Index

A

activation_color() (VirtualMicrobes.plotting.Graphs.AttributeMap method) add() (VirtualMicrobes.my_tools.utility.LinkThroughSet method) (VirtualMicrobes.my_tools.utility.OrderedSet method) add_ancestry_data_point() (VirtualMicrobes.data_tools.store.DataStore method) add_axes() (VirtualMicrobes.my_tools.monkey.Figure method) add_axis() (VirtualMicrobes.plotting.Graphs.MultiGraph method) (VirtualMicrobes.plotting.Graphs.MultiGridGraph method) add_axobserver() (VirtualMicrobes.my_tools.monkey.Figure method) add_best_data_point() (VirtualMicrobes.data_tools.store.DataStore method) add_callback() (VirtualMicrobes.my_tools.monkey.Artist method) add_cell() (VirtualMicrobes.environment.Environment.Locality method) (VirtualMicrobes.virtual_cell.Population.Population method) add_chromosome() (VirtualMicrobes.virtual_cell.Genome.Genome method) add_collection() (VirtualMicrobes.data_tools.store.DataStore method) add_count_stats_dp() (VirtualMicrobes.data_tools.store.DataStore method) add_data_point() (VirtualMicrobes.simulation.Simulation.Simulation method) add_dp() (VirtualMicrobes.data_tools.store.DataStore method) add_eco_data_point() (VirtualMicrobes.data_tools.store.DataStore method) add_frequency_stats_dp() (VirtualMicrobes.data_tools.store.DataStore method) add_gain_loss_dp() (VirtualMicrobes.data_tools.store.DataStore method) add_gene_copy() (VirtualMicrobes.virtual_cell.Cell.Cell method) add_graphs_data() (VirtualMicrobes.simulation.Simulation.Simulation method) add_grid_graphs_data() (VirtualMicrobes.plotting.Graphs.Graphs method) add_leaf() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) add_lines() (VirtualMicrobes.plotting.Graphs.MultiGraph method) add_list_dp() (VirtualMicrobes.data_tools.store.DataStore method) add_lod_binding_conservation() (VirtualMicrobes.data_tools.store.DataStore method) add_lod_data() (VirtualMicrobes.data_tools.store.DataStore method) add_lod_network_data() (VirtualMicrobes.data_tools.store.DataStore method) add_metabolic_stats_dp() (VirtualMicrobes.data_tools.store.DataStore method) add_mol_evo_time_course_data() (VirtualMicrobes.plotting.Graphs.Graphs method) add_molecule() (VirtualMicrobes.event.Molecule.MoleculeClass method) add_multigraph() (VirtualMicrobes.plotting.Graphs.Graphs method) add_new_cells_to_grid() (VirtualMicrobes.environment.Environment.Environment method) add_node() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) add_phylo_history() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) add_pop_data_point() (VirtualMicrobes.data_tools.store.DataStore method) add_pop_stats_data() (VirtualMicrobes.plotting.Graphs.Graphs method) add_raw_values_dp() (VirtualMicrobes.data_tools.store.DataStore method)

add_root() (VirtualMicrobes.Tree.PhyloTree.PhyloNode method) add_self() (VirtualMicrobes.plotting.Graphs.Network method) add_simple_stats_dp() (VirtualMicrobes.data_tools.store.DataStore method) add_small_molecule() (VirtualMicrobes.environment.Environment.Locality method) (VirtualMicrobes.virtual_cell.Cell.Cell method) add_small_molecules() (VirtualMicrobes.virtual_cell.Cell.Cell method) add_subplot() (VirtualMicrobes.my_tools.monkey.Figure method) AddInheritanceType (class in VirtualMicrobes.virtual_cell.PhyloUnit) alive (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloBase attribute) aname (VirtualMicrobes.my_tools.monkey.Artist attribute) ancestors_all_phylo_units() (VirtualMicrobes.virtual_cell.Population.Population method) ancestral_mutations (VirtualMicrobes.virtual_cell.Cell.Cell attribute) ancestry_stats_dir (VirtualMicrobes.data_tools.store.DataStore attribute) annotate_leafs() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) annotate_phylo_tree() (VirtualMicrobes.virtual_cell.Population.Population method) annotate_phylo_units_feature() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) append() (VirtualMicrobes.my_tools.utility.LinkThroughSequence method) append_data() (VirtualMicrobes.plotting.Graphs.MultiGraph method) (VirtualMicrobes.plotting.Graphs.MultiGridGraph method) append_gene() (VirtualMicrobes.virtual_cell.Chromosome.Chromosome method) append_to_axes() (VirtualMicrobes.plotting.Graphs.MultiGraph method) (VirtualMicrobes.plotting.Graphs.MultiGridGraph method) append_to_lines() (VirtualMicrobes.plotting.Graphs.MultiGraph method) applied (VirtualMicrobes.mutate.Mutation.Mutation attribute) apply_hgt() (VirtualMicrobes.virtual_cell.Cell.Cell method) args (VirtualMicrobes.post_analysis.lod.LOD_Analyser attribute) Artist (class in VirtualMicrobes.my_tools.monkey) as_attrdict() (in module VirtualMicrobes.my_tools.utility) as_numpy_array (VirtualMicrobes.environment.Grid.Grid attribute) asexual() (VirtualMicrobes.virtual_cell.Cell.Cell method) AttributeMap (class in VirtualMicrobes.plotting.Graphs) auto_restart_opts() (VirtualMicrobes.simulation.Simulation.Simulation method) autofmt_xdate() (VirtualMicrobes.my_tools.monkey.Figure method) average_death_rate() (VirtualMicrobes.virtual_cell.Population.Population method) average_production() (VirtualMicrobes.virtual_cell.Population.Population method) average_promoter_strengths() (VirtualMicrobes.virtual_cell.Population.Population method) avrg_promoter_strengths (VirtualMicrobes.virtual_cell.Cell.Cell attribute) axes (VirtualMicrobes.my_tools.monkey.Artist attribute) (VirtualMicrobes.my_tools.monkey.Figure attribute)

B

backup_plots() (VirtualMicrobes.plotting.Graphs.Grapher method) backup_pop_stats() (VirtualMicrobes.simulation.Simulation.Simulation method) BadStoichiometryException base (VirtualMicrobes.my_tools.utility.MutationParamSpace attribute) (VirtualMicrobes.my_tools.utility.ParamSpace attribute) best_match() (VirtualMicrobes.virtual_cell.Sequence.Sequence method) best_producer() (VirtualMicrobes.virtual_cell.Population.Population method) best_stats_dir (VirtualMicrobes.data_tools.store.DataStore attribute) bind (VirtualMicrobes.my_tools.utility.PointMutationRatios attribute) bind_to_bs() (VirtualMicrobes.virtual_cell.Sequence.Operator method)

binding_sequence (VirtualMicrobes.virtual_cell.Gene.TranscriptionFactor attribute) binding_sequences (VirtualMicrobes.virtual_cell.Genome.Genome attribute) (VirtualMicrobes.virtual_cell.Sequence.Operator attribute) binding_tfs_scores() (VirtualMicrobes.virtual_cell.Genome.Genome method) BindingNetwork (class in VirtualMicrobes.plotting.Graphs) BindingSequence (class in VirtualMicrobes.virtual_cell.Sequence) bit_flip() (VirtualMicrobes.virtual_cell.Sequence.Sequence method) bound_operators (VirtualMicrobes.virtual_cell.Sequence.BindingSequence attribute) bs_to_tfs_dict() (VirtualMicrobes.virtual_cell.Genome.Genome method) building block building_blocks (VirtualMicrobes.virtual_cell.Cell.Cell attribute)

C

calc_score_for_bs() (VirtualMicrobes.virtual_cell.Sequence.Operator method) calculate_cells_production() (VirtualMicrobes.virtual_cell.Population.Population method) calculate_death_rates() (VirtualMicrobes.virtual_cell.Population.Population method) calculate_overlap() (in module VirtualMicrobes.post_analysis.network_properties) calculate_raw_death_rate() (VirtualMicrobes.virtual_cell.Cell.Cell method) calculate_reference_production() (VirtualMicrobes.virtual_cell.Population.Population method) calculate_regulation() (VirtualMicrobes.virtual_cell.Sequence.Operator method) cap_death_rates() (VirtualMicrobes.virtual_cell.Population.Population method) CELL (class in VirtualMicrobes.cython_gsl_interface.odes) Cell (class in VirtualMicrobes.virtual_cell.Cell) cell_death() (VirtualMicrobes.virtual_cell.Population.Population method) cell_markers() (VirtualMicrobes.virtual_cell.Population.Population method) cell_sizes() (VirtualMicrobes.virtual_cell.Population.Population method) cells_c (VirtualMicrobes.cython_gsl_interface.odes.POPULATION attribute) cells_grid_diffusion() (VirtualMicrobes.environment.Environment.Environment method) change_save_location() (VirtualMicrobes.data_tools.store.DataCollection method) (VirtualMicrobes.data_tools.store.DataStore method) (VirtualMicrobes.plotting.Graphs.Grapher method) (VirtualMicrobes.plotting.Graphs.Graphs method) check_binding (VirtualMicrobes.virtual_cell.Sequence.Sequence attribute) check_gene_multiplicities() (VirtualMicrobes.virtual_cell.Cell.Cell method) check_sane_concentrations() (VirtualMicrobes.virtual_cell.Population.Population method) check_sane_values() (VirtualMicrobes.virtual_cell.Cell.Cell method) child_of() (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloUnit method) children (VirtualMicrobes.Tree.PhyloTree.PhyloNode attribute) (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloUnit attribute) chrom_del (VirtualMicrobes.my_tools.utility.MutationRates attribute) chrom_dup (VirtualMicrobes.my_tools.utility.MutationRates attribute) chrom_fiss (VirtualMicrobes.my_tools.utility.MutationRates attribute) chrom_fuse (VirtualMicrobes.my_tools.utility.MutationRates attribute) chromosomal_mut (VirtualMicrobes.virtual_cell.Cell.Cell attribute) chromosomal_mut_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) chromosomal_mut_counts() (VirtualMicrobes.virtual_cell.Population.Population method) ChromosomalMutation (class in VirtualMicrobes.mutate.Mutation) Chromosome (class in VirtualMicrobes.virtual_cell.Chromosome) chromosome_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) chromosome_counts() (VirtualMicrobes.virtual_cell.Population.Population method) chromosome_del (VirtualMicrobes.virtual_cell.Cell.Cell attribute) chromosome_del_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) chromosome_dup (VirtualMicrobes.virtual_cell.Cell.Cell attribute) chromosome_dup_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) chromosome_fiss_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) chromosome_fission (VirtualMicrobes.virtual_cell.Cell.Cell attribute) chromosome_fuse_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) chromosome_fusion (VirtualMicrobes.virtual_cell.Cell.Cell attribute) chromosome_mutate_genome() (VirtualMicrobes.virtual_cell.Cell.Cell method) ChromosomeDeletion (class in VirtualMicrobes.mutate.Mutation) ChromosomeDuplication (class in VirtualMicrobes.mutate.Mutation) chunks() (in module VirtualMicrobes.my_tools.utility) CircularList (class in VirtualMicrobes.my_tools.utility) class_version (VirtualMicrobes.data_tools.store.DataStore attribute) (VirtualMicrobes.Tree.PhyloTree.PhyloTree attribute) (VirtualMicrobes.environment.Environment.Environment attribute) (VirtualMicrobes.environment.Environment.Locality attribute) (VirtualMicrobes.event.Molecule.Molecule attribute) (VirtualMicrobes.my_tools.utility.ReusableIndexDict attribute) (VirtualMicrobes.plotting.Graphs.Grapher attribute) (VirtualMicrobes.simulation.Simulation.Simulation attribute) (VirtualMicrobes.virtual_cell.Cell.Cell attribute) (VirtualMicrobes.virtual_cell.Genome.Genome attribute) (VirtualMicrobes.virtual_cell.Population.Population attribute) ClassConvert (class in VirtualMicrobes.event.Reaction) clear() (VirtualMicrobes.my_tools.monkey.Figure method) (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) clear_binding_sequences() (VirtualMicrobes.virtual_cell.Sequence.Operator method) clear_bound_operators() (VirtualMicrobes.virtual_cell.Sequence.BindingSequence method) clear_dead_cells_from_grid() (VirtualMicrobes.environment.Environment.Environment method) clear_graph() (VirtualMicrobes.plotting.Graphs.Network method) clear_locality() (VirtualMicrobes.environment.Environment.Locality method) clear_mol_time_courses() (VirtualMicrobes.environment.Environment.Environment method) (VirtualMicrobes.environment.Environment.Locality method) (VirtualMicrobes.virtual_cell.Cell.Cell method) (VirtualMicrobes.virtual_cell.Population.Population method) clear_offspring() (VirtualMicrobes.virtual_cell.Identifier.Identifier method) clear_pop_changes() (VirtualMicrobes.virtual_cell.Population.Population method) clf() (VirtualMicrobes.my_tools.monkey.Figure method)

clone() (VirtualMicrobes.virtual_cell.Cell.Cell method) cloned_pop() (VirtualMicrobes.virtual_cell.Population.Population method) close() (VirtualMicrobes.my_tools.utility.FIFOLarder method) close_larder() (VirtualMicrobes.my_tools.utility.PartialLinkThroughDict method) close_phylo_shelf() (VirtualMicrobes.simulation.Simulation.Simulation method) coalescent() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) col (VirtualMicrobes.my_tools.utility.GridPos attribute) (VirtualMicrobes.my_tools.utility.GridSubDiv attribute) color_edge_direction() (VirtualMicrobes.plotting.Graphs.Network method) color_mol() (VirtualMicrobes.plotting.Graphs.AttributeMap method) color_mol_class() (VirtualMicrobes.plotting.Graphs.AttributeMap method) color_protein() (VirtualMicrobes.plotting.Graphs.AttributeMap method) color_reaction() (VirtualMicrobes.plotting.Graphs.AttributeMap method) color_reactions() (VirtualMicrobes.plotting.Graphs.MetabolicNetwork method) colorbar() (VirtualMicrobes.my_tools.monkey.Figure method) colors (VirtualMicrobes.plotting.Graphs.MultiGraph attribute) cols (VirtualMicrobes.plotting.Graphs.MultiGraph attribute) columns_iter() (VirtualMicrobes.environment.Grid.Grid method) common_ancestors() (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloUnit method) compare_saves (VirtualMicrobes.post_analysis.lod.LOD_Analyser attribute) compare_to_pop() (VirtualMicrobes.post_analysis.lod.PopulationHistory method) compare_to_pops() (VirtualMicrobes.post_analysis.lod.LOD_Analyser method) compress_root_branch() (VirtualMicrobes.plotting.Graphs.PhyloTreeGraph method) compute_product_toxicity() (VirtualMicrobes.virtual_cell.Cell.Cell method) concentration (VirtualMicrobes.my_tools.utility.GeneProduct attribute) (VirtualMicrobes.my_tools.utility.SmallMol attribute) connect_internal_node() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) connect_leaf() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) connect_phylo_offspring() (VirtualMicrobes.Tree.PhyloTree.PhyloNode method) connect_phylo_parent_child() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) construct_moore_n() (VirtualMicrobes.environment.Grid.Neighborhood method) construct_named_neighborhood() (VirtualMicrobes.environment.Grid.Neighborhood method) construct_neighbors() (VirtualMicrobes.environment.Grid.Neighborhood method) construct_neumann_n() (VirtualMicrobes.environment.Grid.Neighborhood method) Consumer (class in VirtualMicrobes.my_tools.utility) consumer_type (VirtualMicrobes.virtual_cell.Cell.Cell attribute) consumer_type_counts() (VirtualMicrobes.virtual_cell.Population.Population method) consumes (VirtualMicrobes.virtual_cell.Cell.Cell attribute) consumes() (in module VirtualMicrobes.event.Reaction) consuming_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) contains() (VirtualMicrobes.my_tools.monkey.Artist method) (VirtualMicrobes.my_tools.monkey.Figure method) content (VirtualMicrobes.environment.Grid.GridPoint attribute) content_iter (VirtualMicrobes.environment.Grid.Grid attribute) conversions_type (VirtualMicrobes.virtual_cell.Cell.Cell attribute) Convert (class in VirtualMicrobes.event.Reaction) convert_rates() (in module VirtualMicrobes.virtual_cell.Gene) convert_xunits() (VirtualMicrobes.my_tools.monkey.Artist method) convert_yunits() (VirtualMicrobes.my_tools.monkey.Artist method) Coord (class in VirtualMicrobes.my_tools.utility) coord (VirtualMicrobes.environment.Grid.GridPoint attribute) copy() (VirtualMicrobes.my_tools.utility.LinkThroughSet method) copy_config_files() (VirtualMicrobes.simulation.Simulation.Simulation method) copy_number_dist (VirtualMicrobes.virtual_cell.Genome.Genome attribute) copy_numbers (VirtualMicrobes.virtual_cell.Cell.Cell attribute) (VirtualMicrobes.virtual_cell.Genome.Genome attribute) copy_numbers_eff_pumps (VirtualMicrobes.virtual_cell.Cell.Cell attribute) (VirtualMicrobes.virtual_cell.Genome.Genome attribute) copy_numbers_enzymes (VirtualMicrobes.virtual_cell.Cell.Cell attribute) (VirtualMicrobes.virtual_cell.Genome.Genome attribute) copy_numbers_inf_pumps (VirtualMicrobes.virtual_cell.Cell.Cell attribute) (VirtualMicrobes.virtual_cell.Genome.Genome attribute) copy_numbers_tfs (VirtualMicrobes.virtual_cell.Cell.Cell attribute) (VirtualMicrobes.virtual_cell.Genome.Genome attribute) copy_utility_files() (VirtualMicrobes.data_tools.store.DataStore method) count_class_types() (VirtualMicrobes.virtual_cell.Identifier.Identifier class method) create_conversions() (in module VirtualMicrobes.event.Reaction) create_gene_type_time_course_dfs() (in module VirtualMicrobes.data_tools.store) create_leaf() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) create_root_stem() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) create_simulation() (in module VirtualMicrobes.simulation.Simulation) create_stems() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) create_tc_df() (in module VirtualMicrobes.data_tools.store) crossfeed_stats (VirtualMicrobes.data_tools.store.DataStore attribute) cum_time_course (VirtualMicrobes.my_tools.utility.GeneProduct attribute) (VirtualMicrobes.my_tools.utility.SmallMol attribute) customize_lines() (VirtualMicrobes.plotting.Graphs.MultiGraph method)

D

DataCollection (class in VirtualMicrobes.data_tools.store) DataStore (class in VirtualMicrobes.data_tools.store) death_rates() (VirtualMicrobes.virtual_cell.Population.Population method) default_params() (in module VirtualMicrobes.simulation.Simulation) Degradation (class in VirtualMicrobes.event.Reaction) degradation (VirtualMicrobes.my_tools.utility.GeneProduct attribute) (VirtualMicrobes.my_tools.utility.SmallMol attribute) del_chromosome() (VirtualMicrobes.virtual_cell.Genome.Genome method) delaxes() (VirtualMicrobes.my_tools.monkey.Figure method) delete_chromosome() (VirtualMicrobes.virtual_cell.Cell.Cell method) delete_empty_phylo_stems() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) delete_genes() (VirtualMicrobes.virtual_cell.Cell.Cell method) delete_node() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) delete_phylo_hist() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) delete_stretch() (VirtualMicrobes.virtual_cell.Cell.Cell method) (VirtualMicrobes.virtual_cell.Chromosome.Chromosome method) describe_environment() (VirtualMicrobes.simulation.Simulation.Simulation method) detect_rel_path_change() (in module VirtualMicrobes.my_tools.utility) detect_sim_folder_move() (in module VirtualMicrobes.my_tools.utility) DictDataCollection (class in VirtualMicrobes.data_tools.store) die() (VirtualMicrobes.virtual_cell.Cell.Cell method) (VirtualMicrobes.virtual_cell.Genome.Genome method) (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloBase method) (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloUnit method)

die_off() (VirtualMicrobes.virtual_cell.Population.Population method) difference() (VirtualMicrobes.my_tools.utility.LinkThroughSet method) difference_update() (VirtualMicrobes.my_tools.utility.LinkThroughSet method) differential_regulation() (VirtualMicrobes.virtual_cell.Population.Population method) Diffusion (class in VirtualMicrobes.event.Reaction) diffusion (VirtualMicrobes.my_tools.utility.GeneProduct attribute) (VirtualMicrobes.my_tools.utility.SmallMol attribute) diffusion_step() (VirtualMicrobes.cython_gsl_interface.integrate.SpatialIntegrator method) discard() (VirtualMicrobes.my_tools.utility.OrderedSet method) disconnect_direction() (VirtualMicrobes.environment.Grid.Grid method) dist_to_parent() (VirtualMicrobes.Tree.PhyloTree.PhyloNode method) distances() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) divide_volume() (VirtualMicrobes.virtual_cell.Cell.Cell method) dpi (VirtualMicrobes.my_tools.monkey.Figure attribute) draw() (VirtualMicrobes.my_tools.monkey.Artist method) (VirtualMicrobes.my_tools.monkey.Figure method) draw_artist() (VirtualMicrobes.my_tools.monkey.Figure method) draw_network() (VirtualMicrobes.plotting.Graphs.BindingNetwork method) (VirtualMicrobes.plotting.Graphs.MetabolicNetwork method) draw_ref_trees() (VirtualMicrobes.post_analysis.lod.LOD_Analyser method) (VirtualMicrobes.post_analysis.lod.PopulationHistory method) dummy() (VirtualMicrobes.environment.Grid.Grid method) duplicate() (VirtualMicrobes.virtual_cell.Chromosome.Chromosome method) duplicate_chromosome() (VirtualMicrobes.virtual_cell.Cell.Cell method)

E

e_attr_list() (VirtualMicrobes.plotting.Graphs.Network method) eco_diversity_stats_dict (VirtualMicrobes.data_tools.store.DataStore attribute) eco_stats_dir (VirtualMicrobes.data_tools.store.DataStore attribute) eco_type_stats (VirtualMicrobes.data_tools.store.DataStore attribute) eco_type_vector_to_dict() (in module VirtualMicrobes.data_tools.store) edges_with_attr_list() (VirtualMicrobes.plotting.Graphs.Network method) eff_apo (VirtualMicrobes.my_tools.utility.PointMutationRatios attribute) eff_bound (VirtualMicrobes.my_tools.utility.PointMutationRatios attribute) eff_pump_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) eff_pumps (VirtualMicrobes.virtual_cell.Genome.Genome attribute) elements (VirtualMicrobes.virtual_cell.Sequence.Sequence attribute) end1 (VirtualMicrobes.mutate.Mutation.Fusion attribute) end2 (VirtualMicrobes.mutate.Mutation.Fusion attribute) end_pos (VirtualMicrobes.mutate.Mutation.StretchMutation attribute) ene_ks (VirtualMicrobes.my_tools.utility.PointMutationRatios attribute) energy_level (VirtualMicrobes.event.Molecule.Molecule attribute) energy_mols (VirtualMicrobes.environment.Environment.Environment attribute) energy_precursors() (VirtualMicrobes.environment.Environment.Environment method) ensure_dir() (in module VirtualMicrobes.my_tools.utility) env_c (VirtualMicrobes.cython_gsl_interface.odes.SYSTEM attribute) ENVIRONMENT (class in VirtualMicrobes.cython_gsl_interface.odes) Environment (class in VirtualMicrobes.environment.Environment) environment (VirtualMicrobes.event.Molecule.Molecule attribute) (VirtualMicrobes.post_analysis.lod.PopulationHistory attribute) enz (VirtualMicrobes.my_tools.utility.GeneTypeNumbers attribute) enz_average_promoter_strengths() (VirtualMicrobes.virtual_cell.Population.Population method) enz_avrg_promoter_strengths (VirtualMicrobes.virtual_cell.Cell.Cell attribute) enz_promoter_strengths (VirtualMicrobes.virtual_cell.Cell.Cell attribute) enz_subs_differential_ks (VirtualMicrobes.virtual_cell.Cell.Cell attribute) enz_subs_ks (VirtualMicrobes.virtual_cell.Cell.Cell attribute) enz_sum_promoter_strengths (VirtualMicrobes.virtual_cell.Cell.Cell attribute) enz_vmaxs (VirtualMicrobes.virtual_cell.Cell.Cell attribute) ENZYME (class in VirtualMicrobes.cython_gsl_interface.odes) enzyme_average_vmaxs() (VirtualMicrobes.virtual_cell.Population.Population method) enzyme_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) enzyme_counts() (VirtualMicrobes.virtual_cell.Population.Population method) enzyme_substrate_ks() (VirtualMicrobes.virtual_cell.Population.Population method) enzymes (VirtualMicrobes.virtual_cell.Cell.Cell attribute) (VirtualMicrobes.virtual_cell.Genome.Genome attribute)

enzymes_c (VirtualMicrobes.cython_gsl_interface.odes.CELL attribute) errand_boy_server() (in module VirtualMicrobes.my_tools.utility) ete_annotate_tree() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) ete_calc_lca_depth() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) ete_convert_feature_to_cummulative() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) ete_convert_feature_to_rate() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) ete_cummulative_features() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) ete_get_lca() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) ete_get_phylo2ete_dict() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) ete_init_mappings() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) ete_n_most_distant_leafs() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) ete_n_most_distant_phylo_units() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) ete_n_oldest_subtrees() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) ete_named_node_dict (VirtualMicrobes.Tree.PhyloTree.PhyloTree attribute) ete_node_name_to_phylo_node (VirtualMicrobes.Tree.PhyloTree.PhyloTree attribute) ete_node_to_phylo_unit() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) ete_nodes_to_phylo_units() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) ete_phylo_to_ete_birth_nodes() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) ete_phylo_to_ete_death_node() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) ete_phylo_to_ete_stem_nodes() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) ete_prune_external() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) ete_prune_internal() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) ete_prune_leafs() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) ete_rate_features() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) ete_tree (VirtualMicrobes.Tree.PhyloTree.PhyloTree attribute) ETEtreeStruct (class in VirtualMicrobes.my_tools.utility) EvoSystem (class in VirtualMicrobes.simulation.Simulation) excise() (VirtualMicrobes.Tree.PhyloTree.PhyloNode method) exploiting (VirtualMicrobes.virtual_cell.Cell.Cell attribute) exploiting_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) export_type (VirtualMicrobes.virtual_cell.Cell.Cell attribute) export_type_counts() (VirtualMicrobes.virtual_cell.Population.Population method) exporter_counts() (VirtualMicrobes.virtual_cell.Population.Population method) exporter_type (VirtualMicrobes.virtual_cell.Cell.Cell attribute) exporting (VirtualMicrobes.my_tools.utility.PointMutationRatios attribute) exporting_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) external_hgt (VirtualMicrobes.my_tools.utility.MutationRates attribute) (VirtualMicrobes.virtual_cell.Cell.Cell attribute) external_hgt_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) external_molecules (VirtualMicrobes.environment.Environment.Environment attribute)

F

FIFOLarder (class in VirtualMicrobes.my_tools.utility) figimage() (VirtualMicrobes.my_tools.monkey.Figure method) Figure (class in VirtualMicrobes.my_tools.monkey) fill_grid() (VirtualMicrobes.environment.Grid.Grid method) (VirtualMicrobes.plotting.Graphs.MultiGraph method) find_homolog_distances() (in module VirtualMicrobes.post_analysis.network_properties) find_homologs() (in module VirtualMicrobes.post_analysis.network_properties) find_lca() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) find_metabolic_closure() (in module VirtualMicrobes.event.Reaction) find_product_set() (in module VirtualMicrobes.event.Reaction) find_the_one() (VirtualMicrobes.virtual_cell.Population.Population method) findobj() (VirtualMicrobes.my_tools.monkey.Artist method) fiss() (VirtualMicrobes.virtual_cell.Chromosome.Chromosome method) fiss_chromosome() (VirtualMicrobes.virtual_cell.Cell.Cell method) Fission (class in VirtualMicrobes.mutate.Mutation)

fit_stats_names (VirtualMicrobes.data_tools.store.DataStore attribute) flatten() (in module VirtualMicrobes.my_tools.utility) flip_dict (VirtualMicrobes.virtual_cell.Sequence.Sequence attribute) fluctuate() (VirtualMicrobes.environment.Environment.Environment method) format_cursor_data() (VirtualMicrobes.my_tools.monkey.Artist method) FormatMessageFile (class in VirtualMicrobes.my_tools.utility) fraction (VirtualMicrobes.my_tools.utility.PopulationWipe attribute) frequency_stats() (VirtualMicrobes.data_tools.store.DataStore method) from_parent() (VirtualMicrobes.virtual_cell.Identifier.Identifier method) frozen() (VirtualMicrobes.my_tools.monkey.TransformWrapper method) func_on_grid() (VirtualMicrobes.environment.Environment.Environment method) functional_stats_names (VirtualMicrobes.data_tools.store.DataStore attribute) fuse() (VirtualMicrobes.virtual_cell.Chromosome.Chromosome class method) fuse_chromosomes() (VirtualMicrobes.virtual_cell.Cell.Cell method) Fusion (class in VirtualMicrobes.mutate.Mutation)

G

gain_loss() (VirtualMicrobes.data_tools.store.DataStore method) gain_loss_columns (VirtualMicrobes.data_tools.store.DataStore attribute) gca() (VirtualMicrobes.my_tools.monkey.Figure method) Gene (class in VirtualMicrobes.virtual_cell.Gene) gene_node_id() (VirtualMicrobes.plotting.Graphs.Network method) gene_node_label() (VirtualMicrobes.plotting.Graphs.Network method) gene_substrate_differential_ks() (VirtualMicrobes.virtual_cell.Cell.Cell method) gene_substrate_ks() (VirtualMicrobes.virtual_cell.Cell.Cell method) gene_type_counts (VirtualMicrobes.virtual_cell.Cell.Cell attribute) GeneProduct (class in VirtualMicrobes.my_tools.utility) generate_enzymes() (VirtualMicrobes.virtual_cell.Cell.Cell method) generate_pumps() (VirtualMicrobes.virtual_cell.Cell.Cell method) generate_tfs() (VirtualMicrobes.virtual_cell.Cell.Cell method) genes_get_prop_vals() (VirtualMicrobes.virtual_cell.Cell.Cell method) GeneTypeNumbers (class in VirtualMicrobes.my_tools.utility) Genome (class in VirtualMicrobes.plotting.Graphs) (class in VirtualMicrobes.virtual_cell.Genome) genome_dist_stats (VirtualMicrobes.data_tools.store.DataStore attribute) genome_simple_stats_names (VirtualMicrobes.data_tools.store.DataStore attribute) genome_simple_val_stats_names (VirtualMicrobes.data_tools.store.DataStore attribute) genome_size (VirtualMicrobes.virtual_cell.Cell.Cell attribute) genome_sizes() (VirtualMicrobes.virtual_cell.Population.Population method) genomic_target (VirtualMicrobes.mutate.Mutation.Mutation attribute) genomic_unit (VirtualMicrobes.mutate.Mutation.Mutation attribute) GenomicElement (class in VirtualMicrobes.virtual_cell.GenomicElement) genotype (VirtualMicrobes.virtual_cell.Cell.Cell attribute) genotype_counts() (VirtualMicrobes.virtual_cell.Population.Population method) genotype_vector() (VirtualMicrobes.virtual_cell.Cell.Cell method) get() (VirtualMicrobes.my_tools.utility.FIFOLarder method) get_agg_filter() (VirtualMicrobes.my_tools.monkey.Artist method) get_alpha() (VirtualMicrobes.my_tools.monkey.Artist method) get_ancestor() (VirtualMicrobes.virtual_cell.Cell.Cell method) get_ancestor_from_time() (VirtualMicrobes.virtual_cell.Cell.Cell method) get_animated() (VirtualMicrobes.my_tools.monkey.Artist method) get_axes() (VirtualMicrobes.my_tools.monkey.Artist method) (VirtualMicrobes.my_tools.monkey.Figure method) get_building_blocks() (VirtualMicrobes.virtual_cell.Cell.Cell method) get_cell_death_rate() (VirtualMicrobes.virtual_cell.Population.Population method) get_cell_death_rate_dict() (VirtualMicrobes.virtual_cell.Population.Population method) get_cell_pos_production_dict() (VirtualMicrobes.virtual_cell.Population.Population method) get_cell_production() (VirtualMicrobes.virtual_cell.Population.Population method) get_cell_production_dict() (VirtualMicrobes.virtual_cell.Population.Population method) get_cell_production_rate_dict() (VirtualMicrobes.virtual_cell.Population.Population method) get_cell_reproduction_dict() (VirtualMicrobes.virtual_cell.Population.Population method) get_cell_size_dict() (VirtualMicrobes.virtual_cell.Population.Population method) get_cell_size_time_course() (VirtualMicrobes.virtual_cell.Cell.Cell method) get_cell_toxicity_rate_dict() (VirtualMicrobes.virtual_cell.Population.Population method) get_cells() (VirtualMicrobes.environment.Environment.Locality method) get_children() (VirtualMicrobes.my_tools.monkey.Artist method) (VirtualMicrobes.my_tools.monkey.Figure method) get_clip_box() (VirtualMicrobes.my_tools.monkey.Artist method) get_clip_on() (VirtualMicrobes.my_tools.monkey.Artist method) get_clip_path() (VirtualMicrobes.my_tools.monkey.Artist method) get_contains() (VirtualMicrobes.my_tools.monkey.Artist method) get_cursor_data() (VirtualMicrobes.my_tools.monkey.Artist method) get_data_point() (VirtualMicrobes.data_tools.store.DataCollection method) get_default_bbox_extra_artists() (VirtualMicrobes.my_tools.monkey.Figure method) get_dpi() (VirtualMicrobes.my_tools.monkey.Figure method) get_edgecolor() (VirtualMicrobes.my_tools.monkey.Figure method) get_facecolor() (VirtualMicrobes.my_tools.monkey.Figure method) get_figheight() (VirtualMicrobes.my_tools.monkey.Figure method) get_figure() (VirtualMicrobes.my_tools.monkey.Artist method) get_figwidth() (VirtualMicrobes.my_tools.monkey.Figure method) get_frameon() (VirtualMicrobes.my_tools.monkey.Figure method) get_from_linker() (in module VirtualMicrobes.my_tools.utility) get_gene_concentration_dict() (VirtualMicrobes.virtual_cell.Cell.Cell method) get_gene_degradation_dict() (VirtualMicrobes.virtual_cell.Cell.Cell method)

get_gene_diffusion_dict() (VirtualMicrobes.virtual_cell.Cell.Cell method) get_gene_multiplicities_dict() (VirtualMicrobes.virtual_cell.Cell.Cell method) get_gene_prod_conc() (VirtualMicrobes.environment.Environment.Locality method) (VirtualMicrobes.virtual_cell.Cell.Cell method) get_gene_time_course_dict() (VirtualMicrobes.virtual_cell.Cell.Cell method) get_gene_type_time_course_dict() (VirtualMicrobes.virtual_cell.Cell.Cell method) get_gid() (VirtualMicrobes.my_tools.monkey.Artist method) get_gp() (VirtualMicrobes.environment.Grid.Grid method) get_label() (VirtualMicrobes.my_tools.monkey.Artist method) get_mol_concentration_dict() (VirtualMicrobes.environment.Environment.Locality method) (VirtualMicrobes.virtual_cell.Cell.Cell method) get_mol_degradation_dict() (VirtualMicrobes.virtual_cell.Cell.Cell method) get_mol_diffusion_dict() (VirtualMicrobes.virtual_cell.Cell.Cell method) get_mol_influx_dict() (VirtualMicrobes.environment.Environment.Locality method) get_mol_per_class_concentration_dict() (VirtualMicrobes.environment.Environment.Locality method) get_mol_per_class_influx_dict() (VirtualMicrobes.environment.Environment.Locality method) get_mol_time_course_dict() (VirtualMicrobes.environment.Environment.Locality method) (VirtualMicrobes.virtual_cell.Cell.Cell method) get_nei_gp() (VirtualMicrobes.environment.Grid.Grid method) get_neighbor_at() (VirtualMicrobes.environment.Grid.GridPoint method) get_path_effects() (VirtualMicrobes.my_tools.monkey.Artist method) get_picker() (VirtualMicrobes.my_tools.monkey.Artist method) get_pos_prod_time_course() (VirtualMicrobes.virtual_cell.Cell.Cell method) get_rasterized() (VirtualMicrobes.my_tools.monkey.Artist method) get_raw_production_time_course() (VirtualMicrobes.virtual_cell.Cell.Cell method) get_rel_coords() (VirtualMicrobes.environment.Grid.Neighborhood method) get_size_inches() (VirtualMicrobes.my_tools.monkey.Figure method) get_sketch_params() (VirtualMicrobes.my_tools.monkey.Artist method) get_small_mol_conc() (VirtualMicrobes.environment.Environment.Locality method) (VirtualMicrobes.virtual_cell.Cell.Cell method) get_snap() (VirtualMicrobes.my_tools.monkey.Artist method) get_tight_layout() (VirtualMicrobes.my_tools.monkey.Figure method) get_tightbbox() (VirtualMicrobes.my_tools.monkey.Figure method) get_time_points() (VirtualMicrobes.virtual_cell.Cell.Cell method) get_total_reaction_type_time_course_dict() (VirtualMicrobes.virtual_cell.Cell.Cell method) get_toxicity_time_course() (VirtualMicrobes.virtual_cell.Cell.Cell method) get_transform() (VirtualMicrobes.my_tools.monkey.Artist method) get_transformed_clip_path_and_affine() (VirtualMicrobes.my_tools.monkey.Artist method) get_unique_key() (in module VirtualMicrobes.my_tools.utility) get_url() (VirtualMicrobes.my_tools.monkey.Artist method) get_visible() (VirtualMicrobes.my_tools.monkey.Artist method) get_window_extent() (VirtualMicrobes.my_tools.monkey.Artist method) (VirtualMicrobes.my_tools.monkey.Figure method) get_zorder() (VirtualMicrobes.my_tools.monkey.Artist method) ginput() (VirtualMicrobes.my_tools.monkey.Figure method) gp_iter (VirtualMicrobes.environment.Grid.Grid attribute) gp_iter_in_order() (VirtualMicrobes.environment.Grid.Grid method) gp_to_integrators_c_dict (VirtualMicrobes.cython_gsl_interface.integrate.SpatialIntegrator attribute) Grapher (class in VirtualMicrobes.plotting.Graphs) GraphingError GraphNotFoundError Graphs (class in VirtualMicrobes.plotting.Graphs) Grid (class in VirtualMicrobes.environment.Grid) grid (VirtualMicrobes.cython_gsl_interface.integrate.SpatialIntegrator attribute) grid_barriers() (VirtualMicrobes.environment.Grid.Grid method) grid_data_from_func() (VirtualMicrobes.environment.Environment.Environment method) grid_free() (VirtualMicrobes.plotting.Graphs.MultiGraph method) grid_stats (VirtualMicrobes.data_tools.store.DataStore attribute) grid_toggle_update() (VirtualMicrobes.environment.Environment.Environment method) GridError GridPoint (class in VirtualMicrobes.environment.Grid) GridPos (class in VirtualMicrobes.my_tools.utility) GridSubDiv (class in VirtualMicrobes.my_tools.utility) GRN() (VirtualMicrobes.virtual_cell.Cell.Cell method) grn_edits (VirtualMicrobes.data_tools.store.DataStore attribute) grow_array() (in module VirtualMicrobes.my_tools.utility) grow_time_course_arrays() (VirtualMicrobes.virtual_cell.Cell.Cell method) (VirtualMicrobes.virtual_cell.Population.Population method)

H

handle_timeout() (VirtualMicrobes.my_tools.utility.timeout method) has_coord() (VirtualMicrobes.environment.Grid.Neighborhood method) has_inverse (VirtualMicrobes.my_tools.monkey.TransformWrapper attribute) has_key() (VirtualMicrobes.my_tools.utility.FIFOLarder method) has_living_offspring() (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloUnit method) has_root() (VirtualMicrobes.Tree.PhyloTree.PhyloNode method)

have_units() (VirtualMicrobes.my_tools.monkey.Artist method) hgt_external() (VirtualMicrobes.virtual_cell.Cell.Cell method) hgt_internal() (VirtualMicrobes.virtual_cell.Cell.Cell method) hitlist() (VirtualMicrobes.my_tools.monkey.Artist method) hold() (VirtualMicrobes.my_tools.monkey.Figure method) horizontal_transfer() (VirtualMicrobes.virtual_cell.Population.Population method) hybridize() (VirtualMicrobes.virtual_cell.Cell.Cell method)

I

id (VirtualMicrobes.Tree.PhyloTree.PhyloNode attribute) (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloBase attribute) Identifier (class in VirtualMicrobes.virtual_cell.Identifier) identify_lod_ancestor() (VirtualMicrobes.post_analysis.lod.PopulationHistory method) import_type (VirtualMicrobes.virtual_cell.Cell.Cell attribute) import_type_counts() (VirtualMicrobes.virtual_cell.Population.Population method) importer_counts() (VirtualMicrobes.virtual_cell.Population.Population method) importer_type (VirtualMicrobes.virtual_cell.Cell.Cell attribute) importing_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) increment() (in module VirtualMicrobes.virtual_cell.Identifier) increment_func (VirtualMicrobes.virtual_cell.Identifier.Identifier attribute) increment_offspring() (VirtualMicrobes.virtual_cell.Identifier.Identifier method) index (VirtualMicrobes.event.Molecule.Molecule attribute) index_key() (VirtualMicrobes.my_tools.utility.ReusableIndexDict method) inf_pump_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) inf_pumps (VirtualMicrobes.virtual_cell.Genome.Genome attribute) Influx (class in VirtualMicrobes.event.Reaction) influx (VirtualMicrobes.my_tools.utility.SmallMol attribute) influx_change_gamma() (VirtualMicrobes.environment.Environment.Environment method) influx_change_range() (VirtualMicrobes.environment.Environment.Environment method) influx_dict (VirtualMicrobes.my_tools.utility.SubEnv attribute) inform_bss() (VirtualMicrobes.virtual_cell.Sequence.Operator method) inform_operators() (VirtualMicrobes.virtual_cell.Sequence.BindingSequence method) inherit_root() (VirtualMicrobes.Tree.PhyloTree.PhyloNode method) init_anabolic_reactions() (VirtualMicrobes.environment.Environment.Environment method) init_ancestry_compare_stores() (VirtualMicrobes.data_tools.store.DataStore method) init_attribute_mapper() (VirtualMicrobes.plotting.Graphs.Grapher method) init_binding_network() (VirtualMicrobes.plotting.Graphs.Graphs method) init_binding_sequences() (VirtualMicrobes.virtual_cell.Sequence.Operator method) init_bound_operators() (VirtualMicrobes.virtual_cell.Sequence.BindingSequence method) init_building_blocks_dict() (VirtualMicrobes.virtual_cell.Cell.Cell method) init_catabolic_reactions() (VirtualMicrobes.environment.Environment.Environment method) init_cell_params() (VirtualMicrobes.virtual_cell.Cell.Cell method) init_cell_time_courses() (VirtualMicrobes.virtual_cell.Cell.Cell method) init_cells_view() (VirtualMicrobes.virtual_cell.Population.Population method) init_chromosomes() (VirtualMicrobes.virtual_cell.Genome.Genome method) init_class_conversions() (VirtualMicrobes.environment.Environment.Environment method) init_color_maps() (VirtualMicrobes.plotting.Graphs.AttributeMap method) init_current_ancestors() (VirtualMicrobes.virtual_cell.Population.Population method) init_data_store() (VirtualMicrobes.simulation.Simulation.Simulation method) init_degradation() (VirtualMicrobes.environment.Environment.Environment method) init_degradation_dict() (VirtualMicrobes.environment.Environment.Environment method) init_dict_stats_store() (VirtualMicrobes.data_tools.store.DataStore method) init_diffusion() (VirtualMicrobes.environment.Environment.Environment method) init_eco_data_stores() (VirtualMicrobes.data_tools.store.DataStore method) init_energy_mols() (VirtualMicrobes.virtual_cell.Cell.Cell method) init_error_log_file() (VirtualMicrobes.simulation.Simulation.Simulation method) init_evo_rand_gens() (VirtualMicrobes.virtual_cell.Population.Population method) init_external_mol_vals_on_grid() (VirtualMicrobes.environment.Environment.Environment method) init_external_mols() (VirtualMicrobes.environment.Environment.Locality method) init_ffmpeg() (VirtualMicrobes.simulation.Simulation.Simulation method) init_file() (VirtualMicrobes.data_tools.store.DataCollection method) init_gain_loss_store() (VirtualMicrobes.data_tools.store.DataStore method) init_gene_products() (VirtualMicrobes.virtual_cell.Cell.Cell method) init_genome() (VirtualMicrobes.virtual_cell.Cell.Cell method) init_genome_structure() (VirtualMicrobes.plotting.Graphs.Graphs method) init_global_influx_dict() (VirtualMicrobes.environment.Environment.Environment method) init_graphs() (VirtualMicrobes.simulation.Simulation.Simulation method) init_grid() (VirtualMicrobes.environment.Environment.Environment method) (VirtualMicrobes.environment.Grid.Grid method) init_grid_graphs() (VirtualMicrobes.plotting.Graphs.Graphs method) init_influx() (VirtualMicrobes.environment.Environment.Environment method) init_influxed_mols() (VirtualMicrobes.environment.Environment.Environment method) init_integrator() (VirtualMicrobes.post_analysis.lod.PopulationHistory method) init_list_stats_store() (VirtualMicrobes.data_tools.store.DataStore method) init_localities() (VirtualMicrobes.environment.Environment.Environment method) init_lod_stores() (VirtualMicrobes.data_tools.store.DataStore method) init_lods() (VirtualMicrobes.post_analysis.lod.PopulationHistory method) init_log_file() (VirtualMicrobes.simulation.Simulation.Simulation method) init_log_files() (VirtualMicrobes.simulation.Simulation.Simulation method) init_membrane_diffusion_dict() (VirtualMicrobes.environment.Environment.Environment method) init_metabolic_network() (VirtualMicrobes.plotting.Graphs.Graphs method) init_mol_class_color_dict() (VirtualMicrobes.plotting.Graphs.AttributeMap method) init_mol_class_sizes() (VirtualMicrobes.environment.Environment.Environment method) init_mol_classes() (VirtualMicrobes.environment.Environment.Environment method) init_mol_time_course() (VirtualMicrobes.environment.Environment.Locality method) (VirtualMicrobes.virtual_cell.Cell.Cell method) init_mol_toxicities() (VirtualMicrobes.environment.Environment.Environment method) init_mol_views() (VirtualMicrobes.environment.Environment.Locality method) (VirtualMicrobes.virtual_cell.Cell.Cell method) init_mols_to_reactions() (VirtualMicrobes.environment.Environment.Environment method)

init_mutations_dict() (VirtualMicrobes.virtual_cell.Cell.Cell method) init_network() (VirtualMicrobes.plotting.Graphs.BindingNetwork method) (VirtualMicrobes.plotting.Graphs.MetabolicNetwork method) (VirtualMicrobes.plotting.Graphs.Network method) init_phylo_dicts() (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloUnit method) init_phylo_hist_stores() (VirtualMicrobes.data_tools.store.DataStore method) init_phylo_linker_dict() (VirtualMicrobes.simulation.Simulation.Simulation method) init_phylo_tree() (VirtualMicrobes.plotting.Graphs.Graphs method) (VirtualMicrobes.post_analysis.lod.PopulationHistory method) (VirtualMicrobes.virtual_cell.Population.Population method) init_pop() (VirtualMicrobes.virtual_cell.Population.Population method) init_pop_data_stores() (VirtualMicrobes.data_tools.store.DataStore method) init_pop_hist_data_store() (VirtualMicrobes.post_analysis.lod.PopulationHistory method) init_pop_rand_gen() (VirtualMicrobes.virtual_cell.Population.Population method) init_pop_stats() (VirtualMicrobes.plotting.Graphs.Graphs method) init_positions() (VirtualMicrobes.virtual_cell.Chromosome.Chromosome method) init_rand_gen() (VirtualMicrobes.my_tools.utility.ReusableIndexDict method) init_rand_gens() (VirtualMicrobes.environment.Environment.Environment method) (VirtualMicrobes.post_analysis.lod.PopulationHistory method) init_range_dicts() (VirtualMicrobes.virtual_cell.Population.Population method) init_reaction_universe() (VirtualMicrobes.environment.Environment.Environment method) init_reactions() (VirtualMicrobes.environment.Environment.Environment method) init_ref_history() (VirtualMicrobes.post_analysis.lod.LOD_Analyser method) init_regulatory_network() (VirtualMicrobes.virtual_cell.Genome.Genome method) init_roots() (VirtualMicrobes.virtual_cell.Population.Population method) init_save_dir() (VirtualMicrobes.plotting.Graphs.Grapher method) (VirtualMicrobes.simulation.Simulation.Simulation method) init_save_dirs() (VirtualMicrobes.data_tools.store.DataStore method) init_scaling_dict() (VirtualMicrobes.plotting.Graphs.Graphs method) init_simple_stats_plus_store() (VirtualMicrobes.data_tools.store.DataStore method) init_simple_stats_store() (VirtualMicrobes.data_tools.store.DataStore method) init_simple_value_store() (VirtualMicrobes.data_tools.store.DataStore method) init_spatial_integrator() (VirtualMicrobes.simulation.Simulation.ODE_simulation method) init_stats_column_names() (VirtualMicrobes.data_tools.store.DataStore method) init_sub_envs() (VirtualMicrobes.environment.Environment.Environment method) init_sub_reaction_dicts() (VirtualMicrobes.event.Reaction.ClassConvert method) (VirtualMicrobes.event.Reaction.Convert method) (VirtualMicrobes.event.Reaction.Transport method) init_substrates_ks() (VirtualMicrobes.virtual_cell.Gene.MetabolicGene method) init_test_bed() (VirtualMicrobes.post_analysis.lod.PopulationHistory method) init_time_course_graph() (VirtualMicrobes.plotting.Graphs.Graphs method) init_time_courses() (VirtualMicrobes.environment.Environment.Locality method) (VirtualMicrobes.virtual_cell.Cell.Cell method) init_transports() (VirtualMicrobes.environment.Environment.Environment method) init_tree_style_dict() (VirtualMicrobes.plotting.Graphs.PhyloTreeGraph method) init_unique_phylo_key() (VirtualMicrobes.simulation.Simulation.Simulation method) init_variables_map() (VirtualMicrobes.environment.Environment.Locality method) insert() (VirtualMicrobes.my_tools.utility.LinkThroughSequence method) insert_mutate() (VirtualMicrobes.virtual_cell.Sequence.Sequence method) insert_pos (VirtualMicrobes.mutate.Mutation.Insertion attribute) (VirtualMicrobes.mutate.Mutation.Translocation attribute) insert_stretch() (VirtualMicrobes.virtual_cell.Cell.Cell method) (VirtualMicrobes.virtual_cell.Chromosome.Chromosome method) Insertion (class in VirtualMicrobes.mutate.Mutation) Integrator (class in VirtualMicrobes.cython_gsl_interface.integrate) internal_hgt (VirtualMicrobes.my_tools.utility.MutationRates attribute) (VirtualMicrobes.virtual_cell.Cell.Cell attribute) internal_hgt_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) intersection() (VirtualMicrobes.my_tools.utility.LinkThroughSet method) interval (VirtualMicrobes.my_tools.utility.PopulationWipe attribute) Inversion (class in VirtualMicrobes.mutate.Mutation) invert (VirtualMicrobes.mutate.Mutation.Translocation attribute) invert() (VirtualMicrobes.virtual_cell.Chromosome.Chromosome method) invert_stretch() (VirtualMicrobes.virtual_cell.Cell.Cell method) is_affine (VirtualMicrobes.my_tools.monkey.TransformWrapper attribute) is_autotroph() (VirtualMicrobes.virtual_cell.Cell.Cell method) is_building_block (VirtualMicrobes.event.Molecule.Molecule attribute) is_copy() (VirtualMicrobes.virtual_cell.Identifier.Identifier method) is_energy (VirtualMicrobes.event.Molecule.Molecule attribute) is_enzyme (VirtualMicrobes.virtual_cell.Gene.Gene attribute) is_external (VirtualMicrobes.mutate.Mutation.Insertion attribute) is_figure_set() (VirtualMicrobes.my_tools.monkey.Artist method) is_gene_product (VirtualMicrobes.event.Molecule.Molecule attribute) is_heterotroph() (VirtualMicrobes.virtual_cell.Cell.Cell method) is_influxed (VirtualMicrobes.event.Molecule.Molecule attribute) is_internal (VirtualMicrobes.event.Molecule.Molecule attribute) is_leaf (VirtualMicrobes.Tree.PhyloTree.PhyloNode attribute) is_separable (VirtualMicrobes.my_tools.monkey.TransformWrapper attribute) is_transform_set() (VirtualMicrobes.my_tools.monkey.Artist method) iter_prepostorder() (VirtualMicrobes.Tree.PhyloTree.PhyloNode method) iterages() (VirtualMicrobes.virtual_cell.Population.Population method)

J

json_dumper() (in module VirtualMicrobes.my_tools.utility)

K

k_bind_op (VirtualMicrobes.my_tools.utility.PointMutationRatios attribute) keys() (VirtualMicrobes.my_tools.utility.FIFOLarder method) (VirtualMicrobes.my_tools.utility.ReusableIndexDict method)

kill_proc_tree() (in module VirtualMicrobes.my_tools.utility)

L

layout_network_positions() (VirtualMicrobes.plotting.Graphs.BindingNetwork method) (VirtualMicrobes.plotting.Graphs.MetabolicNetwork method) legend() (VirtualMicrobes.my_tools.monkey.Figure method) ligand_class (VirtualMicrobes.my_tools.utility.PointMutationRatios attribute) (VirtualMicrobes.virtual_cell.Gene.TranscriptionFactor attribute) ligand_ks (VirtualMicrobes.my_tools.utility.PointMutationRatios attribute) line_colors() (VirtualMicrobes.plotting.Graphs.Graphs method) line_markers (VirtualMicrobes.plotting.Graphs.MultiGraph attribute) line_styles (VirtualMicrobes.plotting.Graphs.MultiGraph attribute) linkthrough() (in module VirtualMicrobes.my_tools.utility) LinkThroughSequence (class in VirtualMicrobes.my_tools.utility) LinkThroughSet (class in VirtualMicrobes.my_tools.utility) ListDataCollection (class in VirtualMicrobes.data_tools.store) living_offspring() (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloBase method) (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloUnit method) load_sim() (in module VirtualMicrobes.simulation.Simulation) load_sim_params() (in module VirtualMicrobes.simulation.Simulation) load_simulation() (in module VirtualMicrobes.simulation.Simulation) Locality (class in VirtualMicrobes.environment.Environment) LOD (class in VirtualMicrobes.post_analysis.lod)

LOD_Analyser (class in VirtualMicrobes.post_analysis.lod) lod_binding_conservation() (VirtualMicrobes.post_analysis.lod.LOD_Analyser method) (VirtualMicrobes.post_analysis.lod.PopulationHistory method) lod_down_single() (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloUnit method) lod_graphs() (VirtualMicrobes.post_analysis.lod.LOD_Analyser method) lod_network_stats() (VirtualMicrobes.post_analysis.lod.LOD_Analyser method) (VirtualMicrobes.post_analysis.lod.PopulationHistory method) lod_stats() (VirtualMicrobes.post_analysis.lod.LOD_Analyser method) (VirtualMicrobes.post_analysis.lod.PopulationHistory method) lod_stats_dir (VirtualMicrobes.data_tools.store.DataStore attribute) lod_time_course_plots() (VirtualMicrobes.post_analysis.lod.LOD_Analyser method) lod_time_courses() (VirtualMicrobes.post_analysis.lod.LOD_Analyser method) lod_up_single() (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloUnit method) lods_down() (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloUnit method) lods_time_course_data() (VirtualMicrobes.post_analysis.lod.PopulationHistory method) lods_time_course_plots() (VirtualMicrobes.post_analysis.lod.PopulationHistory method) lods_up() (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloUnit method) lower (VirtualMicrobes.my_tools.utility.MutationParamSpace attribute) (VirtualMicrobes.my_tools.utility.ParamSpace attribute)

M

main() (in module VirtualMicrobes.simulation.continue) (in module VirtualMicrobes.simulation.start) (in module VirtualMicrobes.simulation.start_multi) major_id (VirtualMicrobes.virtual_cell.Identifier.Identifier attribute) make_barrier() (VirtualMicrobes.environment.Grid.Grid method) make_inherited_hgt_dict() (in module VirtualMicrobes.virtual_cell.Cell) make_mutations_dict() (in module VirtualMicrobes.virtual_cell.Cell) make_tree_style() (VirtualMicrobes.plotting.Graphs.PhyloTreeGraph method) map_backward_func() (in module VirtualMicrobes.my_tools.utility) map_cell_gene_products() (VirtualMicrobes.environment.Environment.Locality method) map_cell_internal_mols() (VirtualMicrobes.environment.Environment.Locality method) map_external_molecules() (VirtualMicrobes.environment.Environment.Locality method) map_forward_func() (in module VirtualMicrobes.my_tools.utility) map_variables() (VirtualMicrobes.environment.Environment.Environment method) (VirtualMicrobes.environment.Environment.Locality method) mark() (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloBase method) mark_cells_lineage() (VirtualMicrobes.virtual_cell.Population.Population method) mark_cells_metabolic_type() (VirtualMicrobes.virtual_cell.Population.Population method) marker_counts() (VirtualMicrobes.virtual_cell.Population.Population method) marker_dict (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloBase attribute) marker_edge_widths (VirtualMicrobes.plotting.Graphs.MultiGraph attribute) marker_sizes (VirtualMicrobes.plotting.Graphs.MultiGraph attribute) match() (VirtualMicrobes.virtual_cell.Sequence.Sequence method) match_operators() (VirtualMicrobes.virtual_cell.Sequence.BindingSequence method) max (VirtualMicrobes.my_tools.utility.MutationParamSpace attribute) max_node_depth (VirtualMicrobes.Tree.PhyloTree.PhyloNode attribute) mean_life_time_cell_size (VirtualMicrobes.virtual_cell.Cell.Cell attribute) mean_life_time_pos_production (VirtualMicrobes.virtual_cell.Cell.Cell attribute) mean_life_time_production (VirtualMicrobes.virtual_cell.Cell.Cell attribute) mean_life_time_toxicity (VirtualMicrobes.virtual_cell.Cell.Cell attribute) mesh_iter() (VirtualMicrobes.environment.Grid.Grid method) meta_stats_names (VirtualMicrobes.data_tools.store.DataStore attribute) metabolic_categories (VirtualMicrobes.data_tools.store.DataStore attribute) metabolic_complementarity() (VirtualMicrobes.virtual_cell.Population.Population class method) metabolic_complementarity_pop() (VirtualMicrobes.virtual_cell.Population.Population method) metabolic_type (VirtualMicrobes.virtual_cell.Cell.Cell attribute) metabolic_type_color() (VirtualMicrobes.virtual_cell.Population.Population method) metabolic_type_counts() (VirtualMicrobes.virtual_cell.Population.Population method) metabolic_type_layout() (VirtualMicrobes.plotting.Graphs.PhyloTreeGraph method) metabolic_type_vector() (VirtualMicrobes.virtual_cell.Cell.Cell method) metabolic_with_lod_layout() (VirtualMicrobes.plotting.Graphs.PhyloTreeGraph method) MetabolicGene (class in VirtualMicrobes.virtual_cell.Gene) MetabolicNetwork (class in VirtualMicrobes.plotting.Graphs) metabolite metabolite_edge_width() (VirtualMicrobes.plotting.Graphs.Network method) metabolite_grid_data_dict() (VirtualMicrobes.environment.Environment.Environment method) min (VirtualMicrobes.my_tools.utility.MutationParamSpace attribute)

minor_id (VirtualMicrobes.virtual_cell.Identifier.Identifier attribute) mirror_rel_coord() (in module VirtualMicrobes.environment.Grid) mol_class (VirtualMicrobes.event.Molecule.Molecule attribute) Molecule (class in VirtualMicrobes.event.Molecule) molecule_classes (VirtualMicrobes.environment.Environment.Environment attribute) MoleculeClass (class in VirtualMicrobes.event.Molecule) MoleculeIndexer (class in VirtualMicrobes.event.Molecule) mols_per_class_dict (VirtualMicrobes.environment.Environment.Environment attribute) monkeypatch_class() (in module VirtualMicrobes.my_tools.monkey) most_abundant_marker() (VirtualMicrobes.virtual_cell.Population.Population method) most_offspring() (VirtualMicrobes.virtual_cell.Population.Population method) mouseover (VirtualMicrobes.my_tools.monkey.Artist attribute) multifile (class in VirtualMicrobes.my_tools.utility) MultiGraph (class in VirtualMicrobes.plotting.Graphs) MultiGridGraph (class in VirtualMicrobes.plotting.Graphs) multiplicity (VirtualMicrobes.my_tools.utility.GeneProduct attribute) mut_func_single_param() (in module VirtualMicrobes.simulation.Simulation) mut_ks_dict_func() (in module VirtualMicrobes.simulation.Simulation) mut_stats_names (VirtualMicrobes.data_tools.store.DataStore attribute) mutate() (VirtualMicrobes.mutate.Mutation.ChromosomeDeletion method) (VirtualMicrobes.mutate.Mutation.ChromosomeDuplication method) (VirtualMicrobes.mutate.Mutation.Fission method) (VirtualMicrobes.mutate.Mutation.Fusion method) (VirtualMicrobes.mutate.Mutation.Insertion method) (VirtualMicrobes.mutate.Mutation.Inversion method) (VirtualMicrobes.mutate.Mutation.Mutation method) (VirtualMicrobes.mutate.Mutation.OperatorInsertion method) (VirtualMicrobes.mutate.Mutation.PointMutation method) (VirtualMicrobes.mutate.Mutation.SingleGeneMutation method) (VirtualMicrobes.mutate.Mutation.StretchDeletion method) (VirtualMicrobes.mutate.Mutation.TandemDuplication method) (VirtualMicrobes.mutate.Mutation.Translocation method) (VirtualMicrobes.virtual_cell.Cell.Cell method) (VirtualMicrobes.virtual_cell.Gene.Promoter method) (VirtualMicrobes.virtual_cell.Sequence.Sequence method) mutate_bits() (VirtualMicrobes.virtual_cell.Sequence.Sequence method) mutate_new_offspring() (VirtualMicrobes.virtual_cell.Population.Population method) mutated() (VirtualMicrobes.virtual_cell.Gene.Gene method) Mutation (class in VirtualMicrobes.mutate.Mutation) mutation_rates_layout() (VirtualMicrobes.plotting.Graphs.PhyloTreeGraph method) MutationAlreadyAppliedError MutationError MutationNotAppliedError MutationParamSpace (class in VirtualMicrobes.my_tools.utility) MutationRates (class in VirtualMicrobes.my_tools.utility) MyArtist (in module VirtualMicrobes.my_tools.monkey) MyFigure (in module VirtualMicrobes.my_tools.monkey) MyTransformWrapper (in module VirtualMicrobes.my_tools.monkey)

N

n_attr_list() (VirtualMicrobes.plotting.Graphs.Network method) named_node_dict (VirtualMicrobes.my_tools.utility.ETEtreeStruct attribute) namedtuple_with_defaults() (in module VirtualMicrobes.my_tools.utility) nei_grid_coords() (VirtualMicrobes.environment.Grid.GridPoint method) nei_rel_coord_to_gp() (VirtualMicrobes.environment.Grid.GridPoint method) nei_rel_to_grid_coords() (VirtualMicrobes.environment.Grid.GridPoint method) neighbor_gps() (VirtualMicrobes.environment.Grid.GridPoint method) Neighborhood (class in VirtualMicrobes.environment.Grid) neighbors() (VirtualMicrobes.environment.Grid.GridPoint method) Network (class in VirtualMicrobes.plotting.Graphs) network_stats_funcs (VirtualMicrobes.data_tools.store.DataStore attribute) new_val (VirtualMicrobes.mutate.Mutation.OperatorInsertion attribute) (VirtualMicrobes.mutate.Mutation.PointMutation attribute)

newick() (in module VirtualMicrobes.Tree.PhyloTree) newick_id (VirtualMicrobes.Tree.PhyloTree.PhyloNode attribute) nh_branch() (in module VirtualMicrobes.Tree.PhyloTree) nh_format_nr() (VirtualMicrobes.Tree.PhyloTree.PhyloNode method) nh_formats() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) nhx() (in module VirtualMicrobes.Tree.PhyloTree) nhx_features (VirtualMicrobes.Tree.PhyloTree.PhyloNode attribute) node_layouts (VirtualMicrobes.plotting.Graphs.PhyloTreeGraph attribute) node_name_to_phylo_node (VirtualMicrobes.my_tools.utility.ETEtreeStruct attribute) nodes_edges() (VirtualMicrobes.virtual_cell.Cell.Cell method) nodes_iter() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) nodes_with_attr_list() (VirtualMicrobes.plotting.Graphs.Network method) normalize_coord() (VirtualMicrobes.environment.Grid.Grid method)

O

ode_params() (VirtualMicrobes.virtual_cell.Gene.MetabolicGene method) (VirtualMicrobes.virtual_cell.Gene.Transporter method) ODE_simulation (class in VirtualMicrobes.simulation.Simulation) offspring_count (VirtualMicrobes.virtual_cell.Identifier.Identifier attribute) offspring_counts() (VirtualMicrobes.virtual_cell.Population.Population method) oldest_cell() (VirtualMicrobes.virtual_cell.Population.Population method) op_to_tfs_scores_dict() (VirtualMicrobes.virtual_cell.Genome.Genome method) open_fifolarder() (in module VirtualMicrobes.my_tools.utility)

open_log_file() (VirtualMicrobes.simulation.Simulation.Simulation method) open_phylo_shelf() (VirtualMicrobes.simulation.Simulation.Simulation method) Operator (class in VirtualMicrobes.virtual_cell.Sequence) operator (VirtualMicrobes.my_tools.utility.PointMutationRatios attribute) (VirtualMicrobes.virtual_cell.Gene.Gene attribute) OperatorInsertion (class in VirtualMicrobes.mutate.Mutation) operators (VirtualMicrobes.virtual_cell.Genome.Genome attribute) OrderedDefaultdict (class in VirtualMicrobes.my_tools.utility) OrderedSet (class in VirtualMicrobes.my_tools.utility)

P

pad_frequencies() (in module VirtualMicrobes.my_tools.utility) padded_most_frequent() (in module VirtualMicrobes.my_tools.utility) pair_up() (VirtualMicrobes.event.Molecule.Molecule method) pan_metabolome_dict() (VirtualMicrobes.virtual_cell.Population.Population method) par (VirtualMicrobes.mutate.Mutation.OperatorInsertion attribute) (VirtualMicrobes.mutate.Mutation.PointMutation attribute) params (VirtualMicrobes.post_analysis.lod.PopulationHistory attribute) (VirtualMicrobes.virtual_cell.Gene.Gene attribute) ParamSpace (class in VirtualMicrobes.my_tools.utility) parent_of() (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloUnit method) parents (VirtualMicrobes.Tree.PhyloTree.PhyloNode attribute) (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloUnit attribute) parse() (VirtualMicrobes.virtual_cell.Identifier.Identifier method) parse_combining_opts() (in module VirtualMicrobes.simulation.start) (in module VirtualMicrobes.simulation.start_multi) parse_fixed_opts() (in module VirtualMicrobes.simulation.start) (in module VirtualMicrobes.simulation.start_multi) parse_opts() (in module VirtualMicrobes.simulation.continue) partial_mut_func_single_param() (in module VirtualMicrobes.simulation.Simulation) partial_mut_ks_dict_func() (in module VirtualMicrobes.simulation.Simulation) partial_sync() (VirtualMicrobes.my_tools.utility.FIFOLarder method) (VirtualMicrobes.my_tools.utility.PartialLinkThroughDict method) PartialLinkThroughDict (class in VirtualMicrobes.my_tools.utility) pass_through (VirtualMicrobes.my_tools.monkey.TransformWrapper attribute) pchanged() (VirtualMicrobes.my_tools.monkey.Artist method) perfect_mix() (VirtualMicrobes.environment.Environment.Environment method) (VirtualMicrobes.environment.Grid.Grid method) phylo_to_ete_nodes() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) PhyloBase (class in VirtualMicrobes.virtual_cell.PhyloUnit) PhyloGeneticAnalysis (class in VirtualMicrobes.post_analysis.network_properties) PhyloNode (class in VirtualMicrobes.Tree.PhyloTree) PhyloTree (class in VirtualMicrobes.Tree.PhyloTree) PhyloTree.SuperNode (class in VirtualMicrobes.Tree.PhyloTree) PhyloTreeGraph (class in VirtualMicrobes.plotting.Graphs) PhyloUnit (class in VirtualMicrobes.virtual_cell.PhyloUnit) pick() (VirtualMicrobes.my_tools.monkey.Artist method) pick_mol_class() (VirtualMicrobes.environment.Environment.Environment method) pickable() (VirtualMicrobes.my_tools.monkey.Artist method) pickles_adict (class in VirtualMicrobes.my_tools.utility) plot_and_save_graphs() (VirtualMicrobes.simulation.Simulation.Simulation method) plot_and_save_phylo_graphs() (VirtualMicrobes.simulation.Simulation.Simulation method) plot_best_genome_structure() (VirtualMicrobes.simulation.Simulation.Simulation method) plot_binding_network() (VirtualMicrobes.plotting.Graphs.Graphs method) plot_genome_structure() (VirtualMicrobes.plotting.Graphs.Genome method) (VirtualMicrobes.plotting.Graphs.Graphs method) plot_grid_concentrations() (VirtualMicrobes.plotting.Graphs.Graphs method) plot_grid_graphs() (VirtualMicrobes.plotting.Graphs.Graphs method) (VirtualMicrobes.simulation.Simulation.Simulation method) plot_in_axes() (VirtualMicrobes.plotting.Graphs.MultiGridGraph method) plot_lod_graphs() (VirtualMicrobes.post_analysis.lod.PopulationHistory method) plot_metabolic_network() (VirtualMicrobes.plotting.Graphs.Graphs method) plot_mol_class_data() (VirtualMicrobes.plotting.Graphs.Graphs method) plot_networks() (VirtualMicrobes.simulation.Simulation.Simulation method) plot_phylo_tree() (VirtualMicrobes.plotting.Graphs.Graphs method) (VirtualMicrobes.simulation.Simulation.Simulation method) plot_pop_stats() (VirtualMicrobes.plotting.Graphs.Graphs method) (VirtualMicrobes.simulation.Simulation.Simulation method) plot_prot_data() (VirtualMicrobes.plotting.Graphs.Graphs method) plot_time_course() (VirtualMicrobes.plotting.Graphs.Graphs method) (VirtualMicrobes.simulation.Simulation.Simulation method) point_mut (VirtualMicrobes.virtual_cell.Cell.Cell attribute) point_mut_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) point_mut_counts() (VirtualMicrobes.virtual_cell.Population.Population method) point_mutate_gene() (VirtualMicrobes.virtual_cell.Cell.Cell method) point_mutate_genome() (VirtualMicrobes.virtual_cell.Cell.Cell method) point_mutation (VirtualMicrobes.my_tools.utility.MutationRates attribute) PointMutation (class in VirtualMicrobes.mutate.Mutation) PointMutationRatios (class in VirtualMicrobes.my_tools.utility) pop() (VirtualMicrobes.my_tools.utility.LinkThroughSequence method) (VirtualMicrobes.my_tools.utility.LinkThroughSet method) (VirtualMicrobes.my_tools.utility.OrderedSet method) pop_c (VirtualMicrobes.cython_gsl_interface.odes.SYSTEM attribute) pop_genomic_stats_dict (VirtualMicrobes.data_tools.store.DataStore attribute) pop_marker_counts() (VirtualMicrobes.virtual_cell.Population.Population method) pop_simple_stats_dict (VirtualMicrobes.data_tools.store.DataStore attribute) pop_stats_dir (VirtualMicrobes.data_tools.store.DataStore attribute) populate_localities() (VirtualMicrobes.environment.Environment.Environment method) POPULATION (class in VirtualMicrobes.cython_gsl_interface.odes) Population (class in VirtualMicrobes.virtual_cell.Population)

population (VirtualMicrobes.post_analysis.lod.PopulationHistory attribute) population_grid_data() (VirtualMicrobes.environment.Environment.Environment method) population_grid_data_dict() (VirtualMicrobes.environment.Environment.Environment method) population_grid_neighborhood_data() (VirtualMicrobes.environment.Environment.Environment method) PopulationHistory (class in VirtualMicrobes.post_analysis.lod) PopulationWipe (class in VirtualMicrobes.my_tools.utility) pos (VirtualMicrobes.environment.Grid.GridPoint attribute) (VirtualMicrobes.mutate.Mutation.Fission attribute) (VirtualMicrobes.mutate.Mutation.SingleGeneMutation attribute) pos_production (VirtualMicrobes.virtual_cell.Cell.Cell attribute) pos_production() (VirtualMicrobes.virtual_cell.Population.Population method) PositionOutsideGridError, [1] positions (VirtualMicrobes.virtual_cell.Chromosome.Chromosome attribute) positive_positions() (VirtualMicrobes.mutate.Mutation.StretchMutation method) (VirtualMicrobes.mutate.Mutation.Translocation method) post_mutation (VirtualMicrobes.mutate.Mutation.Mutation attribute) pretty_scoring_matrix() (in module VirtualMicrobes.virtual_cell.Sequence) print_spatial_sys_vars() (VirtualMicrobes.cython_gsl_interface.integrate.SpatialIntegrator method) print_state() (VirtualMicrobes.environment.Environment.Environment method) (VirtualMicrobes.virtual_cell.Population.Population method) print_system_details() (VirtualMicrobes.simulation.Simulation.Simulation method) print_values() (VirtualMicrobes.environment.Environment.Environment method) processify() (in module VirtualMicrobes.my_tools.utility) prod_species (VirtualMicrobes.event.Reaction.Convert attribute) producer_type (VirtualMicrobes.virtual_cell.Cell.Cell attribute) producer_type_counts() (VirtualMicrobes.virtual_cell.Population.Population method) produces (VirtualMicrobes.virtual_cell.Cell.Cell attribute) produces() (in module VirtualMicrobes.event.Reaction) producing_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) product_in_reaction() (VirtualMicrobes.event.Molecule.MoleculeClass method) production_rates() (VirtualMicrobes.virtual_cell.Population.Population method) production_values() (VirtualMicrobes.virtual_cell.Population.Population method) products (VirtualMicrobes.my_tools.utility.ReactionScheme attribute) Promoter (class in VirtualMicrobes.virtual_cell.Gene) promoter (VirtualMicrobes.my_tools.utility.PointMutationRatios attribute) (VirtualMicrobes.virtual_cell.Gene.Gene attribute) promoter_strengths (VirtualMicrobes.virtual_cell.Cell.Cell attribute) properties() (VirtualMicrobes.my_tools.monkey.Artist method) protein_type_line_style() (VirtualMicrobes.plotting.Graphs.AttributeMap method) providing (VirtualMicrobes.virtual_cell.Cell.Cell attribute) providing_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) prune_data_file_to_time() (VirtualMicrobes.data_tools.store.DataCollection method) prune_data_files_to_time() (VirtualMicrobes.data_tools.store.DataStore method) prune_data_store_files() (VirtualMicrobes.simulation.Simulation.Simulation method) prune_dead_branch() (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloBase method) (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloUnit method) prune_dead_phylo_branches() (VirtualMicrobes.virtual_cell.Cell.Cell method) prune_depth (VirtualMicrobes.post_analysis.lod.PopulationHistory attribute) prune_genomic_ancestries() (VirtualMicrobes.virtual_cell.Genome.Genome method) prune_GRN() (in module VirtualMicrobes.post_analysis.network_funcs) prune_metabolic_types() (VirtualMicrobes.virtual_cell.Population.Population method) PUMP (class in VirtualMicrobes.cython_gsl_interface.odes) pump (VirtualMicrobes.my_tools.utility.GeneTypeNumbers attribute) pump_average_promoter_strengths() (VirtualMicrobes.virtual_cell.Population.Population method) pump_average_vmaxs() (VirtualMicrobes.virtual_cell.Population.Population method) pump_avrg_promoter_strengths (VirtualMicrobes.virtual_cell.Cell.Cell attribute) pump_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) pump_ene_differential_ks (VirtualMicrobes.virtual_cell.Cell.Cell attribute) pump_ene_ks (VirtualMicrobes.virtual_cell.Cell.Cell attribute) pump_energy_ks() (VirtualMicrobes.virtual_cell.Population.Population method) pump_exporting_mut_func() (in module VirtualMicrobes.simulation.Simulation) pump_promoter_strengths (VirtualMicrobes.virtual_cell.Cell.Cell attribute) pump_rates() (in module VirtualMicrobes.virtual_cell.Gene) pump_subs_differential_ks (VirtualMicrobes.virtual_cell.Cell.Cell attribute) pump_subs_ks (VirtualMicrobes.virtual_cell.Cell.Cell attribute) pump_substrate_ks() (VirtualMicrobes.virtual_cell.Population.Population method) pump_sum_promoter_strengths (VirtualMicrobes.virtual_cell.Cell.Cell attribute) pump_vmaxs (VirtualMicrobes.virtual_cell.Cell.Cell attribute) pumps (VirtualMicrobes.virtual_cell.Cell.Cell attribute) (VirtualMicrobes.virtual_cell.Genome.Genome attribute) pumps_c (VirtualMicrobes.cython_gsl_interface.odes.CELL attribute) push_onto_internal_child() (VirtualMicrobes.Tree.PhyloTree.PhyloNode method) push_up_root() (VirtualMicrobes.Tree.PhyloTree.PhyloNode method) py_cell (VirtualMicrobes.cython_gsl_interface.odes.CELL attribute) py_env (VirtualMicrobes.cython_gsl_interface.odes.ENVIRONMENT attribute) py_enzyme (VirtualMicrobes.cython_gsl_interface.odes.ENZYME attribute) py_loc (VirtualMicrobes.cython_gsl_interface.odes.SYSTEM attribute) py_mol (VirtualMicrobes.cython_gsl_interface.odes.SMALL_MOL attribute) py_pump (VirtualMicrobes.cython_gsl_interface.odes.PUMP attribute) py_tf (VirtualMicrobes.cython_gsl_interface.odes.TF attribute)

Q

queuedprocessor() (in module VirtualMicrobes.my_tools.utility)

R

rand_anabolic_reaction_scheme() (VirtualMicrobes.environment.Environment.Environment method) rand_catabolic_reaction_scheme() (VirtualMicrobes.environment.Environment.Environment method) random_gene() (in module VirtualMicrobes.virtual_cell.Gene) random_insert (VirtualMicrobes.my_tools.utility.RegulatorytMutationRatios attribute) random_neighbor() (VirtualMicrobes.environment.Grid.GridPoint method) random_sequence() (VirtualMicrobes.virtual_cell.Sequence.Sequence method) randomize() (VirtualMicrobes.virtual_cell.Gene.Gene method) (VirtualMicrobes.virtual_cell.Gene.Promoter method) (VirtualMicrobes.virtual_cell.Gene.TranscriptionFactor method) (VirtualMicrobes.virtual_cell.Sequence.Sequence method) randomize_params() (VirtualMicrobes.virtual_cell.Gene.Gene method) (VirtualMicrobes.virtual_cell.Gene.MetabolicGene method) (VirtualMicrobes.virtual_cell.Gene.TranscriptionFactor method) (VirtualMicrobes.virtual_cell.Gene.Transporter method) randomized_param() (in module VirtualMicrobes.virtual_cell.Gene) rate_features (VirtualMicrobes.plotting.Graphs.PhyloTreeGraph attribute) raw_production (VirtualMicrobes.virtual_cell.Cell.Cell attribute) raw_production_change_rate (VirtualMicrobes.virtual_cell.Cell.Cell attribute) reac_species (VirtualMicrobes.event.Reaction.Convert attribute) reactant_in_reaction() (VirtualMicrobes.event.Molecule.MoleculeClass method) reactants (VirtualMicrobes.my_tools.utility.ReactionScheme attribute) Reaction (class in VirtualMicrobes.event.Reaction) reaction (VirtualMicrobes.virtual_cell.Gene.MetabolicGene attribute) (VirtualMicrobes.virtual_cell.Gene.Transporter attribute) reaction_counts() (VirtualMicrobes.virtual_cell.Population.Population method) reaction_counts_split() (VirtualMicrobes.virtual_cell.Population.Population method) reaction_genotype (VirtualMicrobes.virtual_cell.Cell.Cell attribute) reaction_genotype_counts() (VirtualMicrobes.virtual_cell.Population.Population method) reaction_scheme() (VirtualMicrobes.event.Reaction.Degradation method) (VirtualMicrobes.event.Reaction.Diffusion method) (VirtualMicrobes.event.Reaction.Influx method) reaction_set_dict (VirtualMicrobes.virtual_cell.Cell.Cell attribute) reaction_set_dict2 (VirtualMicrobes.virtual_cell.Cell.Cell attribute) reactions_dict (VirtualMicrobes.environment.Environment.Environment attribute) ReactionScheme (class in VirtualMicrobes.my_tools.utility) reapply() (VirtualMicrobes.mutate.Mutation.ChromosomeDeletion method) (VirtualMicrobes.mutate.Mutation.ChromosomeDuplication method) (VirtualMicrobes.mutate.Mutation.Fission method) (VirtualMicrobes.mutate.Mutation.Fusion method) (VirtualMicrobes.mutate.Mutation.Insertion method) (VirtualMicrobes.mutate.Mutation.Inversion method) (VirtualMicrobes.mutate.Mutation.Mutation method) (VirtualMicrobes.mutate.Mutation.OperatorInsertion method) (VirtualMicrobes.mutate.Mutation.PointMutation method) (VirtualMicrobes.mutate.Mutation.SingleGeneMutation method) (VirtualMicrobes.mutate.Mutation.StretchDeletion method) (VirtualMicrobes.mutate.Mutation.TandemDuplication method) (VirtualMicrobes.mutate.Mutation.Translocation method) recalc_max_leaf_depth() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) reconnect_internal_nodes() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) redraw_network() (VirtualMicrobes.plotting.Graphs.Network method) reduce_gene_copies() (VirtualMicrobes.virtual_cell.Cell.Cell method) ref_pop_hist (VirtualMicrobes.post_analysis.lod.LOD_Analyser attribute) ref_sim (VirtualMicrobes.post_analysis.lod.LOD_Analyser attribute) REG_SEQ (class in VirtualMicrobes.cython_gsl_interface.odes) reg_stretch_exp_lambda (VirtualMicrobes.my_tools.utility.MutationRates attribute) regulatory_mutation (VirtualMicrobes.my_tools.utility.MutationRates attribute) regulatory_region_mutate() (VirtualMicrobes.virtual_cell.Cell.Cell method) regulatory_region_mutate_genome() (VirtualMicrobes.virtual_cell.Cell.Cell method)

RegulatorytMutationRatios (class in VirtualMicrobes.my_tools.utility) reinit_system_params() (VirtualMicrobes.simulation.Simulation.EvoSystem method) rejuvenate() (VirtualMicrobes.virtual_cell.Cell.Cell method) reload_unique_count() (VirtualMicrobes.simulation.Simulation.Simulation method) remove() (VirtualMicrobes.my_tools.monkey.Artist method) (VirtualMicrobes.my_tools.utility.LinkThroughSequence method) remove_binding_sequence() (VirtualMicrobes.virtual_cell.Sequence.Operator method) remove_bound_operator() (VirtualMicrobes.virtual_cell.Sequence.BindingSequence method) remove_callback() (VirtualMicrobes.my_tools.monkey.Artist method) remove_cell() (VirtualMicrobes.environment.Environment.Locality method) remove_coord() (VirtualMicrobes.environment.Grid.Neighborhood method) remove_direction() (VirtualMicrobes.environment.Grid.Neighborhood method) remove_key() (VirtualMicrobes.my_tools.utility.ReusableIndexDict method) remove_neighbor_at() (VirtualMicrobes.environment.Grid.GridPoint method) remove_root_stem() (VirtualMicrobes.Tree.PhyloTree.PhyloNode method) remove_unproduced_gene_products() (VirtualMicrobes.virtual_cell.Cell.Cell method) (VirtualMicrobes.virtual_cell.Population.Population method) reopen_db() (VirtualMicrobes.my_tools.utility.FIFOLarder method) reopen_phylo_shelf() (VirtualMicrobes.simulation.Simulation.Simulation method) repopulate_localities() (VirtualMicrobes.environment.Environment.Environment method) reproduce() (VirtualMicrobes.virtual_cell.Cell.Cell method) reproduce_at_minimum_production() (VirtualMicrobes.virtual_cell.Population.Population method) reproduce_cell() (VirtualMicrobes.virtual_cell.Population.Population method) reproduce_on_grid() (VirtualMicrobes.virtual_cell.Population.Population method) reproduce_production_proportional() (VirtualMicrobes.virtual_cell.Population.Population method) reproduce_size_proportional() (VirtualMicrobes.virtual_cell.Population.Population method) reset_divided() (VirtualMicrobes.virtual_cell.Population.Population method) reset_grid_concentrations() (VirtualMicrobes.environment.Environment.Environment method) reset_grid_influx() (VirtualMicrobes.environment.Environment.Environment method) reset_grn() (VirtualMicrobes.virtual_cell.Cell.Cell method) reset_locality_updates() (VirtualMicrobes.environment.Environment.Environment method) reset_production_toxicity_volume() (VirtualMicrobes.virtual_cell.Population.Population method) reset_regulatory_network() (VirtualMicrobes.virtual_cell.Genome.Genome method) resize_time_courses() (VirtualMicrobes.environment.Environment.Environment method) (VirtualMicrobes.environment.Environment.Locality method) (VirtualMicrobes.virtual_cell.Cell.Cell method) (VirtualMicrobes.virtual_cell.Population.Population method) resource_combis_within_energy() (VirtualMicrobes.environment.Environment.Environment method) ReusableIndexDict (class in VirtualMicrobes.my_tools.utility) rewind() (VirtualMicrobes.mutate.Mutation.ChromosomeDeletion method) (VirtualMicrobes.mutate.Mutation.ChromosomeDuplication method) (VirtualMicrobes.mutate.Mutation.Fission method) (VirtualMicrobes.mutate.Mutation.Fusion method) (VirtualMicrobes.mutate.Mutation.Insertion method) (VirtualMicrobes.mutate.Mutation.Inversion method) (VirtualMicrobes.mutate.Mutation.Mutation method) (VirtualMicrobes.mutate.Mutation.OperatorInsertion method) (VirtualMicrobes.mutate.Mutation.PointMutation method) (VirtualMicrobes.mutate.Mutation.SingleGeneMutation method) (VirtualMicrobes.mutate.Mutation.StretchDeletion method) (VirtualMicrobes.mutate.Mutation.TandemDuplication method) (VirtualMicrobes.mutate.Mutation.Translocation method) roulette_wheel_draw() (in module VirtualMicrobes.my_tools.utility) row (VirtualMicrobes.my_tools.utility.GridPos attribute) (VirtualMicrobes.my_tools.utility.GridSubDiv attribute) rows (VirtualMicrobes.plotting.Graphs.MultiGraph attribute) rows_iter() (VirtualMicrobes.environment.Grid.Grid method) run() (VirtualMicrobes.my_tools.utility.Consumer method) run_spatial_system() (VirtualMicrobes.cython_gsl_interface.integrate.SpatialIntegrator method) run_system() (VirtualMicrobes.cython_gsl_interface.integrate.Integrator method)

S

same_content() (in module VirtualMicrobes.my_tools.utility) save() (VirtualMicrobes.simulation.Simulation.Simulation method) save_dir (VirtualMicrobes.data_tools.store.DataStore attribute) (VirtualMicrobes.plotting.Graphs.Grapher attribute) (VirtualMicrobes.simulation.Simulation.Simulation attribute) save_fig() (VirtualMicrobes.plotting.Graphs.Grapher method) (VirtualMicrobes.plotting.Graphs.PhyloTreeGraph method) save_fig2() (VirtualMicrobes.plotting.Graphs.Grapher method) save_phylo_shelf() (VirtualMicrobes.simulation.Simulation.Simulation method) save_pop_cells() (in module VirtualMicrobes.simulation.Simulation) save_sim() (in module VirtualMicrobes.simulation.Simulation) save_simprocessify_func() (in module VirtualMicrobes.my_tools.utility) save_single_cell() (in module VirtualMicrobes.simulation.Simulation) save_video() (VirtualMicrobes.plotting.Graphs.Grapher method) savefig() (VirtualMicrobes.my_tools.monkey.Figure method) sca() (VirtualMicrobes.my_tools.monkey.Figure method) scale_death_rates() (VirtualMicrobes.virtual_cell.Population.Population method) sdi() (in module VirtualMicrobes.my_tools.utility) select_building_blocks() (VirtualMicrobes.environment.Environment.Environment method) select_layout_fn() (VirtualMicrobes.plotting.Graphs.PhyloTreeGraph method) sense_external (VirtualMicrobes.my_tools.utility.PointMutationRatios attribute) Sequence (class in VirtualMicrobes.virtual_cell.Sequence) sequence (VirtualMicrobes.virtual_cell.Sequence.Sequence attribute) sequence_mut (VirtualMicrobes.virtual_cell.Cell.Cell attribute) sequence_mut_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) set() (VirtualMicrobes.my_tools.monkey.Artist method) (VirtualMicrobes.my_tools.monkey.TransformWrapper method) set_agg_filter() (VirtualMicrobes.my_tools.monkey.Artist method) set_alpha() (VirtualMicrobes.my_tools.monkey.Artist method) set_ancestor() (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloUnit method) set_animated() (VirtualMicrobes.my_tools.monkey.Artist method) set_axes() (VirtualMicrobes.my_tools.monkey.Artist method) set_building_block() (VirtualMicrobes.event.Molecule.Molecule method) set_canvas() (VirtualMicrobes.my_tools.monkey.Figure method) set_clip_box() (VirtualMicrobes.my_tools.monkey.Artist method) set_clip_on() (VirtualMicrobes.my_tools.monkey.Artist method) set_clip_path() (VirtualMicrobes.my_tools.monkey.Artist method) set_contains() (VirtualMicrobes.my_tools.monkey.Artist method) set_data_range() (VirtualMicrobes.plotting.Graphs.MultiGridGraph method) set_differences() (in module VirtualMicrobes.my_tools.analysis_tools) set_dpi() (VirtualMicrobes.my_tools.monkey.Figure method) set_edgecolor() (VirtualMicrobes.my_tools.monkey.Figure method) set_facecolor() (VirtualMicrobes.my_tools.monkey.Figure method) set_figheight() (VirtualMicrobes.my_tools.monkey.Figure method) set_figure() (VirtualMicrobes.my_tools.monkey.Artist method) set_figwidth() (VirtualMicrobes.my_tools.monkey.Figure method) set_frameon() (VirtualMicrobes.my_tools.monkey.Figure method) set_gene_prod_conc() (VirtualMicrobes.environment.Environment.Locality method) (VirtualMicrobes.virtual_cell.Cell.Cell method) set_gid() (VirtualMicrobes.my_tools.monkey.Artist method) set_gp() (VirtualMicrobes.environment.Grid.Grid method) set_label() (VirtualMicrobes.my_tools.monkey.Artist method) set_larder() (VirtualMicrobes.my_tools.utility.PartialLinkThroughDict method) set_mol_concentrations_from_time_point() (VirtualMicrobes.environment.Environment.Environment method) (VirtualMicrobes.environment.Environment.Locality method) (VirtualMicrobes.virtual_cell.Cell.Cell method) (VirtualMicrobes.virtual_cell.Population.Population method) set_path_effects() (VirtualMicrobes.my_tools.monkey.Artist method) set_phylo_shelf_file_name() (VirtualMicrobes.simulation.Simulation.Simulation method) set_picker() (VirtualMicrobes.my_tools.monkey.Artist method) set_rasterized() (VirtualMicrobes.my_tools.monkey.Artist method) set_size_inches() (VirtualMicrobes.my_tools.monkey.Figure method) set_sketch_params() (VirtualMicrobes.my_tools.monkey.Artist method) set_small_mol_conc() (VirtualMicrobes.environment.Environment.Locality method) (VirtualMicrobes.virtual_cell.Cell.Cell method) set_snap() (VirtualMicrobes.my_tools.monkey.Artist method) set_tight_layout() (VirtualMicrobes.my_tools.monkey.Figure method) set_tot_volume() (VirtualMicrobes.environment.Environment.Environment method) set_transform() (VirtualMicrobes.my_tools.monkey.Artist method) set_unique_key() (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloUnit method) set_url() (VirtualMicrobes.my_tools.monkey.Artist method) set_visible() (VirtualMicrobes.my_tools.monkey.Artist method) set_zorder() (VirtualMicrobes.my_tools.monkey.Artist method) setup_class() (VirtualMicrobes.mutate.test.TestMutate.Test class method) setup_environment() (VirtualMicrobes.simulation.Simulation.EvoSystem method)

SGDeletion (class in VirtualMicrobes.mutate.Mutation) SGDuplication (class in VirtualMicrobes.mutate.Mutation) show() (VirtualMicrobes.my_tools.monkey.Figure method) sim (VirtualMicrobes.post_analysis.lod.PopulationHistory attribute) simple_stats() (VirtualMicrobes.data_tools.store.DataStore method) simple_stats_columns (VirtualMicrobes.data_tools.store.DataStore attribute) simple_str() (VirtualMicrobes.virtual_cell.Gene.MetabolicGene method) (VirtualMicrobes.virtual_cell.Gene.TranscriptionFactor method) (VirtualMicrobes.virtual_cell.Gene.Transporter method) simple_value() (VirtualMicrobes.data_tools.store.DataStore method) simple_value_column (VirtualMicrobes.data_tools.store.DataStore attribute) simulate() (VirtualMicrobes.simulation.Simulation.Simulation method) Simulation (class in VirtualMicrobes.simulation.Simulation) simulation_burn_in() (VirtualMicrobes.simulation.Simulation.ODE_simulation method) simulation_step() (VirtualMicrobes.simulation.Simulation.ODE_simulation method) SingleGeneMutation (class in VirtualMicrobes.mutate.Mutation) size (VirtualMicrobes.virtual_cell.Genome.Genome attribute) SMALL_MOL (class in VirtualMicrobes.cython_gsl_interface.odes) small_mols_c (VirtualMicrobes.cython_gsl_interface.odes.CELL attribute) (VirtualMicrobes.cython_gsl_interface.odes.ENVIRONMENT attribute) SmallMol (class in VirtualMicrobes.my_tools.utility) snapshot_stats_names (VirtualMicrobes.data_tools.store.DataStore attribute) SpatialIntegrator (class in VirtualMicrobes.cython_gsl_interface.integrate) spill_dead_cell_contents() (VirtualMicrobes.environment.Environment.Locality method) stale (VirtualMicrobes.my_tools.monkey.Artist attribute) standardized_production() (VirtualMicrobes.post_analysis.lod.LOD method) start_concentration_dict() (VirtualMicrobes.environment.Environment.Environment method) start_pos (VirtualMicrobes.mutate.Mutation.StretchMutation attribute) store_command_line_string() (VirtualMicrobes.simulation.Simulation.Simulation method) store_nr_time_points_py() (VirtualMicrobes.cython_gsl_interface.integrate.SpatialIntegrator method) store_pop_characters() (VirtualMicrobes.virtual_cell.Population.Population method) store_previous_save_dir() (VirtualMicrobes.simulation.Simulation.Simulation method) strength (VirtualMicrobes.virtual_cell.Gene.Promoter attribute) stretch (VirtualMicrobes.mutate.Mutation.StretchMutation attribute) stretch_del (VirtualMicrobes.my_tools.utility.MutationRates attribute) (VirtualMicrobes.virtual_cell.Cell.Cell attribute) stretch_del_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) stretch_exp_lambda (VirtualMicrobes.my_tools.utility.MutationRates attribute) stretch_invert (VirtualMicrobes.my_tools.utility.MutationRates attribute) (VirtualMicrobes.virtual_cell.Cell.Cell attribute) stretch_invert_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) stretch_mut (VirtualMicrobes.virtual_cell.Cell.Cell attribute) stretch_mut_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) stretch_mutate_genome() (VirtualMicrobes.virtual_cell.Cell.Cell method) stretch_translocate (VirtualMicrobes.my_tools.utility.MutationRates attribute) StretchDeletion (class in VirtualMicrobes.mutate.Mutation) StretchMutation (class in VirtualMicrobes.mutate.Mutation) strict_exploiting (VirtualMicrobes.virtual_cell.Cell.Cell attribute) strict_exploiting_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) strict_providing (VirtualMicrobes.virtual_cell.Cell.Cell attribute) strict_providing_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) strided_lod() (VirtualMicrobes.post_analysis.lod.LOD method) Struct() (in module VirtualMicrobes.my_tools.utility) sub_envs_influx_combinations() (VirtualMicrobes.environment.Environment.Environment method) sub_envs_partial_influx() (VirtualMicrobes.environment.Environment.Environment method) sub_grid (VirtualMicrobes.my_tools.utility.SubEnv attribute) sub_reactions() (VirtualMicrobes.event.Reaction.Convert method) (VirtualMicrobes.event.Reaction.Degradation method) (VirtualMicrobes.event.Reaction.Diffusion method) (VirtualMicrobes.event.Reaction.Transport method) SubEnv (class in VirtualMicrobes.my_tools.utility) subgrids_gen() (VirtualMicrobes.environment.Environment.Environment method) subplots_adjust() (VirtualMicrobes.my_tools.monkey.Figure method) subprocessor() (in module VirtualMicrobes.my_tools.utility) subs_ks (VirtualMicrobes.my_tools.utility.PointMutationRatios attribute) substring_scoring_matrix() (VirtualMicrobes.virtual_cell.Sequence.Sequence class method) sum_promoter_strengths (VirtualMicrobes.virtual_cell.Cell.Cell attribute) suptitle() (VirtualMicrobes.my_tools.monkey.Figure method) swap_content() (VirtualMicrobes.environment.Grid.Grid method) swap_gps() (VirtualMicrobes.environment.Grid.Grid method) swap_pos() (VirtualMicrobes.environment.Grid.Grid method) symmetric_difference() (VirtualMicrobes.my_tools.utility.LinkThroughSet method) sync() (VirtualMicrobes.my_tools.utility.FIFOLarder method) sys_c (VirtualMicrobes.cython_gsl_interface.integrate.Integrator attribute) SYSTEM (class in VirtualMicrobes.cython_gsl_interface.odes)

T

t_interval_iter() (VirtualMicrobes.post_analysis.lod.LOD method) tandem_dup (VirtualMicrobes.my_tools.utility.MutationRates attribute) (VirtualMicrobes.virtual_cell.Cell.Cell attribute) tandem_dup_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) tandem_duplicate() (VirtualMicrobes.virtual_cell.Chromosome.Chromosome method) tandem_duplicate_stretch() (VirtualMicrobes.virtual_cell.Cell.Cell method) TandemDuplication (class in VirtualMicrobes.mutate.Mutation) Task (class in VirtualMicrobes.my_tools.utility) Test (class in VirtualMicrobes.mutate.test.TestMutate) test_chrom_del() (VirtualMicrobes.mutate.test.TestMutate.Test method) test_chrom_dup() (VirtualMicrobes.mutate.test.TestMutate.Test method) test_chrom_fiss() (VirtualMicrobes.mutate.test.TestMutate.Test method) test_chrom_fuse() (VirtualMicrobes.mutate.test.TestMutate.Test method) test_point_mut() (VirtualMicrobes.mutate.test.TestMutate.Test method) text() (VirtualMicrobes.my_tools.monkey.Figure method) TF (class in VirtualMicrobes.cython_gsl_interface.odes) tf (VirtualMicrobes.my_tools.utility.GeneTypeNumbers attribute) tf_average_promoter_strengths() (VirtualMicrobes.virtual_cell.Population.Population method) tf_avrg_promoter_strengths (VirtualMicrobes.virtual_cell.Cell.Cell attribute) tf_binding_overlap() (in module VirtualMicrobes.post_analysis.network_properties) tf_connections_dict() (VirtualMicrobes.virtual_cell.Genome.Genome method) tf_conservation_to_dict() (in module VirtualMicrobes.data_tools.store) tf_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) tf_counts() (VirtualMicrobes.virtual_cell.Population.Population method) tf_differential_reg (VirtualMicrobes.virtual_cell.Cell.Cell attribute) tf_ext_sense_mut_func() (in module VirtualMicrobes.simulation.Simulation) tf_k_bind_operators() (VirtualMicrobes.virtual_cell.Population.Population method) tf_k_bind_ops (VirtualMicrobes.virtual_cell.Cell.Cell attribute) tf_ligand_differential_ks (VirtualMicrobes.virtual_cell.Cell.Cell attribute) tf_ligand_ks (VirtualMicrobes.virtual_cell.Cell.Cell attribute) tf_ligand_ks() (VirtualMicrobes.virtual_cell.Population.Population method) tf_name() (in module VirtualMicrobes.data_tools.store) tf_promoter_strengths (VirtualMicrobes.virtual_cell.Cell.Cell attribute) tf_sensed (VirtualMicrobes.virtual_cell.Cell.Cell attribute) tf_sum_promoter_strengths (VirtualMicrobes.virtual_cell.Cell.Cell attribute) tfs (VirtualMicrobes.virtual_cell.Cell.Cell attribute) (VirtualMicrobes.virtual_cell.Genome.Genome attribute) tfs_c (VirtualMicrobes.cython_gsl_interface.odes.CELL attribute) tight_layout() (VirtualMicrobes.my_tools.monkey.Figure method) (VirtualMicrobes.plotting.Graphs.MultiGraph method) time (VirtualMicrobes.mutate.Mutation.Mutation attribute) time_birth (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloBase attribute) time_course (VirtualMicrobes.my_tools.utility.GeneProduct attribute) (VirtualMicrobes.my_tools.utility.SmallMol attribute)

time_course_array() (in module VirtualMicrobes.my_tools.utility) time_death (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloBase attribute) time_point (VirtualMicrobes.post_analysis.lod.PopulationHistory attribute) timeout (class in VirtualMicrobes.my_tools.utility) to_argparse_opts() (in module VirtualMicrobes.simulation.continue) (in module VirtualMicrobes.simulation.start) (in module VirtualMicrobes.simulation.start_multi) to_ete_trees() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) toggle_gps_updated() (VirtualMicrobes.environment.Grid.Grid method) toJSON() (VirtualMicrobes.virtual_cell.Chromosome.Chromosome method) (VirtualMicrobes.virtual_cell.Gene.Gene method) (VirtualMicrobes.virtual_cell.Gene.MetabolicGene method) (VirtualMicrobes.virtual_cell.Gene.Promoter method) (VirtualMicrobes.virtual_cell.Gene.TranscriptionFactor method) (VirtualMicrobes.virtual_cell.Gene.Transporter method) (VirtualMicrobes.virtual_cell.Genome.Genome method) (VirtualMicrobes.virtual_cell.Sequence.BindingSequence method) (VirtualMicrobes.virtual_cell.Sequence.Operator method) toxic_level (VirtualMicrobes.event.Molecule.Molecule attribute) toxicity (VirtualMicrobes.virtual_cell.Cell.Cell attribute) toxicity_change_rate (VirtualMicrobes.virtual_cell.Cell.Cell attribute) toxicity_rates() (VirtualMicrobes.virtual_cell.Population.Population method) tp_index (VirtualMicrobes.environment.Environment.Locality attribute) (VirtualMicrobes.virtual_cell.Cell.Cell attribute) TranscriptionFactor (class in VirtualMicrobes.virtual_cell.Gene) TransformWrapper (class in VirtualMicrobes.my_tools.monkey) translocate (VirtualMicrobes.my_tools.utility.RegulatorytMutationRatios attribute) (VirtualMicrobes.virtual_cell.Cell.Cell attribute) translocate_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute) translocate_stretch() (VirtualMicrobes.virtual_cell.Cell.Cell method) (VirtualMicrobes.virtual_cell.Chromosome.Chromosome method) Translocation (class in VirtualMicrobes.mutate.Mutation) Transport (class in VirtualMicrobes.event.Reaction) Transporter (class in VirtualMicrobes.virtual_cell.Gene) tree (VirtualMicrobes.my_tools.utility.ETEtreeStruct attribute) tree_lods (VirtualMicrobes.post_analysis.lod.PopulationHistory attribute) trophic_type() (VirtualMicrobes.virtual_cell.Cell.Cell method) trophic_type_columns (VirtualMicrobes.data_tools.store.DataStore attribute) trophic_type_counts() (VirtualMicrobes.virtual_cell.Population.Population method) trophic_type_layout() (VirtualMicrobes.plotting.Graphs.PhyloTreeGraph method) truncate_time_courses() (VirtualMicrobes.virtual_cell.Cell.Cell method) type_differences_stats() (VirtualMicrobes.data_tools.store.DataStore method) type_shape() (VirtualMicrobes.plotting.Graphs.Network method) type_totals_stats() (VirtualMicrobes.data_tools.store.DataStore method) types (VirtualMicrobes.virtual_cell.GenomicElement.GenomicElement attribute)

U

uid (VirtualMicrobes.mutate.Mutation.Mutation attribute) (VirtualMicrobes.virtual_cell.Cell.Cell attribute) (VirtualMicrobes.virtual_cell.Chromosome.Chromosome attribute) (VirtualMicrobes.virtual_cell.Gene.Promoter attribute) (VirtualMicrobes.virtual_cell.GenomicElement.GenomicElement attribute) (VirtualMicrobes.virtual_cell.Sequence.Sequence attribute) un_neighbor() (VirtualMicrobes.environment.Grid.Grid method) union() (VirtualMicrobes.my_tools.utility.LinkThroughSet method) unique_count() (in module VirtualMicrobes.my_tools.utility) unique_index() (VirtualMicrobes.event.Molecule.Molecule class method) unique_pop() (VirtualMicrobes.virtual_cell.Population.Population method) unique_unit_dict (VirtualMicrobes.virtual_cell.Identifier.Identifier attribute) unwrap_ew() (VirtualMicrobes.environment.Grid.Grid method) unwrap_ns() (VirtualMicrobes.environment.Grid.Grid method) update() (VirtualMicrobes.my_tools.monkey.Artist method) (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) (VirtualMicrobes.my_tools.utility.LinkThroughSet method) (VirtualMicrobes.plotting.Graphs.PhyloTreeGraph method) (VirtualMicrobes.virtual_cell.Cell.Cell method) (VirtualMicrobes.virtual_cell.Genome.Genome method) update_binding_sequences() (VirtualMicrobes.virtual_cell.Sequence.Operator method) update_cell_params() (VirtualMicrobes.virtual_cell.Population.Population method) update_cells_on_grid() (VirtualMicrobes.environment.Environment.Environment method) update_data_location() (VirtualMicrobes.simulation.Simulation.Simulation method) update_data_points() (VirtualMicrobes.data_tools.store.DataCollection method) (VirtualMicrobes.data_tools.store.DictDataCollection method) (VirtualMicrobes.data_tools.store.ListDataCollection method) update_default_params() (in module VirtualMicrobes.simulation.Simulation) update_diffusion_stepping() (VirtualMicrobes.cython_gsl_interface.integrate.SpatialIntegrator method) update_drivers() (VirtualMicrobes.cython_gsl_interface.integrate.SpatialIntegrator method) update_ete_tree() (VirtualMicrobes.virtual_cell.Population.Population method) update_figure() (VirtualMicrobes.plotting.Graphs.Grapher method) (VirtualMicrobes.plotting.Graphs.PhyloTreeGraph method)

update_from() (VirtualMicrobes.my_tools.monkey.Artist method) update_genome_removed_gene() (VirtualMicrobes.virtual_cell.Genome.Genome method) update_genome_removed_genes() (VirtualMicrobes.virtual_cell.Genome.Genome method) update_gp() (VirtualMicrobes.environment.Grid.Grid method) update_grn() (VirtualMicrobes.virtual_cell.Cell.Cell method) update_integrators() (VirtualMicrobes.cython_gsl_interface.integrate.SpatialIntegrator method) update_lineage_markers() (VirtualMicrobes.virtual_cell.Population.Population method) update_mutated_gene_product() (VirtualMicrobes.virtual_cell.Cell.Cell method) update_offspring_regulatory_network() (VirtualMicrobes.virtual_cell.Population.Population method) update_phylogeny() (VirtualMicrobes.virtual_cell.Population.Population method) update_prod_val_hist() (VirtualMicrobes.virtual_cell.Population.Population method) update_regulatory_network() (VirtualMicrobes.virtual_cell.Genome.Genome method) update_shelf_location() (VirtualMicrobes.simulation.Simulation.Simulation method) update_sim_params() (VirtualMicrobes.simulation.Simulation.Simulation method) update_small_mol_concentrations() (VirtualMicrobes.environment.Environment.Locality method) update_small_mol_degradation_rates() (VirtualMicrobes.environment.Environment.Locality method) update_small_mol_influxes() (VirtualMicrobes.environment.Environment.Locality method) update_small_molecules_diff() (VirtualMicrobes.virtual_cell.Cell.Cell method) update_volume() (VirtualMicrobes.environment.Environment.Environment method) updated (VirtualMicrobes.environment.Grid.GridPoint attribute) upgrade() (VirtualMicrobes.data_tools.store.DataStore method) (VirtualMicrobes.Tree.PhyloTree.PhyloTree method) (VirtualMicrobes.environment.Environment.Environment method) (VirtualMicrobes.environment.Environment.Locality method) (VirtualMicrobes.event.Molecule.Molecule method) (VirtualMicrobes.my_tools.utility.ReusableIndexDict method) (VirtualMicrobes.plotting.Graphs.Grapher method) (VirtualMicrobes.simulation.Simulation.Simulation method) (VirtualMicrobes.virtual_cell.Cell.Cell method) (VirtualMicrobes.virtual_cell.Genome.Genome method) (VirtualMicrobes.virtual_cell.Population.Population method) upgrade_graphs() (VirtualMicrobes.simulation.Simulation.Simulation method) upper (VirtualMicrobes.my_tools.utility.MutationParamSpace attribute) (VirtualMicrobes.my_tools.utility.ParamSpace attribute)

V

v_max (VirtualMicrobes.my_tools.utility.PointMutationRatios attribute) ValueNotInRange versioned_id (VirtualMicrobes.virtual_cell.Identifier.Identifier attribute) VirtualMicrobes (module) VirtualMicrobes.cython_gsl_interface (module) VirtualMicrobes.cython_gsl_interface.integrate (module) VirtualMicrobes.cython_gsl_interface.odes (module) VirtualMicrobes.data_tools (module) VirtualMicrobes.data_tools.store (module) VirtualMicrobes.environment (module) VirtualMicrobes.environment.Environment (module) VirtualMicrobes.environment.Grid (module) VirtualMicrobes.event (module) VirtualMicrobes.event.Molecule (module) VirtualMicrobes.event.Reaction (module) VirtualMicrobes.mutate (module) VirtualMicrobes.mutate.Mutation (module) VirtualMicrobes.mutate.test (module) VirtualMicrobes.mutate.test.TestMutate (module) VirtualMicrobes.my_tools (module) VirtualMicrobes.my_tools.analysis_tools (module) VirtualMicrobes.my_tools.monkey (module) VirtualMicrobes.my_tools.utility (module) VirtualMicrobes.plotting (module)

VirtualMicrobes.plotting.Graphs (module) VirtualMicrobes.post_analysis (module) VirtualMicrobes.post_analysis.lod (module) VirtualMicrobes.post_analysis.network_funcs (module) VirtualMicrobes.post_analysis.network_properties (module) VirtualMicrobes.simulation (module) VirtualMicrobes.simulation.class_settings (module) VirtualMicrobes.simulation.continue (module) VirtualMicrobes.simulation.Simulation (module) VirtualMicrobes.simulation.start (module) VirtualMicrobes.simulation.start_multi (module) VirtualMicrobes.simulation.vermicelli (module) VirtualMicrobes.Tree (module) VirtualMicrobes.Tree.PhyloTree (module) VirtualMicrobes.virtual_cell (module) VirtualMicrobes.virtual_cell.Cell (module) VirtualMicrobes.virtual_cell.Chromosome (module) VirtualMicrobes.virtual_cell.Gene (module) VirtualMicrobes.virtual_cell.Genome (module) VirtualMicrobes.virtual_cell.GenomicElement (module) VirtualMicrobes.virtual_cell.Identifier (module) VirtualMicrobes.virtual_cell.PhyloUnit (module) VirtualMicrobes.virtual_cell.Population (module) VirtualMicrobes.virtual_cell.Sequence (module) volume (VirtualMicrobes.virtual_cell.Cell.Cell attribute)

W

waitforbuttonpress() (VirtualMicrobes.my_tools.monkey.Figure method) wipe_pop() (VirtualMicrobes.virtual_cell.Population.Population method) within_grid() (VirtualMicrobes.plotting.Graphs.MultiGraph method) within_range() (in module VirtualMicrobes.my_tools.utility) write() (VirtualMicrobes.my_tools.utility.FormatMessageFile method) write_column_names() (VirtualMicrobes.data_tools.store.DictDataCollection method) write_data() (VirtualMicrobes.data_tools.store.DataCollection method) (VirtualMicrobes.data_tools.store.DataStore method) (VirtualMicrobes.data_tools.store.DictDataCollection method) (VirtualMicrobes.data_tools.store.ListDataCollection method) (VirtualMicrobes.simulation.Simulation.Simulation method)

write_genome_json() (VirtualMicrobes.data_tools.store.DataStore method) write_newick_trees() (VirtualMicrobes.post_analysis.lod.LOD_Analyser method) (VirtualMicrobes.post_analysis.lod.PopulationHistory method) write_params_to_file() (VirtualMicrobes.simulation.Simulation.Simulation method) write_to_file() (VirtualMicrobes.plotting.Graphs.Network method) (VirtualMicrobes.plotting.Graphs.PhyloTreeGraph method)

X

x (VirtualMicrobes.my_tools.utility.Coord attribute)

Y

y (VirtualMicrobes.my_tools.utility.Coord attribute)

Z

zorder (VirtualMicrobes.my_tools.monkey.Artist attribute)