Index

_

_add_adjustments() (reconstruction.ecoli.dataclasses.adjustments.Adjustments method) _add_amino_acid_growth_rates() (validation.ecoli.validation_data.ValidationDataEcoli method) _add_base_codes() (reconstruction.ecoli.simulation_data.SimulationDataEcoli method) _add_compartment_keys() (reconstruction.ecoli.simulation_data.SimulationDataEcoli method) _add_complexation_and_complexes() (ecoli.analysis.causality_network.build_network.BuildNetwork method) _add_condition_data() (reconstruction.ecoli.simulation_data.SimulationDataEcoli method) _add_equilibrium() (ecoli.analysis.causality_network.build_network.BuildNetwork method) _add_genes() (ecoli.analysis.causality_network.build_network.BuildNetwork method) _add_global_nodes() (ecoli.analysis.causality_network.build_network.BuildNetwork method) _add_labels() (wholecell.utils.voronoi_plot_main.VoronoiMaster method) _add_metabolism_and_metabolites() (ecoli.analysis.causality_network.build_network.BuildNetwork method) _add_metabolite_charge() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism method) _add_molecular_weight_keys() (reconstruction.ecoli.simulation_data.SimulationDataEcoli method) _add_molecule_amounts() (reconstruction.ecoli.dataclasses.process.metabolism.ConcentrationUpdates method) _add_regulation() (ecoli.analysis.causality_network.build_network.BuildNetwork method) _add_rna_maturation_and_mature_transcripts() (ecoli.analysis.causality_network.build_network.BuildNetwork method) _add_transcription_and_transcripts() (ecoli.analysis.causality_network.build_network.BuildNetwork method) _add_translation_and_monomers() (ecoli.analysis.causality_network.build_network.BuildNetwork method) _append_edge() (ecoli.analysis.causality_network.build_network.BuildNetwork method) _apply_rnaseq_correction() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) _are_instances_of() (in module runscripts.debug.compare_pickles) _build_all_masses() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) _build_amino_acid_pathways() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism method) _build_attenuation() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) _build_biomass() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism method) _build_bulk_molecule_specs() (reconstruction.ecoli.dataclasses.state.internal_state.InternalState method) (validation.ecoli.validation_data.InternalState method) _build_bulk_molecules() (reconstruction.ecoli.dataclasses.state.internal_state.InternalState method) (validation.ecoli.validation_data.InternalState method) _build_CD_periods() (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.Mass method) (validation.ecoli.validation_data.Mass method) _build_charged_trna() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) _build_cistron_data() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) _build_cistron_to_monomer_mapping() (reconstruction.ecoli.dataclasses.relation.Relation method) (validation.ecoli.validation_data.Relation method) _build_common_names() (reconstruction.ecoli.dataclasses.common_names.CommonNames method) _build_compartments() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (reconstruction.ecoli.dataclasses.state.internal_state.InternalState method) (validation.ecoli.validation_data.GetterFunctions method) (validation.ecoli.validation_data.InternalState method) _build_constants() (reconstruction.ecoli.dataclasses.constants.Constants method) (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.Mass method) (validation.ecoli.validation_data.Constants method) (validation.ecoli.validation_data.Mass method) _build_dependent_constants() (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.Mass method) (validation.ecoli.validation_data.Mass method) _build_elongation_rates() (reconstruction.ecoli.dataclasses.process.replication.Replication method) (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) (reconstruction.ecoli.dataclasses.process.translation.Translation method) _build_full_chromosome_mass() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) _build_gene_data() (reconstruction.ecoli.dataclasses.process.replication.Replication method) _build_genomic_coordinates() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) _build_linked_metabolites() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism method) _build_lookups() (reconstruction.ecoli.dataclasses.process.transcription_regulation.TranscriptionRegulation method) _build_mature_rna_data() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) _build_metabolism() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism method) _build_modified_protein_masses() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) _build_modified_rna_masses() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) _build_molecule_groups() (reconstruction.ecoli.dataclasses.molecule_groups.MoleculeGroups method) (validation.ecoli.validation_data.MoleculeGroups method) _build_monomer_data() (reconstruction.ecoli.dataclasses.process.translation.Translation method) _build_monomer_to_mRNA_cistron_mapping() (reconstruction.ecoli.dataclasses.relation.Relation method) (validation.ecoli.validation_data.Relation method) _build_monomer_to_tu_mapping() (reconstruction.ecoli.dataclasses.relation.Relation method) (validation.ecoli.validation_data.Relation method) _build_motifs() (reconstruction.ecoli.dataclasses.process.replication.Replication method) _build_network() (ecoli.analysis.causality_network.build_network.BuildNetwork method) _build_new_gene_data() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) _build_oric_terc_coordinates() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) _build_polymerized_subunit_masses() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) _build_ppgpp_reactions() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism method) _build_ppgpp_regulation() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) _build_protein_complex_compartments() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) _build_protein_complex_masses() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) _build_protein_masses() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) _build_protein_sequences() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) _build_replication() (reconstruction.ecoli.dataclasses.process.replication.Replication method) _build_rna_data() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) _build_rna_masses() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) _build_rna_sequences() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) _build_RNA_to_tf_mapping() (reconstruction.ecoli.dataclasses.relation.Relation method) (validation.ecoli.validation_data.Relation method) _build_sequence() (reconstruction.ecoli.dataclasses.process.replication.Replication method) _build_sequences() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) _build_sites() (reconstruction.ecoli.dataclasses.process.replication.Replication method) _build_submass_array() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) _build_submasses() (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.Mass method) (validation.ecoli.validation_data.Mass method) _build_supercoiling_parameters() (reconstruction.ecoli.dataclasses.process.chromosome_structure.ChromosomeStructure method) _build_synonyms() (reconstruction.ecoli.dataclasses.common_names.CommonNames method) _build_tf_to_RNA_mapping() (reconstruction.ecoli.dataclasses.relation.Relation method) (validation.ecoli.validation_data.Relation method) _build_transcription() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) _build_translation() (reconstruction.ecoli.dataclasses.process.translation.Translation method) _build_translation_efficiency() (reconstruction.ecoli.dataclasses.process.translation.Translation method) _build_transport_reactions() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism method) _build_trna_data() (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.Mass method) (validation.ecoli.validation_data.Mass method) _build_unique_molecules() (reconstruction.ecoli.dataclasses.state.internal_state.InternalState method) (validation.ecoli.validation_data.InternalState method) _buildComplexToMonomer() (reconstruction.ecoli.dataclasses.process.two_component_system.TwoComponentSystem method) _buildMoleculeIds() (reconstruction.ecoli.dataclasses.molecule_ids.MoleculeIds method) (validation.ecoli.validation_data.MoleculeIds method) _buildRnaDecayData() (reconstruction.ecoli.dataclasses.process.rna_decay.RnaDecay method) _buildStoichMatrixMonomers() (reconstruction.ecoli.dataclasses.process.complexation.Complexation method) _calculate_total_n_to_degrade() (ecoli.processes.rna_degradation.RnaDegradation method) _calculateActivationProb() (ecoli.processes.transcript_initiation.TranscriptInitiation method) _calculateGrowthRateDependentDnaMass() (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.Mass method) (validation.ecoli.validation_data.Mass method) _check_multi_sum() (wholecell.utils.test_parallelization.Test_parallelization method) _check_new_gene_ids() (reconstruction.ecoli.knowledge_base_raw.KnowledgeBaseEcoli method) (validation.ecoli.validation_data.KnowledgeBaseEcoli method) _chromMass() (reconstruction.ecoli.compendium.growth_data.GrowthData method) _clamp_elongation_to_sequence_length() (wholecell.utils.polymerize.polymerize method) _class_cleanups (reconstruction.tests.test_fit_sim_data_1.Test_fitkb1 attribute) (reconstruction.tests.test_spreadsheets.Test_Spreadsheets attribute) (wholecell.tests.io.test_tsv.Test_Tsv attribute) (wholecell.tests.utils.test_blas.Test_blas attribute) (wholecell.tests.utils.test_data.Test_data attribute) (wholecell.tests.utils.test_dependency_graph.TestDependencyGraph attribute) (wholecell.tests.utils.test_fast_nnls.Test_fast_nnls attribute) (wholecell.tests.utils.test_filepath.Test_filepath attribute) (wholecell.tests.utils.test_library_performance.Test_library_performance attribute) (wholecell.tests.utils.test_mc_complexation.Test_mc_complexation attribute) (wholecell.tests.utils.test_memory_debug.Test_memory_debug attribute) (wholecell.tests.utils.test_modular_fba.Test_FluxBalanceAnalysis attribute) (wholecell.tests.utils.test_nf_glpk.Test_NetworkFlowGLPK attribute) (wholecell.tests.utils.test_polymerize.Test_polymerize attribute) (wholecell.tests.utils.test_unit_struct_array.Test_unit_struct_array attribute) (wholecell.tests.utils.test_units.Test_units attribute) (wholecell.utils.test_parallelization.Test_parallelization attribute) _classSetupFailed (reconstruction.tests.test_fit_sim_data_1.Test_fitkb1 attribute) (reconstruction.tests.test_spreadsheets.Test_Spreadsheets attribute) (wholecell.tests.io.test_tsv.Test_Tsv attribute) (wholecell.tests.utils.test_blas.Test_blas attribute) (wholecell.tests.utils.test_data.Test_data attribute) (wholecell.tests.utils.test_dependency_graph.TestDependencyGraph attribute) (wholecell.tests.utils.test_fast_nnls.Test_fast_nnls attribute) (wholecell.tests.utils.test_filepath.Test_filepath attribute) (wholecell.tests.utils.test_library_performance.Test_library_performance attribute) (wholecell.tests.utils.test_mc_complexation.Test_mc_complexation attribute) (wholecell.tests.utils.test_memory_debug.Test_memory_debug attribute) (wholecell.tests.utils.test_modular_fba.Test_FluxBalanceAnalysis attribute) (wholecell.tests.utils.test_nf_glpk.Test_NetworkFlowGLPK attribute) (wholecell.tests.utils.test_polymerize.Test_polymerize attribute) (wholecell.tests.utils.test_unit_struct_array.Test_unit_struct_array attribute) (wholecell.tests.utils.test_units.Test_units attribute) (wholecell.utils.test_parallelization.Test_parallelization attribute)

_clipTau_d() (reconstruction.ecoli.compendium.growth_data.GrowthData method) (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.Mass method) (validation.ecoli.validation_data.Mass method) _compartment_tag (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions attribute) (validation.ecoli.validation_data.GetterFunctions attribute) _compiled_enzymes (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) _compiled_saturation (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) _compute_boundaries() (wholecell.utils.voronoi_plot_main.VoronoiMaster method) _compute_error() (wholecell.utils.voronoi_plot_main.VoronoiMaster method) _compute_new_segment_attributes() (ecoli.processes.chromosome_structure.ChromosomeStructure method) _compute_power_diagram() (wholecell.utils.voronoi_plot_main.VoronoiMaster method) _construct_default_saturation_equation() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism static method) _decode_row() (reconstruction.spreadsheets.JsonReader method) _dict_to_list() (reconstruction.spreadsheets.JsonWriter method) _divide_polygons() (wholecell.utils.voronoi_plot_main.VoronoiMaster method) _edge_list() (ecoli.analysis.causality_network.build_network.BuildNetwork method) _elongate() (wholecell.utils.polymerize.polymerize method) _elongate_to_limit() (wholecell.utils.polymerize.polymerize method) _enzymes (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) _exchange_flux_present() (reconstruction.ecoli.dataclasses.process.metabolism.ConcentrationUpdates method) _expected_row() (in module wholecell.tests.io.test_tsv) _extract_custom_constraint() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism static method) _field() (wholecell.utils.unit_struct_array.UnitStructArray method) _finalize() (ecoli.library.parquet_emitter.ParquetEmitter method) (wholecell.utils.polymerize.polymerize method) _finalize_resource_limited_elongations() (wholecell.utils.polymerize.polymerize method) _find_bisector_positive_ray() (wholecell.utils.voronoi_plot_main.VoronoiMaster method) _find_duplicate_nodes() (ecoli.analysis.causality_network.build_network.BuildNetwork method) _find_multiple_positive_ray() (wholecell.utils.voronoi_plot_main.VoronoiMaster method) _find_total() (wholecell.utils.voronoi_plot_main.VoronoiMaster method) _findColumn() (reconstruction.ecoli.dataclasses.process.complexation.Complexation method) (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) _findRow() (reconstruction.ecoli.dataclasses.process.complexation.Complexation method) (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) _fit_ribosome_elongation_rate_by_ppgpp() (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.GrowthRateParameters method) (validation.ecoli.validation_data.GrowthRateParameters method) _format_dynamics_string() (ecoli.analysis.causality_network.network_components.Node method) _format_time() (in module wholecell.tests.utils.test_library_performance) _gather_input_dimensions() (wholecell.utils.polymerize.polymerize method) _gather_sequence_data() (wholecell.utils.polymerize.polymerize method) _generate_plot() (wholecell.utils.voronoi_plot_main.VoronoiMaster method) _get_all_external_exchange_molecules() (reconstruction.ecoli.dataclasses.state.external_state.ExternalState method) _get_complement_sequence() (reconstruction.ecoli.dataclasses.process.replication.Replication method) _get_environment_molecules_fw() (wholecell.utils.make_media.Media method) _get_fit_parameters() (in module reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters) _get_linearized_fit() (in module reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters) _get_lw() (ecoli.analysis.colony.snapshots.LineWidthData method) _get_motif_coordinates() (reconstruction.ecoli.dataclasses.process.replication.Replication method) _get_new_gene_sequence() (reconstruction.ecoli.knowledge_base_raw.KnowledgeBaseEcoli method) (validation.ecoli.validation_data.KnowledgeBaseEcoli method) _get_path_net_depth() (in module ecoli.processes.engine_process) _get_recipes() (wholecell.utils.make_media.Media method) _get_relative_coordinates() (reconstruction.ecoli.dataclasses.process.replication.Replication method) (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) _get_rnas_to_degrade() (ecoli.processes.rna_degradation.RnaDegradation method) _get_secretion_exchange_molecules() (reconstruction.ecoli.dataclasses.state.external_state.ExternalState method) _get_stock_media() (wholecell.utils.make_media.Media method) _getFitParameters() (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.Mass method) (validation.ecoli.validation_data.Mass method) _initialize_environment() (reconstruction.ecoli.dataclasses.state.external_state.ExternalState method) _InnerComposer (class in ecoli.processes.engine_process) _inverse_update() (in module ecoli.processes.engine_process) _is_transport_rxn() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism method) _join_data() (reconstruction.ecoli.knowledge_base_raw.KnowledgeBaseEcoli method) (validation.ecoli.validation_data.KnowledgeBaseEcoli method) _kcats (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) _lambdify_constraints() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism static method) _linewidth (ecoli.analysis.colony.snapshots.LineWidthData property) _load_essential_genes() (validation.ecoli.validation_data.EssentialGenes method) _load_li() (validation.ecoli.validation_data.Protein method) _load_parameters() (reconstruction.ecoli.knowledge_base_raw.KnowledgeBaseEcoli method) (validation.ecoli.validation_data.KnowledgeBaseEcoli method) _load_sequence() (reconstruction.ecoli.knowledge_base_raw.KnowledgeBaseEcoli method) (validation.ecoli.validation_data.KnowledgeBaseEcoli method) _load_tsv() (reconstruction.ecoli.knowledge_base_raw.KnowledgeBaseEcoli method) (validation.ecoli.validation_data.KnowledgeBaseEcoli method) (validation.ecoli.validation_data_raw.ValidationDataRawEcoli method) _loadGeneFunctions() (validation.ecoli.validation_data.GeneFunctions method) _loadHouser2015Counts() (validation.ecoli.validation_data.Protein method) _loadRow() (in module reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters) _loadSchmidt2015Counts() (validation.ecoli.validation_data.Protein method) _loadTableIntoObjectGivenDoublingTime() (in module reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters) _loadTaniguchi2010Counts() (validation.ecoli.validation_data.Protein method) _loadToya2010Fluxes() (validation.ecoli.validation_data.ReactionFlux method) _loadWisniewski2014Counts() (validation.ecoli.validation_data.Protein method) _make_dependency_matrix() (reconstruction.ecoli.dataclasses.process.two_component_system.TwoComponentSystem method) _make_derivative() (reconstruction.ecoli.dataclasses.process.two_component_system.TwoComponentSystem method) _make_derivative_parca() (reconstruction.ecoli.dataclasses.process.two_component_system.TwoComponentSystem method) _make_rates() (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) _make_y_dy() (reconstruction.ecoli.dataclasses.process.two_component_system.TwoComponentSystem method) _makeMatrices() (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) _matrix_to_array() (in module wholecell.utils.build_ode) _modify_data() (reconstruction.ecoli.knowledge_base_raw.KnowledgeBaseEcoli method) (validation.ecoli.validation_data.KnowledgeBaseEcoli method) _moleculeRecursiveSearch() (reconstruction.ecoli.dataclasses.process.complexation.Complexation method) (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) _NO_UPDATE_NEEDED (in module ecoli.library.updaters) _node_list() (ecoli.analysis.causality_network.build_network.BuildNetwork method) _normalize_ppgpp_expression() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) _OuterComposer (class in ecoli.processes.engine_process) _point_is_within_triangle() (wholecell.utils.voronoi_plot_main.VoronoiMaster method) _polygon_area() (wholecell.utils.voronoi_plot_main.PolygonClass method) _populate_derivative_and_jacobian() (reconstruction.ecoli.dataclasses.process.two_component_system.TwoComponentSystem method) _populateDerivativeAndJacobian() (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) _prepare_outputs() (wholecell.utils.polymerize.polymerize method) _prepare_running_values() (wholecell.utils.polymerize.polymerize method) _ProcA (class in ecoli.processes.engine_process) _ProcB (class in ecoli.processes.engine_process) _ProcC (class in ecoli.processes.engine_process) _proteinDegRates() (ecoli.processes.protein_degradation.ProteinDegradation method) _prune_and_convert_to_ipoints() (wholecell.utils.voronoi_plot_main.VoronoiMaster method) _prune_data() (reconstruction.ecoli.knowledge_base_raw.KnowledgeBaseEcoli method) (validation.ecoli.validation_data.KnowledgeBaseEcoli method) _recompute_power_diagram() (wholecell.utils.voronoi_plot_main.VoronoiMaster method) _remove_hanging_edges() (ecoli.analysis.causality_network.build_network.BuildNetwork method) _remove_private_fields() (in module wholecell.tests.io.test_tsv) _replace_enzyme_reactions() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism static method) _rescale_initiation_probs() (ecoli.processes.transcript_initiation.TranscriptInitiation method) _retrieve_process_configs() (ecoli.experiments.ecoli_master_sim.EcoliSim method) _retrieve_processes() (ecoli.experiments.ecoli_master_sim.EcoliSim method) _retrieve_topology() (ecoli.experiments.ecoli_master_sim.EcoliSim method) _reverse_deep_merge() (in module ecoli.library.updaters) _sanitize_inputs() (wholecell.utils.polymerize.polymerize method) _saturations (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) _seedFromName() (ecoli.library.sim_data.LoadSimData method) _set_lw() (ecoli.analysis.colony.snapshots.LineWidthData method) _set_solver_values() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism method) _setup() (wholecell.utils.polymerize.polymerize method) _solve_ppgpp_km() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) _square() (in module wholecell.utils.test_parallelization) _sum_squares() (in module wholecell.utils.test_parallelization) _topo_sort_dfs() (wholecell.utils.dependency_graph.DependencyGraph method) _update_elongation_resource_demands() (wholecell.utils.polymerize.polymerize method) _update_gene_insertion_location() (reconstruction.ecoli.knowledge_base_raw.KnowledgeBaseEcoli method) (validation.ecoli.validation_data.KnowledgeBaseEcoli method) _update_gene_locations() (reconstruction.ecoli.knowledge_base_raw.KnowledgeBaseEcoli method) (validation.ecoli.validation_data.KnowledgeBaseEcoli method) _update_global_coordinates() (reconstruction.ecoli.knowledge_base_raw.KnowledgeBaseEcoli method) (validation.ecoli.validation_data.KnowledgeBaseEcoli method) _use_linearized_fit() (in module reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters) _useFitParameters() (in module reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters) _validate() (wholecell.utils.unit_struct_array.UnitStructArray method) _voronoi_main_function() (wholecell.utils.voronoi_plot_main.VoronoiMaster method) _voronoi_treemap() (wholecell.utils.voronoi_plot_main.VoronoiMaster method) _voronoi_treemap_recal() (wholecell.utils.voronoi_plot_main.VoronoiMaster method) _write_files() (ecoli.analysis.causality_network.build_network.BuildNetwork method) _write_json() (ecoli.analysis.causality_network.build_network.BuildNetwork method)

A

aa_enzymes (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) aa_export_kms (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) aa_exporter_names (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) aa_forward_stoich (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) aa_import_kis (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) aa_importer_names (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) aa_kcats_fwd (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) aa_kcats_rev (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) aa_kis (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) aa_reverse_kms (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) aa_reverse_stoich (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) aa_supply_scaling() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism method) aa_synthesis_pathways (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) aa_to_exporters (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) aa_to_exporters_matrix (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) aa_to_importers (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) aa_to_importers_matrix (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) aa_upstream_kms (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) aa_upstream_mapping (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) abs() (in module wholecell.utils.units) adapt_positions_weights() (wholecell.utils.voronoi_plot_main.VoronoiClass method) adapt_weights() (wholecell.utils.voronoi_plot_main.VoronoiClass method) add_barriers() (ecoli.library.pymunk_multibody.PymunkMultibody method) add_body_from_center() (ecoli.library.pymunk_multibody.PymunkMultibody method) add_computed_value() (in module ecoli.library.create_timeline) add_computed_value_bulk() (in module ecoli.library.create_timeline) add_dep_relation() (wholecell.utils.dependency_graph.DependencyGraph method) add_ingredients() (wholecell.utils.make_media.Media method) add_nodes() (wholecell.utils.dependency_graph.DependencyGraph method) add_polyribosomes() (in module ecoli.composites.ecoli_spatial) add_time_axis() (in module ecoli.analysis.colony.snapshots) add_to_bulk_state() (reconstruction.ecoli.dataclasses.state.bulkMolecules.BulkMolecules method) add_to_unique_state() (reconstruction.ecoli.dataclasses.state.uniqueMolecules.UniqueMolecules method) add_units() (in module ecoli.library.units) add_updates (ecoli.library.schema.UniqueNumpyUpdater attribute) AddIngredientsError addToStateCommon() (in module reconstruction.ecoli.dataclasses.state.stateFunctions) adjust_final_expression() (reconstruction.ecoli.simulation_data.SimulationDataEcoli method) adjust_new_gene_final_expression() (reconstruction.ecoli.simulation_data.SimulationDataEcoli method) adjust_polymerizing_ppgpp_expression() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) adjust_ppgpp_expression_for_tfs() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) adjust_promoters() (in module reconstruction.ecoli.fit_sim_data_1) adjust_toya_data() (in module wholecell.utils.toya) Adjustments (class in reconstruction.ecoli.dataclasses.adjustments) agent_body_config() (in module ecoli.processes.environment.multibody_physics) agent_data_table() (in module ecoli.analysis.antibiotics_colony.load_data)

agent_summary() (in module ecoli.analysis.antibiotics_colony.amp_plots) Aggregator (class in ecoli.processes.listeners.aggregator) all_negative() (in module ecoli.library.data_predicates) all_nonnegative() (in module ecoli.library.data_predicates) all_nonpositive() (in module ecoli.library.data_predicates) all_positive() (in module ecoli.library.data_predicates) all_vars() (in module runscripts.debug.compare_pickles) Allocator (class in ecoli.processes.allocator) amino_acid_counts() (ecoli.processes.polypeptide_elongation.BaseElongationModel method) (ecoli.processes.polypeptide_elongation.TranslationSupplyElongationModel method) amino_acid_export() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism method) amino_acid_export_jit() (in module reconstruction.ecoli.dataclasses.process.metabolism) amino_acid_export_kms (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) amino_acid_import() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism method) amino_acid_import_jit() (in module reconstruction.ecoli.dataclasses.process.metabolism) amino_acid_synthesis() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism method) amino_acid_synthesis_jit() (in module reconstruction.ecoli.dataclasses.process.metabolism) amp_conc_sweep() (in module ecoli.analysis.antibiotics_colony.amp_plots) ampicillin_pca() (in module ecoli.analysis.antibiotics_colony.amp_plots) ANALYSIS_TYPES (in module runscripts.analysis) angle() (in module wholecell.utils.voronoi_plot_main) animate_frame() (ecoli.processes.environment.multibody_physics.Multibody method) apply_and_save_variants() (in module runscripts.create_variants) apply_async() (wholecell.utils.parallelization.InlinePool method) apply_exchanges() (in module ecoli.library.lattice_utils) apply_jitter_force() (ecoli.library.pymunk_multibody.PymunkMultibody method) apply_motile_force() (ecoli.library.pymunk_multibody.PymunkMultibody method) apply_updates() (in module reconstruction.ecoli.fit_sim_data_1) apply_variant() (in module ecoli.variants.condition) (in module ecoli.variants.new_gene_internal_shift) (in module ecoli.variants.variant_test) apply_viscous_force() (ecoli.library.pymunk_multibody.PymunkMultibody method) ApplyResult (class in wholecell.utils.parallelization) approx_poisson() (in module ecoli.library.data_predicates) array_from() (in module ecoli.composites.ecoli_spatial) (in module ecoli.library.schema) (in module ecoli.processes.spatiality.diffusion_network) array_timeseries() (in module ecoli.analysis.causality_network.read_dynamics) array_to() (in module ecoli.processes.spatiality.diffusion_network) array_to_list() (in module reconstruction.spreadsheets) assertions() (in module ecoli.processes.transcript_elongation) attrs() (in module ecoli.library.schema) avg_1d_array_over_scalar_sql() (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) avg_1d_array_sql() (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) avg_ratio_of_1d_arrays_sql() (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) avg_sum_1d_array_over_scalar_sql() (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) avg_sum_1d_array_sql() (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps)

B

basal_specs() (in module reconstruction.ecoli.fit_sim_data_1) base_reaction_ids (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) BaseElongationModel (class in ecoli.processes.polypeptide_elongation) blame_plot() (in module ecoli.analysis.single.blame) blame_timeseries() (in module ecoli.analysis.single.blame) build_ecoli() (ecoli.experiments.ecoli_master_sim.EcoliSim method) build_functions() (in module wholecell.utils.build_ode) build_half_life_table() (in module reconstruction.ecoli.scripts.protein_half_lives.convert_to_flat) (in module reconstruction.ecoli.scripts.rna_half_lives.convert_to_flat) build_nodes_and_edges() (ecoli.analysis.causality_network.build_network.BuildNetwork method) build_runtime_image() (in module runscripts.workflow)

build_wcm_image() (in module runscripts.workflow) buildBasalCellSpecifications() (in module reconstruction.ecoli.fit_sim_data_1) BuildCausalityNetwork (class in ecoli.analysis.causality_network.buildCausalityNetwork) buildCombinedConditionCellSpecifications() (in module reconstruction.ecoli.fit_sim_data_1) BuildNetwork (class in ecoli.analysis.causality_network.build_network) buildSequences() (in module wholecell.utils.polymerize) buildTfConditionCellSpecifications() (in module reconstruction.ecoli.fit_sim_data_1) bulk_name_to_idx() (in module ecoli.library.schema) bulk_numpy_updater() (in module ecoli.library.schema) BulkMolecules (class in reconstruction.ecoli.dataclasses.state.bulkMolecules) BulkTimelineProcess (class in ecoli.processes.bulk_timeline)

C

calcProteinCounts() (in module wholecell.utils.fitting) calcProteinDistribution() (in module wholecell.utils.fitting) calcProteinTotalCounts() (in module wholecell.utils.fitting) calculate_activation_prob() (ecoli.processes.polypeptide_initiation.PolypeptideInitiation method) calculate_amp_metrics() (in module ecoli.analysis.antibiotics_colony.metrics) calculate_attenuation() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) calculate_cell_mass() (in module ecoli.library.initial_conditions) calculate_glucose_metrics() (in module ecoli.analysis.antibiotics_colony.metrics) calculate_lattice_size() (in module ecoli.library.cell_wall.lattice) calculate_ppgpp_expression() (reconstruction.ecoli.simulation_data.SimulationDataEcoli method) calculate_request() (ecoli.processes.chromosome_replication.ChromosomeReplication method) (ecoli.processes.complexation.Complexation method) (ecoli.processes.equilibrium.Equilibrium method) (ecoli.processes.partition.PartitionedProcess method) (ecoli.processes.polypeptide_elongation.PolypeptideElongation method) (ecoli.processes.polypeptide_initiation.PolypeptideInitiation method) (ecoli.processes.protein_degradation.ProteinDegradation method) (ecoli.processes.rna_degradation.RnaDegradation method) (ecoli.processes.rna_maturation.RnaMaturation method) (ecoli.processes.spatiality.diffusion_network.DiffusionNetwork method) (ecoli.processes.transcript_elongation.TranscriptElongation method) (ecoli.processes.transcript_initiation.TranscriptInitiation method) (ecoli.processes.two_component_system.TwoComponentSystem method) calculate_rp_from_mw() (in module ecoli.processes.spatiality.diffusion_network) calculate_tet_metrics() (in module ecoli.analysis.antibiotics_colony.metrics) calculate_timestep() (ecoli.processes.engine_process.EngineProcess method) (ecoli.processes.global_clock.GlobalClock method) calculate_trna_charging() (in module ecoli.processes.polypeptide_elongation) calculateBulkDistributions() (in module reconstruction.ecoli.fit_sim_data_1) calculateMinPolymerizingEnzymeByProductDistribution() (in module reconstruction.ecoli.fit_sim_data_1) calculateMinPolymerizingEnzymeByProductDistributionRNA() (in module reconstruction.ecoli.fit_sim_data_1) calculatePartition() (in module ecoli.processes.allocator) calculatePromoterBoundProbability() (in module reconstruction.ecoli.fit_sim_data_1) calculateRnapRecruitment() (in module reconstruction.ecoli.fit_sim_data_1) calculateTranslationSupply() (in module reconstruction.ecoli.fit_sim_data_1) can_deserialize() (ecoli.library.serialize.NumpyRandomStateSerializer method) (ecoli.library.serialize.ParameterSerializer method) (ecoli.library.serialize.UnumSerializer method) cap_tunneling_paths() (in module ecoli.processes.engine_process) catalysis_matrix_I (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) catalysis_matrix_J (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) catalysis_matrix_V (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) catalyst_ids (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) charging_stoich_matrix() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) check_fig_pickle() (in module ecoli.composites.ecoli_spatial) Chemostat (class in ecoli.processes.chemostat) ChemotaxisMinimal (class in ecoli.composites.chemotaxis_minimal) ChromosomeReplication (class in ecoli.processes.chromosome_replication) ChromosomeStructure (class in ecoli.processes.chromosome_structure) (class in reconstruction.ecoli.dataclasses.process.chromosome_structure) cistron_id_to_rna_indexes() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) cli() (in module ecoli.analysis.antibiotics_colony.amp_plots) (in module ecoli.analysis.antibiotics_colony.spatial_correlation) close() (wholecell.utils.parallelization.InlinePool method) cofactor_denominator() (in module ecoli.library.kinetic_rate_laws) cofactor_numerator() (in module ecoli.library.kinetic_rate_laws)

colony_save_states() (in module ecoli.experiments.ecoli_engine_process) color_phylogeny() (in module ecoli.analysis.colony.snapshots) combine_media() (wholecell.utils.make_media.Media method) comment_line() (in module reconstruction.spreadsheets) CommonNames (class in reconstruction.ecoli.dataclasses.common_names) compare_data() (in module reconstruction.ecoli.scripts.fold_changes.calculate_fc) compare_floats() (in module runscripts.debug.compare_pickles) compare_half_lives() (in module reconstruction.ecoli.scripts.rna_half_lives.convert_to_flat) compare_ndarrays() (in module runscripts.debug.compare_pickles) Complexation (class in ecoli.processes.complexation) (class in reconstruction.ecoli.dataclasses.process.complexation) ComplexationError compute_diffusion_constant_from_mw() (in module wholecell.utils.spatial_tool) compute_diffusion_constant_from_rp() (in module wholecell.utils.spatial_tool) compute_diffusion_constants_from_rp() (in module ecoli.processes.spatiality.diffusion_network) compute_error() (wholecell.utils.voronoi_plot_main.VoronoiClass method) compute_free_volume_ratio() (in module wholecell.utils.spatial_tool) compute_hydrodynamic_radius() (in module wholecell.utils.spatial_tool) compute_n_blob() (in module wholecell.utils.spatial_tool) compute_nucleoid_size() (in module wholecell.utils.spatial_tool) compute_rg_rna() (in module wholecell.utils.spatial_tool) computeMassIncrease() (in module wholecell.utils.polymerize) conc_dict (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) concentration_updates (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) concentrations_based_on_nutrients() (reconstruction.ecoli.dataclasses.process.metabolism.ConcentrationUpdates method) ConcentrationsDeriver (class in ecoli.processes.concentrations_deriver) concentrationToCounts() (ecoli.processes.metabolism_redux.MetabolismRedux method) (ecoli.processes.metabolism_redux_classic.MetabolismReduxClassic method) ConcentrationUpdates (class in reconstruction.ecoli.dataclasses.process.metabolism) config (ecoli.composites.ecoli_master.Ecoli attribute) (ecoli.experiments.ecoli_master_sim.SimConfig attribute) configure() (ecoli.library.pymunk_multibody.NullScreen method) Constants (class in reconstruction.ecoli.dataclasses.constants) (class in validation.ecoli.validation_data) constants (ecoli.analysis.causality_network.network_components.Node attribute) constraint_is_kcat_only (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) constraints_to_disable (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) construct_convenience_rate_law() (in module ecoli.library.kinetic_rate_laws) convert_dynamics() (in module ecoli.analysis.causality_network.read_dynamics) copy_to_filesystem() (in module runscripts.workflow) corner_from_center() (in module ecoli.library.pymunk_multibody) cosine_similarity() (in module wholecell.utils.fitting) COUNT_INDEX (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) count_to_concentration() (in module ecoli.library.lattice_utils) counts() (in module ecoli.library.schema) countsFromMassAndExpression() (in module wholecell.utils.fitting) cpus() (in module wholecell.utils.parallelization) crc32() (in module reconstruction.ecoli.fit_sim_data_1) create_bulk_container() (in module ecoli.library.initial_conditions) create_bulk_timeline_from_df() (in module ecoli.library.create_timeline) create_duckdb_conn() (in module runscripts.analysis) create_emitter() (ecoli.processes.engine_process.EngineProcess method) create_new_unique_molecules() (in module ecoli.library.initial_conditions) create_timeline_from_csv() (in module ecoli.library.create_timeline) create_timeline_from_df() (in module ecoli.library.create_timeline) create_unique_indexes() (in module ecoli.library.schema) createBulkContainer() (in module reconstruction.ecoli.fit_sim_data_1)

D

daemon (wholecell.utils.parallelization.NoDaemonProcess property) DASHBOARD_FLAG (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) DataStore (class in reconstruction.ecoli.knowledge_base_raw) daughter_locations() (in module ecoli.processes.environment.multibody_physics) daughter_phylogeny_id() (in module ecoli.processes.cell_division) dcdt_jit() (in module ecoli.processes.polypeptide_elongation) default_config_path (ecoli.experiments.ecoli_master_sim.SimConfig attribute) defaults (ecoli.composites.chemotaxis_minimal.ChemotaxisMinimal attribute) (ecoli.composites.ecoli_master.Ecoli attribute) (ecoli.composites.ecoli_spatial.EcoliSpatial attribute) (ecoli.composites.environment.grow_divide.GrowDivide attribute) (ecoli.composites.environment.grow_divide.GrowDivideExchange attribute) (ecoli.composites.environment.lattice.Lattice attribute) (ecoli.experiments.ecoli_engine_process.EcoliEngineProcess attribute) (ecoli.experiments.ecoli_engine_process.EcoliInnerSim attribute) (ecoli.experiments.metabolism_exchanger.MetabolismExchange attribute) (ecoli.library.lattice_utils.ExchangeAgent attribute) (ecoli.library.pymunk_multibody.PymunkMultibody attribute) (ecoli.processes.allocator.Allocator attribute) (ecoli.processes.bulk_timeline.BulkTimelineProcess attribute) (ecoli.processes.cell_division.Division attribute) (ecoli.processes.chemostat.Chemostat attribute) (ecoli.processes.chemotaxis.chemoreceptor_cluster.ReceptorCluster attribute) (ecoli.processes.chemotaxis.coarse_motor.MotorActivity attribute) (ecoli.processes.chemotaxis.flagella_motor.FlagellaMotor attribute) (ecoli.processes.chromosome_replication.ChromosomeReplication attribute) (ecoli.processes.chromosome_structure.ChromosomeStructure attribute) (ecoli.processes.complexation.Complexation attribute) (ecoli.processes.concentrations_deriver.ConcentrationsDeriver attribute) (ecoli.processes.division_detector.DivisionDetector attribute) (ecoli.processes.engine_process.EngineProcess attribute) (ecoli.processes.engine_process.SchemaStub attribute) (ecoli.processes.environment.derive_globals.DeriveGlobals attribute) (ecoli.processes.environment.diffusion_field.DiffusionField attribute) (ecoli.processes.environment.exchange.Exchange attribute) (ecoli.processes.environment.exchange_data.ExchangeData attribute) (ecoli.processes.environment.field_timeline.FieldTimeline attribute) (ecoli.processes.environment.local_field.LocalField attribute) (ecoli.processes.environment.lysis.Lysis attribute) (ecoli.processes.environment.lysis.LysisAgent attribute) (ecoli.processes.environment.lysis.ToyTransportBurst attribute) (ecoli.processes.environment.media_update.MediaUpdate attribute) (ecoli.processes.environment.multibody_physics.Multibody attribute) (ecoli.processes.environment.reaction_diffusion_field.ReactionDiffusion attribute) (ecoli.processes.enzyme_kinetics.EnzymeKinetics attribute) (ecoli.processes.equilibrium.Equilibrium attribute) (ecoli.processes.listeners.aggregator.Aggregator attribute) (ecoli.processes.listeners.dna_supercoiling.DnaSupercoiling attribute) (ecoli.processes.listeners.mass_listener.MassListener attribute) (ecoli.processes.listeners.monomer_counts.MonomerCounts attribute) (ecoli.processes.listeners.replication_data.ReplicationData attribute) (ecoli.processes.listeners.ribosome_data.RibosomeData attribute) (ecoli.processes.listeners.RNA_counts.RNACounts attribute) (ecoli.processes.listeners.rna_synth_prob.RnaSynthProb attribute) (ecoli.processes.listeners.rnap_data.RnapData attribute) (ecoli.processes.listeners.unique_molecule_counts.UniqueMoleculeCounts attribute) (ecoli.processes.membrane.membrane_potential.MembranePotential attribute) (ecoli.processes.metabolism.Metabolism attribute) (ecoli.processes.metabolism_redux.MetabolismRedux attribute) (ecoli.processes.metabolism_redux_classic.MetabolismReduxClassic attribute) (ecoli.processes.partition.Evolver attribute) (ecoli.processes.partition.Requester attribute) (ecoli.processes.polypeptide_elongation.PolypeptideElongation attribute) (ecoli.processes.polypeptide_initiation.PolypeptideInitiation attribute) (ecoli.processes.protein_degradation.ProteinDegradation attribute) (ecoli.processes.rna_degradation.RnaDegradation attribute) (ecoli.processes.rna_interference.RnaInterference attribute) (ecoli.processes.shape.Shape attribute) (ecoli.processes.spatiality.diffusion_network.DiffusionNetwork attribute) (ecoli.processes.spatiality.spatial_geometry.SpatialGeometry attribute) (ecoli.processes.stubs.exchange_stub.Exchange attribute) (ecoli.processes.stubs.exchanger_stub.Exchanger attribute) (ecoli.processes.tf_binding.TfBinding attribute) (ecoli.processes.tf_unbinding.TfUnbinding attribute) (ecoli.processes.transcript_elongation.TranscriptElongation attribute) (ecoli.processes.transcript_initiation.TranscriptInitiation attribute) (ecoli.processes.two_component_system.TwoComponentSystem attribute) (ecoli.processes.unique_update.UniqueUpdate attribute)

define_parameters() (ecoli.analysis.causality_network.buildCausalityNetwork.BuildCausalityNetwork method) delete_updates (ecoli.library.schema.UniqueNumpyUpdater attribute) dependencies (wholecell.utils.dependency_graph.DependencyGraph attribute) DependencyGraph (class in wholecell.utils.dependency_graph) derivatives() (in module wholecell.tests.utils.test_library_performance) (in module wholecell.utils.build_ode) (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) (reconstruction.ecoli.dataclasses.process.two_component_system.TwoComponentSystem method) derivatives_jacobian() (in module wholecell.tests.utils.test_library_performance) (in module wholecell.utils.build_ode) (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) (reconstruction.ecoli.dataclasses.process.two_component_system.TwoComponentSystem method) derivatives_jacobian_jit() (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) (reconstruction.ecoli.dataclasses.process.two_component_system.TwoComponentSystem method) derivatives_jit() (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) (reconstruction.ecoli.dataclasses.process.two_component_system.TwoComponentSystem method) DeriveGlobals (class in ecoli.processes.environment.derive_globals) description() (ecoli.analysis.causality_network.buildCausalityNetwork.BuildCausalityNetwork method) deserialize() (ecoli.library.serialize.NumpyRandomStateSerializer method) (ecoli.library.serialize.ParameterSerializer method) (ecoli.library.serialize.UnumSerializer method) deserialize_and_remove_units() (in module ecoli.analysis.antibiotics_colony.load_data) (in module ecoli.analysis.antibiotics_colony.snapshot_and_hist_plot) detect_holes() (in module ecoli.library.cell_wall.hole_detection) detect_holes_skimage() (in module ecoli.library.cell_wall.hole_detection) detect_leaks() (in module wholecell.utils.memory_debug) determine_chromosome_state() (in module ecoli.library.initial_conditions) dialect (reconstruction.spreadsheets.JsonReader property) (wholecell.io.tsv.dict_reader property) (wholecell.io.tsv.reader property) (wholecell.io.tsv.writer property) dict_reader (class in wholecell.io.tsv) dict_writer() (in module wholecell.io.tsv) diff_dirs() (in module runscripts.debug.compare_pickles) diff_files() (in module runscripts.debug.compare_pickles) diff_trees() (in module runscripts.debug.compare_pickles) diffuse() (ecoli.processes.environment.diffusion_field.DiffusionField method) (ecoli.processes.environment.reaction_diffusion_field.ReactionDiffusion method) diffusion_delta() (ecoli.processes.environment.diffusion_field.DiffusionField method) (ecoli.processes.environment.reaction_diffusion_field.ReactionDiffusion method) DiffusionField (class in ecoli.processes.environment.diffusion_field) DiffusionNetwork (class in ecoli.processes.spatiality.diffusion_network) dissoc() (in module wholecell.utils.data) dissoc_strict() (in module wholecell.utils.data) distribution_from_aa() (ecoli.processes.polypeptide_elongation.SteadyStateElongationModel method) DivergingNormalize (class in ecoli.analysis.single.blame) divide() (in module wholecell.utils.units) divide_binomial() (in module ecoli.library.schema) divide_bulk() (in module ecoli.library.schema) divide_by_domain() (in module ecoli.library.schema) divide_domains() (in module ecoli.library.schema) divide_ribosomes_by_RNA() (in module ecoli.library.schema) divide_RNAs_by_domain() (in module ecoli.library.schema) divide_set_none() (in module ecoli.library.schema) Division (class in ecoli.processes.cell_division) DivisionDetected DivisionDetector (class in ecoli.processes.division_detector) dm_dt (ecoli.processes.metabolism_redux.FlowResult attribute) (ecoli.processes.metabolism_redux_classic.FlowResult attribute) dnaMass() (reconstruction.ecoli.compendium.growth_data.GrowthData method) DnaSupercoiling (class in ecoli.processes.listeners.dna_supercoiling) dot() (in module wholecell.utils.units) dot_product() (in module wholecell.tests.utils.test_blas) DRY_MASS_UNITS (in module reconstruction.ecoli.dataclasses.process.metabolism) dst_id (ecoli.analysis.causality_network.network_components.Edge attribute) dynamics (ecoli.analysis.causality_network.network_components.Node attribute) dynamics_dict() (ecoli.analysis.causality_network.network_components.Node method) dynamics_units (ecoli.analysis.causality_network.network_components.Node attribute)

E

ecoli module Ecoli (class in ecoli.composites.ecoli_master) ecoli (ecoli.experiments.ecoli_master_sim.EcoliSim attribute) ecoli.analysis module ecoli.analysis.antibiotics_colony module ecoli.analysis.antibiotics_colony.amp_plots module ecoli.analysis.antibiotics_colony.exploration module ecoli.analysis.antibiotics_colony.load_data module ecoli.analysis.antibiotics_colony.metrics module ecoli.analysis.antibiotics_colony.plot module ecoli.analysis.antibiotics_colony.plot_utils module ecoli.analysis.antibiotics_colony.snapshot_and_hist_plot module ecoli.analysis.antibiotics_colony.spatial_correlation module ecoli.analysis.antibiotics_colony.tet_dry_mass module ecoli.analysis.antibiotics_colony.timeseries module ecoli.analysis.antibiotics_colony.validation module ecoli.analysis.causality_network module ecoli.analysis.causality_network.build_network module ecoli.analysis.causality_network.buildCausalityNetwork module ecoli.analysis.causality_network.network_components module ecoli.analysis.causality_network.read_dynamics module ecoli.analysis.colony module ecoli.analysis.colony.snapshots module ecoli.analysis.multidaughter module ecoli.analysis.multiexperiment module ecoli.analysis.multigeneration module ecoli.analysis.multigeneration.new_gene_counts module ecoli.analysis.multiseed module ecoli.analysis.multiseed.ecocyc_table module ecoli.analysis.multiseed.subgenerational_expression_table module ecoli.analysis.multivariant module ecoli.analysis.multivariant.average_monomer_counts module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps module ecoli.analysis.single module ecoli.analysis.single.blame module ecoli.analysis.single.mass_fraction_summary module ecoli.composites module ecoli.composites.chemotaxis_minimal module ecoli.composites.ecoli_configs module ecoli.composites.ecoli_master module ecoli.composites.ecoli_master_tests module ecoli.composites.ecoli_spatial module ecoli.composites.environment module ecoli.composites.environment.grow_divide module ecoli.composites.environment.lattice module ecoli.experiments module ecoli.experiments.antibiotics_tests module ecoli.experiments.ecoli_engine_process module ecoli.experiments.ecoli_master_sim module ecoli.experiments.glt_division module ecoli.experiments.metabolism_exchanger module ecoli.experiments.metabolism_redux_sim module ecoli.experiments.tet_amp_sim module ecoli.library module ecoli.library.cell_wall module ecoli.library.cell_wall.column_sampler module ecoli.library.cell_wall.fit_lysis_time module ecoli.library.cell_wall.hole_detection module ecoli.library.cell_wall.lattice module ecoli.library.create_timeline module ecoli.library.data_predicates module ecoli.library.initial_conditions module ecoli.library.json_state module ecoli.library.kinetic_rate_laws module ecoli.library.lattice_utils module ecoli.library.logging_tools module ecoli.library.parameters module ecoli.library.parquet_emitter module ecoli.library.pymunk_multibody module ecoli.library.schema module ecoli.library.serialize module ecoli.library.sim_data module ecoli.library.units module ecoli.library.updaters module ecoli.processes module ecoli.processes.allocator module ecoli.processes.bulk_timeline module ecoli.processes.cell_division module ecoli.processes.chemostat module ecoli.processes.chemotaxis module ecoli.processes.chemotaxis.chemoreceptor_cluster module ecoli.processes.chemotaxis.coarse_motor module ecoli.processes.chemotaxis.flagella_motor module ecoli.processes.chromosome_replication module ecoli.processes.chromosome_structure module ecoli.processes.complexation module ecoli.processes.concentrations_deriver module ecoli.processes.division_detector module ecoli.processes.engine_process module ecoli.processes.environment module

ecoli.processes.environment.derive_globals module ecoli.processes.environment.diffusion_field module ecoli.processes.environment.exchange module ecoli.processes.environment.exchange_data module ecoli.processes.environment.field_timeline module ecoli.processes.environment.local_field module ecoli.processes.environment.lysis module ecoli.processes.environment.media_update module ecoli.processes.environment.multibody_physics module ecoli.processes.environment.reaction_diffusion_field module ecoli.processes.enzyme_kinetics module ecoli.processes.equilibrium module ecoli.processes.global_clock module ecoli.processes.listeners module ecoli.processes.listeners.aggregator module ecoli.processes.listeners.dna_supercoiling module ecoli.processes.listeners.mass_listener module ecoli.processes.listeners.monomer_counts module ecoli.processes.listeners.replication_data module ecoli.processes.listeners.ribosome_data module ecoli.processes.listeners.RNA_counts module ecoli.processes.listeners.rna_synth_prob module ecoli.processes.listeners.rnap_data module ecoli.processes.listeners.unique_molecule_counts module ecoli.processes.membrane module ecoli.processes.membrane.membrane_potential module ecoli.processes.metabolism module ecoli.processes.metabolism_redux module ecoli.processes.metabolism_redux_classic module ecoli.processes.partition module ecoli.processes.polypeptide_elongation module ecoli.processes.polypeptide_initiation module ecoli.processes.protein_degradation module ecoli.processes.registries module ecoli.processes.rna_degradation module ecoli.processes.rna_interference module ecoli.processes.rna_maturation module ecoli.processes.shape module ecoli.processes.spatiality module ecoli.processes.spatiality.diffusion_network module ecoli.processes.spatiality.spatial_geometry module ecoli.processes.stubs module ecoli.processes.stubs.exchange_stub module ecoli.processes.stubs.exchanger_stub module ecoli.processes.tf_binding module ecoli.processes.tf_unbinding module ecoli.processes.transcript_elongation module ecoli.processes.transcript_initiation module ecoli.processes.two_component_system module ecoli.processes.unique_update module ecoli.variants module ecoli.variants.condition module ecoli.variants.new_gene_internal_shift module ecoli.variants.variant_test module ECOLI_DEFAULT_PROCESSES (in module ecoli.composites.ecoli_configs) ECOLI_DEFAULT_TOPOLOGY (in module ecoli.composites.ecoli_configs) ecoli_experiment (ecoli.experiments.ecoli_master_sim.EcoliSim attribute) ecoli_topology_plot() (in module ecoli.composites.ecoli_master) EcoliEngineProcess (class in ecoli.experiments.ecoli_engine_process) EcoliInnerSim (class in ecoli.experiments.ecoli_engine_process) EcoliInnerWrapper (class in ecoli.experiments.ecoli_engine_process) EcoliSim (class in ecoli.experiments.ecoli_master_sim) EcoliSpatial (class in ecoli.composites.ecoli_spatial) Edge (class in ecoli.analysis.causality_network.network_components) edge_type (ecoli.analysis.causality_network.network_components.Edge attribute) elide() (in module runscripts.debug.compare_pickles) elongation_rate() (ecoli.processes.polypeptide_elongation.BaseElongationModel method) (ecoli.processes.polypeptide_elongation.SteadyStateElongationModel method) (ecoli.processes.polypeptide_elongation.TranslationSupplyElongationModel method) emit() (ecoli.library.parquet_emitter.ParquetEmitter method) empty_dict_divider() (in module ecoli.library.schema) EngineProcess (class in ecoli.processes.engine_process) enzyme_to_amino_acid (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) EnzymeKinetics (class in ecoli.processes.enzyme_kinetics) Equilibrium (class in ecoli.processes.equilibrium) (class in reconstruction.ecoli.dataclasses.process.equilibrium) EquilibriumError EssentialGenes (class in validation.ecoli.validation_data) evolve() (ecoli.processes.polypeptide_elongation.BaseElongationModel method) (ecoli.processes.polypeptide_elongation.SteadyStateElongationModel method) evolve_state() (ecoli.processes.chromosome_replication.ChromosomeReplication method) (ecoli.processes.complexation.Complexation method) (ecoli.processes.equilibrium.Equilibrium method) (ecoli.processes.partition.PartitionedProcess method) (ecoli.processes.polypeptide_elongation.PolypeptideElongation method) (ecoli.processes.polypeptide_initiation.PolypeptideInitiation method) (ecoli.processes.protein_degradation.ProteinDegradation method) (ecoli.processes.rna_degradation.RnaDegradation method) (ecoli.processes.rna_maturation.RnaMaturation method) (ecoli.processes.transcript_elongation.TranscriptElongation method) (ecoli.processes.transcript_initiation.TranscriptInitiation method) (ecoli.processes.two_component_system.TwoComponentSystem method) Evolver (class in ecoli.processes.partition) Exchange (class in ecoli.processes.environment.exchange) (class in ecoli.processes.stubs.exchange_stub) exchange_constraints() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism method) exchange_data_from_concentrations() (reconstruction.ecoli.dataclasses.state.external_state.ExternalState method) exchange_data_from_media() (reconstruction.ecoli.dataclasses.state.external_state.ExternalState method) ExchangeAgent (class in ecoli.library.lattice_utils) ExchangeData (class in ecoli.processes.environment.exchange_data) Exchanger (class in ecoli.processes.stubs.exchanger_stub) exchanges (ecoli.processes.metabolism_redux.FlowResult attribute) (ecoli.processes.metabolism_redux_classic.FlowResult attribute) exp2() (in module reconstruction.ecoli.compendium.growth_data) expand_keyed_env_vars() (in module wholecell.utils.data) expected_flagella (ecoli.processes.chemotaxis.flagella_motor.FlagellaMotor attribute) expected_pmf (ecoli.processes.chemotaxis.flagella_motor.FlagellaMotor attribute) expected_thrust (ecoli.processes.chemotaxis.flagella_motor.FlagellaMotor attribute) EXPERIMENT_SCHEMA_SUFFIX (in module ecoli.library.parquet_emitter) ExplorationStatus (class in wholecell.utils.dependency_graph) EXPLORED (wholecell.utils.dependency_graph.ExplorationStatus attribute) EXPLORING (wholecell.utils.dependency_graph.ExplorationStatus attribute) export_figure() (in module wholecell.utils.plotting_tools) export_json() (ecoli.experiments.ecoli_master_sim.EcoliSim method) export_kcats_per_aa (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) expression_from_ppgpp() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) expressionConverge() (in module reconstruction.ecoli.fit_sim_data_1) expressionFromConditionAndFoldChange() (in module reconstruction.ecoli.fit_sim_data_1) ExternalState (class in reconstruction.ecoli.dataclasses.state.external_state) extract_bulk() (in module ecoli.analysis.single.blame) extract_kinetic_constraints() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism static method) extract_metadata() (in module ecoli.experiments.ecoli_master_sim) extract_reactions() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism static method)

F

fast_nnls() (in module wholecell.utils.fast_nonnegative_least_squares) fieldnames (reconstruction.spreadsheets.JsonReader property) (wholecell.io.tsv.dict_reader property) FieldTimeline (class in ecoli.processes.environment.field_timeline) FILTERS (in module runscripts.analysis) final_adjustments() (in module reconstruction.ecoli.fit_sim_data_1) final_amino_acids() (ecoli.processes.polypeptide_elongation.BaseElongationModel method) (ecoli.processes.polypeptide_elongation.SteadyStateElongationModel method) find_intersect_with_canvas() (wholecell.utils.voronoi_plot_main.LineClass method) find_min_dist_to_border() (wholecell.utils.voronoi_plot_main.PolygonClass method) find_ray_intersect_with_canvas() (wholecell.utils.voronoi_plot_main.RayClass method) find_ray_intersect_with_canvas_and_ipoints() (wholecell.utils.voronoi_plot_main.RayClass method) find_sites_causing_displacement() (wholecell.utils.voronoi_plot_main.VoronoiClass method) fit_condition() (in module reconstruction.ecoli.fit_sim_data_1) fit_linearized_transforms() (in module wholecell.utils.fitting) fit_rna_expression() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) fit_strand_term_p() (in module ecoli.library.cell_wall.column_sampler) fit_trna_expression() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) fitCondition() (in module reconstruction.ecoli.fit_sim_data_1) fitExpression() (in module reconstruction.ecoli.fit_sim_data_1) fitLigandConcentrations() (in module reconstruction.ecoli.fit_sim_data_1) fitMaintenanceCosts() (in module reconstruction.ecoli.fit_sim_data_1) fitPromoterBoundProbability() (in module reconstruction.ecoli.fit_sim_data_1)

fitSimData_1() (in module reconstruction.ecoli.fit_sim_data_1) FlagellaMotor (class in ecoli.processes.chemotaxis.flagella_motor) flatten() (in module ecoli.library.schema) flatten_dict() (in module ecoli.library.parquet_emitter) floor() (in module wholecell.utils.units) FlowResult (class in ecoli.processes.metabolism_redux) (class in ecoli.processes.metabolism_redux_classic) FluxBalanceAnalysisModel (class in ecoli.processes.metabolism) fluxes_and_molecules_to_SS() (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) follow_domain_tree() (in module ecoli.library.schema) FONT_SIZE (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) ForkedPdb (class in wholecell.utils) (class in wholecell.utils.forkedPdb) format_data() (in module ecoli.processes.transcript_elongation) format_snapshot_data() (in module ecoli.analysis.colony.snapshots) fraction_import_rate (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) fraction_rnap_bound_ppgpp() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) fraction_supply_rate (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) from_cli() (ecoli.experiments.ecoli_master_sim.EcoliSim static method) from_file() (ecoli.experiments.ecoli_master_sim.EcoliSim static method) front_from_corner() (in module ecoli.library.pymunk_multibody) fullArray() (wholecell.utils.unit_struct_array.UnitStructArray method) fullUnits() (wholecell.utils.unit_struct_array.UnitStructArray method)

G

gaussian() (in module ecoli.library.lattice_utils) GENE_COUNTS_SQL (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) GeneFunctions (class in validation.ecoli.validation_data) generate() (ecoli.experiments.ecoli_engine_process.EcoliInnerSim method) generate_code() (in module runscripts.workflow) generate_colony() (in module runscripts.workflow) generate_data() (in module ecoli.experiments.tet_amp_sim) generate_flow() (ecoli.composites.ecoli_master.Ecoli method) (ecoli.processes.environment.lysis.LysisAgent method) generate_initial_state() (ecoli.library.sim_data.LoadSimData method) generate_lineage() (in module runscripts.workflow) generate_processes() (ecoli.composites.chemotaxis_minimal.ChemotaxisMinimal method) (ecoli.composites.ecoli_master.Ecoli method) (ecoli.composites.ecoli_spatial.EcoliSpatial method) (ecoli.composites.environment.grow_divide.GrowDivide method) (ecoli.composites.environment.grow_divide.GrowDivideExchange method) (ecoli.composites.environment.lattice.Lattice method) (ecoli.experiments.ecoli_engine_process.EcoliEngineProcess method) (ecoli.experiments.ecoli_engine_process.EcoliInnerSim method) (ecoli.experiments.metabolism_exchanger.MetabolismExchange method) (ecoli.processes.engine_process._InnerComposer method) (ecoli.processes.engine_process._OuterComposer method) (ecoli.processes.environment.lysis.LysisAgent method) generate_processes_and_steps() (ecoli.composites.ecoli_master.Ecoli method) generate_steps() (ecoli.composites.ecoli_master.Ecoli method) (ecoli.processes.environment.lysis.LysisAgent method) generate_topology() (ecoli.composites.chemotaxis_minimal.ChemotaxisMinimal method) (ecoli.composites.ecoli_master.Ecoli method) (ecoli.composites.ecoli_spatial.EcoliSpatial method) (ecoli.composites.environment.grow_divide.GrowDivide method) (ecoli.composites.environment.grow_divide.GrowDivideExchange method) (ecoli.composites.environment.lattice.Lattice method) (ecoli.experiments.ecoli_engine_process.EcoliEngineProcess method) (ecoli.experiments.ecoli_engine_process.EcoliInnerSim method) (ecoli.experiments.metabolism_exchanger.MetabolismExchange method) (ecoli.processes.engine_process._InnerComposer method) (ecoli.processes.engine_process._OuterComposer method) (ecoli.processes.environment.lysis.LysisAgent method) generated_initial_state (ecoli.experiments.ecoli_master_sim.EcoliSim attribute) geom_sampler() (in module ecoli.library.cell_wall.column_sampler) get() (ecoli.experiments.ecoli_master_sim.SimConfig method) (ecoli.processes.environment.multibody_physics.InvokeUpdate method) (wholecell.utils.parallelization.ApplyResult method) get_aa_to_transporters_mapping_data() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism method) get_agent_colors() (in module ecoli.analysis.colony.snapshots) get_agent_ids() (in module ecoli.analysis.colony.snapshots) get_all_valid_molecules() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) get_allocator_config() (ecoli.library.sim_data.LoadSimData method) get_amino_acid_conc_conversion() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism method) get_attenuation_stop_probabilities() (in module ecoli.processes.transcript_elongation) (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) get_average_copy_number() (reconstruction.ecoli.dataclasses.process.replication.Replication method) get_avg_cell_dry_mass() (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.Mass method) (validation.ecoli.validation_data.Mass method) get_basal_rna_fractions() (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.Mass method) (validation.ecoli.validation_data.Mass method) get_bernstein_half_lives() (in module reconstruction.ecoli.scripts.rna_half_lives.convert_to_flat) get_bin_site() (ecoli.processes.environment.diffusion_field.DiffusionField method) (ecoli.processes.environment.reaction_diffusion_field.ReactionDiffusion method) (in module ecoli.library.lattice_utils) get_bin_volume() (in module ecoli.library.lattice_utils) get_body_position() (ecoli.library.pymunk_multibody.PymunkMultibody method) get_body_positions() (ecoli.library.pymunk_multibody.PymunkMultibody method) get_brownian_ligand_timeline() (in module ecoli.processes.chemotaxis.chemoreceptor_cluster) get_bulk_counts (class in ecoli.library.schema) get_bulk_processes() (in module ecoli.analysis.single.blame) get_bulk_timeline_config() (ecoli.library.sim_data.LoadSimData method) get_charging_supply_function() (in module ecoli.processes.polypeptide_elongation) get_chemoreceptor_activity_timeline() (in module ecoli.processes.chemotaxis.flagella_motor) get_chen_half_lives() (in module reconstruction.ecoli.scripts.rna_half_lives.convert_to_flat) get_chromosome_replication_config() (ecoli.library.sim_data.LoadSimData method) get_chromosome_structure_config() (ecoli.library.sim_data.LoadSimData method) get_common_ids() (in module wholecell.utils.toya) get_common_name() (reconstruction.ecoli.dataclasses.common_names.CommonNames method) get_compartment() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) get_compartment_tag() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) get_compartments() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) get_complexation_config() (ecoli.library.sim_data.LoadSimData method) get_component_masses() (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.Mass method) (validation.ecoli.validation_data.Mass method) get_config_by_name() (ecoli.library.sim_data.LoadSimData method) get_config_value() (in module ecoli.library.parquet_emitter) get_containing_hole() (ecoli.library.cell_wall.hole_detection.HoleSizeDict method) get_csv_from_database() (in module ecoli.library.create_timeline) get_data() (in module ecoli.analysis.antibiotics_colony.snapshot_and_hist_plot) get_dataset_sql() (in module ecoli.library.parquet_emitter) get_default_global_state() (in module ecoli.processes.environment.derive_globals) get_delta_prob_matrix() (reconstruction.ecoli.dataclasses.process.transcription_regulation.TranscriptionRegulation method) get_depth() (ecoli.library.cell_wall.hole_detection.HoleSizeDict method) get_descendent_domains() (in module ecoli.library.schema) get_dna_critical_mass() (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.Mass method) (validation.ecoli.validation_data.Mass method) get_dna_supercoiling_listener_config() (ecoli.library.sim_data.LoadSimData method) get_dst_id() (ecoli.analysis.causality_network.network_components.Edge method) get_ecoli_partition_topology_plot_settings() (in module ecoli.composites.ecoli_master) get_encoding() (in module ecoli.library.parquet_emitter) get_equilibrium_config() (ecoli.library.sim_data.LoadSimData method) get_exchange_data_config() (ecoli.library.sim_data.LoadSimData method) get_exponential_config() (in module ecoli.processes.environment.diffusion_field) get_exponential_random_timeline() (in module ecoli.processes.chemotaxis.chemoreceptor_cluster) get_field_metadata() (in module ecoli.library.parquet_emitter) get_field_range() (in module ecoli.analysis.colony.snapshots) get_fluxes() (ecoli.library.kinetic_rate_laws.KineticFluxModel method) get_force_with_angle() (in module ecoli.library.pymunk_multibody) get_fraction_active_ribosome() (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.GrowthRateParameters method) (validation.ecoli.validation_data.GrowthRateParameters method) get_fraction_active_rnap() (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.GrowthRateParameters method) (validation.ecoli.validation_data.GrowthRateParameters method) get_free_indices() (in module ecoli.library.schema) get_fwd_rate() (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) get_gaussian_config() (in module ecoli.processes.environment.diffusion_field) get_gene_count_fraction_sql() (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) get_gene_mass_prod_func() (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) get_genomic_coordinates() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) get_git_revision_hash() (in module ecoli.experiments.ecoli_master_sim)

get_git_status() (in module ecoli.experiments.ecoli_master_sim) get_half_lives() (in module reconstruction.ecoli.scripts.protein_half_lives.convert_to_flat) get_import_constraints() (reconstruction.ecoli.dataclasses.state.external_state.ExternalState method) get_indexes() (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) get_inertia() (ecoli.library.pymunk_multibody.PymunkMultibody method) get_kinetic_constraints() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism method) get_length_distributions() (in module ecoli.library.cell_wall.lattice) get_local_environments() (ecoli.processes.environment.diffusion_field.DiffusionField method) (ecoli.processes.environment.reaction_diffusion_field.ReactionDiffusion method) get_mapping_arrays() (in module ecoli.processes.transcript_elongation) get_mass() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) get_mass_config() (ecoli.library.sim_data.LoadSimData method) get_mass_fractions() (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.Mass method) (validation.ecoli.validation_data.Mass method) get_mass_fractions_from_rna_protein_ratio() (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.Mass method) (validation.ecoli.validation_data.Mass method) get_mass_listener_config() (ecoli.library.sim_data.LoadSimData method) get_masses() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) get_mean_and_std_matrices() (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) get_media_update_config() (ecoli.library.sim_data.LoadSimData method) get_metabolism_config() (ecoli.library.sim_data.LoadSimData method) get_metabolism_redux_config() (ecoli.library.sim_data.LoadSimData method) get_metabolite() (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) get_metabolite_coeff() (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) get_metadata() (ecoli.experiments.ecoli_master_sim.EcoliSim method) get_miscrnas_with_singleton_tus() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) get_molecules() (in module ecoli.library.kinetic_rate_laws) get_monomer_counts_indices() (ecoli.library.sim_data.LoadSimData method) get_monomer_counts_listener_config() (ecoli.library.sim_data.LoadSimData method) get_monomers() (reconstruction.ecoli.dataclasses.process.complexation.Complexation method) (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) (reconstruction.ecoli.dataclasses.process.two_component_system.TwoComponentSystem method) get_mrna_counts_indices() (ecoli.library.sim_data.LoadSimData method) get_mRNA_ids_from_monomer_ids() (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) get_new_gene_ids_and_indices() (in module ecoli.variants.new_gene_internal_shift) get_new_gene_mRNA_NTP_fraction_sql() (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) get_node_id() (ecoli.analysis.causality_network.network_components.Node method) get_output_metadata() (ecoli.experiments.ecoli_master_sim.EcoliSim method) get_overcrowding_sql() (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) get_pathway_enzyme_counts_per_aa() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism method) get_phylogeny_colors_from_names() (in module ecoli.analysis.colony.snapshots) get_plot_metadata() (in module ecoli.library.parquet_emitter) get_polypeptide_elongation_config() (ecoli.library.sim_data.LoadSimData method) get_polypeptide_initiation_config() (ecoli.library.sim_data.LoadSimData method) get_ppGpp_conc() (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.GrowthRateParameters method) (validation.ecoli.validation_data.GrowthRateParameters method) get_process() (ecoli.analysis.causality_network.network_components.Edge method) get_protein_degradation_config() (ecoli.library.sim_data.LoadSimData method) get_pulse_timeline() (in module ecoli.processes.chemotaxis.chemoreceptor_cluster) get_random_field_config() (in module ecoli.processes.environment.diffusion_field) get_reaction_name() (reconstruction.ecoli.dataclasses.process.two_component_system.TwoComponentSystem method) get_rev_rate() (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) get_ribosome_counts_projection() (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) get_ribosome_data_listener_config() (ecoli.library.sim_data.LoadSimData method) get_ribosome_elongation_rate() (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.GrowthRateParameters method) (validation.ecoli.validation_data.GrowthRateParameters method) get_ribosome_elongation_rate_by_ppgpp() (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.GrowthRateParameters method) (validation.ecoli.validation_data.GrowthRateParameters method) get_rna_counts_listener_config() (ecoli.library.sim_data.LoadSimData method) get_rna_degradation_config() (ecoli.library.sim_data.LoadSimData method) get_rna_fractions() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) get_rna_indices() (ecoli.library.sim_data.LoadSimData method) get_rna_interference_config() (ecoli.library.sim_data.LoadSimData method) get_rna_maturation_config() (ecoli.library.sim_data.LoadSimData method) get_rna_synth_prob_listener_config() (ecoli.library.sim_data.LoadSimData method) get_rnap_active_fraction_from_ppGpp() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) get_rnap_counts_projection() (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) get_rnap_data_listener_config() (ecoli.library.sim_data.LoadSimData method) get_rnap_elongation_rate() (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.GrowthRateParameters method) (validation.ecoli.validation_data.GrowthRateParameters method) get_rnas_combined_as_genes_projection() (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) get_root_to_id_indices_map() (in module wholecell.utils.toya) get_safe_name() (in module ecoli.analysis.causality_network.read_dynamics) get_sequences() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) get_shape() (ecoli.library.pymunk_multibody.PymunkMultibody method) get_simulated_validation_counts() (in module wholecell.utils.protein_counts) get_single_local_environments() (ecoli.processes.environment.diffusion_field.DiffusionField method) (ecoli.processes.environment.reaction_diffusion_field.ReactionDiffusion method) get_singleton_tu_id() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) get_src_id() (ecoli.analysis.causality_network.network_components.Edge method) get_state_from_file() (in module ecoli.library.json_state) get_submass_array() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) get_symbols_to_ids() (in module reconstruction.ecoli.scripts.rna_half_lives.convert_to_flat) get_symbols_to_monomer_ids() (in module reconstruction.ecoli.scripts.protein_half_lives.convert_to_flat) get_synonyms() (reconstruction.ecoli.dataclasses.common_names.CommonNames method) get_tag_ranges() (in module ecoli.analysis.colony.snapshots) get_tetracycline_ribosome_equilibrium_config() (ecoli.library.sim_data.LoadSimData method) get_tf_config() (ecoli.library.sim_data.LoadSimData method) get_tf_unbinding_config() (ecoli.library.sim_data.LoadSimData method) get_topological_ordering() (wholecell.utils.dependency_graph.DependencyGraph method) get_transcript_elongation_config() (ecoli.library.sim_data.LoadSimData method) get_transcript_initiation_config() (ecoli.library.sim_data.LoadSimData method) get_trna_distribution() (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.Mass method) (validation.ecoli.validation_data.Mass method) get_two_component_system_config() (ecoli.library.sim_data.LoadSimData method) get_unbound() (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) get_unique_fields (class in ecoli.library.schema) get_unique_molecule_counts_config() (ecoli.library.sim_data.LoadSimData method) get_variant_mask() (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) getBiomassAsConcentrations() (ecoli.processes.metabolism_redux.MetabolismRedux method) (ecoli.processes.metabolism_redux_classic.MetabolismReduxClassic method) (reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters.Mass method) (validation.ecoli.validation_data.Mass method) GetterFunctions (class in reconstruction.ecoli.dataclasses.getter_functions) (class in validation.ecoli.validation_data) getUnit() (in module wholecell.utils.units) git_branch() (in module wholecell.utils.filepath) git_hash() (in module wholecell.utils.filepath) GlobalClock (class in ecoli.processes.global_clock) GrowDivide (class in ecoli.composites.environment.grow_divide) GrowDivideExchange (class in ecoli.composites.environment.grow_divide) GrowthData (class in reconstruction.ecoli.compendium.growth_data) GrowthRateParameters (class in reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters) (class in validation.ecoli.validation_data)

H

has_python_vars() (in module runscripts.debug.compare_pickles) hasUnit() (in module wholecell.utils.units) heatmap() (in module wholecell.utils.plotting_tools) help() (ecoli.analysis.causality_network.buildCausalityNetwork.BuildCausalityNetwork method)

hist_by_death_plot() (in module ecoli.analysis.antibiotics_colony.amp_plots) HoleSizeDict (class in ecoli.library.cell_wall.hole_detection) hour_scale_plot() (in module ecoli.analysis.antibiotics_colony.amp_plots) hstack() (in module wholecell.utils.units)

I

idx_array_from() (in module ecoli.analysis.single.blame) IGNORE_FIRST_N_GENS (in module ecoli.analysis.multivariant.average_monomer_counts) import_kcats_per_aa (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) init_axes() (in module ecoli.analysis.colony.snapshots) initial_state() (ecoli.composites.ecoli_master.Ecoli method) (ecoli.composites.ecoli_spatial.EcoliSpatial method) (ecoli.experiments.ecoli_engine_process.EcoliInnerWrapper method) (ecoli.processes.engine_process.EngineProcess method) (ecoli.processes.environment.diffusion_field.DiffusionField method) (ecoli.processes.environment.local_field.LocalField method) (ecoli.processes.environment.reaction_diffusion_field.ReactionDiffusion method) (ecoli.processes.shape.Shape method) (ecoli.processes.spatiality.spatial_geometry.SpatialGeometry method) initialize() (in module reconstruction.ecoli.fit_sim_data_1) (reconstruction.ecoli.simulation_data.SimulationDataEcoli method) (validation.ecoli.validation_data.ValidationDataEcoli method) initialize_bulk_counts() (in module ecoli.library.initial_conditions) initialize_chromosomal_segments() (in module ecoli.library.initial_conditions) initialize_complexation() (in module ecoli.library.initial_conditions) initialize_full_chromosome() (in module ecoli.library.initial_conditions) initialize_mature_RNA() (in module ecoli.library.initial_conditions) initialize_protein_monomers() (in module ecoli.library.initial_conditions) initialize_replication() (in module ecoli.library.initial_conditions) initialize_rna() (in module ecoli.library.initial_conditions) initialize_transcription() (in module ecoli.library.initial_conditions) initialize_transcription_factors() (in module ecoli.library.initial_conditions) initialize_translation() (in module ecoli.library.initial_conditions) initialize_trna_charging() (in module ecoli.library.initial_conditions) initialize_unique_molecules() (in module ecoli.library.initial_conditions)

InlinePool (class in wholecell.utils.parallelization) input_adjustments() (in module reconstruction.ecoli.fit_sim_data_1) InternalState (class in reconstruction.ecoli.dataclasses.state.internal_state) (class in validation.ecoli.validation_data) interpolate_linearized_fit() (in module wholecell.utils.fitting) InvalidDependencyGraphError InvalidProteinComplexError InvalidReactionDirectionError inverse_update_accumulate() (in module ecoli.library.updaters) inverse_update_bulk_numpy() (in module ecoli.library.updaters) inverse_update_merge() (in module ecoli.library.updaters) inverse_update_nonnegative_accumulate() (in module ecoli.library.updaters) inverse_update_null() (in module ecoli.library.updaters) inverse_update_set() (in module ecoli.library.updaters) inverse_update_unique_numpy() (in module ecoli.library.updaters) InvokeUpdate (class in ecoli.processes.environment.multibody_physics) is_leaf() (in module runscripts.debug.compare_pickles) is_macos() (in module wholecell.utils.parallelization) is_on_ray() (wholecell.utils.voronoi_plot_main.RayClass method) is_on_segment() (in module wholecell.utils.voronoi_plot_main) is_valid_molecule() (reconstruction.ecoli.dataclasses.getter_functions.GetterFunctions method) (validation.ecoli.validation_data.GetterFunctions method) isfinite() (in module wholecell.utils.units) isnan() (in module wholecell.utils.units) isTimeStepShortEnough() (ecoli.processes.polypeptide_elongation.BaseElongationModel method) (ecoli.processes.polypeptide_elongation.PolypeptideElongation method) (ecoli.processes.polypeptide_elongation.SteadyStateElongationModel method) (ecoli.processes.transcript_elongation.TranscriptElongation method) iter_variants() (in module wholecell.utils.filepath)

J

join() (wholecell.utils.parallelization.InlinePool method) json_to_parquet() (in module ecoli.library.parquet_emitter)

JsonReader (class in reconstruction.spreadsheets) JsonWriter (class in reconstruction.spreadsheets)

K

K_CAT_UNITS (in module reconstruction.ecoli.dataclasses.process.metabolism) keep_nearest_point_on_ray() (wholecell.utils.voronoi_plot_main.RayClass method) kegg_to_ecocyc() (in module reconstruction.ecoli.scripts.metabolite_concentrations.convert_to_flat) keys() (ecoli.experiments.ecoli_master_sim.SimConfig method) KI_aa_synthesis (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) kinetic_constraint_enzymes (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) kinetic_constraint_reactions (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) kinetic_constraint_substrates (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute)

kinetic_objective_weight (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) kinetic_objective_weight_in_range (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) KineticFluxModel (class in ecoli.library.kinetic_rate_laws) KM_aa_export (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) km_loss_function() (reconstruction.ecoli.dataclasses.process.rna_decay.RnaDecay method) KnowledgeBaseEcoli (class in reconstruction.ecoli.knowledge_base_raw) (class in validation.ecoli.validation_data) kochanowski_concentrations() (in module reconstruction.ecoli.scripts.metabolite_concentrations.convert_to_flat)

L

labeled_indexable_hist() (in module wholecell.utils.plotting_tools) labeled_indexable_scatter() (in module wholecell.utils.plotting_tools) Lattice (class in ecoli.composites.environment.lattice) lempp_concentrations() (in module reconstruction.ecoli.scripts.metabolite_concentrations.convert_to_flat) len_plus_one() (in module ecoli.processes.listeners.aggregator) len_squared() (in module ecoli.processes.listeners.aggregator) length_from_volume() (in module ecoli.processes.environment.derive_globals) (in module ecoli.processes.shape) line_num (reconstruction.spreadsheets.JsonReader property) (wholecell.io.tsv.dict_reader property) (wholecell.io.tsv.reader property) line_profile() (in module wholecell.utils.profiler) linear_regression() (in module reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters) LineClass (class in wholecell.utils.voronoi_plot_main) LineWidthData (class in ecoli.analysis.colony.snapshots) LIST_KEYS_TO_MERGE (in module ecoli.experiments.ecoli_master_sim) list_pickles() (in module runscripts.debug.compare_pickles) listener_schema() (in module ecoli.library.schema)

load_conc() (in module reconstruction.ecoli.scripts.metabolite_concentrations.merge_files) load_data() (in module ecoli.analysis.antibiotics_colony.amp_plots) (in module ecoli.analysis.antibiotics_colony.load_data) (in module ecoli.analysis.antibiotics_colony.spatial_correlation) load_exp_data() (in module ecoli.analysis.antibiotics_colony.plot) load_file() (in module reconstruction.ecoli.scripts.fold_changes.calculate_fc) load_fit_tree() (in module runscripts.debug.compare_pickles) load_kochanowski() (in module reconstruction.ecoli.scripts.metabolite_concentrations.convert_to_flat) load_shifts() (in module reconstruction.ecoli.scripts.fold_changes.calculate_fc) load_sim_data (ecoli.composites.ecoli_master.Ecoli attribute) load_src() (in module reconstruction.ecoli.scripts.fold_changes.calculate_fc) load_states() (in module ecoli.library.json_state) load_tree() (in module runscripts.debug.compare_pickles) load_wcm() (in module reconstruction.ecoli.scripts.fold_changes.calculate_fc) LoadSimData (class in ecoli.library.sim_data) LocalField (class in ecoli.processes.environment.local_field) logistic_explain_death() (in module ecoli.analysis.antibiotics_colony.amp_plots) Lysis (class in ecoli.processes.environment.lysis) LysisAgent (class in ecoli.processes.environment.lysis)

M

main() (in module ecoli.analysis.antibiotics_colony.amp_plots) (in module ecoli.analysis.antibiotics_colony.load_data) (in module ecoli.analysis.antibiotics_colony.metrics) (in module ecoli.analysis.antibiotics_colony.plot) (in module ecoli.analysis.antibiotics_colony.snapshot_and_hist_plot) (in module ecoli.analysis.antibiotics_colony.spatial_correlation) (in module ecoli.analysis.antibiotics_colony.tet_dry_mass) (in module ecoli.analysis.causality_network.buildCausalityNetwork) (in module ecoli.composites.chemotaxis_minimal) (in module ecoli.composites.ecoli_spatial) (in module ecoli.composites.environment.grow_divide) (in module ecoli.composites.environment.lattice) (in module ecoli.experiments.ecoli_master_sim) (in module ecoli.experiments.tet_amp_sim) (in module ecoli.library.cell_wall.column_sampler) (in module ecoli.library.cell_wall.fit_lysis_time) (in module ecoli.library.cell_wall.hole_detection) (in module ecoli.library.cell_wall.lattice) (in module ecoli.library.create_timeline) (in module ecoli.processes.chemotaxis.chemoreceptor_cluster) (in module ecoli.processes.chemotaxis.coarse_motor) (in module ecoli.processes.chemotaxis.flagella_motor) (in module ecoli.processes.environment.lysis) (in module ecoli.processes.environment.multibody_physics) (in module ecoli.processes.environment.reaction_diffusion_field) (in module ecoli.processes.membrane.membrane_potential) (in module ecoli.processes.polypeptide_elongation) (in module ecoli.processes.rna_interference) (in module ecoli.processes.spatiality.spatial_geometry) (in module ecoli.processes.transcript_initiation) (in module runscripts.analysis) (in module runscripts.create_variants) (in module runscripts.parca) (in module runscripts.workflow) (in module validation.ecoli.scripts.rnaDegRates) maintenance_flux (ecoli.processes.metabolism_redux.FlowResult attribute) maintenance_reaction (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) make_configuration() (in module ecoli.library.kinetic_rate_laws) make_diffusion_schema() (in module ecoli.library.lattice_utils) make_elongation_rates() (in module ecoli.processes.transcript_elongation) (in module wholecell.utils.random) (reconstruction.ecoli.dataclasses.process.replication.Replication method) (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) (reconstruction.ecoli.dataclasses.process.translation.Translation method) make_elongation_rates_flat() (in module wholecell.utils.random) make_ete_trees() (in module ecoli.analysis.antibiotics_colony.exploration) make_figure_1a() (in module ecoli.analysis.antibiotics_colony.plot) make_figure_2a() (in module ecoli.analysis.antibiotics_colony.plot) make_figure_2b_d() (in module ecoli.analysis.antibiotics_colony.plot) make_figure_3d_and_3m() (in module ecoli.analysis.antibiotics_colony.plot) make_figure_3f_h() (in module ecoli.analysis.antibiotics_colony.plot) make_figure_3i_k() (in module ecoli.analysis.antibiotics_colony.plot) make_figure_3l() (in module ecoli.analysis.antibiotics_colony.plot) make_figure_4c() (in module ecoli.analysis.antibiotics_colony.plot) make_figure_4l() (in module ecoli.analysis.antibiotics_colony.plot) make_figure_4m() (in module ecoli.analysis.antibiotics_colony.plot) make_figure_4n() (in module ecoli.analysis.antibiotics_colony.plot) make_figure_s1() (in module ecoli.analysis.antibiotics_colony.plot) make_figure_s10() (in module ecoli.analysis.antibiotics_colony.plot) make_figure_s3a() (in module ecoli.analysis.antibiotics_colony.plot) make_figure_s3b() (in module ecoli.analysis.antibiotics_colony.plot) make_figure_s5() (in module ecoli.analysis.antibiotics_colony.plot) make_figure_s6a() (in module ecoli.analysis.antibiotics_colony.plot) make_figure_s6b() (in module ecoli.analysis.antibiotics_colony.plot) make_figure_s7() (in module ecoli.analysis.antibiotics_colony.plot) make_figure_s8() (in module ecoli.analysis.antibiotics_colony.plot) make_figure_videos() (in module ecoli.analysis.antibiotics_colony.plot) make_figures() (in module ecoli.analysis.antibiotics_colony.amp_plots) make_gradient() (in module ecoli.library.lattice_utils) make_initial_state() (in module ecoli.experiments.tet_amp_sim) make_lattice_config() (in module ecoli.composites.environment.lattice) make_logging_process() (in module ecoli.library.logging_tools) make_random_position() (in module ecoli.processes.environment.multibody_physics) make_rate_laws() (in module ecoli.library.kinetic_rate_laws) make_recipe() (wholecell.utils.make_media.Media method) make_relatedness_vs_distance_plot() (in module ecoli.analysis.antibiotics_colony.spatial_correlation) make_saved_media() (wholecell.utils.make_media.Media method) make_snapshot_and_hist_plot() (in module ecoli.analysis.antibiotics_colony.snapshot_and_hist_plot) make_snapshots_figure() (in module ecoli.analysis.colony.snapshots) make_spatial_correlation_plot() (in module ecoli.analysis.antibiotics_colony.spatial_correlation) make_tag_video() (in module ecoli.analysis.antibiotics_colony.timeseries) make_tags_figure() (in module ecoli.analysis.colony.snapshots) make_tet_dry_mass_plot() (in module ecoli.analysis.antibiotics_colony.tet_dry_mass) make_threshold_sweep_plot() (in module ecoli.analysis.antibiotics_colony.spatial_correlation) make_timeline() (wholecell.utils.make_media.Media method) make_video() (in module ecoli.analysis.colony.snapshots) makedirs() (in module wholecell.utils.filepath) makeSequenceMonomers() (wholecell.tests.utils.test_polymerize.Test_polymerize method) map() (wholecell.utils.parallelization.InlinePool method) MarkDPeriod (class in ecoli.processes.cell_division) Mass (class in reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters) (class in validation.ecoli.validation_data) mass_balance() (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) (reconstruction.ecoli.dataclasses.process.two_component_system.TwoComponentSystem method) mass_from_count() (in module ecoli.processes.environment.lysis) mass_matrix() (reconstruction.ecoli.dataclasses.process.complexation.Complexation method) (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) (reconstruction.ecoli.dataclasses.process.two_component_system.TwoComponentSystem method) masses_and_counts_for_homeostatic_target() (in module wholecell.utils.fitting) massFractions() (reconstruction.ecoli.compendium.growth_data.GrowthData method) MassListener (class in ecoli.processes.listeners.mass_listener) match_reaction() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism static method) matmul() (in module wholecell.utils.units) max() (ecoli.library.cell_wall.hole_detection.HoleSizeDict method) MAX_CELL_INDEX (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) max_specific_import_rates (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) maxDiff (wholecell.tests.utils.test_dependency_graph.TestDependencyGraph attribute) mccBuildMatrices() (in module wholecell.utils.mc_complexation) mccFormComplexes() (in module wholecell.utils.mc_complexation) mccFormComplexesWithPrebuiltMatrices() (in module wholecell.utils.mc_complexation) Media (class in wholecell.utils.make_media) MediaUpdate (class in ecoli.processes.environment.media_update) MembranePotential (class in ecoli.processes.membrane.membrane_potential) MemoryDebugNode (class in wholecell.tests.utils.test_memory_debug) merge() (ecoli.experiments.ecoli_master_sim.EcoliSim method) (ecoli.library.cell_wall.hole_detection.HoleSizeDict method) merge_config_dicts() (ecoli.experiments.ecoli_master_sim.SimConfig static method) Metabolism (class in ecoli.processes.metabolism) (class in reconstruction.ecoli.dataclasses.process.metabolism) MetabolismExchange (class in ecoli.experiments.metabolism_exchanger) MetabolismRedux (class in ecoli.processes.metabolism_redux) MetabolismReduxClassic (class in ecoli.processes.metabolism_redux_classic) metabolite_charge (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) METABOLITE_CONCENTRATION_UNITS (in module reconstruction.ecoli.dataclasses.process.metabolism) METADATA_PREFIX (in module ecoli.library.parquet_emitter) MethodSerializer (class in ecoli.library.serialize) MICROMOLAR_UNITS (in module ecoli.processes.polypeptide_elongation) minute_scale_plot() (in module ecoli.analysis.antibiotics_colony.amp_plots) mmol_to_counts_from_volume() (in module ecoli.processes.shape) modify_new_gene_exp_trl() (in module ecoli.variants.new_gene_internal_shift) module ecoli ecoli.analysis ecoli.analysis.antibiotics_colony ecoli.analysis.antibiotics_colony.amp_plots ecoli.analysis.antibiotics_colony.exploration ecoli.analysis.antibiotics_colony.load_data ecoli.analysis.antibiotics_colony.metrics ecoli.analysis.antibiotics_colony.plot ecoli.analysis.antibiotics_colony.plot_utils ecoli.analysis.antibiotics_colony.snapshot_and_hist_plot ecoli.analysis.antibiotics_colony.spatial_correlation ecoli.analysis.antibiotics_colony.tet_dry_mass ecoli.analysis.antibiotics_colony.timeseries ecoli.analysis.antibiotics_colony.validation ecoli.analysis.causality_network ecoli.analysis.causality_network.build_network ecoli.analysis.causality_network.buildCausalityNetwork ecoli.analysis.causality_network.network_components ecoli.analysis.causality_network.read_dynamics ecoli.analysis.colony ecoli.analysis.colony.snapshots ecoli.analysis.multidaughter ecoli.analysis.multiexperiment ecoli.analysis.multigeneration ecoli.analysis.multigeneration.new_gene_counts ecoli.analysis.multiseed ecoli.analysis.multiseed.ecocyc_table ecoli.analysis.multiseed.subgenerational_expression_table ecoli.analysis.multivariant ecoli.analysis.multivariant.average_monomer_counts ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps ecoli.analysis.single ecoli.analysis.single.blame ecoli.analysis.single.mass_fraction_summary ecoli.composites ecoli.composites.chemotaxis_minimal ecoli.composites.ecoli_configs ecoli.composites.ecoli_master ecoli.composites.ecoli_master_tests ecoli.composites.ecoli_spatial ecoli.composites.environment ecoli.composites.environment.grow_divide ecoli.composites.environment.lattice ecoli.experiments ecoli.experiments.antibiotics_tests ecoli.experiments.ecoli_engine_process ecoli.experiments.ecoli_master_sim ecoli.experiments.glt_division ecoli.experiments.metabolism_exchanger ecoli.experiments.metabolism_redux_sim ecoli.experiments.tet_amp_sim ecoli.library ecoli.library.cell_wall ecoli.library.cell_wall.column_sampler ecoli.library.cell_wall.fit_lysis_time ecoli.library.cell_wall.hole_detection ecoli.library.cell_wall.lattice ecoli.library.create_timeline ecoli.library.data_predicates ecoli.library.initial_conditions ecoli.library.json_state ecoli.library.kinetic_rate_laws ecoli.library.lattice_utils ecoli.library.logging_tools ecoli.library.parameters ecoli.library.parquet_emitter ecoli.library.pymunk_multibody ecoli.library.schema ecoli.library.serialize ecoli.library.sim_data ecoli.library.units ecoli.library.updaters ecoli.processes ecoli.processes.allocator ecoli.processes.bulk_timeline ecoli.processes.cell_division ecoli.processes.chemostat ecoli.processes.chemotaxis ecoli.processes.chemotaxis.chemoreceptor_cluster ecoli.processes.chemotaxis.coarse_motor ecoli.processes.chemotaxis.flagella_motor ecoli.processes.chromosome_replication ecoli.processes.chromosome_structure ecoli.processes.complexation ecoli.processes.concentrations_deriver ecoli.processes.division_detector ecoli.processes.engine_process ecoli.processes.environment ecoli.processes.environment.derive_globals ecoli.processes.environment.diffusion_field ecoli.processes.environment.exchange ecoli.processes.environment.exchange_data ecoli.processes.environment.field_timeline ecoli.processes.environment.local_field ecoli.processes.environment.lysis ecoli.processes.environment.media_update ecoli.processes.environment.multibody_physics ecoli.processes.environment.reaction_diffusion_field ecoli.processes.enzyme_kinetics ecoli.processes.equilibrium ecoli.processes.global_clock ecoli.processes.listeners ecoli.processes.listeners.aggregator ecoli.processes.listeners.dna_supercoiling ecoli.processes.listeners.mass_listener ecoli.processes.listeners.monomer_counts ecoli.processes.listeners.replication_data ecoli.processes.listeners.ribosome_data ecoli.processes.listeners.RNA_counts ecoli.processes.listeners.rna_synth_prob ecoli.processes.listeners.rnap_data ecoli.processes.listeners.unique_molecule_counts ecoli.processes.membrane ecoli.processes.membrane.membrane_potential ecoli.processes.metabolism ecoli.processes.metabolism_redux ecoli.processes.metabolism_redux_classic ecoli.processes.partition ecoli.processes.polypeptide_elongation ecoli.processes.polypeptide_initiation ecoli.processes.protein_degradation ecoli.processes.registries ecoli.processes.rna_degradation ecoli.processes.rna_interference ecoli.processes.rna_maturation ecoli.processes.shape ecoli.processes.spatiality ecoli.processes.spatiality.diffusion_network ecoli.processes.spatiality.spatial_geometry ecoli.processes.stubs ecoli.processes.stubs.exchange_stub ecoli.processes.stubs.exchanger_stub ecoli.processes.tf_binding ecoli.processes.tf_unbinding ecoli.processes.transcript_elongation ecoli.processes.transcript_initiation ecoli.processes.two_component_system ecoli.processes.unique_update ecoli.variants ecoli.variants.condition ecoli.variants.new_gene_internal_shift ecoli.variants.variant_test reconstruction reconstruction.ecoli reconstruction.ecoli.compendium reconstruction.ecoli.compendium.growth_data reconstruction.ecoli.dataclasses reconstruction.ecoli.dataclasses.adjustments reconstruction.ecoli.dataclasses.common_names reconstruction.ecoli.dataclasses.constants reconstruction.ecoli.dataclasses.getter_functions reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters reconstruction.ecoli.dataclasses.molecule_groups reconstruction.ecoli.dataclasses.molecule_ids reconstruction.ecoli.dataclasses.process reconstruction.ecoli.dataclasses.process.chromosome_structure reconstruction.ecoli.dataclasses.process.complexation reconstruction.ecoli.dataclasses.process.equilibrium reconstruction.ecoli.dataclasses.process.metabolism reconstruction.ecoli.dataclasses.process.process reconstruction.ecoli.dataclasses.process.replication reconstruction.ecoli.dataclasses.process.rna_decay reconstruction.ecoli.dataclasses.process.transcription reconstruction.ecoli.dataclasses.process.transcription_regulation reconstruction.ecoli.dataclasses.process.translation reconstruction.ecoli.dataclasses.process.two_component_system reconstruction.ecoli.dataclasses.relation reconstruction.ecoli.dataclasses.state reconstruction.ecoli.dataclasses.state.bulkMolecules reconstruction.ecoli.dataclasses.state.external_state reconstruction.ecoli.dataclasses.state.internal_state reconstruction.ecoli.dataclasses.state.stateFunctions reconstruction.ecoli.dataclasses.state.uniqueMolecules reconstruction.ecoli.fit_sim_data_1 reconstruction.ecoli.knowledge_base_raw reconstruction.ecoli.scripts reconstruction.ecoli.scripts.fold_changes reconstruction.ecoli.scripts.fold_changes.calculate_fc reconstruction.ecoli.scripts.metabolism_kinetics reconstruction.ecoli.scripts.metabolism_kinetics.convert_to_flat reconstruction.ecoli.scripts.metabolite_concentrations reconstruction.ecoli.scripts.metabolite_concentrations.convert_to_flat reconstruction.ecoli.scripts.metabolite_concentrations.merge_files reconstruction.ecoli.scripts.protein_half_lives reconstruction.ecoli.scripts.protein_half_lives.convert_to_flat reconstruction.ecoli.scripts.rna_half_lives reconstruction.ecoli.scripts.rna_half_lives.convert_to_flat reconstruction.ecoli.scripts.update_biocyc_files reconstruction.ecoli.simulation_data reconstruction.spreadsheets reconstruction.tests reconstruction.tests.test_fit_sim_data_1 reconstruction.tests.test_spreadsheets runscripts runscripts.analysis runscripts.create_variants runscripts.debug runscripts.debug.compare_pickles runscripts.debug.diff_simouts runscripts.parca runscripts.workflow validation validation.ecoli validation.ecoli.scripts validation.ecoli.scripts.rnaDegRates validation.ecoli.validation_data validation.ecoli.validation_data_raw wholecell wholecell.io wholecell.io.tsv wholecell.tests wholecell.tests.io wholecell.tests.io.test_tsv wholecell.tests.utils wholecell.tests.utils.profile_polymerize wholecell.tests.utils.test_blas wholecell.tests.utils.test_data wholecell.tests.utils.test_dependency_graph wholecell.tests.utils.test_fast_nnls wholecell.tests.utils.test_filepath wholecell.tests.utils.test_library_performance wholecell.tests.utils.test_mc_complexation wholecell.tests.utils.test_memory_debug wholecell.tests.utils.test_modular_fba wholecell.tests.utils.test_nf_glpk wholecell.tests.utils.test_polymerize wholecell.tests.utils.test_unit_struct_array wholecell.tests.utils.test_units wholecell.utils wholecell.utils.build_ode wholecell.utils.constants wholecell.utils.data wholecell.utils.dependency_graph wholecell.utils.fast_nonnegative_least_squares wholecell.utils.filepath wholecell.utils.fitting wholecell.utils.forkedPdb wholecell.utils.make_media wholecell.utils.mc_complexation wholecell.utils.memory_debug wholecell.utils.modular_fba wholecell.utils.parallelization wholecell.utils.plotting_tools wholecell.utils.polymerize wholecell.utils.profiler wholecell.utils.protein_counts wholecell.utils.random wholecell.utils.sparkline wholecell.utils.spatial_tool wholecell.utils.test_parallelization wholecell.utils.toya wholecell.utils.unit_struct_array wholecell.utils.units wholecell.utils.voronoi_plot_main

molecule_compartment() (in module ecoli.analysis.causality_network.build_network) MoleculeGroups (class in reconstruction.ecoli.dataclasses.molecule_groups) (class in validation.ecoli.validation_data) MoleculeIds (class in reconstruction.ecoli.dataclasses.molecule_ids) (class in validation.ecoli.validation_data) MoleculeNotFoundError, [1] molecules_to_next_time_step() (reconstruction.ecoli.dataclasses.process.two_component_system.TwoComponentSystem method) molecules_to_ss() (reconstruction.ecoli.dataclasses.process.two_component_system.TwoComponentSystem method) monomer_to_mRNA_cistron_mapping() (reconstruction.ecoli.dataclasses.relation.Relation method) (validation.ecoli.validation_data.Relation method) MonomerCounts (class in ecoli.processes.listeners.monomer_counts) monotonically_decreasing() (in module ecoli.library.data_predicates) monotonically_increasing() (in module ecoli.library.data_predicates) MotorActivity (class in ecoli.processes.chemotaxis.coarse_motor) mRNADistributionFromProtein() (in module reconstruction.ecoli.fit_sim_data_1) Multibody (class in ecoli.processes.environment.multibody_physics) multiply() (in module wholecell.utils.units) multitest_dot() (wholecell.tests.utils.test_library_performance.Test_library_performance method) mutate_color() (in module ecoli.analysis.colony.snapshots)

N

name (ecoli.analysis.causality_network.network_components.Node attribute) (ecoli.composites.chemotaxis_minimal.ChemotaxisMinimal attribute) (ecoli.composites.environment.grow_divide.GrowDivideExchange attribute) (ecoli.composites.environment.lattice.Lattice attribute) (ecoli.processes.allocator.Allocator attribute) (ecoli.processes.bulk_timeline.BulkTimelineProcess attribute) (ecoli.processes.cell_division.Division attribute) (ecoli.processes.cell_division.MarkDPeriod attribute) (ecoli.processes.cell_division.StopAfterDivision attribute) (ecoli.processes.chemostat.Chemostat attribute) (ecoli.processes.chemotaxis.chemoreceptor_cluster.ReceptorCluster attribute) (ecoli.processes.chemotaxis.coarse_motor.MotorActivity attribute) (ecoli.processes.chemotaxis.flagella_motor.FlagellaMotor attribute) (ecoli.processes.chromosome_replication.ChromosomeReplication attribute) (ecoli.processes.chromosome_structure.ChromosomeStructure attribute) (ecoli.processes.complexation.Complexation attribute) (ecoli.processes.concentrations_deriver.ConcentrationsDeriver attribute) (ecoli.processes.division_detector.DivisionDetector attribute) (ecoli.processes.environment.derive_globals.DeriveGlobals attribute) (ecoli.processes.environment.diffusion_field.DiffusionField attribute) (ecoli.processes.environment.exchange_data.ExchangeData attribute) (ecoli.processes.environment.field_timeline.FieldTimeline attribute) (ecoli.processes.environment.local_field.LocalField attribute) (ecoli.processes.environment.lysis.Lysis attribute) (ecoli.processes.environment.media_update.MediaUpdate attribute) (ecoli.processes.environment.multibody_physics.Multibody attribute) (ecoli.processes.environment.reaction_diffusion_field.ReactionDiffusion attribute) (ecoli.processes.enzyme_kinetics.EnzymeKinetics attribute) (ecoli.processes.equilibrium.Equilibrium attribute) (ecoli.processes.global_clock.GlobalClock attribute) (ecoli.processes.listeners.aggregator.Aggregator attribute) (ecoli.processes.listeners.dna_supercoiling.DnaSupercoiling attribute) (ecoli.processes.listeners.mass_listener.MassListener attribute) (ecoli.processes.listeners.mass_listener.PostDivisionMassListener attribute) (ecoli.processes.listeners.monomer_counts.MonomerCounts attribute) (ecoli.processes.listeners.replication_data.ReplicationData attribute) (ecoli.processes.listeners.ribosome_data.RibosomeData attribute) (ecoli.processes.listeners.RNA_counts.RNACounts attribute) (ecoli.processes.listeners.rna_synth_prob.RnaSynthProb attribute) (ecoli.processes.listeners.rnap_data.RnapData attribute) (ecoli.processes.listeners.unique_molecule_counts.UniqueMoleculeCounts attribute) (ecoli.processes.membrane.membrane_potential.MembranePotential attribute) (ecoli.processes.metabolism.Metabolism attribute) (ecoli.processes.metabolism_redux.MetabolismRedux attribute) (ecoli.processes.metabolism_redux_classic.MetabolismReduxClassic attribute) (ecoli.processes.polypeptide_elongation.PolypeptideElongation attribute) (ecoli.processes.polypeptide_initiation.PolypeptideInitiation attribute) (ecoli.processes.protein_degradation.ProteinDegradation attribute) (ecoli.processes.rna_degradation.RnaDegradation attribute) (ecoli.processes.rna_interference.RnaInterference attribute) (ecoli.processes.rna_maturation.RnaMaturation attribute) (ecoli.processes.shape.Shape attribute) (ecoli.processes.spatiality.diffusion_network.DiffusionNetwork attribute) (ecoli.processes.spatiality.spatial_geometry.SpatialGeometry attribute) (ecoli.processes.stubs.exchange_stub.Exchange attribute) (ecoli.processes.tf_binding.TfBinding attribute) (ecoli.processes.tf_unbinding.TfUnbinding attribute) (ecoli.processes.transcript_elongation.TranscriptElongation attribute) (ecoli.processes.transcript_initiation.TranscriptInitiation attribute) (ecoli.processes.two_component_system.TwoComponentSystem attribute) (ecoli.processes.unique_update.UniqueUpdate attribute) named_idx() (in module ecoli.library.parquet_emitter) ndarray_to_ndlist() (in module ecoli.library.parquet_emitter) ndidx_to_duckdb_expr() (in module ecoli.library.parquet_emitter) ndlist_to_ndarray() (in module ecoli.library.parquet_emitter) NegativeCountsError netLossRateFromDilutionAndDegradationProtein() (in module reconstruction.ecoli.fit_sim_data_1) netLossRateFromDilutionAndDegradationRNA() (in module reconstruction.ecoli.fit_sim_data_1) netLossRateFromDilutionAndDegradationRNALinear() (in module reconstruction.ecoli.fit_sim_data_1) NetworkFlowModel (class in ecoli.processes.metabolism_redux) (class in ecoli.processes.metabolism_redux_classic) next() (wholecell.io.tsv.reader method) next_update() (ecoli.library.lattice_utils.ExchangeAgent method) (ecoli.processes.allocator.Allocator method) (ecoli.processes.bulk_timeline.BulkTimelineProcess method) (ecoli.processes.cell_division.Division method) (ecoli.processes.cell_division.MarkDPeriod method) (ecoli.processes.cell_division.StopAfterDivision method) (ecoli.processes.chemostat.Chemostat method) (ecoli.processes.chemotaxis.chemoreceptor_cluster.ReceptorCluster method) (ecoli.processes.chemotaxis.coarse_motor.MotorActivity method) (ecoli.processes.chemotaxis.flagella_motor.FlagellaMotor method) (ecoli.processes.chromosome_structure.ChromosomeStructure method) (ecoli.processes.concentrations_deriver.ConcentrationsDeriver method) (ecoli.processes.division_detector.DivisionDetector method) (ecoli.processes.engine_process._ProcA method) (ecoli.processes.engine_process._ProcB method) (ecoli.processes.engine_process._ProcC method) (ecoli.processes.engine_process.EngineProcess method) (ecoli.processes.engine_process.SchemaStub method) (ecoli.processes.environment.derive_globals.DeriveGlobals method) (ecoli.processes.environment.diffusion_field.DiffusionField method) (ecoli.processes.environment.exchange.Exchange method) (ecoli.processes.environment.exchange_data.ExchangeData method) (ecoli.processes.environment.local_field.LocalField method) (ecoli.processes.environment.lysis.Lysis method) (ecoli.processes.environment.lysis.ToyTransportBurst method) (ecoli.processes.environment.media_update.MediaUpdate method) (ecoli.processes.environment.multibody_physics.Multibody method) (ecoli.processes.environment.reaction_diffusion_field.ReactionDiffusion method) (ecoli.processes.enzyme_kinetics.EnzymeKinetics method) (ecoli.processes.global_clock.GlobalClock method) (ecoli.processes.listeners.aggregator.Aggregator method) (ecoli.processes.listeners.dna_supercoiling.DnaSupercoiling method) (ecoli.processes.listeners.mass_listener.MassListener method) (ecoli.processes.listeners.monomer_counts.MonomerCounts method) (ecoli.processes.listeners.replication_data.ReplicationData method) (ecoli.processes.listeners.ribosome_data.RibosomeData method) (ecoli.processes.listeners.RNA_counts.RNACounts method) (ecoli.processes.listeners.rna_synth_prob.RnaSynthProb method) (ecoli.processes.listeners.rnap_data.RnapData method) (ecoli.processes.listeners.unique_molecule_counts.UniqueMoleculeCounts method) (ecoli.processes.membrane.membrane_potential.MembranePotential method) (ecoli.processes.metabolism.Metabolism method) (ecoli.processes.metabolism_redux.MetabolismRedux method) (ecoli.processes.metabolism_redux_classic.MetabolismReduxClassic method) (ecoli.processes.partition.Evolver method) (ecoli.processes.partition.PartitionedProcess method) (ecoli.processes.partition.Requester method) (ecoli.processes.rna_interference.RnaInterference method) (ecoli.processes.shape.Shape method) (ecoli.processes.spatiality.diffusion_network.DiffusionNetwork method) (ecoli.processes.spatiality.spatial_geometry.SpatialGeometry method) (ecoli.processes.stubs.exchange_stub.Exchange method) (ecoli.processes.stubs.exchanger_stub.Exchanger method) (ecoli.processes.tf_binding.TfBinding method) (ecoli.processes.tf_unbinding.TfUnbinding method) (ecoli.processes.unique_update.UniqueUpdate method)

NoChargeError NoDaemonContext (class in wholecell.utils.parallelization) NoDaemonPool (class in wholecell.utils.parallelization) NoDaemonProcess (class in wholecell.utils.parallelization) Node (class in ecoli.analysis.causality_network.network_components) node_class (ecoli.analysis.causality_network.network_components.Node attribute) node_id (ecoli.analysis.causality_network.network_components.Node attribute) node_type (ecoli.analysis.causality_network.network_components.Node attribute) normalize() (in module wholecell.utils.fitting) not_a_process() (in module ecoli.library.schema) np_apply_along_axis() (in module reconstruction.ecoli.dataclasses.process.metabolism) np_prod() (in module reconstruction.ecoli.dataclasses.process.metabolism) NullScreen (class in ecoli.library.pymunk_multibody) num_cells() (in module ecoli.library.parquet_emitter) numpy_molecules() (in module ecoli.library.json_state) numpy_schema() (in module ecoli.library.schema) NumpyRandomStateSerializer (class in ecoli.library.serialize) nutrients_to_internal_conc (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute)

O

object_tree() (in module runscripts.debug.compare_pickles) objective (ecoli.processes.metabolism_redux.FlowResult attribute) (ecoli.processes.metabolism_redux_classic.FlowResult attribute)

ones_field() (ecoli.processes.environment.diffusion_field.DiffusionField method) (ecoli.processes.environment.reaction_diffusion_field.ReactionDiffusion method) open_arbitrary_sim_data() (in module ecoli.library.parquet_emitter) open_output_file() (in module ecoli.library.parquet_emitter)

P

p_promoter_bound_SKd() (reconstruction.ecoli.dataclasses.process.transcription_regulation.TranscriptionRegulation method) p_promoter_bound_tf() (reconstruction.ecoli.dataclasses.process.transcription_regulation.TranscriptionRegulation method) PAD_VALUE (wholecell.utils.polymerize.polymerize attribute) pairplot() (in module ecoli.analysis.antibiotics_colony.amp_plots) ParameterSerializer (class in ecoli.library.serialize) park_concentrations() (in module reconstruction.ecoli.scripts.metabolite_concentrations.convert_to_flat) ParquetEmitter (class in ecoli.library.parquet_emitter) parse_args() (ecoli.analysis.causality_network.buildCausalityNetwork.BuildCausalityNetwork method) (in module reconstruction.ecoli.scripts.fold_changes.calculate_fc) (in module reconstruction.ecoli.scripts.update_biocyc_files) parse_key_value_args() (in module ecoli.experiments.ecoli_master_sim) parse_variant_data_dir() (in module runscripts.analysis) parse_variants() (in module runscripts.create_variants) parser (ecoli.experiments.ecoli_master_sim.SimConfig attribute) PartitionedProcess (class in ecoli.processes.partition) plot() (in module ecoli.analysis.colony.snapshots) (in module ecoli.analysis.multigeneration.new_gene_counts) (in module ecoli.analysis.multiseed.ecocyc_table) (in module ecoli.analysis.multiseed.subgenerational_expression_table) (in module ecoli.analysis.multivariant.average_monomer_counts) (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) (in module ecoli.analysis.single.blame) (in module ecoli.analysis.single.mass_fraction_summary) (wholecell.utils.voronoi_plot_main.VoronoiMaster method) plot_activity() (in module ecoli.processes.chemotaxis.flagella_motor) plot_agent() (in module ecoli.analysis.colony.snapshots) plot_agents() (in module ecoli.analysis.colony.snapshots) plot_ampc_phylo() (in module ecoli.analysis.antibiotics_colony.exploration) plot_bulk_molecules() (in module ecoli.composites.ecoli_spatial) plot_colony_growth() (in module ecoli.analysis.antibiotics_colony.validation) plot_death_timescale_analysis() (in module ecoli.analysis.antibiotics_colony.validation) plot_diff_range() (in module ecoli.processes.spatiality.diffusion_network) plot_distributions_timeseries() (in module ecoli.library.cell_wall.lattice) plot_exp_growth_rate() (in module ecoli.analysis.antibiotics_colony.exploration) plot_field_snapshots() (in module ecoli.analysis.antibiotics_colony.timeseries) plot_fields() (in module ecoli.processes.environment.diffusion_field) plot_heatmaps() (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) plot_large_molecules() (in module ecoli.composites.ecoli_spatial) plot_lattice() (in module ecoli.library.cell_wall.lattice) plot_length_vs_location() (in module ecoli.library.cell_wall.lattice) plot_locational() (in module ecoli.library.cell_wall.column_sampler) plot_mass_fraction() (in module ecoli.analysis.antibiotics_colony.validation) plot_molecule_characterizations() (in module ecoli.composites.ecoli_spatial) plot_motor_PMF() (in module ecoli.processes.chemotaxis.flagella_motor) plot_mrna_fc() (in module ecoli.analysis.antibiotics_colony.validation) plot_NT_availability() (in module ecoli.composites.ecoli_spatial) plot_nucleoid_diff() (in module ecoli.composites.ecoli_spatial) plot_output() (in module ecoli.processes.spatiality.diffusion_network) plot_polyribosomes() (in module ecoli.composites.ecoli_spatial) plot_polyribosomes_diff() (in module ecoli.composites.ecoli_spatial) plot_protein_synth_inhib() (in module ecoli.analysis.antibiotics_colony.validation) plot_receptor_output() (in module ecoli.processes.chemotaxis.chemoreceptor_cluster) plot_signal_transduction() (in module ecoli.processes.chemotaxis.flagella_motor) plot_single_molecule_diff() (in module ecoli.composites.ecoli_spatial) plot_snapshots() (in module ecoli.analysis.colony.snapshots) plot_spatial_snapshots() (in module ecoli.composites.ecoli_master_tests) plot_splom() (in module wholecell.utils.plotting_tools) plot_strand_length_distribution() (in module ecoli.library.cell_wall.lattice) plot_tag_snapshots() (in module ecoli.analysis.antibiotics_colony.timeseries) plot_tags() (in module ecoli.analysis.colony.snapshots) plot_timeseries() (in module ecoli.analysis.antibiotics_colony.timeseries) plot_variable_receptor() (in module ecoli.processes.chemotaxis.coarse_motor) plots() (in module ecoli.processes.transcript_elongation) point_is_within_canvas() (wholecell.utils.voronoi_plot_main.PolygonClass method) PolygonClass (class in wholecell.utils.voronoi_plot_main) polymerize (class in wholecell.utils.polymerize) PolypeptideElongation (class in ecoli.processes.polypeptide_elongation) PolypeptideInitiation (class in ecoli.processes.polypeptide_initiation) pool() (in module wholecell.utils.parallelization) porosity() (in module ecoli.library.cell_wall.lattice) ports_schema() (ecoli.library.lattice_utils.ExchangeAgent method) (ecoli.processes.allocator.Allocator method) (ecoli.processes.bulk_timeline.BulkTimelineProcess method) (ecoli.processes.cell_division.Division method) (ecoli.processes.cell_division.MarkDPeriod method) (ecoli.processes.cell_division.StopAfterDivision method) (ecoli.processes.chemostat.Chemostat method) (ecoli.processes.chemotaxis.chemoreceptor_cluster.ReceptorCluster method) (ecoli.processes.chemotaxis.coarse_motor.MotorActivity method) (ecoli.processes.chemotaxis.flagella_motor.FlagellaMotor method) (ecoli.processes.chromosome_replication.ChromosomeReplication method) (ecoli.processes.chromosome_structure.ChromosomeStructure method) (ecoli.processes.complexation.Complexation method) (ecoli.processes.concentrations_deriver.ConcentrationsDeriver method) (ecoli.processes.division_detector.DivisionDetector method) (ecoli.processes.engine_process._ProcA method) (ecoli.processes.engine_process._ProcB method) (ecoli.processes.engine_process._ProcC method) (ecoli.processes.engine_process.EngineProcess method) (ecoli.processes.engine_process.SchemaStub method) (ecoli.processes.environment.derive_globals.DeriveGlobals method) (ecoli.processes.environment.diffusion_field.DiffusionField method) (ecoli.processes.environment.exchange.Exchange method) (ecoli.processes.environment.exchange_data.ExchangeData method) (ecoli.processes.environment.local_field.LocalField method) (ecoli.processes.environment.lysis.Lysis method) (ecoli.processes.environment.lysis.ToyTransportBurst method) (ecoli.processes.environment.media_update.MediaUpdate method) (ecoli.processes.environment.multibody_physics.Multibody method) (ecoli.processes.environment.reaction_diffusion_field.ReactionDiffusion method) (ecoli.processes.enzyme_kinetics.EnzymeKinetics method) (ecoli.processes.equilibrium.Equilibrium method) (ecoli.processes.global_clock.GlobalClock method) (ecoli.processes.listeners.aggregator.Aggregator method) (ecoli.processes.listeners.dna_supercoiling.DnaSupercoiling method) (ecoli.processes.listeners.mass_listener.MassListener method) (ecoli.processes.listeners.monomer_counts.MonomerCounts method) (ecoli.processes.listeners.replication_data.ReplicationData method) (ecoli.processes.listeners.ribosome_data.RibosomeData method) (ecoli.processes.listeners.RNA_counts.RNACounts method) (ecoli.processes.listeners.rna_synth_prob.RnaSynthProb method) (ecoli.processes.listeners.rnap_data.RnapData method) (ecoli.processes.listeners.unique_molecule_counts.UniqueMoleculeCounts method) (ecoli.processes.membrane.membrane_potential.MembranePotential method) (ecoli.processes.metabolism.Metabolism method) (ecoli.processes.metabolism_redux.MetabolismRedux method) (ecoli.processes.metabolism_redux_classic.MetabolismReduxClassic method) (ecoli.processes.partition.Evolver method) (ecoli.processes.partition.PartitionedProcess method) (ecoli.processes.partition.Requester method) (ecoli.processes.polypeptide_elongation.PolypeptideElongation method) (ecoli.processes.polypeptide_initiation.PolypeptideInitiation method) (ecoli.processes.protein_degradation.ProteinDegradation method) (ecoli.processes.rna_degradation.RnaDegradation method) (ecoli.processes.rna_interference.RnaInterference method) (ecoli.processes.rna_maturation.RnaMaturation method) (ecoli.processes.shape.Shape method) (ecoli.processes.spatiality.diffusion_network.DiffusionNetwork method) (ecoli.processes.spatiality.spatial_geometry.SpatialGeometry method) (ecoli.processes.stubs.exchange_stub.Exchange method) (ecoli.processes.stubs.exchanger_stub.Exchanger method) (ecoli.processes.tf_binding.TfBinding method) (ecoli.processes.tf_unbinding.TfUnbinding method) (ecoli.processes.transcript_elongation.TranscriptElongation method) (ecoli.processes.transcript_initiation.TranscriptInitiation method) (ecoli.processes.two_component_system.TwoComponentSystem method) (ecoli.processes.unique_update.UniqueUpdate method)

PostDivisionMassListener (class in ecoli.processes.listeners.mass_listener) ppgpp_degradation_reaction (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) ppgpp_metabolite_changes() (in module ecoli.processes.polypeptide_elongation) ppgpp_reaction_metabolites (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) ppgpp_reaction_names (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) ppgpp_reaction_stoich (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) ppgpp_synthesis_reaction (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) pprint_diffs() (in module runscripts.debug.compare_pickles) prepare_save_state() (in module ecoli.experiments.ecoli_master_sim) preprocess_data() (in module ecoli.analysis.single.blame) prettify_axis() (in module ecoli.analysis.antibiotics_colony.plot_utils) Process (class in reconstruction.ecoli.dataclasses.process.process) (class in validation.ecoli.validation_data) (wholecell.utils.parallelization.NoDaemonContext attribute) process_simulated_fluxes() (in module wholecell.utils.toya) process_toya_data() (in module wholecell.utils.toya) processes (ecoli.processes.allocator.Allocator attribute) processes_and_steps (ecoli.composites.ecoli_master.Ecoli attribute) promoter_binding() (in module reconstruction.ecoli.fit_sim_data_1) Protein (class in validation.ecoli.validation_data) ProteinDegradation (class in ecoli.processes.protein_degradation) proteinDistributionFrommRNA() (in module reconstruction.ecoli.fit_sim_data_1) prune_subtree() (ecoli.library.cell_wall.hole_detection.HoleSizeDict method) PymunkMultibody (class in ecoli.library.pymunk_multibody) python_type (ecoli.library.serialize.MethodSerializer attribute) (ecoli.library.serialize.NumpyRandomStateSerializer attribute) (ecoli.library.serialize.UnumSerializer attribute)

Q

query() (ecoli.experiments.ecoli_master_sim.EcoliSim method)

R

randCounts() (in module wholecell.utils.random) random_body_position() (in module ecoli.library.pymunk_multibody) (in module ecoli.processes.environment.multibody_physics) random_points_in_canvas() (wholecell.utils.voronoi_plot_main.PolygonClass method) randomlySelectNRows() (in module wholecell.utils.random) randomlySelectRows() (in module wholecell.utils.random) rate_laws (ecoli.library.kinetic_rate_laws.KineticFluxModel attribute) rates() (in module wholecell.utils.build_ode) rates_jacobian() (in module wholecell.utils.build_ode) ray_intersect_with_edge() (wholecell.utils.voronoi_plot_main.RayClass method) RayClass (class in wholecell.utils.voronoi_plot_main) react() (ecoli.processes.environment.reaction_diffusion_field.ReactionDiffusion method) reaction_catalysts (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) reaction_id_to_base_reaction_id (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) reaction_stoich (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) ReactionDiffusion (class in ecoli.processes.environment.reaction_diffusion_field) ReactionFlux (class in validation.ecoli.validation_data) reactions_with_catalyst (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) read_attributes() (ecoli.analysis.causality_network.network_components.Edge method) (ecoli.analysis.causality_network.network_components.Node method) read_attributes_from_tsv() (ecoli.analysis.causality_network.network_components.Node method) read_charging_dynamics() (in module ecoli.analysis.causality_network.read_dynamics) read_complexation_dynamics() (in module ecoli.analysis.causality_network.read_dynamics) read_dynamics() (ecoli.analysis.causality_network.network_components.Node method) read_equilibrium_dynamics() (in module ecoli.analysis.causality_network.read_dynamics) read_gene_dynamics() (in module ecoli.analysis.causality_network.read_dynamics) read_global_dynamics() (in module ecoli.analysis.causality_network.read_dynamics) read_json_file() (in module wholecell.utils.filepath) read_metabolism_dynamics() (in module ecoli.analysis.causality_network.read_dynamics) read_metabolite_dynamics() (in module ecoli.analysis.causality_network.read_dynamics) read_protein_dynamics() (in module ecoli.analysis.causality_network.read_dynamics) read_regulation_dynamics() (in module ecoli.analysis.causality_network.read_dynamics) read_rna_dynamics() (in module ecoli.analysis.causality_network.read_dynamics) read_rna_maturation_dynamics() (in module ecoli.analysis.causality_network.read_dynamics) read_stacked_columns() (in module ecoli.library.parquet_emitter) read_tf_binding_dynamics() (in module ecoli.analysis.causality_network.read_dynamics) read_transcription_dynamics() (in module ecoli.analysis.causality_network.read_dynamics) read_translation_dynamics() (in module ecoli.analysis.causality_network.read_dynamics) read_tsv() (in module reconstruction.spreadsheets) reader (class in wholecell.io.tsv) ready() (wholecell.utils.parallelization.ApplyResult method) ReceptorCluster (class in ecoli.processes.chemotaxis.chemoreceptor_cluster) reconstruction module reconstruction.ecoli module reconstruction.ecoli.compendium module reconstruction.ecoli.compendium.growth_data module reconstruction.ecoli.dataclasses module reconstruction.ecoli.dataclasses.adjustments module reconstruction.ecoli.dataclasses.common_names module reconstruction.ecoli.dataclasses.constants module reconstruction.ecoli.dataclasses.getter_functions module reconstruction.ecoli.dataclasses.growth_rate_dependent_parameters module reconstruction.ecoli.dataclasses.molecule_groups module reconstruction.ecoli.dataclasses.molecule_ids module reconstruction.ecoli.dataclasses.process module reconstruction.ecoli.dataclasses.process.chromosome_structure module reconstruction.ecoli.dataclasses.process.complexation module reconstruction.ecoli.dataclasses.process.equilibrium module reconstruction.ecoli.dataclasses.process.metabolism module reconstruction.ecoli.dataclasses.process.process module reconstruction.ecoli.dataclasses.process.replication module reconstruction.ecoli.dataclasses.process.rna_decay module reconstruction.ecoli.dataclasses.process.transcription module reconstruction.ecoli.dataclasses.process.transcription_regulation module reconstruction.ecoli.dataclasses.process.translation module reconstruction.ecoli.dataclasses.process.two_component_system module reconstruction.ecoli.dataclasses.relation module reconstruction.ecoli.dataclasses.state module reconstruction.ecoli.dataclasses.state.bulkMolecules module reconstruction.ecoli.dataclasses.state.external_state module reconstruction.ecoli.dataclasses.state.internal_state module reconstruction.ecoli.dataclasses.state.stateFunctions module reconstruction.ecoli.dataclasses.state.uniqueMolecules module reconstruction.ecoli.fit_sim_data_1 module reconstruction.ecoli.knowledge_base_raw module reconstruction.ecoli.scripts module

reconstruction.ecoli.scripts.fold_changes module reconstruction.ecoli.scripts.fold_changes.calculate_fc module reconstruction.ecoli.scripts.metabolism_kinetics module reconstruction.ecoli.scripts.metabolism_kinetics.convert_to_flat module reconstruction.ecoli.scripts.metabolite_concentrations module reconstruction.ecoli.scripts.metabolite_concentrations.convert_to_flat module reconstruction.ecoli.scripts.metabolite_concentrations.merge_files module reconstruction.ecoli.scripts.protein_half_lives module reconstruction.ecoli.scripts.protein_half_lives.convert_to_flat module reconstruction.ecoli.scripts.rna_half_lives module reconstruction.ecoli.scripts.rna_half_lives.convert_to_flat module reconstruction.ecoli.scripts.update_biocyc_files module reconstruction.ecoli.simulation_data module reconstruction.spreadsheets module reconstruction.tests module reconstruction.tests.test_fit_sim_data_1 module reconstruction.tests.test_spreadsheets module Relation (class in reconstruction.ecoli.dataclasses.relation) (class in validation.ecoli.validation_data) remove_border() (in module wholecell.utils.plotting_tools) remove_empty_values() (in module ecoli.experiments.antibiotics_tests) remove_properties() (in module ecoli.library.schema) remove_units() (in module ecoli.library.units) REMOVED_FROM_CHARGING (in module ecoli.processes.polypeptide_elongation) replace_uncertain_entries() (in module reconstruction.ecoli.scripts.fold_changes.calculate_fc) Replication (class in reconstruction.ecoli.dataclasses.process.replication) ReplicationData (class in ecoli.processes.listeners.replication_data) report_profiling() (in module ecoli.experiments.ecoli_master_sim) reposition_ticks() (in module ecoli.analysis.single.blame) Repr (class in runscripts.debug.compare_pickles) request() (ecoli.processes.polypeptide_elongation.BaseElongationModel method) (ecoli.processes.polypeptide_elongation.SteadyStateElongationModel method) Requester (class in ecoli.processes.partition) rescale_initiation_probs() (in module ecoli.library.initial_conditions) rescaleMassForSolubleMetabolites() (in module reconstruction.ecoli.fit_sim_data_1) restrict_data() (in module ecoli.analysis.antibiotics_colony) RFC RFC 2119 RibosomeData (class in ecoli.processes.listeners.ribosome_data) rna_id_to_cistron_indexes() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) RNACounts (class in ecoli.processes.listeners.RNA_counts) RnaDecay (class in reconstruction.ecoli.dataclasses.process.rna_decay) RnaDegradation (class in ecoli.processes.rna_degradation) RnaInterference (class in ecoli.processes.rna_interference) RnaMaturation (class in ecoli.processes.rna_maturation) RnapData (class in ecoli.processes.listeners.rnap_data) RnaSynthProb (class in ecoli.processes.listeners.rna_synth_prob) run() (ecoli.analysis.causality_network.build_network.BuildNetwork method) (ecoli.analysis.causality_network.buildCausalityNetwork.BuildCausalityNetwork method) (ecoli.experiments.ecoli_master_sim.EcoliSim method) (ecoli.library.pymunk_multibody.PymunkMultibody method) (ecoli.processes.chemotaxis.flagella_motor.FlagellaMotor method) (in module ecoli.processes.chemotaxis.coarse_motor) run_cmd() (in module wholecell.utils.filepath) run_cmd2() (in module wholecell.utils.filepath) run_cmdline() (in module wholecell.utils.filepath) run_colony() (in module ecoli.experiments.metabolism_redux_sim) run_diffusion_field() (in module ecoli.processes.environment.diffusion_field) run_division() (in module ecoli.experiments.glt_division) run_ecoli() (in module ecoli.composites.ecoli_master) run_ecoli_with_default_metabolism() (in module ecoli.experiments.metabolism_redux_sim) run_ecoli_with_metabolism_redux() (in module ecoli.experiments.metabolism_redux_sim) run_ecoli_with_metabolism_redux_classic() (in module ecoli.experiments.metabolism_redux_sim) run_growth_division() (in module ecoli.processes.environment.multibody_physics) run_metabolism() (in module ecoli.experiments.metabolism_exchanger) run_metabolism_composite() (in module ecoli.experiments.metabolism_exchanger) run_parca() (in module runscripts.parca) run_plot() (in module ecoli.processes.polypeptide_elongation) (in module ecoli.processes.transcript_initiation) run_sim() (in module ecoli.experiments.tet_amp_sim) run_simulation() (in module ecoli.experiments.ecoli_engine_process) run_spatial_ecoli() (in module ecoli.composites.ecoli_spatial) run_spatial_geometry_process() (in module ecoli.processes.spatiality.spatial_geometry) run_step() (in module ecoli.processes.chemotaxis.chemoreceptor_cluster) run_test_case() (in module ecoli.library.cell_wall.hole_detection) run_to_steady_state() (in module ecoli.processes.chemotaxis.chemoreceptor_cluster) runscripts module runscripts.analysis module runscripts.create_variants module runscripts.debug module runscripts.debug.compare_pickles module runscripts.debug.diff_simouts module runscripts.parca module runscripts.workflow module

S

sample_column() (in module ecoli.library.cell_wall.column_sampler) sample_histogram() (in module ecoli.library.cell_wall.fit_lysis_time) sample_lattice() (in module ecoli.library.cell_wall.column_sampler) sander_concentrations() (in module reconstruction.ecoli.scripts.metabolite_concentrations.convert_to_flat) save_conc() (in module reconstruction.ecoli.scripts.metabolite_concentrations.merge_files) save_concentrations() (in module reconstruction.ecoli.scripts.metabolite_concentrations.convert_to_flat) save_file() (in module ecoli.analysis.multiseed.ecocyc_table) (in module ecoli.analysis.multivariant.average_monomer_counts) save_kochanowski_relative_changes() (in module reconstruction.ecoli.scripts.metabolite_concentrations.convert_to_flat) save_sim_output() (in module ecoli.experiments.metabolism_redux_sim) save_snapshot_figure() (in module ecoli.analysis.colony.snapshots) save_state() (in module reconstruction.ecoli.fit_sim_data_1) save_states() (ecoli.experiments.ecoli_master_sim.EcoliSim method) save_tags_figure() (in module ecoli.analysis.colony.snapshots) save_timeseries_figure() (in module ecoli.analysis.colony.snapshots) SchemaStub (class in ecoli.processes.engine_process) secretion_penalty_coeff (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) select_keys() (in module wholecell.utils.data) send_command() (ecoli.processes.engine_process.EngineProcess method) serialize() (ecoli.library.schema.get_bulk_counts method) (ecoli.library.schema.get_unique_fields method) (ecoli.library.serialize.MethodSerializer method) (ecoli.library.serialize.NumpyRandomStateSerializer method) (ecoli.library.serialize.UnumSerializer method) set() (ecoli.analysis.colony.snapshots.LineWidthData method) set_balanced_translation_efficiencies() (in module reconstruction.ecoli.fit_sim_data_1) set_conditions() (in module reconstruction.ecoli.fit_sim_data_1) set_fwd_rate() (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) set_mechanistic_export_constants() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism method) set_mechanistic_supply_constants() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism method) set_mechanistic_uptake_constants() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism method) set_molecule_levels() (ecoli.processes.metabolism.FluxBalanceAnalysisModel method) set_phenomological_supply_constants() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism method) set_ppgpp_expression() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) set_ppgpp_kinetics_parameters() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method) set_reaction_bounds() (ecoli.processes.metabolism.FluxBalanceAnalysisModel method) set_reaction_targets() (ecoli.processes.metabolism.FluxBalanceAnalysisModel method) set_rev_rate() (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) set_small_molecule_counts() (in module ecoli.library.initial_conditions) set_trace() (wholecell.utils.ForkedPdb method) (wholecell.utils.forkedPdb.ForkedPdb method) set_up_exchanges() (ecoli.processes.metabolism_redux.NetworkFlowModel method) (ecoli.processes.metabolism_redux_classic.NetworkFlowModel method) set_updates (ecoli.library.schema.UniqueNumpyUpdater attribute) setAxisMaxMinX() (in module wholecell.utils.sparkline) setAxisMaxMinY() (in module wholecell.utils.sparkline) setInitialRnaExpression() (in module reconstruction.ecoli.fit_sim_data_1) setKmCooperativeEndoRNonLinearRNAdecay() (in module reconstruction.ecoli.fit_sim_data_1) setProteinDegRates() (in module reconstruction.ecoli.fit_sim_data_1) setRibosomeCountsConstrainedByPhysiology() (in module reconstruction.ecoli.fit_sim_data_1) setRNADegRates() (in module reconstruction.ecoli.fit_sim_data_1) setRNAExpression() (in module reconstruction.ecoli.fit_sim_data_1)

setRNAPCountsConstrainedByPhysiology() (in module reconstruction.ecoli.fit_sim_data_1) setTranslationEfficiencies() (in module reconstruction.ecoli.fit_sim_data_1) setUp() (wholecell.tests.utils.test_fast_nnls.Test_fast_nnls method) (wholecell.tests.utils.test_filepath.Test_filepath method) (wholecell.tests.utils.test_modular_fba.Test_FluxBalanceAnalysis method) (wholecell.tests.utils.test_polymerize.Test_polymerize method) (wholecell.tests.utils.test_unit_struct_array.Test_unit_struct_array method) setUpClass() (wholecell.tests.utils.test_modular_fba.Test_FluxBalanceAnalysis class method) (wholecell.tests.utils.test_polymerize.Test_polymerize class method) Shape (class in ecoli.processes.shape) shift_column_to_boundary() (in module ecoli.library.cell_wall.lattice) sign_str() (in module ecoli.analysis.single.blame) signed_stacked_bar() (in module ecoli.analysis.single.blame) SignNormalize (class in ecoli.analysis.single.blame) SimConfig (class in ecoli.experiments.ecoli_master_sim) SimData (class in runscripts.create_variants) simpleSparklineAxis() (in module wholecell.utils.sparkline) simplify_error_message() (in module runscripts.debug.compare_pickles) SimulationDataEcoli (class in reconstruction.ecoli.simulation_data) single_agent_config() (in module ecoli.processes.environment.multibody_physics) SiteNotFoundError size_tree() (in module runscripts.debug.compare_pickles) skip_n_gens() (in module ecoli.library.parquet_emitter) solve() (ecoli.processes.metabolism_redux.NetworkFlowModel method) (ecoli.processes.metabolism_redux_classic.NetworkFlowModel method) solver (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) sparklineAxis() (in module wholecell.utils.sparkline) SpatialGeometry (class in ecoli.processes.spatiality.spatial_geometry) specific_import_rates (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) src_id (ecoli.analysis.causality_network.network_components.Edge attribute) startswith() (in module wholecell.utils.data) STD_DEV_FLAG (in module ecoli.analysis.multivariant.new_gene_translation_efficiency_heatmaps) SteadyStateElongationModel (class in ecoli.processes.polypeptide_elongation) stochasticRound() (in module wholecell.utils.random) stoich_matrix() (reconstruction.ecoli.dataclasses.process.complexation.Complexation method) (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) (reconstruction.ecoli.dataclasses.process.two_component_system.TwoComponentSystem method) stoich_matrix_monomers() (reconstruction.ecoli.dataclasses.process.complexation.Complexation method) (reconstruction.ecoli.dataclasses.process.equilibrium.Equilibrium method) (reconstruction.ecoli.dataclasses.process.two_component_system.TwoComponentSystem method) stoichiometry (ecoli.analysis.causality_network.network_components.Edge attribute) StopAfterDivision (class in ecoli.processes.cell_division) strictly_decreasing() (in module ecoli.library.data_predicates) strictly_increasing() (in module ecoli.library.data_predicates) strip_empty_units() (in module wholecell.utils.units) successful() (wholecell.utils.parallelization.ApplyResult method) sum() (in module wholecell.utils.units) sum_monomers_reference_implementation() (in module wholecell.utils.polymerize) surface_area_from_length() (in module ecoli.processes.environment.derive_globals) (in module ecoli.processes.shape) synonyms (ecoli.analysis.causality_network.network_components.Node attribute) synth_prob_from_ppgpp() (reconstruction.ecoli.dataclasses.process.transcription.Transcription method)

T

tearDown() (wholecell.tests.utils.test_filepath.Test_filepath method) (wholecell.tests.utils.test_modular_fba.Test_FluxBalanceAnalysis method) (wholecell.tests.utils.test_polymerize.Test_polymerize method) tearDownClass() (wholecell.tests.utils.test_modular_fba.Test_FluxBalanceAnalysis class method) (wholecell.tests.utils.test_polymerize.Test_polymerize class method) temperature_adjusted_kcat() (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism static method) terminate() (wholecell.utils.parallelization.InlinePool method) Test_blas (class in wholecell.tests.utils.test_blas) Test_data (class in wholecell.tests.utils.test_data) Test_fast_nnls (class in wholecell.tests.utils.test_fast_nnls) Test_filepath (class in wholecell.tests.utils.test_filepath) Test_fitkb1 (class in reconstruction.tests.test_fit_sim_data_1) Test_FluxBalanceAnalysis (class in wholecell.tests.utils.test_modular_fba) Test_library_performance (class in wholecell.tests.utils.test_library_performance) Test_mc_complexation (class in wholecell.tests.utils.test_mc_complexation) Test_memory_debug (class in wholecell.tests.utils.test_memory_debug) Test_NetworkFlowGLPK (class in wholecell.tests.utils.test_nf_glpk) Test_parallelization (class in wholecell.utils.test_parallelization) Test_polymerize (class in wholecell.tests.utils.test_polymerize) Test_Spreadsheets (class in reconstruction.tests.test_spreadsheets) Test_Tsv (class in wholecell.tests.io.test_tsv) Test_unit_struct_array (class in wholecell.tests.utils.test_unit_struct_array) Test_units (class in wholecell.tests.utils.test_units) TestDependencyGraph (class in wholecell.tests.utils.test_dependency_graph) tf_condition_specs() (in module reconstruction.ecoli.fit_sim_data_1) TfBinding (class in ecoli.processes.tf_binding) TfUnbinding (class in ecoli.processes.tf_unbinding) time_it() (in module wholecell.tests.utils.test_library_performance) time_node() (in module ecoli.analysis.causality_network.read_dynamics) time_this() (in module wholecell.tests.utils.test_fast_nnls) (wholecell.tests.utils.test_library_performance.Test_library_performance method) TimeLimitError timeseries_death_plot() (in module ecoli.analysis.antibiotics_colony.amp_plots) timestamp() (in module wholecell.utils.filepath) to_dict() (ecoli.analysis.causality_network.network_components.Node method) (ecoli.experiments.ecoli_master_sim.SimConfig method) topology (ecoli.processes.allocator.Allocator attribute) (ecoli.processes.chromosome_replication.ChromosomeReplication attribute) (ecoli.processes.chromosome_structure.ChromosomeStructure attribute) (ecoli.processes.complexation.Complexation attribute) (ecoli.processes.environment.exchange_data.ExchangeData attribute) (ecoli.processes.environment.media_update.MediaUpdate attribute) (ecoli.processes.equilibrium.Equilibrium attribute) (ecoli.processes.listeners.dna_supercoiling.DnaSupercoiling attribute) (ecoli.processes.listeners.mass_listener.MassListener attribute) (ecoli.processes.listeners.monomer_counts.MonomerCounts attribute) (ecoli.processes.listeners.replication_data.ReplicationData attribute) (ecoli.processes.listeners.ribosome_data.RibosomeData attribute) (ecoli.processes.listeners.RNA_counts.RNACounts attribute) (ecoli.processes.listeners.rna_synth_prob.RnaSynthProb attribute) (ecoli.processes.listeners.rnap_data.RnapData attribute) (ecoli.processes.listeners.unique_molecule_counts.UniqueMoleculeCounts attribute) (ecoli.processes.metabolism.Metabolism attribute) (ecoli.processes.metabolism_redux.MetabolismRedux attribute) (ecoli.processes.metabolism_redux_classic.MetabolismReduxClassic attribute) (ecoli.processes.polypeptide_elongation.PolypeptideElongation attribute) (ecoli.processes.polypeptide_initiation.PolypeptideInitiation attribute) (ecoli.processes.protein_degradation.ProteinDegradation attribute) (ecoli.processes.rna_degradation.RnaDegradation attribute) (ecoli.processes.rna_interference.RnaInterference attribute) (ecoli.processes.rna_maturation.RnaMaturation attribute) (ecoli.processes.tf_binding.TfBinding attribute) (ecoli.processes.tf_unbinding.TfUnbinding attribute) (ecoli.processes.transcript_elongation.TranscriptElongation attribute) (ecoli.processes.transcript_initiation.TranscriptInitiation attribute) (ecoli.processes.two_component_system.TwoComponentSystem attribute)

topology_registry (in module ecoli.processes.registries) totalCountFromMassesAndRatios() (in module reconstruction.ecoli.fit_sim_data_1) totalCountIdDistributionProtein() (in module reconstruction.ecoli.fit_sim_data_1) totalCountIdDistributionRNA() (in module reconstruction.ecoli.fit_sim_data_1) ToyTransportBurst (class in ecoli.processes.environment.lysis) TranscriptElongation (class in ecoli.processes.transcript_elongation) TranscriptInitiation (class in ecoli.processes.transcript_initiation) Transcription (class in reconstruction.ecoli.dataclasses.process.transcription) TranscriptionDirectionError, [1] TranscriptionRegulation (class in reconstruction.ecoli.dataclasses.process.transcription_regulation) Translation (class in reconstruction.ecoli.dataclasses.process.translation) TranslationSupplyElongationModel (class in ecoli.processes.polypeptide_elongation) transport_reactions (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) transpose() (in module wholecell.utils.units) tsv_reader() (in module reconstruction.spreadsheets) tsv_writer() (in module reconstruction.spreadsheets) tumble() (ecoli.processes.chemotaxis.flagella_motor.FlagellaMotor method) (in module ecoli.processes.chemotaxis.coarse_motor) tuplify_topology() (in module ecoli.experiments.ecoli_master_sim) TwoComponentSystem (class in ecoli.processes.two_component_system) (class in reconstruction.ecoli.dataclasses.process.two_component_system)

U

UNEXPLORED (wholecell.utils.dependency_graph.ExplorationStatus attribute) UNIQUE_DIVIDERS (in module ecoli.library.schema) UniqueMoleculeCounts (class in ecoli.processes.listeners.unique_molecule_counts) UniqueMolecules (class in reconstruction.ecoli.dataclasses.state.uniqueMolecules) UniqueNumpyUpdater (class in ecoli.library.schema) UniqueUpdate (class in ecoli.processes.unique_update) UnitStructArray (class in wholecell.utils.unit_struct_array) UnknownModifiedRnaError UnknownMolecularWeightError UnumSerializer (class in ecoli.library.serialize) update_agent() (in module ecoli.experiments.tet_amp_sim) update_amino_acid_targets() (ecoli.processes.metabolism.Metabolism method) (ecoli.processes.metabolism_redux.MetabolismRedux method) update_biocyc_files() (in module reconstruction.ecoli.scripts.update_biocyc_files) update_bodies() (ecoli.library.pymunk_multibody.PymunkMultibody method) update_body() (ecoli.library.pymunk_multibody.PymunkMultibody method) update_condition() (ecoli.processes.chromosome_structure.ChromosomeStructure method) (ecoli.processes.listeners.dna_supercoiling.DnaSupercoiling method) (ecoli.processes.listeners.mass_listener.MassListener method) (ecoli.processes.listeners.mass_listener.PostDivisionMassListener method) (ecoli.processes.listeners.monomer_counts.MonomerCounts method) (ecoli.processes.listeners.replication_data.ReplicationData method) (ecoli.processes.listeners.ribosome_data.RibosomeData method) (ecoli.processes.listeners.RNA_counts.RNACounts method) (ecoli.processes.listeners.rna_synth_prob.RnaSynthProb method) (ecoli.processes.listeners.rnap_data.RnapData method) (ecoli.processes.listeners.unique_molecule_counts.UniqueMoleculeCounts method) (ecoli.processes.metabolism.Metabolism method) (ecoli.processes.metabolism_redux.MetabolismRedux method) (ecoli.processes.metabolism_redux_classic.MetabolismReduxClassic method) (ecoli.processes.partition.Evolver method) (ecoli.processes.partition.Requester method) (ecoli.processes.tf_binding.TfBinding method) (ecoli.processes.tf_unbinding.TfUnbinding method)

update_external_molecule_levels() (ecoli.processes.metabolism.FluxBalanceAnalysisModel method) update_flagellum() (ecoli.processes.chemotaxis.flagella_motor.FlagellaMotor method) update_from_cli() (ecoli.experiments.ecoli_master_sim.SimConfig method) update_from_dict() (ecoli.experiments.ecoli_master_sim.SimConfig method) update_from_json() (ecoli.experiments.ecoli_master_sim.SimConfig method) update_screen() (ecoli.library.pymunk_multibody.NullScreen method) updater() (ecoli.library.schema.UniqueNumpyUpdater method) url (ecoli.analysis.causality_network.network_components.Node attribute) URL_TEMPLATE_COMPOUND (in module ecoli.analysis.causality_network.build_network) use_all_constraints (reconstruction.ecoli.dataclasses.process.metabolism.Metabolism attribute) USE_UINT16 (in module ecoli.library.parquet_emitter) USE_UINT32 (in module ecoli.library.parquet_emitter)

V

validation module validation.ecoli module validation.ecoli.scripts module validation.ecoli.scripts.rnaDegRates module validation.ecoli.validation_data module validation.ecoli.validation_data_raw module

ValidationDataEcoli (class in validation.ecoli.validation_data) ValidationDataRawEcoli (class in validation.ecoli.validation_data_raw) variant_test_2() (in module ecoli.variants.variant_test) velocities (ecoli.processes.metabolism_redux.FlowResult attribute) (ecoli.processes.metabolism_redux_classic.FlowResult attribute) verify_dir_exists() (in module wholecell.utils.filepath) verify_file_exists() (in module wholecell.utils.filepath) video_from_images() (in module ecoli.analysis.colony.snapshots) volume_from_length() (in module ecoli.processes.environment.derive_globals) (in module ecoli.processes.shape) VoronoiClass (class in wholecell.utils.voronoi_plot_main) VoronoiMaster (class in wholecell.utils.voronoi_plot_main)

W

wait() (wholecell.utils.parallelization.ApplyResult method) whitePadSparklineAxis() (in module wholecell.utils.sparkline) wholecell module wholecell.io module wholecell.io.tsv module wholecell.tests module wholecell.tests.io module wholecell.tests.io.test_tsv module wholecell.tests.utils module wholecell.tests.utils.profile_polymerize module wholecell.tests.utils.test_blas module wholecell.tests.utils.test_data module wholecell.tests.utils.test_dependency_graph module wholecell.tests.utils.test_fast_nnls module wholecell.tests.utils.test_filepath module wholecell.tests.utils.test_library_performance module wholecell.tests.utils.test_mc_complexation module wholecell.tests.utils.test_memory_debug module wholecell.tests.utils.test_modular_fba module wholecell.tests.utils.test_nf_glpk module wholecell.tests.utils.test_polymerize module wholecell.tests.utils.test_unit_struct_array module wholecell.tests.utils.test_units module wholecell.utils module wholecell.utils.build_ode module wholecell.utils.constants module wholecell.utils.data module wholecell.utils.dependency_graph module

wholecell.utils.fast_nonnegative_least_squares module wholecell.utils.filepath module wholecell.utils.fitting module wholecell.utils.forkedPdb module wholecell.utils.make_media module wholecell.utils.mc_complexation module wholecell.utils.memory_debug module wholecell.utils.modular_fba module wholecell.utils.parallelization module wholecell.utils.plotting_tools module wholecell.utils.polymerize module wholecell.utils.profiler module wholecell.utils.protein_counts module wholecell.utils.random module wholecell.utils.sparkline module wholecell.utils.spatial_tool module wholecell.utils.test_parallelization module wholecell.utils.toya module wholecell.utils.unit_struct_array module wholecell.utils.units module wholecell.utils.voronoi_plot_main module write_dynamics() (ecoli.analysis.causality_network.network_components.Node method) write_edgelist() (ecoli.analysis.causality_network.network_components.Edge method) write_file() (in module wholecell.utils.filepath) write_json() (in module ecoli.library.logging_tools) write_json_file() (in module wholecell.utils.filepath) write_nodelist() (ecoli.analysis.causality_network.network_components.Node method) writeheader() (reconstruction.spreadsheets.JsonWriter method) writer (class in wholecell.io.tsv) writerow() (wholecell.io.tsv.writer method) writerows() (wholecell.io.tsv.writer method)

Z

zeros_field() (ecoli.processes.environment.reaction_diffusion_field.ReactionDiffusion method)