Pushed Revisions

Merge pull request #5909 from RosettaCommons/aleaverfay/fix_lr_bg_energy_accum_in_pack_daemon Fixing a bug in MSD background long-range energy calc; only affected multistate design runs. Previously, long range two body energies for pairs of background residues were not being accumulated into the background_energies_ which would lead to 1) inaccurate representation of total energies of the states that were being repacked and 2) a significant delta between those states and poses that were not being packed at all. This affected both the disulfide and rama_prepro terms.

Merge pull request #5914 from RosettaCommons/revert-5573-vmullig/citation_info_in_docs Temporarily revert "Ensure that the CitationManager exports citation information in the auto-generated documentation" Reverts RosettaCommons/main#5573 This PR created the following problems: - Unit tests time out on older hardware. - Profile tests use more memory. Both are likely due to some subset of movers, filters, etc. loading large amounts of data on instantiation (since all movers, filters, etc. are now instantiated once during XSD generation). This likely needs to be fixed before re-merging this. @JackMaguire @roccomoretti

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Test: linux.clang.code_quality.submodule_regression

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

Failed sub-tests (click for more details):
backbonegridsampler_nstruct_mode features_pdb_mpi helical_bundle_predict helical_bundle_predict_psipred helical_bundle_predict_psipred_with_helix_globals helical_bundle_predict_sequence helical_bundle_predict_skipping_residues recon_design_mpi threefold_symm_peptide_design

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
AddConstraintsToCurrentConformationMover AlignPDBInfoToSequences ConsensusLoopDesign ContactMolecularSurface DumpTrajectoryEnergy DumpTrajectoryEnergy_packing Enzrevert_xml FilterReportAsPoseExtraScoresMover FlipChirality HelixBendFilter InterfaceAnalyzer InterfaceDdG LayerDesign LayerDesign_symm LayerSelector LoopAnalyzer LoopLengthChange ModifyVariantTypeMover MutateResidue_selector OversaturatedHbondAcceptorFilter PeptideCyclizeMover PeptideStubMover_prependRepeat PolarDesign2019 RBOut ReadResfile_with_selector SSElementSelector SecondaryStructureFilter StrandCurvatureByLevels StrandHelixGeometryFilter TryDisulfPermutations UnsatSelector add_constraints_to_current_conformation add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup add_job_pair_data antibody_designer_xml autosetup_metals_centroid backbonegridsampler backbonegridsampler_multiresidue backbonegridsampler_nstruct_mode backrub backrub_interface_ddG bin_initialization bin_perturbation binselector binselector_probins bundlegridsampler bundlegridsampler_composition_energy bundlegridsampler_composition_energy_fract_range bundlegridsampler_copy_pitch bundlegridsampler_design bundlegridsampler_design_nstruct_mode bundlegridsampler_epsilon bundlegridsampler_multirepeat bundlegridsampler_z0_offset bundlegridsampler_z1_offset bundlereporter_filter buried_area_filter buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm cart_min_glycans ccd_ends_graft_mover_rs central_class_modification centroid_from_fullatom cleanAlignment coarse_rna_scoring composition_energy_layers constraints_metric control_flow_rs copy_rotamer_mover create_sequence_motif crosslinkermover_1_4_bbmb_asymm crosslinkermover_1_4_bbmb_c2_symmetry crosslinkermover_1_4_bbmb_s2_symm crosslinkermover_octahedral crosslinkermover_octahedral_s2_symm crosslinkermover_square_planar crosslinkermover_square_planar_d2_symm crosslinkermover_square_pyramidal crosslinkermover_tetrahedral_metal crosslinkermover_tetrahedral_metal_asp crosslinkermover_tetrahedral_metal_c2_symmetry crosslinkermover_tetrahedral_metal_d2_symmetry crosslinkermover_tma crosslinkermover_tma_symm crosslinkermover_trigonal_planar crosslinkermover_trigonal_planar_c3_symm crosslinkermover_trigonal_pyramidal crosslinkermover_trigonal_pyramidal_c3_symm cst_info custom_basetype_packer_palette cycpep_design_pipeline cycpep_rdkit_metric cycpep_rigid_body_permutation_mover cycpep_symmetry_filter d_workflow database_session_resource ddG_scan ddG_sym design_w_custom_palette-CAAs design_w_custom_palette-NCAAs design_w_custom_palette-RNA disulfidize_beta_cys dna_interface_design dock_with_hotspot_place_simultaneously enumerative_sampling enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym evolution farnesyl fast_relax_scripts favor_coupling_tensor favor_native_residue features features_parallel features_pdb fold_from_loops fuzzy ga_ligand_dock ga_ligand_dock_amino_acid genkic_bin_perturbing genkic_bin_sampling genkic_bin_setting genkic_dihedral_copying genkic_lowmemory_mode genkic_rama_filter genkic_ramaprepro_sampling genkic_sugars glycan_anomers glycan_refinment glycan_relax glycan_sequon_scanner glycan_tree_relax grid_scores_features hbnet hbnet_asymm hbnet_energy hbnet_energy_rosettascripts_linear hbnet_energy_symm hbnet_use_input_rot hbondstoresidue_selector helical_bundle helical_bundle_nonideal helical_bundle_predict helical_bundle_predict_psipred helical_bundle_predict_psipred_with_helix_globals helical_bundle_predict_sequence helical_bundle_predict_skipping_residues homodimer_fnd_ref2015_memb hotspot_graft hotspot_stub_constraints hts_io hybridization interaction_graph_summary_metric iphold job_definition_script_vars kinemage_grid_output 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 match_xml metropolis_hastings mf_fixbb_des mf_fixbb_sc mf_flexbb_sc mhc_epitope mhc_epitope_nmer_preload minimize_with_elec_dens mirror_symm motif_score_filter mp_ligand_interface mp_quick_relax_ref2015_memb mp_relax mp_span_ang_ref2015_memb mp_symmetry_load multistage_rosetta_scripts multistage_rosetta_scripts_clustering netcharge_design netcharge_design_symm nonideal_rtmin oligourea_design pertmin perturb_helical_bundle perturb_helical_bundle_copying_pitch perturb_helical_bundle_epsilon perturb_helical_bundle_setting perturb_helical_bundle_z_offset phiselector place_simultaneously pna_base_pairs pose_sewing posttranslationalmod_io ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG ppk protocol_metric rama_mutation_selector rdkit_metrics real_virt_mover recon_design referencepose_mutateresidue remodel_disulfides_rosettascripts remodel_helical_repeat repack_with_elec_dens repeat_propagate repeat_propagate_v2 repeat_propagate_v3 repeat_relax res_lipo_ref2015_memb resource_database_locator rollmover rosetta_scripts_hbond_options rosetta_scripts_include rosetta_scripts_info rosetta_scripts_jd3 rosetta_scripts_loops rosetta_scripts_setup rosie_ligand_docking rotamer_probability rs_flexbbmoves rs_loophash sasa_metric_options score12_docking score_only_silence sdf_reader secondary_structure_output seed_ensemble_JD2_JI selected_residue_count_metric sequence_profile_constraints set_torsion simple_glycosylation simple_grafting_movers simple_hbondstoatom simple_metric_cache simple_metric_features simple_metric_filter simple_metrics simple_metrics_in_protocols simple_metrics_per_residue small_molecule_lattice_dock smallmover_resselector 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 swm_add_rosettascripts symm_disulfidize symm_rotamer_boltzmann symmetric_cycpep_align_and_symmetrize symmetrical_residue_selector symmetry_data_resource target_clash task_selector threefold_symm_peptide_design threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric tna_base_pairs trRosettaConstraintGenerator_rosettascripts trRosettaProtocolMover_rosettascripts trRosettaProtocolMover_rosettascripts_diskwrite trRosettaProtocolMover_rosettascripts_diskwrite_only voids_penalty_energy_design voids_penalty_energy_design_symmetry write_mol_file

Test: linux.clang.tensorflow.integration.tensorflow

Failed sub-tests (click for more details):
abinitio_with_trRosetta smart_annealer tensorflow_manager trRosettaConstraintGenerator trRosettaConstraintGenerator_rosettascripts trRosettaProtocolMover trRosettaProtocolMover_rosettascripts trRosettaProtocolMover_rosettascripts_diskwrite trRosettaProtocolMover_rosettascripts_diskwrite_only trRosetta_test_predict trRosetta_test_predict_ubiquitin trRosetta_test_predict_ubiquitin_cst_file_write trRosetta_test_predict_ubiquitin_cst_file_write_only trRosetta_test_predict_ubiquitin_init_by_bins

Test: linux.gcc.cxx11thread.integration.thread

Failed sub-tests (click for more details):
multithreaded_fastdesign multithreaded_fixbb multithreaded_packrotamersmover

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):
AddConstraintsToCurrentConformationMover AlignPDBInfoToSequences ConsensusLoopDesign ContactMolecularSurface DumpTrajectoryEnergy DumpTrajectoryEnergy_packing Enzrevert_xml FilterReportAsPoseExtraScoresMover FlipChirality HelixBendFilter InterfaceAnalyzer InterfaceDdG LayerDesign LayerDesign_symm LayerSelector LoopAnalyzer LoopLengthChange ModifyVariantTypeMover MutateResidue_selector OversaturatedHbondAcceptorFilter PeptideCyclizeMover PeptideStubMover_prependRepeat PolarDesign2019 RBOut ReadResfile_with_selector SSElementSelector SecondaryStructureFilter StrandCurvatureByLevels StrandHelixGeometryFilter TryDisulfPermutations UnsatSelector add_constraints_to_current_conformation add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup add_job_pair_data antibody_designer_xml autosetup_metals_centroid backbonegridsampler backbonegridsampler_multiresidue backbonegridsampler_nstruct_mode backrub backrub_interface_ddG bin_initialization bin_perturbation binselector binselector_probins bridge_chains bundlegridsampler bundlegridsampler_composition_energy bundlegridsampler_composition_energy_fract_range bundlegridsampler_copy_pitch bundlegridsampler_design bundlegridsampler_design_nstruct_mode bundlegridsampler_epsilon bundlegridsampler_multirepeat bundlegridsampler_z0_offset bundlegridsampler_z1_offset bundlereporter_filter buried_area_filter buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm cart_min_glycans ccd_ends_graft_mover_rs central_class_modification centroid_from_fullatom cleanAlignment coarse_rna_scoring composition_energy_layers constraints_metric control_flow_rs copy_rotamer_mover create_sequence_motif crosslinkermover_1_4_bbmb_asymm crosslinkermover_1_4_bbmb_c2_symmetry crosslinkermover_1_4_bbmb_s2_symm crosslinkermover_octahedral crosslinkermover_octahedral_s2_symm crosslinkermover_square_planar crosslinkermover_square_planar_d2_symm crosslinkermover_square_pyramidal crosslinkermover_tetrahedral_metal crosslinkermover_tetrahedral_metal_asp crosslinkermover_tetrahedral_metal_c2_symmetry crosslinkermover_tetrahedral_metal_d2_symmetry crosslinkermover_tma crosslinkermover_tma_symm crosslinkermover_trigonal_planar crosslinkermover_trigonal_planar_c3_symm crosslinkermover_trigonal_pyramidal crosslinkermover_trigonal_pyramidal_c3_symm cst_info custom_basetype_packer_palette cycpep_design_pipeline cycpep_rdkit_metric cycpep_rigid_body_permutation_mover cycpep_symmetry_filter d_workflow database_session_resource ddG_scan ddG_sym design_w_custom_palette-CAAs design_w_custom_palette-NCAAs design_w_custom_palette-RNA disulfidize_beta_cys dna_interface_design dock_with_hotspot_place_simultaneously enumerative_sampling enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym evolution farnesyl fast_relax_scripts favor_coupling_tensor favor_native_residue features features_parallel features_pdb fold_from_loops fuzzy ga_ligand_dock ga_ligand_dock_amino_acid genkic_bin_perturbing genkic_bin_sampling genkic_bin_setting genkic_dihedral_copying genkic_lowmemory_mode genkic_rama_filter genkic_ramaprepro_sampling genkic_sugars glycan_anomers glycan_refinment glycan_relax glycan_sequon_scanner glycan_tree_relax grid_scores_features hbnet hbnet_asymm hbnet_energy hbnet_energy_rosettascripts_linear hbnet_energy_symm hbnet_use_input_rot hbondstoresidue_selector helical_bundle helical_bundle_nonideal helical_bundle_predict helical_bundle_predict_psipred helical_bundle_predict_psipred_with_helix_globals helical_bundle_predict_sequence helical_bundle_predict_skipping_residues homodimer_fnd_ref2015_memb hotspot_graft hotspot_stub_constraints hts_io hybridization interaction_graph_summary_metric inverse_rotamer_remodel iphold job_definition_script_vars kinemage_grid_output 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 match_xml metropolis_hastings mf_fixbb_des mf_fixbb_sc mf_flexbb_sc mhc_epitope mhc_epitope_nmer_preload minimize_with_elec_dens mirror_symm motif_score_filter mp_ligand_interface mp_quick_relax_ref2015_memb mp_relax mp_relax_w_ligand mp_span_ang_ref2015_memb mp_symmetry_load multistage_rosetta_scripts multistage_rosetta_scripts_clustering netcharge_design netcharge_design_symm nonideal_rtmin oligourea_design pertmin perturb_helical_bundle perturb_helical_bundle_copying_pitch perturb_helical_bundle_epsilon perturb_helical_bundle_setting perturb_helical_bundle_z_offset phiselector place_simultaneously pna_base_pairs pose_sewing posttranslationalmod_io ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG ppk protocol_metric rama_mutation_selector rdkit_metrics real_virt_mover recon_design referencepose_mutateresidue remodel_disulfides_rosettascripts remodel_helical_repeat repack_with_elec_dens repeat_propagate repeat_propagate_v2 repeat_propagate_v3 repeat_relax res_lipo_ref2015_memb resource_database_locator rollmover rosetta_scripts_hbond_options rosetta_scripts_include rosetta_scripts_info rosetta_scripts_jd3 rosetta_scripts_loops rosetta_scripts_setup rosie_ligand_docking rotamer_probability rs_flexbbmoves rs_loophash sasa_metric_options score12_docking score_only_silence sdf_reader secondary_structure_output seed_ensemble_JD2_JI selected_residue_count_metric sequence_profile_constraints set_torsion simple_glycosylation simple_grafting_movers simple_hbondstoatom simple_metric_cache simple_metric_features simple_metric_filter simple_metrics simple_metrics_in_protocols simple_metrics_per_residue small_molecule_lattice_dock smallmover_resselector 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 swm_add_rosettascripts symm_disulfidize symm_rotamer_boltzmann symmetric_cycpep_align_and_symmetrize symmetrical_residue_selector symmetry_data_resource target_clash task_selector threefold_symm_peptide_design threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric tna_base_pairs trRosettaConstraintGenerator_rosettascripts trRosettaProtocolMover_rosettascripts trRosettaProtocolMover_rosettascripts_diskwrite trRosettaProtocolMover_rosettascripts_diskwrite_only voids_penalty_energy_design voids_penalty_energy_design_symmetry write_mol_file

Test: linux.clang.profile

Failed sub-tests (click for more details):
build_rotamers ligand_dock_7cpa monte_carlo_hbnet relax_native rosie_ligand_dock

Merge pull request #5888 from RosettaCommons/BYachnin/add_setters_for_sheettopology_helixkink Add getters and setters to HelixKinkFilter and SheetTopologyFilter These classes have very little in the way of getters and setters to access and modify member data. This makes it tricky to use natively in PyRosetta without XML parsing. This PR simply adds getters and setters to the classes. Thanks Vikram for the review.

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running	Test is Running right now
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	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit