branch: master 「№62008」
Commited by: Rocco Moretti
GitHub commit link: 「2490d4c2089049cc」 「№6346」
Difference from previous tested commit:  code diff
Commit date: 2023-05-10 12:28:20
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.clang.cxx11thread.serialization.python37.PyRosetta.unit mac.clang.python38.PyRosetta.unit mpi mpi.serialization build.header build.levels build.ninja_debug beautification code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.mpi integration.release_debug integration.tensorflow integration.thread integration performance profile linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify util.apps windows.build.debug windows.build.release

Merge pull request #6346 from RosettaCommons/roccomoretti/obey_ssbond Add option to obey SSBOND info during PDB loading. One of the time sinks in PDB loading is the disulfide bond detection. There is currently a way to turn it off entirely (-detect_disulf false) or use an external file to specify things (-fix_disulf), but there's not currently a way to specify that you want to obey the disulfide annotations in the PDB file and not do a general scan. This is less than ideal, as from-wwPDB and Rosetta output files should have the complete SSBOND information in them already. This PR adds a -in:obey_ssbond option to the command line, which tells the loader code to take the SSBOND information from the PDB/StructFileRep as the only disulfides which should be used. Adding this flag shaves the time in initialize_disulfide_bonds() in half, saving somewhere between 1-2% in PDB loading speed.

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Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
AnchorFinder BFactorSelector ContactMolecularSurface InterfaceAnalyzer_ligand PDB_diagnostic RBOut SID_rescore antibody_H3 antibody_H3_camelid antibody_designer antibody_designer_camelid antibody_designer_xml antibody_graft antibody_numbering_converter assemble_domains_jd2 binselector binselector_probins cart_min_glycans ccd_ends_graft_mover_rs cluster_alns control_flow_rs create_clash-based_repack_shell create_sequence_motif custom_basetype_packer_palette density_refine dock_with_hotspot_place_simultaneously docking_ensemble docking_ensemble_prepack exclusively_shared_jumps features flexpepdock genkic_sugars glycan_clash_check glycan_relax glycan_sequon_scanner glycan_tree_relax glycopeptidedocking glycopeptidedocking_diglyco_long helical_bundle_predict helical_bundle_predict_sequence helical_bundle_predict_skipping_residues hotspot_graft hotspot_hashing hotspot_stub_constraints hts_io identify_cdr_clusters interface_energy iphold ligand_dock_cholesterol ligand_dock_ensemble ligand_motif_discovery ligand_motif_identification loop_grower_N_term_symm make_symmdef_file match_6cpa match_xml metal_setup minimize_with_elec_dens motif_extraction mp_domain_assembly mp_ligand_interface mp_score_jd2 mpil_find_pore_ahelical mpil_load_implicit_lipids mr_protocols non-canonical_connectivities pH_mode phiselector phosphonate place_simultaneously pose_sewing ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG ppk protocol_metric repack_with_elec_dens resource_database_locator rollmover rosetta_scripts_include rosetta_scripts_jd3 rosetta_scripts_setup rosie_ligand_docking rotamer_probability rs_loophash sasa_metric_options score12_docking score_only_silence secondary_structure_output selected_residue_count_metric simple_glycosylation simple_metric_cache simple_metric_features simple_metric_filter simple_metrics simple_metrics_in_protocols simple_metrics_per_residue site_constraint splice_in_4loops_longer splice_in_4loops_shorter splice_out_H1_H2_longer splice_out_H1_H2_same splice_out_H1_H2_shorter splice_out_H3_longer splice_out_H3_same splice_out_H3_shorter splice_out_L1_L2_longer splice_out_L1_L2_same splice_out_L1_L2_shorter splice_out_L3_longer splice_out_L3_same splice_out_L3_shorter swa_protein_loop_sampler symmetry_data_resource tcrmodel
Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
AnchorFinder BFactorSelector ContactMolecularSurface InterfaceAnalyzer_ligand PDB_diagnostic RBOut SID_rescore antibody_H3 antibody_H3_camelid antibody_designer antibody_designer_camelid antibody_designer_xml antibody_graft antibody_numbering_converter assemble_domains_jd2 binselector binselector_probins cart_min_glycans ccd_ends_graft_mover_rs cluster_alns control_flow_rs create_clash-based_repack_shell create_sequence_motif custom_basetype_packer_palette density_refine dock_with_hotspot_place_simultaneously docking_ensemble docking_ensemble_prepack exclusively_shared_jumps flexpepdock genkic_sugars glycan_clash_check glycan_relax glycan_sequon_scanner glycan_tree_relax glycopeptidedocking glycopeptidedocking_diglyco_long helical_bundle_predict helical_bundle_predict_sequence helical_bundle_predict_skipping_residues hotspot_graft hotspot_hashing hotspot_stub_constraints hts_io identify_cdr_clusters interface_energy iphold ligand_dock_cholesterol ligand_dock_ensemble ligand_motif_discovery ligand_motif_identification loop_grower_N_term_symm make_symmdef_file match_6cpa match_xml metal_setup minimize_with_elec_dens motif_extraction mp_domain_assembly mp_ligand_interface mp_relax_w_ligand mp_score_jd2 mpil_find_pore_ahelical mpil_load_implicit_lipids mr_protocols non-canonical_connectivities pH_mode phiselector phosphonate place_simultaneously pose_sewing ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG ppk protocol_metric repack_with_elec_dens resource_database_locator rollmover rosetta_scripts_include rosetta_scripts_jd3 rosetta_scripts_setup rosie_ligand_docking rotamer_probability rs_loophash sasa_metric_options score12_docking score_only_silence secondary_structure_output selected_residue_count_metric simple_glycosylation simple_metric_cache simple_metric_features simple_metric_filter simple_metrics simple_metrics_in_protocols simple_metrics_per_residue site_constraint splice_in_4loops_longer splice_in_4loops_shorter splice_out_H1_H2_longer splice_out_H1_H2_same splice_out_H1_H2_shorter splice_out_H3_longer splice_out_H3_same splice_out_H3_shorter splice_out_L1_L2_longer splice_out_L1_L2_same splice_out_L1_L2_shorter splice_out_L3_longer splice_out_L3_same splice_out_L3_shorter swa_protein_loop_sampler symmetry_data_resource tcrmodel


branch: master 「№62007」
Commited by: Rocco Moretti
GitHub commit link: 「bc76d3d54a80c178」 「№5694」
Difference from previous tested commit:  code diff
Commit date: 2023-05-10 12:27:20
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.clang.cxx11thread.serialization.python37.PyRosetta.unit mac.clang.python38.PyRosetta.unit mpi mpi.serialization build.header build.levels build.ninja_debug beautification code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.mpi integration.release_debug integration.tensorflow integration.thread integration performance profile linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify util.apps windows.build.debug windows.build.release

Merge pull request #5694 from RosettaCommons/roccomoretti/fix_ssbond_shift Fix how PDB output calculates output residues for SSBONDs. Centralize the calculation of the numbering of output residues. Putting the logic in a single place should yield a consistent calculation for both ATOM and SSBOND lines.

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Test: linux.gcc.mpi.serialization.integration.mpi

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


branch: master 「№62006」
Commited by: Guangfeng Zhou
GitHub commit link: 「d7aa7f94e8be5e9d」 「№6394」
Difference from previous tested commit:  code diff
Commit date: 2023-05-08 19:22:16
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 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.build.debug gcc-9.gcc.build.debug icc.icc.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 mac.clang.bcl.build.debug OpenCL ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics gcc-10.gcc.build.release gcc-11.gcc.build.release gcc-9.gcc.build.release static mac.clang.static.build.release torch.gcc.pytorch.python39.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 performance profile linux.clang.python310.release.PyRosetta.Debug linux.clang.python311.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.python311.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.python311.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel mac.clang.python310.release.PyRosetta.MinSizeRel mac.clang.python311.release.PyRosetta.MinSizeRel mac.clang.python38.release.PyRosetta.MinSizeRel mac.clang.python39.release.PyRosetta.MinSizeRel ubuntu.clang.python310.release.PyRosetta.MinSizeRel ubuntu.clang.python311.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.python311.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.python311.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release mac.clang.python310.release.PyRosetta.Release mac.clang.python311.release.PyRosetta.Release mac.clang.python38.release.PyRosetta.Release mac.clang.python39.release.PyRosetta.Release ubuntu.clang.python310.release.PyRosetta.Release ubuntu.clang.python311.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.sb_talaris13_loop_modeling_ngk_12res.debug 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.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 #6394 from RosettaCommons/guangfeng/galiganddock_vsx_update [GALigandDock] A few updates

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Test: ubuntu.gcc.integration.addsan

Failed sub-tests (click for more details):
ligand_dock_ensemble
Test: linux.gcc.mpi.serialization.integration.mpi

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

Failed sub-tests (click for more details):
Protein-Protein-Docking
Test: mac.clang.python311.release.PyRosetta.MinSizeRel

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Test: mac.clang.python311.release.PyRosetta.Release

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branch: master 「№62005」
Commited by: Rocco Moretti
GitHub commit link: 「b3411a49afedb45f」 「№6389」
Difference from previous tested commit:  code diff
Commit date: 2023-04-27 10:32:30
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.build.debug gcc-9.gcc.build.debug icc.icc.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 mac.clang.bcl.build.debug OpenCL ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug graphics gcc-10.gcc.build.release gcc-11.gcc.build.release gcc-9.gcc.build.release static mac.clang.static.build.release torch.gcc.pytorch.python39.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 performance profile linux.clang.python310.release.PyRosetta.Debug linux.clang.python311.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.python311.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.python311.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel mac.clang.python310.release.PyRosetta.MinSizeRel mac.clang.python311.release.PyRosetta.MinSizeRel mac.clang.python38.release.PyRosetta.MinSizeRel mac.clang.python39.release.PyRosetta.MinSizeRel ubuntu.clang.python310.release.PyRosetta.MinSizeRel ubuntu.clang.python311.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.python311.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.python311.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release mac.clang.python310.release.PyRosetta.Release mac.clang.python311.release.PyRosetta.Release mac.clang.python38.release.PyRosetta.Release mac.clang.python39.release.PyRosetta.Release ubuntu.clang.python310.release.PyRosetta.Release ubuntu.clang.python311.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.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.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.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.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 #6389 from RosettaCommons/roccomoretti/master_fixes Attempt to fix failing tests in master. Assorted fixes for failing tests in master

...
Test: linux.gcc.mpi.serialization.integration.mpi

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

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

Failed sub-tests (click for more details):
FloppyTail
Test: mac.clang.python311.release.PyRosetta.MinSizeRel

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Test: mac.clang.python311.release.PyRosetta.Release

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Test: ubuntu-20.04.clang.python36.scientific.fragments_picking.debug

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Test: ubuntu-20.04.clang.python36.scientific.ligand_scoring_ranking

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Test: ubuntu-20.04.clang.python36.scientific.make_fragments.debug

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Test: ubuntu-20.04.clang.python36.scientific.make_fragments

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Test: ubuntu-20.04.clang.python36.scientific.mp_f19_sequence_recovery

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Test: ubuntu-20.04.clang.python36.scientific.mp_lipid_acc

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branch: master 「№62004」
Commited by: Rocco Moretti
GitHub commit link: 「f1578235c0dc7800」 「№5801」
Difference from previous tested commit:  code diff
Commit date: 2023-04-25 12:16:26
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.python38.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.build.debug gcc-9.gcc.build.debug icc.icc.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 ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug gcc-10.gcc.build.release gcc-11.gcc.build.release gcc-9.gcc.build.release static torch.gcc.pytorch.python39.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 performance profile linux.clang.python310.release.PyRosetta.Debug linux.clang.python311.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.python311.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.python311.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel ubuntu.clang.python310.release.PyRosetta.MinSizeRel ubuntu.clang.python311.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.python311.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.python311.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release ubuntu.clang.python310.release.PyRosetta.Release ubuntu.clang.python311.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.ligand_scoring_ranking 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 unit.ubsan unit.valgrind gcc-10.gcc.unit gcc-11.gcc.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 #5801 from RosettaCommons/roccomoretti/lDDT Add functions to compute lDDT. Code to compute lDDT of two structures. The default settings give results which match that given by https://swissmodel.expasy.org/lddt Unlike the website, this can handle substructures (by passing a residue map), as well as ligand/non-protein residues. You can also pass an rmsd Predicate object to select only certain atoms within the residue (e.g. backbone only or Calpha only). You can also get atom-level statistics, if you want. Not implemented is any consideration for penalties for bond/angle deviations. I also haven't implemented the one-to-many comparison. (Run it multiple times with multiple references and pick the lowest.) It's probably going to be slower than an rmsd calculation. I tried to keep efficiency in mind, but things are slowed down by the need to consider alternate states (e.g. PHE ring flips) to match the official implementation. There's an option to turn that off if you don't want it, or if you're using an atom set (e.g. backbone-only) where it's not relevant. There's probably also other ways of improving the efficiency, but I don't have time at the moment to do efficiency profiling.

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Test: linux.gcc.mpi.serialization.integration.mpi

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

Failed sub-tests (click for more details):
FloppyTail
Test: ubuntu-20.04.clang.python36.scientific.ligand_scoring_ranking

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branch: master 「№62003」
Commited by: Rocco Moretti
GitHub commit link: 「75d0e58efa87407d」 「№6345」
Difference from previous tested commit:  code diff
Commit date: 2023-04-25 12:14:13
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.clang.cxx11thread.serialization.python37.PyRosetta.unit mac.clang.python38.PyRosetta.unit mpi mpi.serialization build.header build.levels build.ninja_debug beautification 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.MinSizeRel release.PyRosetta.Release scientific.ligand_scoring_ranking linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify util.apps windows.build.debug windows.build.release

Merge pull request #6345 from RosettaCommons/roccomoretti/pdb_loading_small_tweaks A set of small efficiency tweaks for PDB Loading Small inefficiencies I found when looking into PDB loading speeds. Mostly doing work we don't really have to do (refolding, creating new objects which aren't used). These probably account for a ~2% speedup in my test set.

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Test: linux.gcc.mpi.serialization.integration.mpi

Failed sub-tests (click for more details):
replica_docking
Test: mac.clang.python311.release.PyRosetta.MinSizeRel

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Test: mac.clang.python311.release.PyRosetta.Release

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branch: master 「№62002」
Commited by: Rocco Moretti
GitHub commit link: 「28b344ef7da98efe」 「№6353」
Difference from previous tested commit:  code diff
Commit date: 2023-04-25 12:12:13
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.clang.cxx11thread.serialization.python37.PyRosetta.unit mac.clang.python38.PyRosetta.unit mpi mpi.serialization build.header build.levels build.ninja_debug beautification 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.MinSizeRel release.PyRosetta.Release scientific.ligand_scoring_ranking scientific.mp_f19_sequence_recovery linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify util.apps windows.build.debug windows.build.release

Merge pull request #6353 from RosettaCommons/roccomoretti/speed_VDDistanceMatrix Speed up NBR distance calculation. It looks like the slow bit of loading types from the Chemical Components Dictionary is the find_nbr_dist() calc. The slow bit looks to be data structure access in the Floyd-Warshall. Right now we're using a map of maps. If we can use compact data storage (and integer indexes), we can speed this up greatly. The find_nbr_dist() function gets ~50 times faster, though given the total time we spend in it, the overall speedup due to this fix is probably ~1% at most (depending on how many CCD components you have.)

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Test: linux.gcc.mpi.serialization.integration.mpi

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

Failed sub-tests (click for more details):
per_residue_solvent_exposure
Test: mac.clang.python311.release.PyRosetta.MinSizeRel

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Test: mac.clang.python311.release.PyRosetta.Release

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Test: ubuntu-20.04.clang.python36.scientific.mp_f19_sequence_recovery

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branch: master 「№62001」
Commited by: Sergey Lyskov
GitHub commit link: 「9045c942a9345d58」
Difference from previous tested commit:  code diff
Commit date: 2023-04-20 14:31:51
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.python38.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.build.debug gcc-9.gcc.build.debug icc.icc.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 ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug gcc-10.gcc.build.release gcc-11.gcc.build.release gcc-9.gcc.build.release static torch.gcc.pytorch.python39.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 performance profile linux.clang.python310.release.PyRosetta.Debug linux.clang.python311.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.python311.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.python311.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel mac.clang.python311.release.PyRosetta.MinSizeRel ubuntu.clang.python310.release.PyRosetta.MinSizeRel ubuntu.clang.python311.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.python311.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.python311.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release mac.clang.python311.release.PyRosetta.Release ubuntu.clang.python310.release.PyRosetta.Release ubuntu.clang.python311.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.mp_f19_sequence_recovery 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 unit.ubsan unit.valgrind gcc-10.gcc.unit gcc-11.gcc.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

triggering clean rebuild

...
Test: linux.gcc.mpi.serialization.integration.mpi

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

Failed sub-tests (click for more details):
instantiate_modules_packer_palettes
Test: mac.clang.python311.release.PyRosetta.MinSizeRel

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Test: mac.clang.python311.release.PyRosetta.Release

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Test: ubuntu-20.04.clang.python36.scientific.mp_f19_sequence_recovery

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branch: master 「№62000」
Commited by: hochshi
GitHub commit link: 「263f6d95f6fd3e44」 「№6385」
Difference from previous tested commit:  code diff
Commit date: 2023-04-15 01:05:18
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.python38.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.build.debug gcc-9.gcc.build.debug icc.icc.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 ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug gcc-10.gcc.build.release gcc-11.gcc.build.release gcc-9.gcc.build.release static torch.gcc.pytorch.python39.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 performance profile linux.clang.python310.release.PyRosetta.Debug linux.clang.python311.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.python311.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.python311.release.PyRosetta.MinSizeRel m1.clang.python38.release.PyRosetta.MinSizeRel m1.clang.python39.release.PyRosetta.MinSizeRel mac.clang.python310.release.PyRosetta.MinSizeRel mac.clang.python311.release.PyRosetta.MinSizeRel mac.clang.python38.release.PyRosetta.MinSizeRel mac.clang.python39.release.PyRosetta.MinSizeRel ubuntu.clang.python310.release.PyRosetta.MinSizeRel ubuntu.clang.python311.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.python311.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.python311.release.PyRosetta.Release m1.clang.python38.release.PyRosetta.Release m1.clang.python39.release.PyRosetta.Release mac.clang.python310.release.PyRosetta.Release mac.clang.python311.release.PyRosetta.Release mac.clang.python38.release.PyRosetta.Release mac.clang.python39.release.PyRosetta.Release ubuntu.clang.python310.release.PyRosetta.Release ubuntu.clang.python311.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.docking_ensemble scientific.mp_f19_sequence_recovery 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 unit.ubsan unit.valgrind gcc-10.gcc.unit gcc-11.gcc.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 #6385 from RosettaCommons/hochshi/feat/c14_c17 Making Rosetta c++14/17 compliant.

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Test: linux.clang.build.release

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Test: linux.gcc.mpi.serialization.integration.mpi

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

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Test: mac.clang.python39.integration

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


branch: master 「№61999」
Commited by: Andy Watkins
GitHub commit link: 「05235b789e20edd7」 「№6386」
Difference from previous tested commit:  code diff
Commit date: 2023-04-12 21:59:31
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.python38.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.build.debug gcc-9.gcc.build.debug icc.icc.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 ubuntu.clang.bcl.build.debug ubuntu.gcc.bcl.build.debug build.header build.levels build.ninja_debug gcc-10.gcc.build.release gcc-11.gcc.build.release gcc-9.gcc.build.release static torch.gcc.pytorch.python39.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 performance profile linux.clang.python310.release.PyRosetta.Debug linux.clang.python311.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.python311.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