Index

_

__all__ (in module ovo.core.database.models) __call__() (ovo.app.components.molstar_custom_component.color_picker.ColorPicker method) __do_not_serialize__ (ovo.core.database.models.UnknownWorkflow attribute) __eq__() (ovo.core.database.models.Threshold method) __getattr__() (ovo.core.database.base_db.DBEngine method) __post_init__() (ovo.app.components.molstar_custom_component.dataclasses.StructureVisualization method) (ovo.core.database.models.Design method) __table_args__ (ovo.core.database.models.Pool attribute) (ovo.core.database.models.Project attribute) __tablename__ (ovo.core.database.models.DescriptorJob attribute) (ovo.core.database.models.DescriptorValue attribute) (ovo.core.database.models.Design attribute) (ovo.core.database.models.DesignJob attribute) (ovo.core.database.models.Pool attribute) (ovo.core.database.models.Project attribute) (ovo.core.database.models.Round attribute) (ovo.core.database.models.UserSettings attribute) __version__ (in module ovo) _align_sequences_and_get_indices() (in module ovo.core.utils.pdb) _cache_read() (ovo.core.storage.Storage method) _cache_store() (ovo.core.storage.Storage method) _check_updated() (ovo.core.database.sql_db.SqlDBEngine method) _clear_all_cache() (ovo.core.database.cache_clearing.CacheClearingEngine method) _clear_temp_dir() (ovo.core.storage.Storage method)

_component_func (in module ovo.app.components.contigs_organizer) (in module ovo.app.components.molstar_custom_component) _create_filters() (ovo.core.database.sql_db.SqlDBEngine method) _create_order_by() (ovo.core.database.sql_db.SqlDBEngine method) _create_order_by_single() (ovo.core.database.sql_db.SqlDBEngine method) _create_query() (ovo.core.database.sql_db.SqlDBEngine method) _create_run_command() (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) _create_session() (ovo.core.aws.AWSSessionManager method) (ovo.core.database.sql_db.SqlDBEngine method) _db() (ovo.core.database.db_proxy.DBProxy method) _descriptors_by_key (in module ovo.core.database.descriptors_bindcraft) _get_cached_design_jobs_table() (in module ovo.app.utils.cached_db) _get_default_config_path() (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) _get_exec_dir() (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) _get_module_path() (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) _get_pid() (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) _get_pipeline_dir() (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) _get_shared_module_paths() (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) _get_shared_modules_string() (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) _parse_contigs_with_tuples() (ovo.app.components.molstar_custom_component.contigs_parser.ContigsParser method) _queue_get_address() (ovo.core.scheduler.simple_queue_mixin.SimpleQueueMixin method) _queue_get_auth_key() (ovo.core.scheduler.simple_queue_mixin.SimpleQueueMixin method) _registry (ovo.core.database.models.WorkflowTypes attribute) _run_subprocess() (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) _static_files (in module ovo.app.components.molstar_custom_component)

A

A_PERC (in module ovo.core.database.descriptors_proteinqc) aa2long (in module ovo.core.utils.pdb) aa2num (in module ovo.core.utils.pdb) aa3to1 (in module ovo.core.utils.pdb) accept_atom() (ovo.core.utils.pdb.PDBSegmentSelector method) accept_chain() (ovo.core.utils.pdb.PDBSegmentSelector method) accept_designs_dialog() (in module ovo.app.components.acceptance_thresholds_components) accept_model() (ovo.core.utils.pdb.PDBSegmentSelector method) accept_residue() (ovo.core.utils.pdb.PDBSegmentSelector method) acceptance_thresholds (ovo.core.database.models.DesignWorkflow attribute) (ovo.core.database.models_rfdiffusion.RFdiffusionBinderDesignWorkflow attribute) (ovo.core.database.models_rfdiffusion.RFdiffusionScaffoldDesignWorkflow attribute) accepted (ovo.core.database.models.Design attribute) add_glycan_to_pdb() (in module ovo.core.utils.pdb) admin_debug_page (in module ovo.app.pages) admin_import_export_page (in module ovo.app.pages) admin_users (ovo.core.configuration.AuthConfig attribute) AF2_PRIMARY_BINDER_PAE (in module ovo.core.database.descriptors_refolding) AF2_PRIMARY_DESCRIPTORS (in module ovo.core.database.descriptors_refolding) AF2_PRIMARY_DESIGN_RMSD (in module ovo.core.database.descriptors_refolding) AF2_PRIMARY_IPAE (in module ovo.core.database.descriptors_refolding) AF2_PRIMARY_IPTM (in module ovo.core.database.descriptors_refolding) AF2_PRIMARY_NATIVE_MOTIF_RMSD (in module ovo.core.database.descriptors_refolding) AF2_PRIMARY_PAE (in module ovo.core.database.descriptors_refolding) AF2_PRIMARY_PLDDT (in module ovo.core.database.descriptors_refolding) AF2_PRIMARY_PLDDT_BINDER (in module ovo.core.database.descriptors_refolding) AF2_PRIMARY_PTM (in module ovo.core.database.descriptors_refolding) AF2_PRIMARY_STRUCTURE_PATH (in module ovo.core.database.descriptors_refolding) AF2_PRIMARY_TARGET_ALIGNED_BINDER_RMSD (in module ovo.core.database.descriptors_refolding) AF2_STRUCTURE_PATHS (in module ovo.core.database.descriptors_refolding)

align_multiple_proteins_pdb() (in module ovo.core.utils.pdb) align_protein_global() (in module ovo.core.utils.seq) ALL_DESCRIPTOR_KEYS (in module ovo.core.database.descriptors) ALL_DESCRIPTOR_KEYS_SET (in module ovo.core.database.descriptors) ALL_DESCRIPTORS (in module ovo.core.database.descriptors) ALL_DESCRIPTORS_BY_KEY (in module ovo.core.database.descriptors) allow_private_project_link_access (ovo.core.configuration.AuthConfig attribute) ALPHAFOLD_MODEL_FILES (in module ovo.cli.init) always_require_token (ovo.core.configuration.AuthConfig attribute) app (in module ovo.cli.app) (in module ovo.cli.init) (in module ovo.cli.main) (in module ovo.cli.module) (in module ovo.cli.scheduler_cli) approx_max_width() (in module ovo.app.components.custom_elements) AROMATIC_PERC (in module ovo.core.database.descriptors_proteinqc) AROMATICITY (in module ovo.core.database.descriptors_proteinqc) ASPHERICITY (in module ovo.core.database.descriptors_proteinqc) assert_similar_sequence() (in module ovo.core.utils.tests) ASSETS_PATH (in module ovo.app.utils.page_init) assume_role_arn (ovo.core.configuration.AWSConfig attribute) auth (ovo.core.configuration.OVOConfig attribute) AuthConfig (class in ovo.core.configuration) author (ovo.core.database.models.MetadataMixin attribute) AVG_CHARGE (in module ovo.core.database.descriptors_proteinqc) AVG_CHARGE_NEGATIVE (in module ovo.core.database.descriptors_proteinqc) AVG_CHARGE_POSITIVE (in module ovo.core.database.descriptors_proteinqc) aws (ovo.core.configuration.SchedulerConfig attribute) (ovo.core.configuration.StorageConfig attribute) AWSConfig (class in ovo.core.configuration) AWSSessionManager (class in ovo.core.aws)

B

b_factor_value (ovo.core.database.models.StructureFileDescriptor attribute) backbone_filters (ovo.core.database.models_rfdiffusion.RFdiffusionParams attribute) BACKBONE_METRIC_FIELD_NAMES (in module ovo.core.database.descriptors_rfdiffusion) BACKBONE_METRICS (in module ovo.core.database.descriptors_rfdiffusion) Base (class in ovo.core.database.models) BaseConfigModel (class in ovo.core.configuration) batch_size (ovo.core.database.models_rfdiffusion.RFdiffusionParams attribute) BEND_PERCENTAGE (in module ovo.core.database.descriptors_proteinqc) bias_aa (ovo.core.database.models_rfdiffusion.ProteinMPNNParams attribute)

bindcraft_binder_design_page (in module ovo.app.pages) bindcraft_binder_design_visualization() (in module ovo.app.components.workflow_visualization_components) bindcraft_params (ovo.core.database.models_bindcraft.BindCraftBinderDesignWorkflow attribute) BindCraftBinderDesignWorkflow (class in ovo.core.database.models_bindcraft) BindCraftParams (class in ovo.core.database.models_bindcraft) binder_length (ovo.core.database.models_bindcraft.BindCraftParams attribute) (ovo.core.database.models_rfdiffusion.RFdiffusionBinderDesignWorkflow attribute) BOLTZ_MODEL_FILES (in module ovo.cli.init) build_dir (in module ovo.app.components.contigs_organizer) (in module ovo.app.components.molstar_custom_component)

C

C_PERC (in module ovo.core.database.descriptors_proteinqc) cache_ok (ovo.core.database.encoder.DataclassType attribute) CacheClearingEngine (class in ovo.core.database.cache_clearing) calculate_coords_from_transformed_displacements() (in module ovo.core.utils.pdb) calculate_file_hash() (in module ovo.cli.common) cancel() (in module ovo.cli.scheduler_cli) (ovo.core.scheduler.base_scheduler.Scheduler method) (ovo.core.scheduler.healthomics_scheduler.HealthOmicsScheduler method) (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) CategoricalResidueDescriptor (class in ovo.core.database.models) category_labels (ovo.core.database.models.CategoricalResidueDescriptor attribute) ccd (ovo.core.database.models.DesignChain attribute) chain_id (ovo.app.components.molstar_custom_component.dataclasses.ChainVisualization attribute) chain_ids (ovo.core.database.models.DesignChain attribute) ChainNotFoundError chains (ovo.app.components.molstar_custom_component.dataclasses.StructureVisualization attribute) (ovo.core.database.models.DescriptorValue attribute) (ovo.core.database.models.DescriptorWorkflow attribute) (ovo.core.database.models.DesignSpec attribute) (ovo.core.database.models_bindcraft.BindCraftBinderDesignWorkflow attribute) (ovo.core.database.models_refolding.RefoldingWorkflow attribute) (ovo.core.database.models_rfdiffusion.RFdiffusionBinderDesignWorkflow attribute) ChainVisualization (class in ovo.app.components.molstar_custom_component.dataclasses) CHARGE_5_5 (in module ovo.core.database.descriptors_proteinqc) CHARGE_7_4 (in module ovo.core.database.descriptors_proteinqc) CHARGED_INTEGRAL_5_5 (in module ovo.core.database.descriptors_proteinqc) CHARGED_INTEGRAL_7_4 (in module ovo.core.database.descriptors_proteinqc) CHARGED_INTEGRAL_HIGH_5_5 (in module ovo.core.database.descriptors_proteinqc) CHARGED_INTEGRAL_HIGH_7_4 (in module ovo.core.database.descriptors_proteinqc) CHARGED_INTEGRAL_LOW_5_5 (in module ovo.core.database.descriptors_proteinqc) CHARGED_INTEGRAL_LOW_7_4 (in module ovo.core.database.descriptors_proteinqc) CHARGED_INTEGRAL_NEGATIVE_5_5 (in module ovo.core.database.descriptors_proteinqc) CHARGED_INTEGRAL_NEGATIVE_7_4 (in module ovo.core.database.descriptors_proteinqc) CHARGED_INTEGRAL_POSITIVE_5_5 (in module ovo.core.database.descriptors_proteinqc) CHARGED_INTEGRAL_POSITIVE_7_4 (in module ovo.core.database.descriptors_proteinqc) CHARGED_NEGATIVE_5_5_TOP_PATCH_AREA (in module ovo.core.database.descriptors_proteinqc) CHARGED_NEGATIVE_5_5_TOP_PATCH_AREA_NORM (in module ovo.core.database.descriptors_proteinqc) CHARGED_NEGATIVE_5_5_TOTAL_AREA (in module ovo.core.database.descriptors_proteinqc) CHARGED_NEGATIVE_5_5_TOTAL_AREA_NORM (in module ovo.core.database.descriptors_proteinqc) CHARGED_NEGATIVE_7_4_TOP_PATCH_AREA (in module ovo.core.database.descriptors_proteinqc) CHARGED_NEGATIVE_7_4_TOP_PATCH_AREA_NORM (in module ovo.core.database.descriptors_proteinqc) CHARGED_NEGATIVE_7_4_TOTAL_AREA (in module ovo.core.database.descriptors_proteinqc) CHARGED_NEGATIVE_7_4_TOTAL_AREA_NORM (in module ovo.core.database.descriptors_proteinqc) CHARGED_POSITIVE_5_5_TOP_PATCH_AREA (in module ovo.core.database.descriptors_proteinqc) CHARGED_POSITIVE_5_5_TOP_PATCH_AREA_NORM (in module ovo.core.database.descriptors_proteinqc) CHARGED_POSITIVE_5_5_TOTAL_AREA (in module ovo.core.database.descriptors_proteinqc) CHARGED_POSITIVE_5_5_TOTAL_AREA_NORM (in module ovo.core.database.descriptors_proteinqc) CHARGED_POSITIVE_7_4_TOP_PATCH_AREA (in module ovo.core.database.descriptors_proteinqc) CHARGED_POSITIVE_7_4_TOP_PATCH_AREA_NORM (in module ovo.core.database.descriptors_proteinqc) CHARGED_POSITIVE_7_4_TOTAL_AREA (in module ovo.core.database.descriptors_proteinqc) CHARGED_POSITIVE_7_4_TOTAL_AREA_NORM (in module ovo.core.database.descriptors_proteinqc) check_hotspots() (in module ovo.app.components.trim_components) check_read_only() (ovo.core.database.sql_db.SqlDBEngine method)

CLEAR_FUNCTIONS (in module ovo.core.database.cache_clearing) clear_when_modified() (in module ovo.core.database.cache_clearing) co (in module ovo.app.components.contigs_organizer.main) coerce_types() (in module ovo.core.utils.param_validation) collect_storage_paths() (in module ovo.core.logic.design_logic) color (ovo.app.components.descriptor_scatterplot.PlotSettings attribute) (ovo.app.components.molstar_custom_component.dataclasses.ChainVisualization attribute) (ovo.app.components.molstar_custom_component.dataclasses.ContigSegment attribute) (ovo.app.components.molstar_custom_component.dataclasses.StructureVisualization attribute) color_by (ovo.app.components.descriptor_explorer.HistogramSettings attribute) COLOR_BY_OPTIONS (in module ovo.app.components.descriptor_explorer) color_params (ovo.app.components.molstar_custom_component.dataclasses.ChainVisualization attribute) (ovo.app.components.molstar_custom_component.dataclasses.StructureVisualization attribute) color_scale (ovo.core.database.models.NumericDescriptor attribute) color_type (ovo.app.components.descriptor_scatterplot.PlotSettings attribute) ColorPicker (class in ovo.app.components.molstar_custom_component.color_picker) combine_histograms() (in module ovo.app.utils.protein_qc_plots) comparison (ovo.core.database.models.NumericDescriptor attribute) ConfigProps (class in ovo.core.configuration) confirm_download_button() (in module ovo.app.components.custom_elements) connect_to_queue() (ovo.core.scheduler.simple_queue_mixin.SimpleQueueMixin method) console (in module ovo.cli.common) contig (ovo.core.database.models.DesignChain attribute) (ovo.core.database.models_rfdiffusion.RFdiffusionParams property) contig_index (ovo.core.database.models.Design attribute) contigmap_length (ovo.core.database.models_rfdiffusion.RFdiffusionParams attribute) contigs (ovo.app.components.molstar_custom_component.dataclasses.StructureVisualization attribute) (ovo.core.database.models_rfdiffusion.RFdiffusionParams attribute) contigs_organizer() (in module ovo.app.components.contigs_organizer) contigs_organizer_fragment() (in module ovo.app.components.preview_components) ContigSegment (class in ovo.app.components.molstar_custom_component.dataclasses) ContigsParser (class in ovo.app.components.molstar_custom_component.contigs_parser) copy() (ovo.core.database.models.Threshold method) count() (ovo.core.database.base_db.DBEngine method) (ovo.core.database.db_proxy.DBProxy method) (ovo.core.database.sql_db.SqlDBEngine method) count_distinct() (ovo.core.database.base_db.DBEngine method) (ovo.core.database.db_proxy.DBProxy method) (ovo.core.database.sql_db.SqlDBEngine method) create_new_pool() (in module ovo.app.components.create_new_pool) create_new_round_dialog() (in module ovo.app.components.submission_components) create_partial_diffusion_binder_contig() (in module ovo.core.utils.residue_selection) create_project_dialog() (in module ovo.app.components.sidebar) create_queue_server() (ovo.core.scheduler.simple_queue_mixin.SimpleQueueMixin method) create_zip() (ovo.core.storage.Storage method) created_date_utc (ovo.core.database.models.MetadataMixin attribute) CSS (in module ovo.app.utils.page_init) CURRENT_SECTION_PREFIX (in module ovo.app.components.navigation) custom_advanced_settings (ovo.core.database.models_bindcraft.BindCraftParams attribute) custom_filter_settings (ovo.core.database.models_bindcraft.BindCraftParams attribute) customize_json_settings_component() (in module ovo.app.components.submission_components) cyclic (ovo.core.database.models.DesignChain attribute) cyclic_offset (ovo.core.database.models_rfdiffusion.RFdiffusionParams attribute)

D

D_PERC (in module ovo.core.database.descriptors_proteinqc) data (ovo.core.database.models.UnknownWorkflow attribute) DataclassEncoder (class in ovo.core.database.encoder) DataclassType (class in ovo.core.database.encoder) db (ovo.core.configuration.OVOConfig attribute) DBConfig (class in ovo.core.configuration) DBEngine (class in ovo.core.database.base_db) DBProxy (class in ovo.core.database.db_proxy) default() (ovo.app.components.molstar_custom_component.dataclasses.EnhancedJSONEncoder method) (ovo.core.configuration.OVOConfig class method) (ovo.core.database.encoder.DataclassEncoder method) default_data (in module ovo.core.configuration) default_nextflow_config() (ovo.core.configuration.OVOConfig static method) DEFAULT_OVO_HOME (in module ovo.core.configuration) default_scheduler (ovo.core.configuration.OVOConfig attribute) DENQ_PERC (in module ovo.core.database.descriptors_proteinqc) description (ovo.core.database.models.Descriptor attribute) (ovo.core.database.models.Pool attribute) (ovo.core.database.models.Round attribute) Descriptor (class in ovo.core.database.models) descriptor (ovo.app.components.descriptor_explorer.HistogramSettings attribute) descriptor_explorer() (in module ovo.app.components.descriptor_explorer) descriptor_histogram_component() (in module ovo.app.components.acceptance_thresholds_components) descriptor_histograms() (in module ovo.app.utils.protein_qc_plots) descriptor_job_df (in module ovo.app.pages.debug) descriptor_job_id (ovo.core.database.models.DescriptorValue attribute) descriptor_key (ovo.core.database.models.DescriptorValue attribute) descriptor_overview_tiles() (in module ovo.app.components.descriptor_tiles) descriptor_scatterplot_design_explorer_component() (in module ovo.app.components.descriptor_scatterplot) descriptor_scatterplot_input_component() (in module ovo.app.components.descriptor_scatterplot) descriptor_scatterplot_pool_details_component() (in module ovo.app.components.descriptor_scatterplot) descriptor_table() (in module ovo.app.components.descriptor_table) descriptor_tiles() (in module ovo.app.components.descriptor_tiles) DescriptorJob (class in ovo.core.database.models) DESCRIPTORS (in module ovo.core.database.descriptors_bindcraft) (in module ovo.core.database.descriptors_proteinqc) (in module ovo.core.database.descriptors_refolding) (in module ovo.core.database.descriptors_rfdiffusion)

DescriptorValue (class in ovo.core.database.models) DescriptorWorkflow (class in ovo.core.database.models) deserialize() (ovo.core.database.models.Descriptor method) (ovo.core.database.models.StringResidueDescriptor method) Design (class in ovo.core.database.models) design_df (in module ovo.app.pages.debug) design_id (ovo.core.database.models.DescriptorValue attribute) design_id_to_pool_id() (ovo.core.database.models.Design class method) design_ids (ovo.core.database.models.DescriptorWorkflow attribute) (ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow attribute) DESIGN_IDS_QUERY_PARAM (in module ovo.app.components.navigation) design_job_df (in module ovo.app.pages.debug) design_job_id (ovo.core.database.models.DesignDescriptorWorkflow attribute) (ovo.core.database.models.Pool attribute) design_navigation_selector() (in module ovo.app.components.navigation) design_protocol (ovo.core.database.models_bindcraft.BindCraftParams attribute) design_type (ovo.core.database.models_refolding.RefoldingWorkflow attribute) DesignChain (class in ovo.core.database.models) DesignChainType (in module ovo.core.database.models) DesignDescriptorWorkflow (class in ovo.core.database.models) DesignJob (class in ovo.core.database.models) designs_page (in module ovo.app.pages) DesignSpec (class in ovo.core.database.models) DesignWorkflow (class in ovo.core.database.models) detail_button() (in module ovo.app.components.descriptor_tiles) detail_descriptor_dialog() (in module ovo.app.components.descriptor_tiles) detect_glycosylation_sites() (in module ovo.core.utils.pdb) dir (ovo.core.configuration.OVOConfig attribute) display_current_thresholds() (in module ovo.app.components.acceptance_thresholds_components) download() (in module ovo.cli.scheduler_cli) download_descriptor_table() (in module ovo.app.components.download_component) download_design_files() (in module ovo.app.components.download_component) download_file() (in module ovo.cli.common) download_files() (in module ovo.cli.common) download_job_designs_component() (in module ovo.app.components.download_component) DSSP (in module ovo.core.database.models_proteinqc) DSSP_DESCRIPTORS (in module ovo.core.database.descriptors_proteinqc)

E

E_PERC (in module ovo.core.database.descriptors_proteinqc) enabled (ovo.core.database.models.Threshold attribute) end_res_trimmed_chain (ovo.core.database.models_rfdiffusion.RFdiffusionBinderDesignWorkflow attribute) EnhancedJSONEncoder (class in ovo.app.components.molstar_custom_component.dataclasses) ENTROPY (in module ovo.core.database.descriptors_proteinqc) error (ovo.core.database.models.UnknownWorkflow attribute) error_value (ovo.core.database.models.NumericDescriptor attribute) ESM1V (in module ovo.core.database.descriptors_proteinqc) ESM1V_MODEL_FILES (in module ovo.cli.init) ESM_1V (in module ovo.core.database.models_proteinqc) ESM_DESCRIPTORS (in module ovo.core.database.descriptors_proteinqc) ESM_IF (in module ovo.core.database.models_proteinqc) ESM_IF_MODEL_FILES (in module ovo.cli.init) ESM_IF_NATIVE_SEQ_AVG_LOGITS (in module ovo.core.database.descriptors_proteinqc) ESM_IF_NATIVE_SEQ_SUM_LOGITS (in module ovo.core.database.descriptors_proteinqc)

ESMFOLD_DESCRIPTORS (in module ovo.core.database.descriptors_refolding) ESMFOLD_DESIGN_ALL_ATOM_RMSD (in module ovo.core.database.descriptors_refolding) ESMFOLD_DESIGN_BACKBONE_RMSD (in module ovo.core.database.descriptors_refolding) esmfold_fp16 (ovo.core.database.models_rfdiffusion.RefoldingParams attribute) ESMFOLD_PAE (in module ovo.core.database.descriptors_refolding) ESMFOLD_PLDDT (in module ovo.core.database.descriptors_refolding) ESMFOLD_PTM (in module ovo.core.database.descriptors_refolding) ESMFOLD_STRUCTURE_PATH (in module ovo.core.database.descriptors_refolding) ESMIF (in module ovo.core.database.descriptors_proteinqc) exists() (ovo.core.database.models.WorkflowTypes class method) export_design_descriptors_excel() (in module ovo.core.logic.descriptor_logic) EXPORT_DESIGNS_LIMIT (in module ovo.app.pages.import_export) export_import_project() (in module ovo.core.logic.import_export_logic) export_project() (in module ovo.core.logic.import_export_logic) export_proteinqc_excel() (in module ovo.core.logic.descriptor_logic) export_tab() (in module ovo.app.pages.import_export)

F

F_PERC (in module ovo.core.database.descriptors_proteinqc) fastrelax_cycles (ovo.core.database.models_rfdiffusion.ProteinMPNNParams attribute) FASTRELAX_STRUCTURE_PATH (in module ovo.core.database.descriptors_rfdiffusion) file_exists() (ovo.core.storage.Storage method) FileDescriptor (class in ovo.core.database.models) filter_designs_by_thresholds() (in module ovo.core.logic.filtering_logic) filter_designs_by_thresholds_cached() (in module ovo.app.components.acceptance_thresholds_components) filter_pdb_str() (in module ovo.core.utils.pdb) filter_type (ovo.core.database.models_bindcraft.BindCraftParams attribute) find_id_column() (in module ovo.core.logic.descriptor_logic) find_storage_path_fields() (in module ovo.core.logic.import_export_logic) fix_contigs() (in module ovo.core.utils.pdb) FLAG_ICONS (in module ovo.app.components.descriptor_tiles) flatten_schema() (in module ovo.core.utils.param_validation) FLEXIBILITY_AVG (in module ovo.core.database.descriptors_proteinqc) format() (ovo.core.database.models.NumericDescriptor method) (ovo.core.database.models.Threshold method) format_descriptor_name() (in module ovo.app.components.descriptor_scatterplot) format_duration() (in module ovo.core.utils.formatting)

format_help() (in module ovo.cli.scheduler_cli) format_job_duration() (in module ovo.core.logic.job_logic) format_label() (in module ovo.app.components.history_components) format_pool_status() (in module ovo.core.logic.design_logic) format_range() (in module ovo.app.components.descriptor_scatterplot) format_threshold_value() (in module ovo.app.utils.protein_qc_plots) from_contig_to_residues() (in module ovo.core.utils.residue_selection) from_dict() (ovo.core.database.models.DesignSpec class method) (ovo.core.database.models.Workflow class method) (ovo.core.database.models.WorkflowParams class method) (ovo.core.database.models_bindcraft.BindCraftParams class method) from_hotspots_to_segments() (in module ovo.core.utils.residue_selection) from_pdb_file() (ovo.core.database.models.Design class method) from_pdb_str() (ovo.core.database.models.DesignSpec class method) from_query_params() (ovo.app.components.descriptor_explorer.HistogramSettings class method) (ovo.app.components.descriptor_scatterplot.PlotSettings class method) from_residues_to_chain_breaks() (in module ovo.core.utils.residue_selection) from_residues_to_hotspots() (in module ovo.core.utils.residue_selection) from_residues_to_segments() (in module ovo.core.utils.residue_selection) from_segments_to_hotspots() (in module ovo.core.utils.residue_selection)

G

G_PERC (in module ovo.core.database.descriptors_proteinqc) generate_descriptor_values_for_design() (in module ovo.core.logic.descriptor_logic) generate_id() (in module ovo.core.utils.formatting) (ovo.core.database.models.DescriptorJob class method) (ovo.core.database.models.Pool class method) get() (ovo.core.database.base_db.DBEngine method) (ovo.core.database.db_proxy.DBProxy method) (ovo.core.database.models.WorkflowTypes class method) (ovo.core.database.sql_db.SqlDBEngine method) (ovo.core.scheduler.simple_queue_mixin.TaskQueue method) get_account_id() (ovo.core.aws.AWSSessionManager method) get_aligned_structure_as_string() (in module ovo.core.utils.pdb) get_alphanumeric_sort_key() (in module ovo.core.utils.formatting) get_approx_screen_width() (in module ovo.app.components.custom_elements) get_atom_coordinates() (in module ovo.core.utils.pdb) get_available_descriptors() (in module ovo.core.logic.descriptor_logic) get_available_schedulers() (in module ovo.core.logic.proteinqc_logic) get_available_tools() (in module ovo.core.logic.proteinqc_logic) get_binder_contig() (ovo.core.database.models_rfdiffusion.RFdiffusionBinderDesignWorkflow method) get_bounds() (ovo.core.database.models.Threshold method) get_cached_available_descriptors() (in module ovo.app.utils.cached_db) get_cached_descriptor_values() (in module ovo.app.utils.cached_db) get_cached_design() (in module ovo.app.utils.cached_db) get_cached_design_descriptors() (in module ovo.app.utils.cached_db) get_cached_design_ids() (in module ovo.app.utils.cached_db) get_cached_design_job() (in module ovo.app.utils.cached_db) get_cached_design_jobs() (in module ovo.app.utils.cached_db) get_cached_design_jobs_table() (in module ovo.app.utils.cached_db) get_cached_designs() (in module ovo.app.utils.cached_db) get_cached_designs_accept_field() (in module ovo.app.utils.cached_db) get_cached_pool() (in module ovo.app.utils.cached_db) get_cached_pools() (in module ovo.app.utils.cached_db) get_cached_pools_table() (in module ovo.app.utils.cached_db) get_cached_project_ids_and_names() (in module ovo.app.utils.cached_db) get_cached_round() (in module ovo.app.utils.cached_db) get_cached_rounds() (in module ovo.app.utils.cached_db) get_cached_workflow_pools_and_jobs() (in module ovo.app.utils.cached_db) get_chain() (ovo.core.database.models.DesignSpec method) get_chain_and_indices_fixed_region() (ovo.app.components.molstar_custom_component.contigs_parser.ContigsParser method) get_chains_and_contigs() (in module ovo.core.utils.residue_selection) get_client() (ovo.core.aws.AWSSessionManager method) get_color_from_str() (in module ovo.core.utils.colors) get_contig() (ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow method) get_cyclic_offset() (ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow method) get_descriptor_cmap() (in module ovo.core.logic.proteinqc_logic) get_descriptor_colormap() (in module ovo.core.logic.proteinqc_logic) get_descriptor_column_config() (in module ovo.app.components.descriptor_table) get_descriptor_comment() (in module ovo.core.logic.proteinqc_logic) get_descriptor_plot_setting() (in module ovo.core.logic.proteinqc_logic) get_design_accepted_values() (ovo.core.database.sql_db.SqlDBEngine method) get_design_jobs_table() (in module ovo.core.logic.design_logic) get_dict_diff() (in module ovo.app.utils.bindcraft_utils) get_download_fields() (ovo.core.database.models.Workflow class method) (ovo.core.database.models_bindcraft.BindCraftBinderDesignWorkflow class method) (ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow class method) get_failed_message() (ovo.core.scheduler.base_scheduler.Scheduler method) (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) get_flag_color() (in module ovo.core.logic.proteinqc_logic) get_hash_of_bytes() (in module ovo.core.utils.formatting) get_hashed_path_for_bytes() (in module ovo.core.utils.formatting) get_higher_is_better_colormap() (in module ovo.core.logic.proteinqc_logic) get_histogram_alt() (in module ovo.app.utils.protein_qc_plots) get_hotspots() (ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow method) get_input_pdb_path() (ovo.core.database.models_bindcraft.BindCraftBinderDesignWorkflow method) (ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow method) get_input_pdb_paths() (ovo.core.database.models_bindcraft.BindCraftBinderDesignWorkflow method) get_job_ids() (ovo.core.scheduler.simple_queue_mixin.TaskQueue method) get_job_start_time() (ovo.core.scheduler.base_scheduler.Scheduler method) (ovo.core.scheduler.healthomics_scheduler.HealthOmicsScheduler method) (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) get_job_stop_time() (ovo.core.scheduler.base_scheduler.Scheduler method) (ovo.core.scheduler.healthomics_scheduler.HealthOmicsScheduler method) (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) get_latest_workflow_id() (ovo.core.aws.AWSSessionManager method) get_log() (in module ovo.core.logic.descriptor_logic) (in module ovo.core.logic.design_logic) (ovo.core.scheduler.base_scheduler.Scheduler method) (ovo.core.scheduler.healthomics_scheduler.HealthOmicsScheduler method) (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) get_lower_is_better_colormap() (in module ovo.core.logic.proteinqc_logic) get_neutral_colormap() (in module ovo.core.logic.proteinqc_logic)

get_or_create_personal_project() (in module ovo.core.logic.project_logic) get_or_create_project() (in module ovo.core.logic.project_logic) get_or_create_project_round() (in module ovo.core.logic.project_logic) get_or_create_project_rounds() (in module ovo.core.logic.round_logic) get_or_create_user_settings() (in module ovo.core.logic.user_settings_logic) get_output_chain() (ovo.app.components.molstar_custom_component.contigs_parser.ContigsParser method) get_output_dir() (ovo.core.scheduler.base_scheduler.Scheduler method) (ovo.core.scheduler.healthomics_scheduler.HealthOmicsScheduler method) (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) get_pae_colormap() (in module ovo.core.logic.proteinqc_logic) get_param_dict() (ovo.core.database.models.Workflow method) get_param_fields() (ovo.core.database.models.Workflow method) get_param_schema() (ovo.core.scheduler.base_scheduler.Scheduler method) (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) get_pdb() (in module ovo.core.utils.pdb) get_pipeline_name() (ovo.core.database.models.Workflow method) (ovo.core.database.models_bindcraft.BindCraftBinderDesignWorkflow method) (ovo.core.database.models_proteinqc.ProteinQCWorkflow method) (ovo.core.database.models_refolding.RefoldingWorkflow method) (ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow method) get_pipeline_names() (ovo.core.scheduler.base_scheduler.Scheduler method) (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) get_plddt_color() (in module ovo.core.logic.proteinqc_logic) get_plot_range() (ovo.core.database.models.NumericDescriptor method) get_pool_inputs() (in module ovo.app.components.submission_components) get_pools_table() (in module ovo.core.logic.design_logic) get_posit_user_info() (in module ovo.core.auth) get_precomputed_histogram_alt() (in module ovo.app.utils.protein_qc_plots) get_query_arg_project() (in module ovo.app.components.sidebar) get_refolding_design_paths() (ovo.core.database.models_refolding.RefoldingSupportedDesignWorkflow method) (ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow method) get_refolding_design_type() (ovo.core.database.models_refolding.RefoldingSupportedDesignWorkflow method) (ovo.core.database.models_rfdiffusion.RFdiffusionBinderDesignWorkflow method) (ovo.core.database.models_rfdiffusion.RFdiffusionScaffoldDesignWorkflow method) get_refolding_native_pdb_path() (ovo.core.database.models_refolding.RefoldingSupportedDesignWorkflow method) (ovo.core.database.models_rfdiffusion.RFdiffusionBinderDesignWorkflow method) (ovo.core.database.models_rfdiffusion.RFdiffusionScaffoldDesignWorkflow method) get_remark_header() (in module ovo.core.utils.pdb) get_residue_number_column_config() (in module ovo.app.components.descriptor_table) get_residue_presence_df() (in module ovo.app.components.descriptor_tiles) get_result() (ovo.core.scheduler.base_scheduler.Scheduler method) (ovo.core.scheduler.healthomics_scheduler.HealthOmicsScheduler method) (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) get_rfdiffusion_run_parameters() (in module ovo.core.logic.design_logic_rfdiffusion) get_rmsd_colormap() (in module ovo.core.logic.proteinqc_logic) get_s3_bytes() (ovo.core.aws.AWSSessionManager method) get_selected_segments() (ovo.core.database.models_bindcraft.BindCraftBinderDesignWorkflow method) (ovo.core.database.models_rfdiffusion.RFdiffusionBinderDesignWorkflow method) (ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow method) get_sequences_from_pdb_str() (in module ovo.core.utils.pdb) get_settings_paths() (ovo.core.database.models_bindcraft.BindCraftBinderDesignWorkflow method) get_shell_config_path() (in module ovo.core.configuration) get_source_command() (in module ovo.core.configuration) get_standardized_remarks_from_pdb_str() (in module ovo.core.utils.pdb) get_startup_time_minutes() (ovo.core.scheduler.base_scheduler.Scheduler method) (ovo.core.scheduler.healthomics_scheduler.HealthOmicsScheduler method) get_status_label() (ovo.core.scheduler.base_scheduler.Scheduler method) (ovo.core.scheduler.healthomics_scheduler.HealthOmicsScheduler method) (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) get_subclass_names() (ovo.core.database.models.WorkflowTypes class method) get_table_row() (ovo.core.database.models.DesignWorkflow method) (ovo.core.database.models.Workflow method) (ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow method) get_target_chain() (ovo.core.database.models_rfdiffusion.RFdiffusionBinderDesignWorkflow method) get_target_contig() (ovo.core.database.models_rfdiffusion.RFdiffusionBinderDesignWorkflow method) get_target_trim_boundary() (ovo.core.database.models_rfdiffusion.RFdiffusionBinderDesignWorkflow method) get_test_scheduler() (in module ovo.core.utils.tests) get_time_estimate() (ovo.core.database.models.Workflow method) (ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow method) get_trace_table() (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) get_trimmed_min_max() (in module ovo.app.components.descriptor_scatterplot) get_username() (in module ovo.core.auth) get_value() (ovo.core.database.base_db.DBEngine method) (ovo.core.database.db_proxy.DBProxy method) (ovo.core.database.sql_db.SqlDBEngine method) get_wide_descriptor_table() (in module ovo.core.logic.descriptor_logic) get_workflows_table() (in module ovo.core.logic.design_logic) get_x_key() (ovo.app.components.descriptor_scatterplot.PlotSettings method) get_y_key() (ovo.app.components.descriptor_scatterplot.PlotSettings method) global_config_flag (in module ovo.core.configuration) GLOBAL_OVO_HOME (in module ovo.core.configuration) GRAVY (in module ovo.core.database.descriptors_proteinqc)

H

H_PERC (in module ovo.core.database.descriptors_proteinqc) has_queue() (ovo.core.scheduler.simple_queue_mixin.SimpleQueueMixin method) heading_with_value() (in module ovo.app.components.custom_elements) HealthOmicsScheduler (class in ovo.core.scheduler.healthomics_scheduler) HELIX_3_10_PERCENTAGE (in module ovo.core.database.descriptors_proteinqc) HELIX_PERCENTAGE (in module ovo.core.database.descriptors_proteinqc) HELIX_SEQ_PERC (in module ovo.core.database.descriptors_proteinqc) hide_admin_warning (ovo.core.configuration.AuthConfig attribute) hide_test_dialog() (in module ovo.app.utils.testing) highlighted_selections (ovo.app.components.molstar_custom_component.dataclasses.StructureVisualization attribute) HISTOGRAMS (in module ovo.app.components.descriptor_tiles)

HistogramSettings (class in ovo.app.components.descriptor_explorer) history_dropdown_component() (in module ovo.app.components.history_components) home() (in module ovo.cli.init) hotspots (ovo.core.database.models_bindcraft.BindCraftParams attribute) (ovo.core.database.models_rfdiffusion.RFdiffusionParams attribute) HYDROPHOBIC_SAP_SCORE (in module ovo.core.database.descriptors_proteinqc) HYDROPHOBIC_SASA (in module ovo.core.database.descriptors_proteinqc) HYDROPHOBIC_SURFACE_INTEGRAL (in module ovo.core.database.descriptors_proteinqc) HYDROPHOBIC_TOP_PATCH_AREA (in module ovo.core.database.descriptors_proteinqc) HYDROPHOBIC_TOP_PATCH_AREA_NORM (in module ovo.core.database.descriptors_proteinqc) HYDROPHOBIC_TOTAL_AREA (in module ovo.core.database.descriptors_proteinqc) HYDROPHOBIC_TOTAL_AREA_NORM (in module ovo.core.database.descriptors_proteinqc)

I

I_PERC (in module ovo.core.database.descriptors_proteinqc) id (ovo.core.database.models.DescriptorJob attribute) (ovo.core.database.models.Design attribute) (ovo.core.database.models.DesignJob attribute) (ovo.core.database.models.Pool attribute) (ovo.core.database.models.Project attribute) (ovo.core.database.models.Round attribute) impl (ovo.core.database.encoder.DataclassType attribute) IMPORT_EXPORT_CONFIGS (in module ovo.core.logic.import_export_logic) import_project() (in module ovo.core.logic.import_export_logic) import_tab() (in module ovo.app.pages.import_export) init() (ovo.core.database.base_db.DBEngine method) (ovo.core.database.sql_db.SqlDBEngine method) init_nextflow() (in module ovo.cli.common) initialize_page() (in module ovo.app.utils.page_init) initialize_workflow() (in module ovo.app.components.input_components) inpaint_seq (ovo.core.database.models_rfdiffusion.RFdiffusionParams attribute) input_name (ovo.core.database.models_bindcraft.BindCraftBinderDesignWorkflow attribute) (ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow attribute)

input_pdb (ovo.core.database.models_rfdiffusion.RFdiffusionParams property) input_pdb_path (ovo.core.database.models_bindcraft.BindCraftParams attribute) input_pdb_paths (ovo.core.database.models_rfdiffusion.RFdiffusionParams attribute) input_res_chain (ovo.app.components.molstar_custom_component.dataclasses.ContigSegment attribute) input_res_end (ovo.app.components.molstar_custom_component.dataclasses.ContigSegment attribute) input_res_start (ovo.app.components.molstar_custom_component.dataclasses.ContigSegment attribute) INSTABILITY_INDEX (in module ovo.core.database.descriptors_proteinqc) interface_protocol (ovo.core.database.models_bindcraft.BindCraftParams attribute) INTERFACE_TARGET_RESIDUES (in module ovo.core.database.descriptors_rfdiffusion) is_instance() (ovo.core.database.models.Workflow method) is_local_path() (ovo.core.storage.Storage method) is_running_in_streamlit() (in module ovo.core.auth) is_subclass() (ovo.core.database.models.Workflow class method) is_test_dialog_shown() (in module ovo.app.utils.testing) ISOELECTRIC_POINT (in module ovo.core.database.descriptors_proteinqc) ISOLATED_BETA_BRIDGE_PERCENTAGE (in module ovo.core.database.descriptors_proteinqc) iter_progress() (in module ovo.app.components.custom_elements)

J

job_finished_date_utc (ovo.core.database.models.JobMixin attribute) job_id (ovo.core.database.models.JobMixin attribute) job_result (ovo.core.database.models.JobMixin attribute) job_started_date_utc (ovo.core.database.models.JobMixin attribute)

JobMixin (class in ovo.core.database.models) JobNotFound jobs_page (in module ovo.app.pages) jupyter() (in module ovo.cli.scheduler_cli)

K

K_PERC (in module ovo.core.database.descriptors_proteinqc)

key (ovo.core.database.models.Descriptor attribute) kwargs (in module ovo.app.pages.debug)

L

L_PERC (in module ovo.core.database.descriptors_proteinqc) label (ovo.app.components.molstar_custom_component.dataclasses.ChainVisualization attribute) last_project_id (ovo.core.database.models.UserSettings attribute) LENGTH (in module ovo.core.database.descriptors_proteinqc) length (ovo.app.components.molstar_custom_component.dataclasses.ContigSegment attribute) LIGANDMPNN_STRUCTURE_PATH (in module ovo.core.database.descriptors_rfdiffusion) list_dir() (ovo.core.storage.Storage method)

load_config() (in module ovo.core.configuration) load_histograms() (in module ovo.app.utils.protein_qc_plots) load_json_from_file() (in module ovo.app.utils.bindcraft_utils) load_plots_data() (in module ovo.app.utils.protein_qc_plots) load_plugins() (in module ovo.core.plugins) load_variable() (in module ovo.core.plugins) local_scheduler (ovo.core.configuration.OVOConfig attribute)

M

M_PERC (in module ovo.core.database.descriptors_proteinqc) main() (in module ovo.cli.app) (in module ovo.cli.main) make_bg_color_func() (in module ovo.app.components.descriptor_table) max_value (ovo.core.database.models.NumericDescriptor attribute) (ovo.core.database.models.Threshold attribute) MEC_CYSTINES (in module ovo.core.database.descriptors_proteinqc) MEC_REDUCED (in module ovo.core.database.descriptors_proteinqc) merge_dictionaries() (in module ovo.app.utils.bindcraft_utils) MetadataMixin (class in ovo.core.database.models) min_value (ovo.core.database.models.NumericDescriptor attribute) (ovo.core.database.models.Threshold attribute) mix_colors() (in module ovo.app.components.molstar_custom_component.color_picker) model_config (ovo.core.configuration.BaseConfigModel attribute) model_weights (ovo.core.database.models_rfdiffusion.RFdiffusionParams attribute) MODEL_WEIGHTS_BINDER (in module ovo.core.database.models) (in module ovo.core.database.models_rfdiffusion) MODEL_WEIGHTS_SCAFFOLD (in module ovo.core.database.models) (in module ovo.core.database.models_rfdiffusion) module ovo ovo.app ovo.app.components ovo.app.components.acceptance_thresholds_components ovo.app.components.contigs_organizer ovo.app.components.contigs_organizer.main ovo.app.components.create_new_pool ovo.app.components.custom_elements ovo.app.components.descriptor_explorer ovo.app.components.descriptor_job_components ovo.app.components.descriptor_scatterplot ovo.app.components.descriptor_table ovo.app.components.descriptor_tiles ovo.app.components.download_component ovo.app.components.history_components ovo.app.components.input_components ovo.app.components.molstar_custom_component ovo.app.components.molstar_custom_component.color_picker ovo.app.components.molstar_custom_component.contigs_parser ovo.app.components.molstar_custom_component.dataclasses ovo.app.components.molstar_custom_component.main ovo.app.components.navigation ovo.app.components.preview_components ovo.app.components.scheduler_components ovo.app.components.sidebar ovo.app.components.submission_components ovo.app.components.trim_components ovo.app.components.workflow_visualization_components ovo.app.pages ovo.app.pages.debug ovo.app.pages.import_export ovo.app.pages.welcome ovo.app.utils ovo.app.utils.bindcraft_utils ovo.app.utils.cached_db ovo.app.utils.page_init ovo.app.utils.protein_qc_plots ovo.app.utils.testing ovo.cli ovo.cli.app ovo.cli.common ovo.cli.init ovo.cli.main ovo.cli.module ovo.cli.scheduler_cli ovo.core ovo.core.auth ovo.core.aws ovo.core.configuration ovo.core.database ovo.core.database.base_db ovo.core.database.cache_clearing ovo.core.database.db_proxy ovo.core.database.descriptors ovo.core.database.descriptors_bindcraft ovo.core.database.descriptors_proteinqc ovo.core.database.descriptors_refolding ovo.core.database.descriptors_rfdiffusion ovo.core.database.encoder ovo.core.database.models ovo.core.database.models_bindcraft ovo.core.database.models_proteinqc ovo.core.database.models_refolding ovo.core.database.models_rfdiffusion ovo.core.database.sql_db ovo.core.logic ovo.core.logic.descriptor_logic ovo.core.logic.design_logic ovo.core.logic.design_logic_bindcraft ovo.core.logic.design_logic_rfdiffusion ovo.core.logic.filtering_logic ovo.core.logic.import_export_logic ovo.core.logic.job_logic ovo.core.logic.project_logic ovo.core.logic.proteinqc_logic ovo.core.logic.round_logic ovo.core.logic.user_settings_logic ovo.core.plugins ovo.core.scheduler ovo.core.scheduler.base_scheduler ovo.core.scheduler.healthomics_scheduler ovo.core.scheduler.nextflow_scheduler ovo.core.scheduler.simple_queue_mixin ovo.core.storage ovo.core.utils ovo.core.utils.colors ovo.core.utils.export ovo.core.utils.formatting ovo.core.utils.param_validation ovo.core.utils.pdb ovo.core.utils.residue_selection ovo.core.utils.resources ovo.core.utils.seq ovo.core.utils.tests

module() (in module ovo.cli.module) MOLECULEAR_WEIGHT (in module ovo.core.database.descriptors_proteinqc) molstar_custom_component() (in module ovo.app.components.molstar_custom_component) molstar_html() (in module ovo.app.components.molstar_custom_component) molstar_notebook() (in module ovo.app.components.molstar_custom_component) mpnn_sequences_limit (ovo.core.configuration.ConfigProps attribute)

N

N_CONTACTS_TO_HOTSPOTS (in module ovo.core.database.descriptors_rfdiffusion) N_CONTACTS_TO_INTERFACE (in module ovo.core.database.descriptors_rfdiffusion) N_HOTSPOTS_ON_INTERFACE (in module ovo.core.database.descriptors_rfdiffusion) N_PERC (in module ovo.core.database.descriptors_proteinqc) name (ovo.core.configuration.SchedulerConfig attribute) (ovo.core.database.models.Descriptor attribute) (ovo.core.database.models.Pool attribute) (ovo.core.database.models.Project attribute) (ovo.core.database.models.Round attribute) (ovo.core.database.models.Workflow attribute) (ovo.core.database.models_proteinqc.ProteinQCTool attribute) native_pdb_path (ovo.core.database.models_refolding.RefoldingWorkflow attribute) NEGATIVE_PERC (in module ovo.core.database.descriptors_proteinqc)

next_design_idx() (in module ovo.app.components.navigation) nextflow_home (ovo.core.configuration.OVOConfig attribute) NextflowScheduler (class in ovo.core.scheduler.nextflow_scheduler) NONE_PERCENTAGE (in module ovo.core.database.descriptors_proteinqc) NONPOLAR_PERC (in module ovo.core.database.descriptors_proteinqc) num2aa (in module ovo.core.utils.pdb) num_designs (ovo.core.database.models_rfdiffusion.RFdiffusionParams attribute) num_replicas (ovo.core.database.models_bindcraft.BindCraftParams attribute) num_sequences (ovo.core.database.models_rfdiffusion.ProteinMPNNParams attribute) number_of_final_designs (ovo.core.database.models_bindcraft.BindCraftParams attribute) NumericDescriptor (class in ovo.core.database.models) NumericGlobalDescriptor (class in ovo.core.database.models) NumericResidueDescriptor (class in ovo.core.database.models)

O

omics (ovo.core.aws.AWSSessionManager property) omit_aa (ovo.core.database.models_rfdiffusion.ProteinMPNNParams attribute) on_dismiss_dialog() (in module ovo.app.components.descriptor_tiles) open_first_section() (in module ovo.app.components.navigation) out_res_chain (ovo.app.components.molstar_custom_component.dataclasses.ContigSegment attribute) out_res_end (ovo.app.components.molstar_custom_component.dataclasses.ContigSegment attribute) out_res_start (ovo.app.components.molstar_custom_component.dataclasses.ContigSegment attribute) ovo module ovo.app module ovo.app.components module ovo.app.components.acceptance_thresholds_components module ovo.app.components.contigs_organizer module ovo.app.components.contigs_organizer.main module ovo.app.components.create_new_pool module ovo.app.components.custom_elements module ovo.app.components.descriptor_explorer module ovo.app.components.descriptor_job_components module ovo.app.components.descriptor_scatterplot module ovo.app.components.descriptor_table module ovo.app.components.descriptor_tiles module ovo.app.components.download_component module ovo.app.components.history_components module ovo.app.components.input_components module ovo.app.components.molstar_custom_component module ovo.app.components.molstar_custom_component.color_picker module ovo.app.components.molstar_custom_component.contigs_parser module ovo.app.components.molstar_custom_component.dataclasses module ovo.app.components.molstar_custom_component.main module ovo.app.components.navigation module ovo.app.components.preview_components module ovo.app.components.scheduler_components module ovo.app.components.sidebar module ovo.app.components.submission_components module ovo.app.components.trim_components module ovo.app.components.workflow_visualization_components module ovo.app.pages module ovo.app.pages.debug module ovo.app.pages.import_export module ovo.app.pages.welcome module ovo.app.utils module ovo.app.utils.bindcraft_utils module ovo.app.utils.cached_db module ovo.app.utils.page_init module ovo.app.utils.protein_qc_plots module ovo.app.utils.testing module ovo.cli module ovo.cli.app module ovo.cli.common module ovo.cli.init module ovo.cli.main module ovo.cli.module module ovo.cli.scheduler_cli module ovo.core module

ovo.core.auth module ovo.core.aws module ovo.core.configuration module ovo.core.database module ovo.core.database.base_db module ovo.core.database.cache_clearing module ovo.core.database.db_proxy module ovo.core.database.descriptors module ovo.core.database.descriptors_bindcraft module ovo.core.database.descriptors_proteinqc module ovo.core.database.descriptors_refolding module ovo.core.database.descriptors_rfdiffusion module ovo.core.database.encoder module ovo.core.database.models module ovo.core.database.models_bindcraft module ovo.core.database.models_proteinqc module ovo.core.database.models_refolding module ovo.core.database.models_rfdiffusion module ovo.core.database.sql_db module ovo.core.logic module ovo.core.logic.descriptor_logic module ovo.core.logic.design_logic module ovo.core.logic.design_logic_bindcraft module ovo.core.logic.design_logic_rfdiffusion module ovo.core.logic.filtering_logic module ovo.core.logic.import_export_logic module ovo.core.logic.job_logic module ovo.core.logic.project_logic module ovo.core.logic.proteinqc_logic module ovo.core.logic.round_logic module ovo.core.logic.user_settings_logic module ovo.core.plugins module ovo.core.scheduler module ovo.core.scheduler.base_scheduler module ovo.core.scheduler.healthomics_scheduler module ovo.core.scheduler.nextflow_scheduler module ovo.core.scheduler.simple_queue_mixin module ovo.core.storage module ovo.core.utils module ovo.core.utils.colors module ovo.core.utils.export module ovo.core.utils.formatting module ovo.core.utils.param_validation module ovo.core.utils.pdb module ovo.core.utils.residue_selection module ovo.core.utils.resources module ovo.core.utils.seq module ovo.core.utils.tests module OVOCliError OVOConfig (class in ovo.core.configuration) OVONotInitializedError

P

P_PERC (in module ovo.core.database.descriptors_proteinqc) pad_line() (in module ovo.core.utils.pdb) parameters_binder_preview_component() (in module ovo.app.components.preview_components) parameters_trim_structure_component() (in module ovo.app.components.trim_components) parent_dir (in module ovo.app.components.contigs_organizer) (in module ovo.app.components.molstar_custom_component) parse_args() (in module ovo.core.utils.formatting) parse_contigs_str() (ovo.app.components.molstar_custom_component.contigs_parser.ContigsParser method) parse_contigs_trb() (ovo.app.components.molstar_custom_component.contigs_parser.ContigsParser method) parse_partial_diffusion_binder_contig() (in module ovo.core.utils.residue_selection) parse_path() (ovo.core.storage.Storage static method) parse_pdb() (in module ovo.core.utils.pdb) parse_pdb_lines() (in module ovo.core.utils.pdb) parse_region_fixed() (ovo.app.components.molstar_custom_component.contigs_parser.ContigsParser method) parse_region_fixed_no_mapping() (ovo.app.components.molstar_custom_component.contigs_parser.ContigsParser method) parse_region_generated() (ovo.app.components.molstar_custom_component.contigs_parser.ContigsParser method) parse_selections() (in module ovo.core.utils.residue_selection) partial_diffusion (ovo.core.database.models_rfdiffusion.RFdiffusionParams attribute) path (ovo.core.configuration.StorageConfig attribute) paths (in module ovo.app.components.molstar_custom_component.main) pdb (ovo.app.components.molstar_custom_component.dataclasses.StructureVisualization attribute) pdb_input_component() (in module ovo.app.components.input_components) pdb_to_mmcif() (in module ovo.core.utils.pdb) pdb_to_mmcif_iter() (in module ovo.core.utils.pdb) PDBSegmentSelector (class in ovo.core.utils.pdb) PEP_PATCH_CHARGE_DESCRIPTORS (in module ovo.core.database.descriptors_proteinqc) PEP_PATCH_CHARGE_DESCRIPTORS_BY_KEY (in module ovo.core.database.descriptors_proteinqc) PEP_PATCH_DESCRIPTORS (in module ovo.core.database.descriptors_proteinqc) PEP_PATCH_HYDROPHOBICITY_DESCRIPTORS (in module ovo.core.database.descriptors_proteinqc) PEP_PATCH_HYDROPHOBICITY_DESCRIPTORS_BY_KEY (in module ovo.core.database.descriptors_proteinqc) PEPPATCH (in module ovo.core.database.models_proteinqc) PERC_NEGATIVE (in module ovo.core.database.descriptors_proteinqc) PERC_POSITIVE (in module ovo.core.database.descriptors_proteinqc) PERC_SOLUBILITY (in module ovo.core.database.descriptors_proteinqc) PERSONAL_PROJECT_NAME (in module ovo.core.logic.project_logic) PI_HELIX_PERCENTAGE (in module ovo.core.database.descriptors_proteinqc) PlotSettings (class in ovo.app.components.descriptor_scatterplot) POLAR_UNCHARGED_PERC (in module ovo.core.database.descriptors_proteinqc) Pool (class in ovo.core.database.models) pool_df (in module ovo.app.pages.debug) pool_id (ovo.core.database.models.Design attribute) pool_selector_table() (in module ovo.app.components.navigation) pool_submission_inputs() (in module ovo.app.components.submission_components) POSITIVE_PERC (in module ovo.core.database.descriptors_proteinqc) prediction_protocol (ovo.core.database.models_bindcraft.BindCraftParams attribute) prepare_bindcraft_params() (in module ovo.core.logic.design_logic_bindcraft) prepare_params() (ovo.core.database.models.Workflow method) (ovo.core.database.models_bindcraft.BindCraftBinderDesignWorkflow method) (ovo.core.database.models_proteinqc.ProteinQCWorkflow method) (ovo.core.database.models_refolding.RefoldingWorkflow method) (ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow method) prepare_proteinqc_params() (in module ovo.core.logic.descriptor_logic) prepare_refolding_params() (in module ovo.core.logic.descriptor_logic) prepare_rfdiffusion_workflow_params() (in module ovo.core.logic.design_logic_rfdiffusion) prepare_test_output_dir() (in module ovo.core.utils.tests)

prepare_workflow_input() (ovo.core.storage.Storage method) prepare_workflow_inputs() (ovo.core.storage.Storage method) PRESETS (in module ovo.core.database.descriptors) (in module ovo.core.database.descriptors_bindcraft) (in module ovo.core.database.descriptors_proteinqc) (in module ovo.core.database.descriptors_refolding) (in module ovo.core.database.descriptors_rfdiffusion) preview() (in module ovo.cli.init) preview_job_id (ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow attribute) previous_design_idx() (in module ovo.app.components.navigation) primary_test (ovo.core.database.models_rfdiffusion.RefoldingParams attribute) print_missing() (in module ovo.app.components.descriptor_scatterplot) process_bind_param() (ovo.core.database.encoder.DataclassType method) process_result_value() (ovo.core.database.encoder.DataclassType method) process_results() (in module ovo.core.logic.descriptor_logic) (in module ovo.core.logic.design_logic) (ovo.core.database.models.Workflow method) (ovo.core.database.models_bindcraft.BindCraftBinderDesignWorkflow method) (ovo.core.database.models_proteinqc.ProteinQCWorkflow method) (ovo.core.database.models_refolding.RefoldingWorkflow method) (ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow method) process_rfdiffusion_design() (in module ovo.core.logic.design_logic_rfdiffusion) process_workflow_results() (in module ovo.core.logic.design_logic_bindcraft) (in module ovo.core.logic.design_logic_rfdiffusion) processed (ovo.core.database.models.DescriptorJob attribute) (ovo.core.database.models.Pool attribute) Project (class in ovo.core.database.models) project_df (in module ovo.app.pages.debug) project_id (ovo.core.database.models.Round attribute) project_round_selector() (in module ovo.app.components.navigation) project_sidebar_component() (in module ovo.app.components.sidebar) props (ovo.core.configuration.OVOConfig attribute) protein_mpnn_params (ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow attribute) PROTEIN_SOL_DESCRIPTORS (in module ovo.core.database.descriptors_proteinqc) ProteinMPNNParams (class in ovo.core.database.models_rfdiffusion) proteinqc() (in module ovo.cli.init) PROTEINQC_MAIN_DESCRIPTORS (in module ovo.core.database.descriptors_proteinqc) PROTEINQC_SEQUENCE_DESCRIPTORS (in module ovo.core.database.descriptors_proteinqc) PROTEINQC_STRUCTURE_DESCRIPTORS (in module ovo.core.database.descriptors_proteinqc) PROTEINQC_TOOLS (in module ovo.core.database.models_proteinqc) PROTEINQC_TOOLS_BY_KEY (in module ovo.core.database.models_proteinqc) ProteinQCTool (class in ovo.core.database.models_proteinqc) ProteinQCWorkflow (class in ovo.core.database.models_proteinqc) PROTEINSOL (in module ovo.core.database.models_proteinqc) public (ovo.core.database.models.Project attribute) put() (ovo.core.scheduler.simple_queue_mixin.TaskQueue method) PYDSSP_HELIX_PERCENT (in module ovo.core.database.descriptors_rfdiffusion) PYDSSP_LOOP_PERCENT (in module ovo.core.database.descriptors_rfdiffusion) PYDSSP_SHEET_PERCENT (in module ovo.core.database.descriptors_rfdiffusion) PYDSSP_STRING (in module ovo.core.database.descriptors_rfdiffusion) PYROSETTA_CMS (in module ovo.core.database.descriptors_rfdiffusion) PYROSETTA_DDG (in module ovo.core.database.descriptors_rfdiffusion) PYROSETTA_INTERFACE_DESCRIPTORS (in module ovo.core.database.descriptors_rfdiffusion) pyrosetta_license (ovo.core.configuration.ConfigProps attribute) PYROSETTA_SAP_SCORE (in module ovo.core.database.descriptors_rfdiffusion)

Q

Q_PERC (in module ovo.core.database.descriptors_proteinqc) queue_put() (ovo.core.scheduler.simple_queue_mixin.SimpleQueueMixin method) queue_run_task() (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) (ovo.core.scheduler.simple_queue_mixin.SimpleQueueMixin method)

queue_size() (ovo.core.scheduler.simple_queue_mixin.SimpleQueueMixin method) queue_worker() (ovo.core.scheduler.simple_queue_mixin.SimpleQueueMixin method)

R

R_PERC (in module ovo.core.database.descriptors_proteinqc) RADIUS_OF_GYRATION (in module ovo.core.database.descriptors_rfdiffusion) RADIUS_OF_GYRATION_ALL_ATOM (in module ovo.core.database.descriptors_proteinqc) RADIUS_OF_GYRATION_NORM (in module ovo.core.database.descriptors_proteinqc) RAMACHANDRAN_ALLOWED_PERCENTAGE (in module ovo.core.database.descriptors_proteinqc) RAMACHANDRAN_MARGINALLY_ALLOWED_PERCENTAGE (in module ovo.core.database.descriptors_proteinqc) RAMACHANDRAN_OUTLIERS_PERCENTAGE (in module ovo.core.database.descriptors_proteinqc) read_css() (in module ovo.app.utils.page_init) read_descriptor_file_values() (in module ovo.core.logic.descriptor_logic) read_file_bytes() (ovo.core.storage.Storage method) read_file_pickle() (ovo.core.storage.Storage method) read_file_str() (ovo.core.storage.Storage method) read_only (ovo.core.configuration.ConfigProps attribute) read_static_files() (in module ovo.app.components.molstar_custom_component) reference_files_dir (ovo.core.configuration.OVOConfig attribute) REFOLDING_DESCRIPTORS (in module ovo.core.database.descriptors_refolding) refolding_params (ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow attribute) REFOLDING_TESTS (in module ovo.core.database.descriptors_refolding) REFOLDING_TESTS_BINDER (in module ovo.core.database.descriptors_refolding) REFOLDING_TESTS_BY_TYPE (in module ovo.core.database.descriptors_refolding) REFOLDING_TESTS_SCAFFOLD (in module ovo.core.database.descriptors_refolding) RefoldingParams (class in ovo.core.database.models_rfdiffusion) RefoldingSupportedDesignWorkflow (class in ovo.core.database.models_refolding) RefoldingWorkflow (class in ovo.core.database.models_refolding) refresh_descriptors() (in module ovo.app.components.descriptor_job_components) region (ovo.core.configuration.AWSConfig attribute) register() (ovo.core.database.models.WorkflowTypes class method) (ovo.core.scheduler.base_scheduler.SchedulerTypes class method) REGISTERED_CLASSES (ovo.core.scheduler.base_scheduler.SchedulerTypes attribute) REMARK_KEYS (in module ovo.core.utils.pdb) remove() (ovo.core.database.base_db.DBEngine method) (ovo.core.database.cache_clearing.CacheClearingEngine method) (ovo.core.database.db_proxy.DBProxy method) (ovo.core.database.sql_db.SqlDBEngine method) representation_type (ovo.app.components.molstar_custom_component.dataclasses.ChainVisualization attribute) (ovo.app.components.molstar_custom_component.dataclasses.StructureVisualization attribute)

residue_number_descriptor_detail_table() (in module ovo.app.components.descriptor_tiles) ResidueNumberDescriptor (class in ovo.core.database.models) residues (ovo.app.components.molstar_custom_component.dataclasses.ChainVisualization attribute) resolve_path() (ovo.core.storage.Storage method) resolve_relative_paths() (ovo.core.configuration.OVOConfig method) RESOURCES_DIR (in module ovo.core.utils.resources) review_workflow_submission() (in module ovo.app.components.submission_components) rf_binder_design_page (in module ovo.app.pages) rf_binder_diversification_page (in module ovo.app.pages) rf_scaffold_design_page (in module ovo.app.pages) rfdiffusion() (in module ovo.cli.init) rfdiffusion_backbones_limit (ovo.core.configuration.ConfigProps attribute) rfdiffusion_backbones_limit_admin (ovo.core.configuration.ConfigProps attribute) rfdiffusion_binder_design_visualization() (in module ovo.app.components.workflow_visualization_components) RFDIFFUSION_MODEL_FILES (in module ovo.cli.init) rfdiffusion_multiple_binder_designs_visualization() (in module ovo.app.components.workflow_visualization_components) rfdiffusion_params (ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow attribute) rfdiffusion_scaffold_design_visualization() (in module ovo.app.components.workflow_visualization_components) RFDIFFUSION_STRUCTURE_PATH (in module ovo.core.database.descriptors_rfdiffusion) RFDIFFUSION_TRB_PATH (in module ovo.core.database.descriptors_rfdiffusion) RFdiffusionBinderDesignWorkflow (class in ovo.core.database.models_rfdiffusion) RFdiffusionParams (class in ovo.core.database.models_rfdiffusion) RFdiffusionScaffoldDesignWorkflow (class in ovo.core.database.models_rfdiffusion) RFdiffusionWorkflow (class in ovo.core.database.models_rfdiffusion) Round (class in ovo.core.database.models) round_id (ovo.core.database.models.DescriptorJob attribute) (ovo.core.database.models.Pool attribute) ROUND_IDS_QUERY_PARAM (in module ovo.app.components.navigation) rounds_df (in module ovo.app.pages.debug) run() (in module ovo.cli.scheduler_cli) (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) run_nextflow() (in module ovo.cli.common) run_parameters (ovo.core.database.models_rfdiffusion.ProteinMPNNParams attribute) (ovo.core.database.models_rfdiffusion.RFdiffusionParams attribute)

S

s (in module ovo.app.pages.debug) s3 (ovo.core.aws.AWSSessionManager property) s3_file_exists() (ovo.core.aws.AWSSessionManager method) S_PERC (in module ovo.core.database.descriptors_proteinqc) safe_filename() (in module ovo.core.utils.formatting) sampling_temp (ovo.core.database.models_rfdiffusion.ProteinMPNNParams attribute) sanitize_excel_sheet_name() (in module ovo.core.utils.export) save() (ovo.core.database.base_db.DBEngine method) (ovo.core.database.cache_clearing.CacheClearingEngine method) (ovo.core.database.sql_db.SqlDBEngine method) save_all() (ovo.core.database.base_db.DBEngine method) (ovo.core.database.cache_clearing.CacheClearingEngine method) (ovo.core.database.sql_db.SqlDBEngine method) save_default_config() (in module ovo.core.configuration) save_descriptor_job_for_design_job() (in module ovo.core.logic.descriptor_logic) save_global_home_dir() (in module ovo.core.configuration) save_value() (ovo.core.database.base_db.DBEngine method) (ovo.core.database.cache_clearing.CacheClearingEngine method) (ovo.core.database.db_proxy.DBProxy method) (ovo.core.database.sql_db.SqlDBEngine method) scaffold_contig_preview() (in module ovo.app.components.preview_components) Scheduler (class in ovo.core.scheduler.base_scheduler) scheduler_key (ovo.core.database.models.JobMixin attribute) SchedulerConfig (class in ovo.core.configuration) schedulers (ovo.core.configuration.OVOConfig attribute) SchedulerTypes (class in ovo.core.scheduler.base_scheduler) select() (ovo.core.database.base_db.DBEngine method) (ovo.core.database.db_proxy.DBProxy method) (ovo.core.database.sql_db.SqlDBEngine method) select_dataframe() (ovo.core.database.db_proxy.DBProxy method) (ovo.core.database.sql_db.SqlDBEngine method) select_descriptor_values() (ovo.core.database.base_db.DBEngine method) (ovo.core.database.sql_db.SqlDBEngine method) select_design_descriptors() (ovo.core.database.sql_db.SqlDBEngine method) select_dict() (ovo.core.database.base_db.DBEngine method) (ovo.core.database.db_proxy.DBProxy method) (ovo.core.database.sql_db.SqlDBEngine method) select_structure_prediction_descriptor() (in module ovo.app.components.workflow_visualization_components) select_unique_values() (ovo.core.database.base_db.DBEngine method) (ovo.core.database.db_proxy.DBProxy method) (ovo.core.database.sql_db.SqlDBEngine method) select_values() (ovo.core.database.base_db.DBEngine method) (ovo.core.database.db_proxy.DBProxy method) (ovo.core.database.sql_db.SqlDBEngine method) select_wide_descriptor_table() (ovo.core.database.base_db.DBEngine method) (ovo.core.database.sql_db.SqlDBEngine method) selected_segments (ovo.core.database.models_bindcraft.BindCraftBinderDesignWorkflow attribute) (ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow attribute) SEQ_COMPOSITION (in module ovo.core.database.models_proteinqc) SEQ_COMPOSITION_DESCRIPTORS (in module ovo.core.database.descriptors_proteinqc) sequence (ovo.core.database.models.DesignChain attribute) SEQUENCE_DESIGN_PATH_DESCRIPTORS (in module ovo.core.database.descriptors) sequence_selection_fragment() (in module ovo.app.components.input_components) serialize() (ovo.core.database.models.Descriptor method) (ovo.core.database.models.StringResidueDescriptor method) set_binder_contig() (ovo.core.database.models_rfdiffusion.RFdiffusionBinderDesignWorkflow method) set_contig() (ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow method) set_designs_accepted() (in module ovo.core.logic.design_logic) set_selected_segments() (ovo.core.database.models_bindcraft.BindCraftBinderDesignWorkflow method) (ovo.core.database.models_rfdiffusion.RFdiffusionBinderDesignWorkflow method) (ovo.core.database.models_rfdiffusion.RFdiffusionWorkflow method)

SHAPE_DESCRIPTORS (in module ovo.core.database.descriptors_proteinqc) SHAPE_PARAMETER (in module ovo.core.database.descriptors_proteinqc) SHEET_PERCENTAGE (in module ovo.core.database.descriptors_proteinqc) SHEET_SEQ_PERC (in module ovo.core.database.descriptors_proteinqc) shorten_sheet_names() (in module ovo.core.utils.export) show_bindcraft_advanced_settings() (in module ovo.app.components.submission_components) show_buttons() (in module ovo.app.components.navigation) show_counts() (in module ovo.app.pages.import_export) show_design_metrics() (in module ovo.app.components.workflow_visualization_components) show_flag_counts() (in module ovo.app.components.descriptor_tiles) show_login_dialog() (in module ovo.app.utils.page_init) show_prev_next_sections() (in module ovo.app.components.navigation) show_rfdiffusion_advanced_settings() (in module ovo.app.components.submission_components) show_rfdiffusion_binder_seq_design_inputs() (in module ovo.app.components.submission_components) show_test_dialog() (in module ovo.app.utils.testing) SimpleQueueMixin (class in ovo.core.scheduler.simple_queue_mixin) single_threshold_input_component() (in module ovo.app.components.acceptance_thresholds_components) site_packages_dir (in module ovo.core.configuration) smiles (ovo.core.database.models.DesignChain attribute) SOLUBILITY (in module ovo.core.database.descriptors_proteinqc) sorted_alphanumeric() (in module ovo.core.utils.formatting) source (ovo.app.components.descriptor_explorer.HistogramSettings attribute) SOURCE_OPTIONS (in module ovo.app.components.descriptor_explorer) spec (ovo.core.database.models.Design attribute) SqlDBEngine (class in ovo.core.database.sql_db) start_res_trimmed_chain (ovo.core.database.models_rfdiffusion.RFdiffusionBinderDesignWorkflow attribute) status() (in module ovo.cli.scheduler_cli) Storage (class in ovo.core.storage) storage (ovo.core.configuration.OVOConfig attribute) StorageConfig (class in ovo.core.configuration) store_file_bytes() (ovo.core.storage.Storage method) store_file_path() (ovo.core.storage.Storage method) store_file_str() (ovo.core.storage.Storage method) store_input() (ovo.core.storage.Storage method) streamlit_auth (ovo.core.configuration.AuthConfig attribute) StringGlobalDescriptor (class in ovo.core.database.models) StringResidueDescriptor (class in ovo.core.database.models) structure_descriptor_key (ovo.core.database.models.Design attribute) structure_path (ovo.core.database.models.Design attribute) STRUCTURE_PATH_DESCRIPTORS (in module ovo.core.database.descriptors) structure_type (ovo.core.database.models.StructureFileDescriptor attribute) StructureFileDescriptor (class in ovo.core.database.models) StructureVisualization (class in ovo.app.components.molstar_custom_component.dataclasses) subheading_with_value() (in module ovo.app.components.custom_elements) submission_args (ovo.core.configuration.SchedulerConfig attribute) submit() (in module ovo.cli.scheduler_cli) (ovo.core.scheduler.base_scheduler.Scheduler method) (ovo.core.scheduler.healthomics_scheduler.HealthOmicsScheduler method) (ovo.core.scheduler.nextflow_scheduler.NextflowScheduler method) submit_descriptor_workflow() (in module ovo.core.logic.descriptor_logic) submit_design_workflow() (in module ovo.core.logic.design_logic) submit_rfdiffusion_preview() (in module ovo.core.logic.design_logic_rfdiffusion) submit_workflow_dialog() (in module ovo.app.components.submission_components) supports_conda (ovo.core.database.models_proteinqc.ProteinQCTool attribute) supports_multichain (ovo.core.database.models_proteinqc.ProteinQCTool attribute) sync_directory() (ovo.core.storage.Storage method) sync_file() (ovo.core.storage.Storage method) sync_files() (ovo.core.storage.Storage method)

T

T (in module ovo.core.database.base_db) T_PERC (in module ovo.core.database.descriptors_proteinqc) target_chain (ovo.core.database.models_rfdiffusion.RFdiffusionBinderDesignWorkflow attribute) target_chains (ovo.core.database.models_bindcraft.BindCraftParams attribute) TaskQueue (class in ovo.core.scheduler.simple_queue_mixin) template_protocol (ovo.core.database.models_bindcraft.BindCraftParams attribute) templates (ovo.core.configuration.OVOConfig attribute) TemplatesConfig (class in ovo.core.configuration) TEST_OUTPUT_DIR (in module ovo.core.utils.tests) TEST_PROJECT_NAME (in module ovo.core.utils.tests) TEST_SCHEDULER_KEY (in module ovo.core.utils.tests) tests (ovo.core.database.models_refolding.RefoldingWorkflow attribute) Threshold (class in ovo.core.database.models) thresholds_and_histograms_component() (in module ovo.app.components.acceptance_thresholds_components) thresholds_input_component() (in module ovo.app.components.acceptance_thresholds_components) time_limit_hours (ovo.core.database.models_bindcraft.BindCraftParams attribute)

timesteps (ovo.core.database.models_rfdiffusion.RFdiffusionParams attribute) to_dict() (ovo.app.components.molstar_custom_component.dataclasses.StructureVisualization method) (ovo.core.database.models.WorkflowParams method) tool (ovo.core.database.models.Descriptor attribute) tool_key (ovo.core.database.models_proteinqc.ProteinQCTool attribute) tool_supports_scheduler() (in module ovo.core.logic.proteinqc_logic) tools (ovo.core.database.models_proteinqc.ProteinQCWorkflow attribute) transformed_displacements (in module ovo.core.utils.pdb) trim_pdb_str() (in module ovo.core.utils.pdb) trimmed_structure_visualizer() (in module ovo.app.components.trim_components) truncated_list() (in module ovo.core.utils.formatting) TURN_FORMING_PERC (in module ovo.core.database.descriptors_proteinqc) TURN_PERCENTAGE (in module ovo.core.database.descriptors_proteinqc) TURN_SEQ_PERC (in module ovo.core.database.descriptors_proteinqc) type (ovo.app.components.molstar_custom_component.dataclasses.ContigSegment attribute) (ovo.core.configuration.SchedulerConfig attribute) (ovo.core.database.models.DesignChain attribute)

U

unit (ovo.core.database.models.NumericDescriptor attribute) UnknownWorkflow (class in ovo.core.database.models) update_acceptance_thresholds() (in module ovo.core.logic.design_logic) update_accepted_design_ids() (in module ovo.core.logic.design_logic) update_and_process_descriptors() (in module ovo.core.logic.descriptor_logic) update_bins() (in module ovo.app.utils.protein_qc_plots)

update_contig_based_on_selected_segments() (in module ovo.app.components.preview_components) update_job_status() (in module ovo.core.logic.job_logic) update_query_params() (ovo.app.components.descriptor_explorer.HistogramSettings method) (ovo.app.components.descriptor_scatterplot.PlotSettings method) url (ovo.core.configuration.DBConfig attribute) username (ovo.core.database.models.UserSettings attribute) UserSettings (class in ovo.core.database.models)

V

V_PERC (in module ovo.core.database.descriptors_proteinqc) validate() (ovo.core.database.models.DescriptorWorkflow method) (ovo.core.database.models.DesignWorkflow method) (ovo.core.database.models.Workflow method) (ovo.core.database.models.WorkflowParams method) (ovo.core.database.models_bindcraft.BindCraftParams method) (ovo.core.database.models_proteinqc.ProteinQCWorkflow method) (ovo.core.database.models_refolding.RefoldingWorkflow method) (ovo.core.database.models_rfdiffusion.ProteinMPNNParams method) (ovo.core.database.models_rfdiffusion.RefoldingParams method) (ovo.core.database.models_rfdiffusion.RFdiffusionParams method) validate_params() (in module ovo.core.utils.param_validation) value (ovo.app.components.molstar_custom_component.dataclasses.ContigSegment attribute) (ovo.core.database.models.DescriptorValue attribute)

verbose (ovo.core.configuration.DBConfig attribute) (ovo.core.configuration.StorageConfig attribute) visualize_design_sequence() (in module ovo.app.components.workflow_visualization_components) visualize_design_structure() (in module ovo.app.components.workflow_visualization_components) visualize_multiple_designs_structures() (ovo.core.database.models.DesignWorkflow class method) (ovo.core.database.models_rfdiffusion.RFdiffusionBinderDesignWorkflow class method) visualize_rfdiffusion_design_sequence() (in module ovo.app.components.workflow_visualization_components) visualize_rfdiffusion_preview() (in module ovo.app.components.preview_components) visualize_single_design_sequences() (ovo.core.database.models.DesignWorkflow class method) (ovo.core.database.models_rfdiffusion.RFdiffusionScaffoldDesignWorkflow class method) visualize_single_design_structures() (ovo.core.database.models.DesignWorkflow class method) (ovo.core.database.models_bindcraft.BindCraftBinderDesignWorkflow class method) (ovo.core.database.models_rfdiffusion.RFdiffusionBinderDesignWorkflow class method) (ovo.core.database.models_rfdiffusion.RFdiffusionScaffoldDesignWorkflow class method)

W

W_PERC (in module ovo.core.database.descriptors_proteinqc) wait() (ovo.core.scheduler.base_scheduler.Scheduler method) wait_with_statusbar() (in module ovo.app.components.scheduler_components) warning_value (ovo.core.database.models.NumericDescriptor attribute) warnings (ovo.core.database.models.JobMixin attribute) welcome (ovo.core.configuration.TemplatesConfig attribute) welcome_appendix (ovo.core.configuration.TemplatesConfig attribute) welcome_page (in module ovo.app.pages) workdir (ovo.core.configuration.SchedulerConfig attribute)

worker() (in module ovo.cli.scheduler_cli) Workflow (class in ovo.core.database.models) workflow (ovo.core.database.models.DescriptorJob attribute) (ovo.core.database.models.DesignJob attribute) WorkflowParams (class in ovo.core.database.models) WorkflowTypes (class in ovo.core.database.models) wrapped_columns() (in module ovo.app.components.custom_elements) write_sheet() (in module ovo.core.utils.export) write_sheets() (in module ovo.core.utils.export)

X

x (in module ovo.core.database.models) (ovo.app.components.descriptor_scatterplot.PlotSettings attribute)

Y

y (ovo.app.components.descriptor_scatterplot.PlotSettings attribute)

Y_PERC (in module ovo.core.database.descriptors_proteinqc)