Virtual Microbes Evolutionary Simulator
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Virtual Microbes Evolutionary Simulator
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A
activation_color() (VirtualMicrobes.plotting.Graphs.AttributeMap method)
add_ancestry_data_point() (VirtualMicrobes.data_tools.store.DataStore method)
add_axis() (VirtualMicrobes.plotting.Graphs.MultiGraph method)
(VirtualMicrobes.plotting.Graphs.MultiGridGraph method)
add_best_data_point() (VirtualMicrobes.data_tools.store.DataStore method)
add_cell() (VirtualMicrobes.environment.Environment.Locality method)
(VirtualMicrobes.virtual_cell.Population.Population method)
add_cell_tc() (VirtualMicrobes.data_tools.store.DataStore 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_dp() (VirtualMicrobes.data_tools.store.DataStore method)
add_eco_data_point() (VirtualMicrobes.data_tools.store.DataStore method)
add_expression_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_gene_product() (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_prot_grid_graphs_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)
AddInheritanceType (class in VirtualMicrobes.virtual_cell.PhyloUnit)
ages() (VirtualMicrobes.virtual_cell.Population.Population method)
alive (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloBase attribute)
anc_cells() (VirtualMicrobes.post_analysis.lod.LOD_Analyser method)
(VirtualMicrobes.post_analysis.lod.PopulationHistory method)
ancestral_mutations (VirtualMicrobes.virtual_cell.Cell.Cell attribute)
annotate_leafs() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method)
annotate_phylo_units_feature() (VirtualMicrobes.Tree.PhyloTree.PhyloTree 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)
,
[1]
apply_hgt() (VirtualMicrobes.virtual_cell.Cell.Cell method)
args (VirtualMicrobes.post_analysis.lod.LOD_Analyser attribute)
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)
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)
B
backup_plots() (VirtualMicrobes.plotting.Graphs.Grapher method)
backup_pop_stats() (VirtualMicrobes.simulation.Simulation.Simulation method)
BadStoichiometryException
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_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_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_lineage_marker() (VirtualMicrobes.virtual_cell.Cell.Cell method)
Cell (class in VirtualMicrobes.virtual_cell.Cell)
cell_death() (VirtualMicrobes.virtual_cell.Population.Population method)
cell_dict (VirtualMicrobes.virtual_cell.Population.Population attribute)
cell_markers() (VirtualMicrobes.virtual_cell.Population.Population method)
cell_sizes() (VirtualMicrobes.virtual_cell.Population.Population method)
cells (VirtualMicrobes.virtual_cell.Population.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_ete_mapping() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method)
child_of() (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloUnit method)
children (VirtualMicrobes.Tree.PhyloTree.PhyloNode attribute)
(VirtualMicrobes.virtual_cell.PhyloUnit.PhyloUnit 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)
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.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.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)
clone() (VirtualMicrobes.virtual_cell.Cell.Cell method)
cloned_pop() (VirtualMicrobes.virtual_cell.Population.Population method)
cloned_pop_from_files() (VirtualMicrobes.virtual_cell.Population.Population method)
close_phylo_shelf() (VirtualMicrobes.simulation.Simulation.Simulation method)
coalescent() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method)
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)
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_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)
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_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)
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)
coord (VirtualMicrobes.environment.Grid.GridPoint attribute)
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_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)
current_ancestors (VirtualMicrobes.virtual_cell.Population.Population attribute)
current_pop_size (VirtualMicrobes.virtual_cell.Population.Population 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)
del_chromosome() (VirtualMicrobes.virtual_cell.Genome.Genome 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)
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)
died (VirtualMicrobes.virtual_cell.Population.Population attribute)
differential_regulation() (VirtualMicrobes.virtual_cell.Population.Population method)
Diffusion (class in VirtualMicrobes.event.Reaction)
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)
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)
dump_anc_cells() (VirtualMicrobes.post_analysis.lod.PopulationHistory method)
dump_lod_cells() (VirtualMicrobes.post_analysis.lod.PopulationHistory method)
dump_pop_cells() (VirtualMicrobes.post_analysis.lod.PopulationHistory 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_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)
energy_level (VirtualMicrobes.event.Molecule.Molecule attribute)
energy_mols (VirtualMicrobes.environment.Environment.Environment attribute)
energy_precursors() (VirtualMicrobes.environment.Environment.Environment method)
Environment (class in VirtualMicrobes.environment.Environment)
environment (VirtualMicrobes.event.Molecule.Molecule attribute)
(VirtualMicrobes.post_analysis.lod.PopulationHistory 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_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)
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)
evo_rand_gen (VirtualMicrobes.virtual_cell.Population.Population attribute)
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_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute)
expression_grid_data_dict() (VirtualMicrobes.environment.Environment.Environment method)
external_hgt (VirtualMicrobes.virtual_cell.Cell.Cell attribute)
external_hgt_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute)
external_molecules (VirtualMicrobes.environment.Environment.Environment attribute)
F
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_reaction() (VirtualMicrobes.environment.Environment.Environment 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)
flip_dict (VirtualMicrobes.virtual_cell.Sequence.Sequence attribute)
fluctuate() (VirtualMicrobes.environment.Environment.Environment method)
frequency_stats() (VirtualMicrobes.data_tools.store.DataStore method)
from_file() (VirtualMicrobes.virtual_cell.Cell.Cell class method)
from_params() (VirtualMicrobes.virtual_cell.Cell.Cell class method)
from_parent() (VirtualMicrobes.virtual_cell.Identifier.Identifier 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)
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)
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)
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)
,
[1]
genomic_unit (VirtualMicrobes.mutate.Mutation.Mutation attribute)
,
[1]
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_ancestor() (VirtualMicrobes.virtual_cell.Cell.Cell method)
get_ancestor_at_time() (VirtualMicrobes.virtual_cell.Cell.Cell method)
get_cell_age_dict() (VirtualMicrobes.virtual_cell.Population.Population method)
get_cell_death_rate_dict() (VirtualMicrobes.virtual_cell.Population.Population method)
get_cell_divided_dict() (VirtualMicrobes.virtual_cell.Population.Population method)
get_cell_genome_size_dict() (VirtualMicrobes.virtual_cell.Population.Population method)
get_cell_pos_production_dict() (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_data_point() (VirtualMicrobes.data_tools.store.DataCollection method)
get_expression_level() (VirtualMicrobes.environment.Environment.Locality method)
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_gp() (VirtualMicrobes.environment.Grid.Grid method)
get_internal_mol_conc() (VirtualMicrobes.environment.Environment.Locality 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_pos_prod_time_course() (VirtualMicrobes.virtual_cell.Cell.Cell method)
get_raw_production_time_course() (VirtualMicrobes.virtual_cell.Cell.Cell method)
get_rel_coords() (VirtualMicrobes.environment.Grid.Neighborhood method)
get_small_mol_conc() (VirtualMicrobes.environment.Environment.Locality method)
(VirtualMicrobes.virtual_cell.Cell.Cell method)
get_time_points() (VirtualMicrobes.virtual_cell.Cell.Cell method)
get_total_expression_level() (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)
gp_iter (VirtualMicrobes.environment.Grid.Grid attribute)
gp_iter_in_order() (VirtualMicrobes.environment.Grid.Grid method)
Grapher (class in VirtualMicrobes.plotting.Graphs)
GraphingError
GraphNotFoundError
Graphs (class in VirtualMicrobes.plotting.Graphs)
Grid (class in VirtualMicrobes.environment.Grid)
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)
GRN() (VirtualMicrobes.virtual_cell.Cell.Cell method)
grn_edits (VirtualMicrobes.data_tools.store.DataStore attribute)
grow_time_course_arrays() (VirtualMicrobes.virtual_cell.Cell.Cell method)
(VirtualMicrobes.virtual_cell.Population.Population method)
H
has_coord() (VirtualMicrobes.environment.Grid.Neighborhood method)
has_living_offspring() (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloUnit method)
has_root() (VirtualMicrobes.Tree.PhyloTree.PhyloNode method)
hgt_external() (VirtualMicrobes.virtual_cell.Cell.Cell method)
hgt_internal() (VirtualMicrobes.virtual_cell.Cell.Cell method)
hgt_neighs() (VirtualMicrobes.virtual_cell.Population.Population method)
historic_production_max (VirtualMicrobes.virtual_cell.Population.Population attribute)
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)
inf_pump_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute)
inf_pumps (VirtualMicrobes.virtual_cell.Genome.Genome attribute)
Influx (class in VirtualMicrobes.event.Reaction)
influx_change_gamma() (VirtualMicrobes.environment.Environment.Environment method)
influx_change_range() (VirtualMicrobes.environment.Environment.Environment method)
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_compare_saves() (VirtualMicrobes.post_analysis.lod.LOD_Analyser 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_expression_data_stores() (VirtualMicrobes.data_tools.store.DataStore 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_ligand() (VirtualMicrobes.virtual_cell.Gene.TranscriptionFactor 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_microfluid_cycle() (VirtualMicrobes.environment.Environment.Environment 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_molecule_ks() (in module VirtualMicrobes.virtual_cell.Gene)
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.post_analysis.lod.PopulationHistory method)
(VirtualMicrobes.virtual_cell.Population.Population method)
init_phylo_tree_graph() (VirtualMicrobes.plotting.Graphs.Graphs method)
init_pop() (VirtualMicrobes.virtual_cell.Population.Population method)
init_pop_data_stores() (VirtualMicrobes.data_tools.store.DataStore 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_prot_grid_graphs() (VirtualMicrobes.plotting.Graphs.Graphs 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() (in module VirtualMicrobes.virtual_cell.Gene)
init_time_course_graph() (VirtualMicrobes.plotting.Graphs.Graphs method)
init_time_course_lengths() (VirtualMicrobes.simulation.Simulation.ODE_simulation method)
init_time_courses() (VirtualMicrobes.environment.Environment.Locality method)
(VirtualMicrobes.virtual_cell.Cell.Cell method)
init_transports() (VirtualMicrobes.environment.Environment.Environment method)
init_unique_gene_key() (VirtualMicrobes.simulation.Simulation.Simulation method)
init_unique_phylo_key() (VirtualMicrobes.simulation.Simulation.Simulation method)
init_variables_map() (VirtualMicrobes.environment.Environment.Locality 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)
internal_hgt (VirtualMicrobes.virtual_cell.Cell.Cell attribute)
internal_hgt_count (VirtualMicrobes.virtual_cell.Cell.Cell 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_autotroph() (VirtualMicrobes.virtual_cell.Cell.Cell method)
is_building_block (VirtualMicrobes.event.Molecule.Molecule attribute)
is_clone() (VirtualMicrobes.virtual_cell.Cell.Cell method)
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_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)
iter_prepostorder() (VirtualMicrobes.Tree.PhyloTree.PhyloNode method)
iterages() (VirtualMicrobes.virtual_cell.Population.Population method)
K
kill_cells_lineage() (VirtualMicrobes.virtual_cell.Population.Population method)
L
layout_network_positions() (VirtualMicrobes.plotting.Graphs.BindingNetwork method)
(VirtualMicrobes.plotting.Graphs.MetabolicNetwork method)
ligand_class (VirtualMicrobes.virtual_cell.Gene.TranscriptionFactor attribute)
line_colors() (VirtualMicrobes.plotting.Graphs.Graphs method)
line_markers (VirtualMicrobes.plotting.Graphs.MultiGraph attribute)
line_styles (VirtualMicrobes.plotting.Graphs.MultiGraph attribute)
lineages() (VirtualMicrobes.virtual_cell.Population.Population method)
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_cells() (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)
M
major_id (VirtualMicrobes.virtual_cell.Identifier.Identifier attribute)
make_anc_clones() (VirtualMicrobes.virtual_cell.Population.Population method)
make_barrier() (VirtualMicrobes.environment.Grid.Grid method)
make_cell_clones() (VirtualMicrobes.virtual_cell.Population.Population method)
make_inherited_hgt_dict() (in module VirtualMicrobes.virtual_cell.Cell)
make_mutations_dict() (in module VirtualMicrobes.virtual_cell.Cell)
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_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)
mark_for_death() (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)
markers_range_dict (VirtualMicrobes.virtual_cell.Population.Population attribute)
match() (VirtualMicrobes.virtual_cell.Sequence.Sequence method)
match_operators() (VirtualMicrobes.virtual_cell.Sequence.BindingSequence method)
max_node_depth (VirtualMicrobes.Tree.PhyloTree.PhyloNode attribute)
max_time_course_length() (VirtualMicrobes.simulation.Simulation.ODE_simulation method)
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_types() (VirtualMicrobes.virtual_cell.Population.Population 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)
metabolite_internal_grid_data_dict() (VirtualMicrobes.environment.Environment.Environment method)
microfluid_chemostat() (VirtualMicrobes.environment.Environment.Environment method)
minor_id (VirtualMicrobes.virtual_cell.Identifier.Identifier attribute)
mirror_rel_coord() (in module VirtualMicrobes.environment.Grid)
mix_metabolites() (VirtualMicrobes.environment.Environment.Environment method)
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)
most_abundant_marker() (VirtualMicrobes.virtual_cell.Population.Population method)
most_offspring() (VirtualMicrobes.virtual_cell.Population.Population method)
MultiGraph (class in VirtualMicrobes.plotting.Graphs)
MultiGridGraph (class in VirtualMicrobes.plotting.Graphs)
mut_func_single_param() (in module VirtualMicrobes.simulation.Simulation)
mut_func_single_param_step_uniform() (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_neigh() (VirtualMicrobes.virtual_cell.Cell.Cell method)
mutate_new_offspring() (VirtualMicrobes.virtual_cell.Population.Population method)
mutate_uptake() (VirtualMicrobes.virtual_cell.Cell.Cell 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
N
n_attr_list() (VirtualMicrobes.plotting.Graphs.Network method)
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_offspring (VirtualMicrobes.virtual_cell.Population.Population 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)
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_log_file() (VirtualMicrobes.simulation.Simulation.Simulation method)
open_phylo_shelf() (VirtualMicrobes.simulation.Simulation.Simulation method)
Operator (class in VirtualMicrobes.virtual_cell.Sequence)
operator (VirtualMicrobes.virtual_cell.Gene.Gene attribute)
OperatorInsertion (class in VirtualMicrobes.mutate.Mutation)
operators (VirtualMicrobes.virtual_cell.Genome.Genome attribute)
P
pair_up() (VirtualMicrobes.event.Molecule.Molecule method)
pan_reactome_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)
(VirtualMicrobes.virtual_cell.Population.Population attribute)
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)
partial_mut_func_single_param() (in module VirtualMicrobes.simulation.Simulation)
partial_mut_ks_dict_func() (in module VirtualMicrobes.simulation.Simulation)
perfect_mix() (VirtualMicrobes.environment.Environment.Environment method)
(VirtualMicrobes.environment.Grid.Grid method)
phy_dir (VirtualMicrobes.data_tools.store.DataStore attribute)
phylo_to_ete_nodes() (VirtualMicrobes.Tree.PhyloTree.PhyloTree method)
phylo_tree (VirtualMicrobes.virtual_cell.Population.Population attribute)
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_mol_class() (VirtualMicrobes.environment.Environment.Environment method)
plot_and_save_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_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_gene_param() (VirtualMicrobes.virtual_cell.Cell.Cell method)
point_mutate_genome() (VirtualMicrobes.virtual_cell.Cell.Cell method)
PointMutation (class in VirtualMicrobes.mutate.Mutation)
pop_cells() (VirtualMicrobes.post_analysis.lod.LOD_Analyser method)
pop_genomic_stats_dict (VirtualMicrobes.data_tools.store.DataStore attribute)
pop_marker_counts() (VirtualMicrobes.virtual_cell.Population.Population method)
pop_rand_gen (VirtualMicrobes.virtual_cell.Population.Population attribute)
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.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)
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)
,
[1]
pretty_scoring_matrix() (in module VirtualMicrobes.virtual_cell.Sequence)
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)
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)
production_rates() (VirtualMicrobes.virtual_cell.Population.Population method)
production_val_history (VirtualMicrobes.virtual_cell.Population.Population attribute)
production_values() (VirtualMicrobes.virtual_cell.Population.Population method)
Promoter (class in VirtualMicrobes.virtual_cell.Gene)
promoter (VirtualMicrobes.virtual_cell.Gene.Gene attribute)
promoter_strengths (VirtualMicrobes.virtual_cell.Cell.Cell attribute)
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)
pruned_cells (VirtualMicrobes.virtual_cell.Population.Population attribute)
,
[1]
pruned_chromosomes (VirtualMicrobes.virtual_cell.Population.Population attribute)
pruned_genes (VirtualMicrobes.virtual_cell.Population.Population 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)
push_onto_internal_child() (VirtualMicrobes.Tree.PhyloTree.PhyloNode method)
push_up_root() (VirtualMicrobes.Tree.PhyloTree.PhyloNode method)
Q
qual_expr_diff() (VirtualMicrobes.virtual_cell.Cell.Cell method)
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_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_good_params() (VirtualMicrobes.virtual_cell.Gene.TranscriptionFactor 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)
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)
read_gene() (in module VirtualMicrobes.virtual_cell.Gene)
read_genome() (VirtualMicrobes.virtual_cell.Cell.Cell method)
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)
regulator_score() (VirtualMicrobes.virtual_cell.Population.Population method)
regulatory_region_mutate() (VirtualMicrobes.virtual_cell.Cell.Cell method)
regulatory_region_mutate_genome() (VirtualMicrobes.virtual_cell.Cell.Cell method)
reinit_system_params() (VirtualMicrobes.simulation.Simulation.EvoSystem method)
reload_unique_gene_count() (VirtualMicrobes.simulation.Simulation.Simulation method)
reload_unique_phylo_count() (VirtualMicrobes.simulation.Simulation.Simulation method)
remove_binding_sequence() (VirtualMicrobes.virtual_cell.Sequence.Operator method)
remove_bound_operator() (VirtualMicrobes.virtual_cell.Sequence.BindingSequence method)
remove_cell() (VirtualMicrobes.environment.Environment.Locality method)
remove_coord() (VirtualMicrobes.environment.Grid.Neighborhood method)
remove_direction() (VirtualMicrobes.environment.Grid.Neighborhood 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)
reopen_phylo_shelf() (VirtualMicrobes.simulation.Simulation.Simulation 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_neutral() (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)
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)
roots (VirtualMicrobes.virtual_cell.Population.Population attribute)
rows (VirtualMicrobes.plotting.Graphs.MultiGraph attribute)
rows_iter() (VirtualMicrobes.environment.Grid.Grid method)
S
save() (VirtualMicrobes.simulation.Simulation.Simulation method)
save_anc_cells() (VirtualMicrobes.data_tools.store.DataStore 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_lod_cells() (VirtualMicrobes.data_tools.store.DataStore method)
save_phylo_shelf() (VirtualMicrobes.simulation.Simulation.Simulation method)
save_phylo_tree() (VirtualMicrobes.data_tools.store.DataStore method)
save_pop_cells() (in module VirtualMicrobes.simulation.Simulation)
save_sim() (in module VirtualMicrobes.simulation.Simulation)
save_single_cell() (in module VirtualMicrobes.simulation.Simulation)
save_video() (VirtualMicrobes.plotting.Graphs.Grapher method)
scale_death_rates() (VirtualMicrobes.virtual_cell.Population.Population method)
scale_mol_degr_rate() (VirtualMicrobes.virtual_cell.Cell.Cell method)
select_building_blocks() (VirtualMicrobes.environment.Environment.Environment method)
select_layout_fn() (VirtualMicrobes.plotting.Graphs.PhyloTreeGraph method)
select_reproducing_cell() (VirtualMicrobes.virtual_cell.Population.Population method)
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_ancestor() (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloUnit method)
set_building_block() (VirtualMicrobes.event.Molecule.Molecule method)
set_data_range() (VirtualMicrobes.plotting.Graphs.MultiGridGraph method)
set_gene_prod_conc() (VirtualMicrobes.environment.Environment.Locality method)
(VirtualMicrobes.virtual_cell.Cell.Cell method)
set_gp() (VirtualMicrobes.environment.Grid.Grid method)
set_mol_concentrations_from_time_point() (VirtualMicrobes.environment.Environment.Environment method)
(VirtualMicrobes.environment.Environment.Locality method)
(VirtualMicrobes.virtual_cell.Cell.Cell method)
set_molconcs() (VirtualMicrobes.virtual_cell.Cell.Cell method)
set_phylo_shelf_file_name() (VirtualMicrobes.simulation.Simulation.Simulation method)
set_properties() (VirtualMicrobes.virtual_cell.Cell.Cell method)
set_small_mol_conc() (VirtualMicrobes.environment.Environment.Locality method)
(VirtualMicrobes.virtual_cell.Cell.Cell method)
set_small_mol_degr() (VirtualMicrobes.virtual_cell.Cell.Cell method)
set_small_mol_diff() (VirtualMicrobes.virtual_cell.Cell.Cell method)
set_state_from_file() (VirtualMicrobes.virtual_cell.Cell.Cell method)
set_state_from_ref_cell_tp() (VirtualMicrobes.virtual_cell.Cell.Cell method)
set_tot_volume() (VirtualMicrobes.environment.Environment.Environment method)
set_unique_key() (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloUnit method)
setup_environment() (VirtualMicrobes.simulation.Simulation.EvoSystem method)
SGDeletion (class in VirtualMicrobes.mutate.Mutation)
SGDuplication (class in VirtualMicrobes.mutate.Mutation)
short_repr() (VirtualMicrobes.event.Molecule.Molecule method)
(VirtualMicrobes.event.Molecule.MoleculeClass method)
(VirtualMicrobes.event.Reaction.Reaction 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)
snapshot_stats_names (VirtualMicrobes.data_tools.store.DataStore attribute)
spill_dead_cell_contents() (VirtualMicrobes.environment.Environment.Locality method)
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_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.virtual_cell.Cell.Cell attribute)
stretch_del_count (VirtualMicrobes.virtual_cell.Cell.Cell attribute)
stretch_invert (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)
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)
sub_envs_influx_combinations() (VirtualMicrobes.environment.Environment.Environment method)
sub_envs_partial_influx() (VirtualMicrobes.environment.Environment.Environment method)
sub_reactions() (VirtualMicrobes.event.Reaction.Convert method)
(VirtualMicrobes.event.Reaction.Degradation method)
(VirtualMicrobes.event.Reaction.Diffusion method)
(VirtualMicrobes.event.Reaction.Transport method)
subgrids_gen() (VirtualMicrobes.environment.Environment.Environment method)
substring_scoring_matrix() (VirtualMicrobes.virtual_cell.Sequence.Sequence class method)
sum_promoter_strengths (VirtualMicrobes.virtual_cell.Cell.Cell attribute)
swap_content() (VirtualMicrobes.environment.Grid.Grid method)
swap_gps() (VirtualMicrobes.environment.Grid.Grid method)
swap_pos() (VirtualMicrobes.environment.Grid.Grid method)
T
t_interval_iter() (VirtualMicrobes.post_analysis.lod.LOD method)
tandem_dup (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)
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)
tight_layout() (VirtualMicrobes.plotting.Graphs.MultiGraph method)
time (VirtualMicrobes.mutate.Mutation.Mutation attribute)
,
[1]
time_birth (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloBase attribute)
time_death (VirtualMicrobes.virtual_cell.PhyloUnit.PhyloBase attribute)
time_point (VirtualMicrobes.post_analysis.lod.PopulationHistory attribute)
times_divided() (VirtualMicrobes.virtual_cell.Population.Population 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)
translocate (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_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)
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.plotting.Graphs.PhyloTreeGraph method)
(VirtualMicrobes.Tree.PhyloTree.PhyloTree 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_ete_tree() (VirtualMicrobes.virtual_cell.Population.Population method)
update_figure() (VirtualMicrobes.plotting.Graphs.Grapher method)
(VirtualMicrobes.plotting.Graphs.PhyloTreeGraph 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_lineage_markers() (VirtualMicrobes.virtual_cell.Population.Population method)
update_localities() (VirtualMicrobes.environment.Environment.Environment 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_reaction_universe() (VirtualMicrobes.environment.Environment.Environment 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() (VirtualMicrobes.virtual_cell.Cell.Cell method)
update_small_molecules_degr() (VirtualMicrobes.virtual_cell.Cell.Cell method)
update_small_molecules_diff() (VirtualMicrobes.virtual_cell.Cell.Cell method)
update_stored_variables() (VirtualMicrobes.virtual_cell.Population.Population 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.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)
uptake_rates() (VirtualMicrobes.virtual_cell.Population.Population method)
V
value_range_dict (VirtualMicrobes.virtual_cell.Population.Population attribute)
versioned_id (VirtualMicrobes.virtual_cell.Identifier.Identifier attribute)
VirtualMicrobes (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.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.Simulation (module)
VirtualMicrobes.simulation.virtualmicrobes (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
wipe_pop() (VirtualMicrobes.virtual_cell.Population.Population method)
within_grid() (VirtualMicrobes.plotting.Graphs.MultiGraph 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)
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