rdc

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Test: linux.clang.scientific.docking.debug

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Test: linux.clang.scientific.loop_modeling_kic_12res

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Test: linux.clang.scientific.mp_domain_assembly

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Test: linux.clang.scientific.mp_symdock.debug

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Test: linux.gcc.cxx11thread.mpi.serialization.scientific.peptide_pnear_vs_ic50

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branch: master 「№61908」
Commited by: Vikram K. Mulligan
GitHub commit link: 「5fc6a2f0d6a637e8」 「№6093」
Difference from previous tested commit:  code diff
Commit date: 2022-07-20 14:01:16
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta.notebook gcc-9.gcc.python37.PyRosetta.unit linux.clang.cxx11thread.serialization.python37.PyRosetta.unit linux.clang.python310.PyRosetta.unit linux.gcc.python36.PyRosetta.unit m1.clang.python310.PyRosetta.unit m1.clang.python38.PyRosetta.unit m1.clang.python39.PyRosetta.unit mac.clang.python310.PyRosetta.unit mac.clang.python38.PyRosetta.unit mac.clang.python39.PyRosetta.unit ubuntu-20.04.clang.python39.PyRosetta.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.python39.build.debug gcc-9.gcc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization linux.icc.build.debug mac.clang.bcl.build.debug OpenCL ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics static beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.addsan integration.mpi integration.release_debug integration.tensorflow integration.thread integration performance profile mac.clang.python310.release.PyRosetta.Debug mac.clang.python39.release.PyRosetta.Debug m1.clang.python38.release.PyRosetta.MinSizeRel mac.clang.python310.release.PyRosetta.MinSizeRel mac.clang.python310.release.PyRosetta.Release mac.clang.python38.release.PyRosetta.Release mac.clang.python39.release.PyRosetta.Release release.source scientific.FlexPepDock scientific.design_fast scientific.ligand_docking.debug scientific.loop_modeling_ccd_12res.debug scientific.mp_f19_sequence_recovery scientific.mp_lipid_acc scientific.peptide_pnear_vs_ic50 linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release mac.clang.unit.release gcc-10.gcc.unit gcc-11.gcc.python39.unit gcc-9.gcc.unit m1.clang.python39.unit ubuntu-20.04.clang.python39.unit ubuntu-20.04.gcc.python39.unit util.apps windows.build.debug windows.build.release

Merge pull request #6093 from RosettaCommons/vmullig/fix_thioether_cyclization_patch Fixing the oxygen atom placement in the AcetylatedProteinNtermConnection patch. The backbone carbon depended on the oxygen rather than the converse. This created bad geometry in GenKIC.

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Test: ubuntu.gcc.integration.addsan

Failed sub-tests (click for more details):
simple_cycpep_predict_square_pyramidal_metal
Test: linux.gcc.cxx11thread.integration.thread

Failed sub-tests (click for more details):
database_md5
Test: linux.clang.profile

Failed sub-tests (click for more details):
relax_native
Test: linux.clang.scientific.FlexPepDock

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Test: linux.clang.scientific.design_fast

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Test: linux.clang.scientific.ligand_docking.debug

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Test: linux.clang.scientific.loop_modeling_ccd_12res.debug

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Test: linux.clang.scientific.mp_f19_sequence_recovery

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Test: linux.clang.scientific.mp_lipid_acc

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Test: linux.gcc.cxx11thread.mpi.serialization.scientific.peptide_pnear_vs_ic50

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branch: master 「№61907」
Commited by: Sergey Lyskov
GitHub commit link: 「f80ea672c2432d30」 「№6087」
Difference from previous tested commit:  code diff
Commit date: 2022-07-18 16:32:42
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta.notebook gcc-9.gcc.python37.PyRosetta.unit linux.clang.cxx11thread.serialization.python37.PyRosetta.unit linux.clang.python310.PyRosetta.unit linux.gcc.python36.PyRosetta.unit m1.clang.python310.PyRosetta.unit m1.clang.python38.PyRosetta.unit m1.clang.python39.PyRosetta.unit mac.clang.python310.PyRosetta.unit mac.clang.python38.PyRosetta.unit mac.clang.python39.PyRosetta.unit ubuntu-20.04.clang.python39.PyRosetta.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.python39.build.debug gcc-9.gcc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization linux.icc.build.debug mac.clang.bcl.build.debug OpenCL mac.clang.python36.build.debug ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics static mac.clang.static.build.release beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.addsan integration.mpi integration.release_debug integration.tensorflow integration.thread integration.tutorials integration.ubsan integration.valgrind integration maintenance.documentation performance profile linux.clang.python310.release.PyRosetta.Debug linux.clang.python36.release.PyRosetta.Debug linux.clang.python37.release.PyRosetta.Debug linux.clang.python38.release.PyRosetta.Debug linux.clang.python39.release.PyRosetta.Debug mac.clang.python310.release.PyRosetta.Debug mac.clang.python38.release.PyRosetta.Debug mac.clang.python39.release.PyRosetta.Debug linux.clang.python310.release.PyRosetta.MinSizeRel linux.clang.python36.release.PyRosetta.MinSizeRel linux.clang.python37.release.PyRosetta.MinSizeRel linux.clang.python38.release.PyRosetta.MinSizeRel linux.clang.python39.release.PyRosetta.MinSizeRel m1.clang.python310.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel mac.clang.python310.release.PyRosetta.MinSizeRel mac.clang.python38.release.PyRosetta.MinSizeRel mac.clang.python39.release.PyRosetta.MinSizeRel ubuntu.clang.python310.release.PyRosetta.MinSizeRel ubuntu.clang.python36.release.PyRosetta.MinSizeRel ubuntu.clang.python37.release.PyRosetta.MinSizeRel ubuntu.clang.python38.release.PyRosetta.MinSizeRel ubuntu.clang.python39.release.PyRosetta.MinSizeRel linux.clang.python310.release.PyRosetta.Release linux.clang.python36.release.PyRosetta.Release linux.clang.python37.release.PyRosetta.Release linux.clang.python38.release.PyRosetta.Release linux.clang.python39.release.PyRosetta.Release m1.clang.python310.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release mac.clang.python310.release.PyRosetta.Release mac.clang.python38.release.PyRosetta.Release mac.clang.python39.release.PyRosetta.Release ubuntu.clang.python310.release.PyRosetta.Release ubuntu.clang.python36.release.PyRosetta.Release ubuntu.clang.python37.release.PyRosetta.Release ubuntu.clang.python38.release.PyRosetta.Release ubuntu.clang.python39.release.PyRosetta.Release release.PyRosetta.conda.Release release.source scientific.FlexPepDock.debug scientific.FlexPepDock scientific.RosettaCM.debug scientific.abinitio_RosettaNMR_rdc scientific.antibody_h3_modeling scientific.ddg_ala_scan.debug scientific.ddg_ala_scan scientific.design_fast scientific.docking.debug scientific.glycan_structure_prediction.debug scientific.ligand_docking.debug scientific.loop_modeling_ccd_12res.debug scientific.loop_modeling_ccd_12res scientific.mhc_epitope_energy.debug scientific.mp_domain_assembly.debug scientific.mp_domain_assembly scientific.mp_f19_ddG_of_mutation.debug scientific.mp_f19_ddG_of_mutation scientific.mp_f19_sequence_recovery scientific.mp_lipid_acc scientific.mp_symdock.debug scientific.peptide_pnear_vs_ic50 scientific.protein_data_bank_diagnostic.cif scientific.protein_data_bank_diagnostic.full linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release mac.clang.unit.release unit.ubsan unit.valgrind gcc-10.gcc.unit gcc-11.gcc.python39.unit gcc-9.gcc.unit m1.clang.python39.unit ubuntu-20.04.clang.python39.unit ubuntu-20.04.gcc.python39.unit util.apps windows.build.debug windows.build.release

Merge pull request #6087 from RosettaCommons/benchmark Fixing Mac builds, fixing Conda releases and updating default Python to 3.9.

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Test: ubuntu.gcc.integration.addsan

Failed sub-tests (click for more details):
simple_cycpep_predict_square_pyramidal_metal
Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
Protein-Protein-Docking
Test: ubuntu.gcc.integration.ubsan

Failed sub-tests (click for more details):
simple_cycpep_predict_square_pyramidal_metal
Test: linux.clang.scientific.ddg_ala_scan

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Test: linux.clang.scientific.docking.debug

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Test: linux.gcc.mpi.serialization.scientific.glycan_structure_prediction.debug

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Test: linux.clang.scientific.ligand_docking.debug

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Test: linux.clang.scientific.loop_modeling_ccd_12res.debug

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Test: linux.clang.scientific.loop_modeling_ccd_12res

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Test: linux.clang.scientific.mhc_epitope_energy.debug

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Test: linux.clang.scientific.mp_domain_assembly.debug

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Test: linux.clang.scientific.mp_domain_assembly

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Test: linux.clang.scientific.mp_f19_ddG_of_mutation

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Test: linux.clang.scientific.mp_f19_sequence_recovery

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Test: linux.clang.scientific.mp_lipid_acc

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Test: linux.clang.scientific.mp_symdock.debug

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Test: linux.gcc.cxx11thread.mpi.serialization.scientific.peptide_pnear_vs_ic50

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branch: master 「№61906」
Commited by: Rocco Moretti
GitHub commit link: 「fde602ce59a2d14b」 「№6091」
Difference from previous tested commit:  code diff
Commit date: 2022-07-18 12:05:14
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta.notebook gcc-9.gcc.python37.PyRosetta.unit linux.clang.cxx11thread.serialization.python37.PyRosetta.unit linux.clang.python310.PyRosetta.unit linux.gcc.python36.PyRosetta.unit m1.clang.python310.PyRosetta.unit m1.clang.python38.PyRosetta.unit m1.clang.python39.PyRosetta.unit mac.clang.python310.PyRosetta.unit mac.clang.python38.PyRosetta.unit mac.clang.python39.PyRosetta.unit ubuntu-20.04.clang.python39.PyRosetta.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.python39.build.debug gcc-9.gcc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization linux.icc.build.debug mac.clang.bcl.build.debug OpenCL mac.clang.python36.build.debug ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics static beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.mpi integration.release_debug integration.tensorflow integration.thread integration performance profile release.source scientific.FlexPepDock.debug scientific.FlexPepDock scientific.RosettaCM.debug scientific.abinitio_RosettaNMR_rdc scientific.antibody_h3_modeling scientific.ddg_ala_scan.debug scientific.ddg_ala_scan scientific.design_fast scientific.docking.debug scientific.glycan_structure_prediction.debug scientific.ligand_docking.debug scientific.loop_modeling_ccd_12res.debug scientific.loop_modeling_ccd_12res scientific.loop_modeling_kic_12res scientific.mhc_epitope_energy.debug scientific.mp_domain_assembly.debug scientific.mp_domain_assembly scientific.mp_f19_ddG_of_mutation.debug scientific.mp_f19_ddG_of_mutation scientific.mp_f19_sequence_recovery scientific.mp_lipid_acc scientific.mp_symdock.debug scientific.peptide_pnear_vs_ic50 linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release mac.clang.unit.release gcc-10.gcc.unit gcc-11.gcc.python39.unit gcc-9.gcc.unit m1.clang.python39.unit ubuntu-20.04.clang.python39.unit ubuntu-20.04.gcc.python39.unit util.apps windows.build.debug windows.build.release

Merge pull request #6091 from RosettaCommons/roccomoretti/replica_dock_fix (Partially) Fix replica_docking integration test Looks like we need a pre-existing directory to put the logs into. We're still getting timeouts on the server, but we're not hard crashing anymore.

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Test: mac.clang.bcl.build.debug

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Test: mac.clang.build.debug

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Test: mac.clang.opencl.build.debug

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Test: mac.clang.python36.build.debug

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Test: mac.clang.build.ninja_graphics

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Test: mac.clang.build.release

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Test: linux.clang.scientific.FlexPepDock

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Test: linux.clang.scientific.mp_f19_ddG_of_mutation

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Test: linux.clang.scientific.mp_lipid_acc

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Test: mac.clang.score

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Test: mac.clang.unit.release

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Test: gcc-9.gcc.unit

Failed sub-tests (click for more details):
core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_current_default_scorefxn core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_dslf_fa13 core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_fa_dun_dev core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_fa_dun_semi core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_fa_intra_atr_xover4 core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_fa_intra_rep core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_fa_intra_rep_xover4 core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_fa_rep core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_lk_ball_bridge core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_lk_ball_bridge_uncpl core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_p_aa_pp core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_pro_close core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_rama_prepro core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_beta core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_cart_bonded core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_fa_atr core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_fa_dun_rot core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_fa_elec core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_fa_intra_elec core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_fa_intra_sol_xover4 core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_fa_sol core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_hbonds core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_hxl_tors core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_lk_ball core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_lk_ball_iso core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_omega core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_rama core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_beta_nov16 core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_cart_bonded core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_current_default_scorefxn core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_dslf_fa13 core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_atr core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_dun_dev core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_dun_rot core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_dun_semi core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_elec core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_intra_atr_xover4 core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_intra_elec core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_intra_rep core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_intra_rep_xover4 core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_intra_sol_xover4 core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_rep core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_sol core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_hbonds core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_hxl_tors core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_lk_ball core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_lk_ball_bridge core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_lk_ball_bridge_uncpl core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_lk_ball_iso core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_omega core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_p_aa_pp core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_pro_close core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_rama core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_rama_prepro
Test: mac.clang.unit

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branch: master 「№61905」
Commited by: Sergey Lyskov
GitHub commit link: 「6c2ddeccd31e780d」
Difference from previous tested commit:  code diff
Commit date: 2022-07-12 17:12:13
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta.notebook gcc-9.gcc.python37.PyRosetta.unit linux.clang.cxx11thread.serialization.python37.PyRosetta.unit linux.clang.python310.PyRosetta.unit linux.gcc.python36.PyRosetta.unit m1.clang.python310.PyRosetta.unit m1.clang.python38.PyRosetta.unit m1.clang.python39.PyRosetta.unit mac.clang.python310.PyRosetta.unit mac.clang.python36.PyRosetta.unit ubuntu-20.04.clang.python39.PyRosetta.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.python39.build.debug gcc-9.gcc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization linux.icc.build.debug mac.clang.bcl.build.debug OpenCL mac.clang.python36.build.debug ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics static mac.clang.static.build.release beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.addsan integration.mpi integration.release_debug integration.tensorflow integration.thread integration.tutorials integration.ubsan integration.valgrind integration maintenance.documentation performance profile linux.clang.python310.release.PyRosetta.Debug linux.clang.python36.release.PyRosetta.Debug linux.clang.python37.release.PyRosetta.Debug linux.clang.python38.release.PyRosetta.Debug linux.clang.python39.release.PyRosetta.Debug mac.clang.python36.release.PyRosetta.Debug linux.clang.python310.release.PyRosetta.MinSizeRel linux.clang.python36.release.PyRosetta.MinSizeRel linux.clang.python37.release.PyRosetta.MinSizeRel linux.clang.python38.release.PyRosetta.MinSizeRel linux.clang.python39.release.PyRosetta.MinSizeRel m1.clang.python310.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel ubuntu.clang.python310.release.PyRosetta.MinSizeRel ubuntu.clang.python36.release.PyRosetta.MinSizeRel ubuntu.clang.python37.release.PyRosetta.MinSizeRel ubuntu.clang.python38.release.PyRosetta.MinSizeRel ubuntu.clang.python39.release.PyRosetta.MinSizeRel linux.clang.python310.release.PyRosetta.Release linux.clang.python36.release.PyRosetta.Release linux.clang.python37.release.PyRosetta.Release linux.clang.python38.release.PyRosetta.Release linux.clang.python39.release.PyRosetta.Release m1.clang.python310.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release mac.clang.python36.release.PyRosetta.Release ubuntu.clang.python310.release.PyRosetta.Release ubuntu.clang.python36.release.PyRosetta.Release ubuntu.clang.python37.release.PyRosetta.Release ubuntu.clang.python38.release.PyRosetta.Release ubuntu.clang.python39.release.PyRosetta.Release release.PyRosetta.conda.Release release.source scientific.FlexPepDock.debug scientific.abinitio_RosettaNMR_pcs.debug scientific.abinitio_RosettaNMR_pcs scientific.abinitio_RosettaNMR_rdc.debug scientific.abinitio_RosettaNMR_rdc scientific.antibody_grafting.debug scientific.antibody_grafting scientific.antibody_h3_modeling.debug scientific.antibody_snugdock.debug scientific.antibody_snugdock scientific.cofactor_binding_sites.debug scientific.cofactor_binding_sites scientific.design_fast.debug scientific.docking.debug scientific.docking_ensemble.debug scientific.enzyme_design.debug scientific.enzyme_design scientific.glycan_dock.debug scientific.glycan_structure_prediction scientific.ligand_docking scientific.ligand_scoring_ranking.debug scientific.ligand_scoring_ranking scientific.loop_modeling_kic_12res.debug scientific.loop_modeling_ngk_12res.debug scientific.make_fragments.debug scientific.make_fragments scientific.mp_dock.debug scientific.mp_dock scientific.mp_domain_assembly scientific.mp_f19_decoy_discrimination.debug scientific.mp_f19_decoy_discrimination scientific.mp_f19_sequence_recovery.debug scientific.mp_f19_tilt_angle.debug scientific.mp_f19_tilt_angle scientific.mp_lipid_acc.debug scientific.mp_relax.debug scientific.mp_relax scientific.mp_symdock.debug scientific.peptide_pnear_vs_ic50.debug scientific.relax_cartesian.debug scientific.relax_cartesian scientific.relax_fast.debug scientific.relax_fast_5iter.debug scientific.relax_fast_5iter scientific.relax_fast scientific.rna_denovo_favorites.debug scientific.rna_denovo_favorites scientific.sb_ligand_docking scientific.sb_talaris14_docking scientific.sewing.debug scientific.sewing scientific.stepwise_rna_favorites.debug scientific.stepwise_rna_favorites linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release mac.clang.unit.release unit.ubsan unit.valgrind gcc-10.gcc.unit gcc-11.gcc.python39.unit gcc-9.gcc.unit m1.clang.python39.unit util.apps windows.build.debug windows.build.release

reverting #5520 Revert "Degreaser v 1.0"

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Test: ubuntu.gcc.integration.addsan

Failed sub-tests (click for more details):
simple_cycpep_predict_square_pyramidal_metal
Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
Protein-Protein-Docking
Test: ubuntu.gcc.integration.ubsan

Failed sub-tests (click for more details):
simple_cycpep_predict_square_pyramidal_metal
Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
match_xml
Test: linux.clang.scientific.make_fragments.debug

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Test: linux.clang.scientific.make_fragments

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Test: linux.clang.scientific.mp_f19_decoy_discrimination.debug

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Test: linux.clang.scientific.mp_f19_decoy_discrimination

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Test: linux.gcc.cxx11thread.mpi.serialization.scientific.peptide_pnear_vs_ic50.debug

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branch: master 「№61904」
Commited by: John Wang
GitHub commit link: 「7ce5e3ea8ba2597e」 「№5520」
Difference from previous tested commit:  code diff
Commit date: 2022-07-12 11:41:38
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta.notebook gcc-9.gcc.python37.PyRosetta.unit linux.clang.cxx11thread.serialization.python37.PyRosetta.unit linux.clang.python310.PyRosetta.unit linux.gcc.python36.PyRosetta.unit m1.clang.python310.PyRosetta.unit m1.clang.python38.PyRosetta.unit m1.clang.python39.PyRosetta.unit mac.clang.python310.PyRosetta.unit mac.clang.python36.PyRosetta.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.python39.build.debug gcc-9.gcc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization linux.icc.build.debug mac.clang.bcl.build.debug OpenCL mac.clang.python36.build.debug ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics static beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.mpi integration.release_debug integration.tensorflow integration.thread integration.ubsan integration maintenance.documentation performance profile release.PyRosetta.Debug linux.clang.python37.release.PyRosetta.MinSizeRel linux.clang.python39.release.PyRosetta.MinSizeRel m1.clang.python310.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel ubuntu.clang.python36.release.PyRosetta.MinSizeRel ubuntu.clang.python37.release.PyRosetta.MinSizeRel ubuntu.clang.python39.release.PyRosetta.MinSizeRel linux.clang.python310.release.PyRosetta.Release m1.clang.python310.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release release.PyRosetta.conda.Release release.source scientific.FlexPepDock scientific.RosettaCM.debug scientific.antibody_h3_modeling scientific.ddg_ala_scan.debug scientific.ddg_ala_scan scientific.design_fast scientific.glycan_structure_prediction.debug scientific.ligand_docking.debug scientific.loop_modeling_ccd_12res.debug scientific.loop_modeling_ccd_12res scientific.mhc_epitope_energy.debug scientific.mp_domain_assembly.debug scientific.mp_f19_ddG_of_mutation.debug scientific.mp_f19_ddG_of_mutation scientific.mp_f19_sequence_recovery scientific.mp_lipid_acc linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release mac.clang.unit.release unit.ubsan gcc-10.gcc.unit gcc-11.gcc.python39.unit gcc-9.gcc.unit m1.clang.python39.unit util.apps windows.build.debug windows.build.release

Merge pull request #5520 from RosettaCommons/jyjwang/degreaser-fresh Degreaser v 1.0

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Test: gcc-9.gcc.serialization.python37.PyRosetta.notebook

Failed sub-tests (click for more details):
01.00-How-to-Get-Started 02.01-Pose-Basics 02.02-Working-with-Pose-Residues 02.03-Accessing-PyRosetta-Documentation 02.04-Getting-Spatial-Features-from-Pose 02.05-Protein-Geometry 02.06-Visualization-and-PyMOL-Mover 02.06-Visualization-and-PyMOL-Mover.PyRosetta-ColabPyMOL-integration 02.07-RosettaScripts-in-PyRosetta 02.08-Visualization-and-pyrosetta.distributed.viewer 03.01-Score-Function-Basics 03.02-Analyzing-energy-between-residues 03.03-Energies-and-the-PyMOLMover 04.01-Basic-Folding-Algorithm 04.02-Low-Res-Scoring-and-Fragments 05.01-High-Res-Movers 05.02-Refinement-Protocol 06.01-Side-Chain-Conformations-and-Dunbrack-Energies 06.02-Packing-design-and-regional-relax 06.03-Design-with-a-resfile-and-relax 06.04-Protein-Design-2 06.05-HBNet-Before-Design 06.06-Introduction-to-Parametric-backbone-design 06.07-Introduction-to-DeNovo-protein-design 06.08-Point-Mutation-Scan 07.02-Docking-Moves-in-Rosetta 08.00-Ligand-Docking-PyRosetta 08.01-Ligand-Docking-XMLObjects 08.02-Ligand-Docking-pyrosetta.distributed 10.00-Working-With-Symmetry 11.00-Working-With-Density 12.01-RosettaAntibody-Framework-and-SimpleMetrics 12.02-RosettaAntibodyDesign-RAbD 13.00-RosettaCarbohydrates-Working-with-Glycans 13.01-Glycan-Trees-Selectors-and-Movers 13.02-Glycan-Modeling-and-Design 14.00-RNA-Basics 15.01-Accounting-for-the-lipid-bilayer 15.02-Membrane-Protein-ddG-of-mutation 16.01-PyData-ddG-pssm 16.02-PyData-miniprotein-design 16.04-dask.delayed-Via-Slurm 16.05-Ligand-Docking-dask 16.06-PyRosettaCluster-Simple-protocol 16.07-PyRosettaCluster-Reproduce-simple-protocol 16.08-PyRosettaCluster-Multiple-protocols 16.09-PyRosettaCluster-Multiple-decoys 16.10-PyRosettaCluster-Ligand-params
Test: clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug

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Test: mac.clang.bcl.build.debug

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Test: mac.clang.build.release

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Test: linux.gcc.code_quality.beautification

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Test: linux.clang.scientific.FlexPepDock

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Test: linux.clang.scientific.RosettaCM.debug

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Test: linux.clang.scientific.antibody_h3_modeling

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Test: linux.clang.scientific.ddg_ala_scan.debug

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Test: linux.clang.scientific.design_fast

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Test: linux.clang.scientific.ligand_docking.debug

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Test: linux.clang.scientific.loop_modeling_ccd_12res.debug

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Test: linux.clang.scientific.loop_modeling_ccd_12res

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Test: linux.clang.scientific.mhc_epitope_energy.debug

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Test: linux.clang.scientific.mp_domain_assembly.debug

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Test: linux.clang.scientific.mp_f19_ddG_of_mutation.debug

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Test: linux.clang.scientific.mp_f19_ddG_of_mutation

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Test: linux.clang.scientific.mp_f19_sequence_recovery

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Test: linux.clang.scientific.mp_lipid_acc

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Test: linux.clang.python36.scripts.pyrosetta

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branch: master 「№61903」
Commited by: Vikram K. Mulligan
GitHub commit link: 「f0932dcdc69a51e5」 「№6076」
Difference from previous tested commit:  code diff
Commit date: 2022-07-07 21:30:40
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta.notebook gcc-9.gcc.python37.PyRosetta.unit linux.clang.cxx11thread.serialization.python37.PyRosetta.unit linux.clang.python310.PyRosetta.unit linux.gcc.python36.PyRosetta.unit m1.clang.python310.PyRosetta.unit m1.clang.python38.PyRosetta.unit m1.clang.python39.PyRosetta.unit mac.clang.python310.PyRosetta.unit mac.clang.python36.PyRosetta.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.python39.build.debug gcc-9.gcc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization linux.icc.build.debug mac.clang.bcl.build.debug OpenCL mac.clang.python36.build.debug ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics static mac.clang.static.build.release beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.addsan integration.mpi integration.release_debug integration.tensorflow integration.thread integration.tutorials integration.ubsan integration.valgrind integration maintenance.documentation performance profile linux.clang.python310.release.PyRosetta.Debug linux.clang.python36.release.PyRosetta.Debug linux.clang.python37.release.PyRosetta.Debug linux.clang.python38.release.PyRosetta.Debug linux.clang.python39.release.PyRosetta.Debug linux.clang.python310.release.PyRosetta.MinSizeRel linux.clang.python36.release.PyRosetta.MinSizeRel linux.clang.python37.release.PyRosetta.MinSizeRel linux.clang.python38.release.PyRosetta.MinSizeRel linux.clang.python39.release.PyRosetta.MinSizeRel m1.clang.python310.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel ubuntu.clang.python310.release.PyRosetta.MinSizeRel ubuntu.clang.python36.release.PyRosetta.MinSizeRel ubuntu.clang.python37.release.PyRosetta.MinSizeRel ubuntu.clang.python38.release.PyRosetta.MinSizeRel ubuntu.clang.python39.release.PyRosetta.MinSizeRel linux.clang.python310.release.PyRosetta.Release linux.clang.python36.release.PyRosetta.Release linux.clang.python37.release.PyRosetta.Release linux.clang.python38.release.PyRosetta.Release linux.clang.python39.release.PyRosetta.Release m1.clang.python310.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release ubuntu.clang.python310.release.PyRosetta.Release ubuntu.clang.python36.release.PyRosetta.Release ubuntu.clang.python37.release.PyRosetta.Release ubuntu.clang.python38.release.PyRosetta.Release ubuntu.clang.python39.release.PyRosetta.Release release.PyRosetta.conda.Release release.source scientific.fragments_picking.debug scientific.loop_modeling_kic_fragments_12res.debug scientific.loop_modeling_kic_fragments_12res scientific.simple_cycpep_predict.debug scientific.simple_cycpep_predict linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release mac.clang.unit.release unit.ubsan unit.valgrind gcc-10.gcc.unit gcc-11.gcc.python39.unit gcc-9.gcc.unit m1.clang.python39.unit util.apps windows.build.debug windows.build.release

Merge pull request #6076 from RosettaCommons/vmullig/fix_symmetrical_residue_selector Fix the SymmetricalResidueSelector's internal logic The SymmetricalResidueSelector would copy selections from the independent set to the dependent residues, but not vice versa. This PR fixes this, so that it's guaranteed to produce a symmetrical selection every time. This requires a two-pass process: - In the first pass, every independent residue that has a dependent selected is selected. - In the second pass, every independent residue that is selected selects all of its dependents.

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Test: ubuntu.gcc.integration.addsan

Failed sub-tests (click for more details):
simple_cycpep_predict_square_pyramidal_metal
Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
Protein-Protein-Docking
Test: ubuntu.gcc.integration.ubsan

Failed sub-tests (click for more details):
simple_cycpep_predict_square_pyramidal_metal


branch: master 「№61902」
Commited by: Vikram K. Mulligan
GitHub commit link: 「776897c0457a671f」 「№6072」
Difference from previous tested commit:  code diff
Commit date: 2022-07-06 22:03:53
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta.notebook gcc-9.gcc.python37.PyRosetta.unit linux.clang.cxx11thread.serialization.python37.PyRosetta.unit linux.clang.python310.PyRosetta.unit linux.gcc.python36.PyRosetta.unit m1.clang.python310.PyRosetta.unit m1.clang.python38.PyRosetta.unit m1.clang.python39.PyRosetta.unit mac.clang.python310.PyRosetta.unit mac.clang.python36.PyRosetta.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.python39.build.debug gcc-9.gcc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization linux.icc.build.debug mac.clang.bcl.build.debug OpenCL mac.clang.python36.build.debug ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics static mac.clang.static.build.release beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.addsan integration.mpi integration.release_debug integration.tensorflow integration.thread integration.tutorials integration.ubsan integration.valgrind integration maintenance.documentation performance profile linux.clang.python310.release.PyRosetta.Debug linux.clang.python36.release.PyRosetta.Debug linux.clang.python37.release.PyRosetta.Debug linux.clang.python38.release.PyRosetta.Debug linux.clang.python39.release.PyRosetta.Debug linux.clang.python310.release.PyRosetta.MinSizeRel linux.clang.python36.release.PyRosetta.MinSizeRel linux.clang.python37.release.PyRosetta.MinSizeRel linux.clang.python38.release.PyRosetta.MinSizeRel linux.clang.python39.release.PyRosetta.MinSizeRel m1.clang.python310.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel ubuntu.clang.python310.release.PyRosetta.MinSizeRel ubuntu.clang.python36.release.PyRosetta.MinSizeRel ubuntu.clang.python37.release.PyRosetta.MinSizeRel ubuntu.clang.python38.release.PyRosetta.MinSizeRel ubuntu.clang.python39.release.PyRosetta.MinSizeRel linux.clang.python310.release.PyRosetta.Release linux.clang.python36.release.PyRosetta.Release linux.clang.python37.release.PyRosetta.Release linux.clang.python38.release.PyRosetta.Release linux.clang.python39.release.PyRosetta.Release m1.clang.python310.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release ubuntu.clang.python310.release.PyRosetta.Release ubuntu.clang.python36.release.PyRosetta.Release ubuntu.clang.python37.release.PyRosetta.Release ubuntu.clang.python38.release.PyRosetta.Release ubuntu.clang.python39.release.PyRosetta.Release release.PyRosetta.conda.Release release.source scientific.RosettaCM scientific.docking_ensemble scientific.docking scientific.glycan_dock scientific.loop_modeling_kic_12res scientific.loop_modeling_ngk_12res scientific.mhc_epitope_energy scientific.mp_symdock scientific.peptide_pnear_vs_ic50 linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release mac.clang.unit.release unit.ubsan unit.valgrind gcc-10.gcc.unit gcc-11.gcc.python39.unit gcc-9.gcc.unit m1.clang.python39.unit util.apps windows.build.debug windows.build.release

Merge pull request #6072 from RosettaCommons/vmullig/fix_cycpep_bug_identified_by_jared Fix a simple_cycpep_predict bug in cis-trans sampling with lariats, identified by Jared The bug is actually in N-terminal N-methylated thioether-cyclized variants, which are introduced in the `jadolfbr/cycpep` branch. This branch has `jadolfbr/cycpep` merged into it. @jadolfbr, is it okay to merge the contents of `jadolfbr/cycpep` into `master`, or do you want to keep that private for now? Tasks: - [x] Add integration test that should trigger the bug. - [x] Track down the bug. - [x] Check whether `jadolfbr/cycpep` can be merged into master. - [x] Fix the bug. - [x] Beauty. From `jadolfbr/cycpep`: - [x] This adds support to the AcetylatedProteinNterm for N-methylation. - [x] This adds support for the `out::path::pdb`, `out::path::all`, `out::path::path`, `out::suffix`, and `out::prefix` commandline flags to the `simple_cycpep_predict` application.

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Test: ubuntu.gcc.integration.addsan

Failed sub-tests (click for more details):
simple_cycpep_predict_square_pyramidal_metal
Test: linux.clang.tensorflow.integration.tensorflow

Failed sub-tests (click for more details):
database_md5
Test: linux.gcc.cxx11thread.integration.thread

Failed sub-tests (click for more details):
database_md5
Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
Protein-Protein-Docking
Test: ubuntu.gcc.integration.ubsan

Failed sub-tests (click for more details):
simple_cycpep_predict_square_pyramidal_metal


branch: master 「№61901」
Commited by: Vikram K. Mulligan
GitHub commit link: 「7c85da316d6f1b52」 「№6074」
Difference from previous tested commit:  code diff
Commit date: 2022-07-06 18:23:39
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta.notebook gcc-9.gcc.python37.PyRosetta.unit linux.clang.cxx11thread.serialization.python37.PyRosetta.unit linux.clang.python310.PyRosetta.unit linux.gcc.python36.PyRosetta.unit m1.clang.python310.PyRosetta.unit m1.clang.python38.PyRosetta.unit m1.clang.python39.PyRosetta.unit mac.clang.python310.PyRosetta.unit mac.clang.python36.PyRosetta.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.python39.build.debug gcc-9.gcc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization linux.icc.build.debug mac.clang.bcl.build.debug OpenCL mac.clang.python36.build.debug ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics static mac.clang.static.build.release beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.mpi integration.release_debug integration.tensorflow integration.thread integration.tutorials integration maintenance.documentation performance profile linux.clang.python310.release.PyRosetta.MinSizeRel m1.clang.python310.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python310.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release release.source scientific.FlexPepDock.debug scientific.abinitio_RosettaNMR_rdc scientific.docking.debug scientific.mp_domain_assembly scientific.mp_symdock.debug linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release mac.clang.unit.release gcc-10.gcc.unit gcc-11.gcc.python39.unit gcc-9.gcc.unit m1.clang.python39.unit util.apps windows.build.debug windows.build.release

Merge pull request #6074 from RosettaCommons/vmullig/tweak_rosettascript_filter_reevaluation Some minor tweaks to filters to reduce reevaluation Currently, filters are recomputed several times by default in RosettaScripts: - Three times on application (once to filter, once to store the filter value in the pose, and once to report the filter's calculation to the tracer). - Once more on script completion. There are two options that reduce this. The `never_rerun_filters="true"` option ensures that only the computation to filter is performed, but returns no values. The `report_at_end="false"` option disables the final reporting, but doesn't alter the threefold computation. Obviously this is far from ideal, especially with filters with some stochasticity to their calculation or filters that are expensive to apply. Cleaning up the threefold computation is hard -- it comes down to poor design of the virtual functions of the filter class, and would require touching every filter to refactor. However, we can add options to remove at least one of the triplicated calculations. This pull request: - [x] Disables the third calculation for reporting if the report tracer (`protocols.rosetta_scripts.ParsedProtocol.REPORT`) is muted. - [x] Ensures that the `never_rerun_filters` option is correctly set from RosettaScripts. - [x] Cleans up a visually ambiguous mix of nots and ors in `parse_my_tag()`. - [x] Corrects a few typos in error and warning messages. Note that Jack made a good point about merging the never_rerun and report time options. Although it's outside of the scope of this pull request, I'll make an issue for doing that in the future.

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Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
ContactMolecularSurface Enzrevert_xml FilterReportAsPoseExtraScoresMover LoopAnalyzer buried_area_filter buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm cmaes_minimizer cycpep_design_pipeline cycpep_rdkit_metric cycpep_symmetry_filter ddG_sym dock_with_hotspot_place_simultaneously enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym hbondstoresidue_selector homodimer_fnd_ref2015_memb hotspot_graft longest_continuous_polar_segment_filter match_xml mmtfIO_score_test motif_score_filter mp_quick_relax_ref2015_memb mp_span_ang_ref2015_memb oligourea_design oligourea_predict place_simultaneously ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG ppk res_lipo_ref2015_memb rnp_ddg_finalize rotamer_probability sasa_metric_options score12_docking score_only_silence simple_cycpep_predict simple_cycpep_predict_1_4_bbmb simple_cycpep_predict_angle simple_cycpep_predict_anglelength simple_cycpep_predict_beta_thioether_lariat simple_cycpep_predict_cartesian simple_cycpep_predict_cispro simple_cycpep_predict_cterm_isopeptide_lariat simple_cycpep_predict_cterm_isopeptide_lariat_tailless simple_cycpep_predict_design simple_cycpep_predict_nmethyl simple_cycpep_predict_nterm_isopeptide_lariat simple_cycpep_predict_nterm_isopeptide_lariat_tailless simple_cycpep_predict_peptoid simple_cycpep_predict_setting simple_cycpep_predict_sidechain_isopeptide simple_cycpep_predict_sidechain_isopeptide_reverse simple_cycpep_predict_square_planar_metal simple_cycpep_predict_square_pyramidal_metal simple_cycpep_predict_symm_gly simple_cycpep_predict_tbmb simple_cycpep_predict_terminal_disulfide simple_cycpep_predict_terminal_disulfide_internal_permutations simple_cycpep_predict_terminal_disulfide_tails simple_cycpep_predict_tetrahedral_metal simple_cycpep_predict_tetrahedral_metal_asp simple_cycpep_predict_thioether_lariat simple_cycpep_predict_tma simple_cycpep_predict_trigonal_planar_metal simple_cycpep_predict_trigonal_pyramidal_metal simple_metric_cache simple_metric_filter symm_rotamer_boltzmann threefold_symm_peptide_design voids_penalty_energy_design voids_penalty_energy_design_symmetry
Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
Protein-Protein-Docking
Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
ContactMolecularSurface Enzrevert_xml FilterReportAsPoseExtraScoresMover LoopAnalyzer buried_area_filter buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm cycpep_design_pipeline cycpep_rdkit_metric cycpep_symmetry_filter ddG_sym dock_with_hotspot_place_simultaneously enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym hbondstoresidue_selector homodimer_fnd_ref2015_memb hotspot_graft longest_continuous_polar_segment_filter match_xml motif_score_filter mp_quick_relax_ref2015_memb mp_span_ang_ref2015_memb oligourea_design oligourea_predict place_simultaneously ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG ppk res_lipo_ref2015_memb rotamer_probability sasa_metric_options score12_docking score_only_silence simple_cycpep_predict simple_cycpep_predict_1_4_bbmb simple_cycpep_predict_angle simple_cycpep_predict_anglelength simple_cycpep_predict_beta_thioether_lariat simple_cycpep_predict_cartesian simple_cycpep_predict_cispro simple_cycpep_predict_cterm_isopeptide_lariat simple_cycpep_predict_cterm_isopeptide_lariat_tailless simple_cycpep_predict_design simple_cycpep_predict_nmethyl simple_cycpep_predict_nterm_isopeptide_lariat simple_cycpep_predict_nterm_isopeptide_lariat_tailless simple_cycpep_predict_peptoid simple_cycpep_predict_setting simple_cycpep_predict_sidechain_isopeptide simple_cycpep_predict_sidechain_isopeptide_reverse simple_cycpep_predict_square_planar_metal simple_cycpep_predict_square_pyramidal_metal simple_cycpep_predict_symm_gly simple_cycpep_predict_tbmb simple_cycpep_predict_terminal_disulfide simple_cycpep_predict_terminal_disulfide_internal_permutations simple_cycpep_predict_terminal_disulfide_tails simple_cycpep_predict_tetrahedral_metal simple_cycpep_predict_tetrahedral_metal_asp simple_cycpep_predict_thioether_lariat simple_cycpep_predict_tma simple_cycpep_predict_trigonal_planar_metal simple_cycpep_predict_trigonal_pyramidal_metal simple_metric_cache simple_metric_filter symm_rotamer_boltzmann threefold_symm_peptide_design voids_penalty_energy_design voids_penalty_energy_design_symmetry


branch: master 「№61900」
Commited by: Vikram K. Mulligan
GitHub commit link: 「924f2f00012a153c」 「№6071」
Difference from previous tested commit:  code diff
Commit date: 2022-07-04 15:50:58
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta.notebook gcc-9.gcc.python37.PyRosetta.unit linux.clang.cxx11thread.serialization.python37.PyRosetta.unit linux.clang.python310.PyRosetta.unit linux.gcc.python36.PyRosetta.unit m1.clang.python310.PyRosetta.unit m1.clang.python38.PyRosetta.unit m1.clang.python39.PyRosetta.unit mac.clang.python310.PyRosetta.unit mac.clang.python36.PyRosetta.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.python39.build.debug gcc-9.gcc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization linux.icc.build.debug mac.clang.bcl.build.debug OpenCL mac.clang.python36.build.debug ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics static mac.clang.static.build.release beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.addsan integration.mpi integration.release_debug integration.tensorflow integration.thread integration.tutorials integration.ubsan integration.valgrind integration maintenance.documentation performance profile linux.clang.python310.release.PyRosetta.Debug linux.clang.python36.release.PyRosetta.Debug linux.clang.python37.release.PyRosetta.Debug linux.clang.python38.release.PyRosetta.Debug linux.clang.python39.release.PyRosetta.Debug linux.clang.python310.release.PyRosetta.MinSizeRel linux.clang.python36.release.PyRosetta.MinSizeRel linux.clang.python37.release.PyRosetta.MinSizeRel linux.clang.python38.release.PyRosetta.MinSizeRel linux.clang.python39.release.PyRosetta.MinSizeRel m1.clang.python310.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel ubuntu.clang.python310.release.PyRosetta.MinSizeRel ubuntu.clang.python36.release.PyRosetta.MinSizeRel ubuntu.clang.python37.release.PyRosetta.MinSizeRel ubuntu.clang.python38.release.PyRosetta.MinSizeRel ubuntu.clang.python39.release.PyRosetta.MinSizeRel linux.clang.python310.release.PyRosetta.Release linux.clang.python36.release.PyRosetta.Release linux.clang.python37.release.PyRosetta.Release linux.clang.python38.release.PyRosetta.Release linux.clang.python39.release.PyRosetta.Release m1.clang.python310.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release ubuntu.clang.python310.release.PyRosetta.Release ubuntu.clang.python36.release.PyRosetta.Release ubuntu.clang.python37.release.PyRosetta.Release ubuntu.clang.python38.release.PyRosetta.Release ubuntu.clang.python39.release.PyRosetta.Release release.PyRosetta.conda.Release release.source scientific.FlexPepDock scientific.RosettaCM.debug scientific.antibody_h3_modeling scientific.ddg_ala_scan.debug scientific.ddg_ala_scan scientific.design_fast scientific.glycan_structure_prediction.debug scientific.ligand_docking.debug scientific.loop_modeling_ccd_12res.debug scientific.loop_modeling_ccd_12res scientific.mhc_epitope_energy.debug scientific.mp_domain_assembly.debug scientific.mp_f19_ddG_of_mutation.debug scientific.mp_f19_ddG_of_mutation scientific.mp_f19_sequence_recovery scientific.mp_lipid_acc scientific.protein_data_bank_diagnostic.cif scientific.protein_data_bank_diagnostic.full linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release mac.clang.unit.release unit.ubsan unit.valgrind gcc-10.gcc.unit gcc-11.gcc.python39.unit gcc-9.gcc.unit m1.clang.python39.unit util.apps windows.build.debug windows.build.release

Merge pull request #6071 from RosettaCommons/vmullig/update_rms_functions Add some RMSD functions. This pull request: - [x] Adds a `superimpose_polymer_heavyatoms()` function, to superimpose based on either _all_ heavyatoms or all _mainchain_ heavyatoms. Our existing functions are peptide and protein-specific. - [x] Adds a `all_atom_rmsd_incl_hydrogens()` function (as well as a Doxygen comment on the existing `all_atom_rmsd()` function indicating that this excludes hydrogens). - [x] Switches a couple of instances of `new` to use `make_shared` instead. - [x] Unit tests this. These new functions are used in a project that will be the subject of a future pull request.

...
Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
Protein-Protein-Docking
Test: ubuntu.gcc.integration.ubsan

Failed sub-tests (click for more details):
simple_cycpep_predict_square_pyramidal_metal
Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
match_xml


branch: master 「№61899」
Commited by: Sergey Lyskov
GitHub commit link: 「33c241a66e25be79」
Difference from previous tested commit:  code diff
Commit date: 2022-07-03 19:44:23
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta.notebook gcc-9.gcc.python37.PyRosetta.unit linux.clang.cxx11thread.serialization.python37.PyRosetta.unit linux.clang.python310.PyRosetta.unit linux.gcc.python36.PyRosetta.unit m1.clang.python310.PyRosetta.unit m1.clang.python38.PyRosetta.unit m1.clang.python39.PyRosetta.unit mac.clang.python310.PyRosetta.unit mac.clang.python36.PyRosetta.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.python39.build.debug gcc-9.gcc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization linux.icc.build.debug mac.clang.bcl.build.debug OpenCL mac.clang.python36.build.debug ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics static mac.clang.static.build.release beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.addsan integration.mpi integration.release_debug integration.tensorflow integration.thread integration.tutorials integration.ubsan integration maintenance.documentation performance profile linux.clang.python310.release.PyRosetta.Debug linux.clang.python36.release.PyRosetta.Debug linux.clang.python37.release.PyRosetta.Debug linux.clang.python38.release.PyRosetta.Debug linux.clang.python39.release.PyRosetta.Debug linux.clang.python310.release.PyRosetta.MinSizeRel linux.clang.python36.release.PyRosetta.MinSizeRel linux.clang.python37.release.PyRosetta.MinSizeRel linux.clang.python38.release.PyRosetta.MinSizeRel linux.clang.python39.release.PyRosetta.MinSizeRel m1.clang.python310.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel ubuntu.clang.python310.release.PyRosetta.MinSizeRel ubuntu.clang.python36.release.PyRosetta.MinSizeRel ubuntu.clang.python37.release.PyRosetta.MinSizeRel ubuntu.clang.python38.release.PyRosetta.MinSizeRel ubuntu.clang.python39.release.PyRosetta.MinSizeRel linux.clang.python310.release.PyRosetta.Release linux.clang.python36.release.PyRosetta.Release linux.clang.python37.release.PyRosetta.Release linux.clang.python38.release.PyRosetta.Release linux.clang.python39.release.PyRosetta.Release m1.clang.python310.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release mac.clang.python36.release.PyRosetta.Release ubuntu.clang.python310.release.PyRosetta.Release ubuntu.clang.python36.release.PyRosetta.Release ubuntu.clang.python37.release.PyRosetta.Release ubuntu.clang.python38.release.PyRosetta.Release ubuntu.clang.python39.release.PyRosetta.Release release.PyRosetta.conda.Release release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release mac.clang.unit.release unit.ubsan gcc-10.gcc.unit gcc-11.gcc.python39.unit gcc-9.gcc.unit m1.clang.python39.unit util.apps windows.build.debug windows.build.release

updating PyRosetta to support Python-3.10

...
Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
Protein-Protein-Docking
Test: ubuntu.gcc.integration.ubsan

Failed sub-tests (click for more details):
simple_cycpep_predict_square_pyramidal_metal
Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
dgdp_script match_xml


branch: master 「№61898」
Commited by: Diego del Alamo
GitHub commit link: 「3248884b8d8cd403」 「№5935」
Difference from previous tested commit:  code diff
Commit date: 2022-06-30 11:26:09
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta.notebook gcc-9.gcc.python37.PyRosetta.unit linux.clang.cxx11thread.serialization.python37.PyRosetta.unit linux.gcc.python36.PyRosetta.unit m1.clang.python38.PyRosetta.unit m1.clang.python39.PyRosetta.unit mac.clang.python36.PyRosetta.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.python39.build.debug gcc-9.gcc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization linux.icc.build.debug mac.clang.bcl.build.debug OpenCL mac.clang.python36.build.debug ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics static mac.clang.static.build.release beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.addsan integration.mpi integration.release_debug integration.tensorflow integration.thread integration.tutorials integration.ubsan integration.valgrind integration maintenance.documentation performance profile linux.clang.python36.release.PyRosetta.Debug linux.clang.python37.release.PyRosetta.Debug linux.clang.python38.release.PyRosetta.Debug linux.clang.python39.release.PyRosetta.Debug mac.clang.python36.release.PyRosetta.Debug linux.clang.python36.release.PyRosetta.MinSizeRel linux.clang.python37.release.PyRosetta.MinSizeRel linux.clang.python38.release.PyRosetta.MinSizeRel linux.clang.python39.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel ubuntu.clang.python36.release.PyRosetta.MinSizeRel ubuntu.clang.python37.release.PyRosetta.MinSizeRel ubuntu.clang.python38.release.PyRosetta.MinSizeRel ubuntu.clang.python39.release.PyRosetta.MinSizeRel linux.clang.python36.release.PyRosetta.Release linux.clang.python37.release.PyRosetta.Release linux.clang.python38.release.PyRosetta.Release linux.clang.python39.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release ubuntu.clang.python36.release.PyRosetta.Release ubuntu.clang.python37.release.PyRosetta.Release ubuntu.clang.python38.release.PyRosetta.Release ubuntu.clang.python39.release.PyRosetta.Release release.PyRosetta.conda.Release release.source scientific.antibody_h3_modeling.debug scientific.antibody_snugdock.debug scientific.antibody_snugdock scientific.cofactor_binding_sites.debug scientific.cofactor_binding_sites scientific.design_fast.debug scientific.docking_ensemble.debug scientific.enzyme_design scientific.glycan_structure_prediction scientific.ligand_scoring_ranking.debug scientific.ligand_scoring_ranking scientific.loop_modeling_ngk_12res.debug scientific.mp_dock.debug scientific.mp_dock scientific.mp_f19_sequence_recovery.debug scientific.mp_lipid_acc.debug scientific.mp_relax.debug scientific.relax_cartesian.debug scientific.relax_cartesian scientific.relax_fast.debug scientific.relax_fast_5iter.debug scientific.relax_fast_5iter scientific.rna_denovo_favorites.debug scientific.sb_talaris13_loop_modeling_kic_12res scientific.sb_talaris13_loop_modeling_kic_fragments_12res scientific.sb_talaris13_loop_modeling_ngk_12res scientific.sb_talaris14_loop_modeling_ccd_12res scientific.sb_talaris14_loop_modeling_kic_12res scientific.sb_talaris14_loop_modeling_kic_fragments_12res scientific.sb_talaris14_loop_modeling_ngk_12res scientific.sewing.debug scientific.stepwise_rna_favorites.debug scientific.stepwise_rna_favorites linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release mac.clang.unit.release unit.ubsan unit.valgrind gcc-10.gcc.unit gcc-11.gcc.python39.unit gcc-9.gcc.unit m1.clang.python39.unit util.apps windows.build.debug windows.build.release

Merge pull request #5935 from RosettaCommons/alamo/deer_optimize_coords_mover New Mover to modify the spin labels used to model proteins with EPR data

...
Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
Protein-Protein-Docking
Test: ubuntu.gcc.integration.ubsan

Failed sub-tests (click for more details):
simple_cycpep_predict_square_pyramidal_metal
Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
match_xml output_schema


branch: master 「№61897」
Commited by: Vikram K. Mulligan
GitHub commit link: 「cd16be2910907fd8」 「№6069」
Difference from previous tested commit:  code diff
Commit date: 2022-06-29 22:22:46
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta.notebook gcc-9.gcc.python37.PyRosetta.unit linux.clang.cxx11thread.serialization.python37.PyRosetta.unit linux.gcc.python36.PyRosetta.unit m1.clang.python38.PyRosetta.unit m1.clang.python39.PyRosetta.unit mac.clang.python36.PyRosetta.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.python39.build.debug gcc-9.gcc.build.debug linux.clang.bcl.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug linux.gcc.bcl.build.debug mpi mpi.serialization linux.icc.build.debug mac.clang.bcl.build.debug OpenCL mac.clang.python36.build.debug ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics static mac.clang.static.build.release beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.mpi integration.release_debug integration.tensorflow integration.thread integration.ubsan integration maintenance.documentation performance profile linux.clang.python38.release.PyRosetta.Debug linux.clang.python39.release.PyRosetta.Debug linux.clang.python36.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel linux.clang.python36.release.PyRosetta.Release linux.clang.python37.release.PyRosetta.Release linux.clang.python38.release.PyRosetta.Release linux.clang.python39.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release ubuntu.clang.python36.release.PyRosetta.Release ubuntu.clang.python38.release.PyRosetta.Release ubuntu.clang.python39.release.PyRosetta.Release release.source scientific.mp_relax scientific.sb_score12_loop_modeling_kic_fragments_12res scientific.sb_talaris13_loop_modeling_ccd_12res linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release mac.clang.unit.release gcc-10.gcc.unit gcc-11.gcc.python39.unit gcc-9.gcc.unit m1.clang.python39.unit util.apps windows.build.debug windows.build.release

Merge pull request #6069 from RosettaCommons/vmullig/custom_real_valued_metric Add a CustomRealValueMetric class, analogous to the CustomStringValueMetric It is convenient to have an easy way to cache an arbitrary floating-point value in a pose from code, without doing a lot of manual steps. Simple metrics let you _compute_ particular types of floating-point values (scores, RMSDs, _etc._) and cache them, but if you've already computed whatever you want to compute, it's not easy to get that stored as a metric. This pull request adds a `CustomRealValueMetric` class, which lets you add an arbitrary input value and label to a pose. For instance, you might be testing an idea in a pilot app: ```c++ core::pose::PoseOP pose( utility::pointer::make_shared< core::pose::Pose >() ); // Create the pose and manipulate it. core::Real const my_computed_value = /*some new calculation to analyze the pose that's experimental enough or specialized enough that it's not worth turning into its own simple metric*/; core::simple_metrics::metrics::CustomRealValueMetric my_metric; my_metric.set_value( my_computed_value ); //I don't want the computation to be done by the metric. my_metric.apply( "custom_computed_value", *pose ); //Cache the computed value in the pose, and give it the label "custom_computed_value". ``` We already have this for string metrics. This pull request adds it for float-valued metrics. Note: this also gives you a way to pass in information from the commandline in RosettaScripts and cache it in the pose. For instance: ```xml <ROSETTASCRIPTS> <SIMPLE_METRICS> <CustomRealValueMetric name="my_metric" value="%%extrernal_val%%" /> </SIMPLE_METRICS> <PROTOCOLS> <Add metrics="my_metric" /> </PROTOCOLS> </ROSETTASCRIPTS> ``` ```sh ~/Rosetta/main/source/src/rosetta_scripts.default.linuxgccrelease -parser:protocol my_script.xml -script_vars external_val=25.3 -in:file:s first_file.pdb ~/Rosetta/main/source/src/rosetta_scripts.default.linuxgccrelease -parser:protocol my_script.xml -script_vars external_val=-12.9 -in:file:s second_file.pdb ``` It should also make it easier to put custom information into a Pose in PyRosetta. TODO: - [x] Unit test. - [x] Beauty. - [x] Documentation. Pull request RosettaCommons/documentation#59 has this.

...
Test: ubuntu.gcc.integration.ubsan

Failed sub-tests (click for more details):
simple_cycpep_predict_square_pyramidal_metal
Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
match_xml output_schema


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