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Revisions №60396

branch: master 「№60396」
Commited by: Vikram K. Mulligan
GitHub commit link: 「89f026f6774b0d60」 「№653」
Difference from previous tested commit:  code diff
Commit date: 2018-09-12 12:14:12
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile 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

Merge pull request #653 from RosettaCommons/vmullig/npro_not_a_donor Removes DONOR property from Npro atom type The Npro atom type was incorrectly listed as a hydrogen bond donor. This results in its Lennard-Jones radius being shrunk, and bad things happening in protocols that iterate over donors and whatnot. We've had the pull request to correct this open for three years, and have agreed at more than one meeting that it should be merged. Frank confirmed in 2016 that while the change does have a small effect on numerical values of scores, it doesn't alter his scientific benchmarks. It seems that everyone's on board with this being merged, so here we go. ***SCORING TESTS WILL SHOW SMALL NUMERICAL CHANGES*** Virtually all integration test trajectories are likely to change. Prepare for lots of observer e-mails as integration tests change. This is expected.

Rocco Moretti 1 year
I don't know if this commit is directly responsible, but it looks like this commit is the first one which causes the mac.clang.integration hotspot_hashing test to consistently hard-fail with a timeout error. It's probably worth looking into if this change substantially alters the runtime of this test (and if so, why and if there's an easy way to correct it.)
Vikram K. Mulligan 1 year
Yes, this change likely resulted in small trajectory changes that are resulting in a big change in runtime (possibly because some filter isn't being satisfied as soon or something like that). The best solution might just be to play with the random seed for the test. [list]
Rocco Moretti 1 year
It also killed the linux.clang.performance.protocols_optimization_Minimizer_dfpmin_armijo_nonmonotone performance test -- it's running about a third of what it once was (consistently in future releases, too). Is that just because of the particular structure being tested, or is that more of a reflection in a global slowdown of minimization?
Vikram K. Mulligan 1 year
Since the only thing that has changed is a database change (removing DONOR from the Npro atom type, with all other changes being corrections to the expected outputs in unit tests), I don't see how this could have fundamentally changed the minimizer. It must be the particular structure being tested. [list]
Rocco Moretti 1 year
Over the weekend I ran a runtime length test across various proteins. On the whole there doesn't seem to be any change pre/post commit, so it does look like it may be just a quirk of the particular structure being tested.
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Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
AnchoredDesign ConsensusLoopDesign DumpTrajectoryEnergy Enzrevert_xml FloppyTail HelixBendFilter InterfaceAnalyzer InterfaceAnalyzer_allscores InterfaceAnalyzer_bothpack InterfaceAnalyzer_ligand InterfaceAnalyzer_prepack InterfaceAnalyzer_resfile InterfaceAnalyzer_tracer KIC_refine KIC_vicinity KIC_with_fragments LayerDesign LayerDesign_ncaas LoopAnalyzer MutateResidue_selector PeptideCyclizeMover RBOut RescorePDDF ResidueDisorder SecondaryStructureFilter SnugDock StrandCurvatureByLevels StrandHelixGeometryFilter UBQ_E2_thioester UBQ_E2_thioester_extra_bodies UBQ_E2_thioester_two_ubiquitins UBQ_Gp_CYD-CYD UBQ_Gp_LYX-Cterm UnsatSelector add_constraints_to_current_conformation antibody_H3 antibody_H3_camelid antibody_designer antibody_graft antibody_numbering_converter assemble_domains_jd2 autosetup_metals_centroid backrub backrub_interface_ddG backrub_pilot batch_relax beta_strand_homodimer broker_membrane bundlegridsampler_multirepeat buried_area_filter cart_min_glycans ccd_ends_graft_mover_rs classic_relax_1a19 cleanAlignment cluster_alns constel copy_rotamer_mover coupled_moves create_sequence_motif cyclization cycpep_design_pipeline d_workflow database_session_resource ddG_ensemble ddG_of_mutation ddG_scan density_refine dna_interface_design dock_glycans dock_with_hotspot_place_simultaneously docking_distance_constraints docking_ensemble docking_ensemble_prepack docking_full_protocol docking_local_refine docking_local_refine_min docking_prepack docking_site_constraints doug_dock_design_min_mod2_cal_cal drrafter_run entropy_correction enumerative_sampling enzdes enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym evolution extract_atomtree_diffs farnesyl fast_relax favor_native_residue features fix_alignment_to_match_pdb fixbb flexpepdock flexpepdock_abinitio fold_from_loops fuzzy genkic_sugars geometric_solvation glycan_relax glycan_sequon_scanner glycan_tree_relax glycan_tree_relax_build_single glycan_tree_relax_quench hbnet_use_input_rot hbonds hbonds_sp2 hbs_design helix_from_sequence hotspot_graft hotspot_hashing hotspot_stub_constraints hts_io hybridization hydrate hydrate_relax identify_cdr_clusters ig_dump inv_kin_lig_loop_design inverse_rotamer_remodel jd2test_PDBIO jd2test_PDBin_mmCIFout jd2test_PDBin_mmCIFout_extra_data_separate jd2test_mmCIFIO jd2test_mmCIFin_PDBout jrelax jscore kinemage_grid_output kinematic_looprelax ligand_database_io ligand_dock_7cpa ligand_dock_ensemble ligand_dock_grid ligand_dock_script ligand_motif_design ligand_water_docking longest_continuous_polar_segment_filter loop_creation loop_grower_N_term_symm loop_modeling make_and_perturb_bundle_multirepeat make_symmdef_file membrane_relax membrane_relax_hbond metal_setup metalloprotein_abrelax metropolis_hastings mf_fixbb_des min_pack_min minimize_with_elec_dens mirror_symm motif_dna_packer_design mp_dock mp_dock_prepack mp_dock_setup mp_domain_assembly mp_find_interface mp_interface_statistics mp_mutate_relax mp_mutate_repack mp_range_relax mp_relax mp_relax_w_ligand mp_score_jd2 mp_symdock mp_symmetry_load mp_transform mp_transform_optimize mp_vis_emb mpi_multistate_design mr_protocols msd_mover multistage_rosetta_scripts mutate ncaa_fixbb next_generation_KIC non-canonical_connectivities nonideal_rtmin oligourea_design oligourea_predict oop_design oop_dock_design orbitals pepspec pepspec_anchor_dock peptiderive per_residue_energies pertmin phosphonate place_simultaneously pna pna_base_pairs pocket_measure pocket_relax ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG ppk protocol_metric pwsho rama_mutation_selector range_relax_w_cst readin_dna_rna_protein relax_w_allatom_cst remodel remodel_disulfides remodel_disulfides_rosettascripts remodel_helical_repeat repack_with_elec_dens repeat_propagate_v2 residue_energy_breakdown resource_database_locator rna_denovo_RNP_refine_native rna_denovo_dna_bridge rnp_ddg_calc_mut rnp_ddg_calc_wt rnp_ddg_relax_command_1 rnp_ddg_relax_command_2 rollmover rosetta_scripts_jd3 rosetta_scripts_loops rosetta_scripts_setup rosie_ligand_docking rotamer_probability rotamer_recovery rs_flexbbmoves rs_loophash sample_tilt_angles scaffold_matcher score12_docking score_jd2 score_only_silence sdf_reader secondary_structure_output selected_residue_count_metric sequence_profile_constraints sequence_tolerance simple_cycpep_predict_angle simple_cycpep_predict_anglelength simple_cycpep_predict_cartesian simple_cycpep_predict_cispro simple_cycpep_predict_nterm_isopeptide_lariat simple_cycpep_predict_nterm_isopeptide_lariat_tailless simple_cycpep_predict_setting simple_cycpep_predict_tbmb simple_dna_test simple_glycosylation simple_grafting_movers simple_hbondstoatom simple_metric_cache simple_metric_features simple_metrics simple_metrics_per_residue small_molecule_lattice_dock 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 startfrom_file stored_residue_subset supercharge swa_protein_CCDclose swa_protein_build_at_Cterminus swa_protein_build_at_Nterminus swa_protein_combine_loops swa_protein_loop_sampler swa_protein_prepack swm_dna_bridge swm_protein_from_scratch symm_rotamer_boltzmann symmetrical_residue_selector symmetry_data_resource task_selector test1_benchmark test_computed_saxs_spectrum threefold_symm_peptide_design threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric torsion_restricted_sampling vip write_mol_file zinc_heterodimer zinc_homodimer_design zinc_homodimer_setup
Test: mac.clang.integration

Failed sub-tests (click for more details):
AnchoredDesign ConsensusLoopDesign DumpTrajectoryEnergy Enzrevert_xml FloppyTail HelixBendFilter InterfaceAnalyzer InterfaceAnalyzer_allscores InterfaceAnalyzer_bothpack InterfaceAnalyzer_ligand InterfaceAnalyzer_prepack InterfaceAnalyzer_resfile InterfaceAnalyzer_tracer KIC_refine KIC_vicinity KIC_with_fragments LayerDesign LayerDesign_ncaas LoopAnalyzer MutateResidue_selector PeptideCyclizeMover RBOut RescorePDDF ResidueDisorder SecondaryStructureFilter SnugDock StrandCurvatureByLevels StrandHelixGeometryFilter UBQ_E2_thioester UBQ_E2_thioester_extra_bodies UBQ_E2_thioester_two_ubiquitins UBQ_Gp_CYD-CYD UBQ_Gp_LYX-Cterm UnsatSelector add_constraints_to_current_conformation antibody_H3 antibody_H3_camelid antibody_designer antibody_graft antibody_numbering_converter assemble_domains_jd2 autosetup_metals_centroid backrub backrub_interface_ddG backrub_pilot batch_relax beta_strand_homodimer broker_membrane bundlegridsampler_multirepeat buried_area_filter cart_min_glycans ccd_ends_graft_mover_rs classic_relax_1a19 cleanAlignment cluster_alns constel copy_rotamer_mover coupled_moves create_sequence_motif cyclization cycpep_design_pipeline d_workflow database_session_resource ddG_ensemble ddG_of_mutation ddG_scan density_refine dna_interface_design dock_glycans dock_with_hotspot_place_simultaneously docking_distance_constraints docking_ensemble docking_ensemble_prepack docking_full_protocol docking_local_refine docking_local_refine_min docking_prepack docking_site_constraints doug_dock_design_min_mod2_cal_cal drrafter_run entropy_correction enumerative_sampling enzdes enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym evolution extract_atomtree_diffs farnesyl fast_relax favor_native_residue features fixbb flexpepdock flexpepdock_abinitio fold_from_loops fuzzy genkic_sugars geometric_solvation glycan_relax glycan_sequon_scanner glycan_tree_relax glycan_tree_relax_build_single glycan_tree_relax_quench hbnet_use_input_rot hbonds hbonds_sp2 hbs_design helix_from_sequence hotspot_graft hotspot_hashing hts_io hybridization hydrate hydrate_relax identify_cdr_clusters ig_dump inv_kin_lig_loop_design inverse_rotamer_remodel jd2test_PDBIO jd2test_PDBin_mmCIFout jd2test_PDBin_mmCIFout_extra_data_separate jd2test_mmCIFIO jd2test_mmCIFin_PDBout jrelax jscore kinemage_grid_output kinematic_looprelax ligand_database_io ligand_dock_7cpa ligand_dock_ensemble ligand_dock_grid ligand_dock_script ligand_motif_design ligand_water_docking longest_continuous_polar_segment_filter loop_creation loop_grower_N_term_symm make_and_perturb_bundle_multirepeat make_symmdef_file membrane_relax membrane_relax_hbond metal_setup metalloprotein_abrelax metropolis_hastings mf_fixbb_des min_pack_min minimize_with_elec_dens mirror_symm motif_dna_packer_design mp_dock mp_dock_prepack mp_dock_setup mp_domain_assembly mp_find_interface mp_interface_statistics mp_mutate_relax mp_mutate_repack mp_range_relax mp_relax mp_relax_w_ligand mp_score_jd2 mp_symdock mp_symmetry_load mp_transform mp_transform_optimize mp_vis_emb mpi_multistate_design mr_protocols msd_mover multistage_rosetta_scripts mutate ncaa_fixbb next_generation_KIC nonideal_rtmin oligourea_design oligourea_predict oop_design oop_dock_design orbitals pepspec pepspec_anchor_dock peptiderive per_residue_energies pertmin phosphonate place_simultaneously pna pna_base_pairs pocket_measure pocket_relax ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG ppk protocol_metric pwsho rama_mutation_selector range_relax_w_cst readin_dna_rna_protein relax_w_allatom_cst remodel remodel_disulfides remodel_disulfides_rosettascripts repack_with_elec_dens repeat_propagate_v2 residue_energy_breakdown resource_database_locator rna_denovo_RNP_refine_native rna_denovo_dna_bridge rnp_ddg_calc_mut rnp_ddg_calc_wt rnp_ddg_relax_command_1 rnp_ddg_relax_command_2 rollmover rosetta_scripts_jd3 rosetta_scripts_loops rosetta_scripts_setup rosie_ligand_docking rotamer_probability rotamer_recovery rs_flexbbmoves rs_loophash sample_tilt_angles scaffold_matcher score12_docking score_jd2 score_only_silence sdf_reader secondary_structure_output selected_residue_count_metric sequence_profile_constraints sequence_tolerance simple_cycpep_predict_angle simple_cycpep_predict_anglelength simple_cycpep_predict_cartesian simple_cycpep_predict_cispro simple_cycpep_predict_nterm_isopeptide_lariat simple_cycpep_predict_nterm_isopeptide_lariat_tailless simple_cycpep_predict_setting simple_cycpep_predict_tbmb simple_dna_test simple_glycosylation simple_grafting_movers simple_hbondstoatom simple_metric_cache simple_metric_features simple_metrics simple_metrics_per_residue small_molecule_lattice_dock 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 startfrom_file stored_residue_subset supercharge swa_protein_CCDclose swa_protein_build_at_Cterminus swa_protein_build_at_Nterminus swa_protein_combine_loops swa_protein_loop_sampler swa_protein_prepack swm_dna_bridge swm_protein_from_scratch symm_rotamer_boltzmann symmetrical_residue_selector symmetry_data_resource task_selector test1_benchmark test_computed_saxs_spectrum threefold_symm_peptide_design threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric torsion_restricted_sampling vip write_mol_file zinc_heterodimer zinc_homodimer_design zinc_homodimer_setup