Index

A

add_comparison() (pykaryote.petri.master.Master method) add_comparisons() (pykaryote.petri.master.Master method) add_family() (pykaryote.sim.families.FamilyTracker method)

Analyzer (class in pykaryote.utils.analysis) AnalyzerAggregator (class in pykaryote.utils.comparison) ancestry (pykaryote.sim.organism.Organism attribute)

B

base (pykaryote.sim.families.Family attribute) base_concentration (built-in variable) binding_affinity (pykaryote.sim.complexes.Complex attribute)

binds() (pykaryote.sim.families.FamilyTracker method) breed() (pykaryote.sim.organism.Organism method) builds (pykaryote.sim.organism.Organism attribute)

C

cell (pykaryote.sim.organism.Organism attribute) chem_fitness() (pykaryote.sim.organism.Organism method) chem_list (built-in variable) chemical_fitnesses (built-in variable) chemicals (pykaryote.sim.organism.Organism attribute) child_location (built-in variable) close_all() (pykaryote.utils.analysis.CreativeAnalyzer method) codon() (in module pykaryote.sim.genome) column (pykaryote.sim.organism.Organism attribute) columns (built-in variable) Comparer (class in pykaryote.utils.comparison) compile_all() (pykaryote.utils.comparison.AnalyzerAggregator method) compile_metric() (pykaryote.utils.comparison.AnalyzerAggregator method)

Complex (class in pykaryote.sim.complexes) complex_complex_binding (built-in variable) complex_lookup (pykaryote.sim.complexes.ComplexTracker attribute) complexes (pykaryote.sim.environment.Environment attribute) (pykaryote.sim.organism.Organism attribute) complexity_limit (built-in variable) ComplexTracker (class in pykaryote.sim.complexes) compute_complexity() (in module pykaryote.utils.analysis) copy_gene() (in module pykaryote.sim.genome) copy_probability (built-in variable) create_fitness_scaler() (pykaryote.sim.simulation.Simulation method) create_function_vector() (in module pykaryote.sim.organism) CreativeAnalyzer (class in pykaryote.utils.analysis) cut_del_length() (in module pykaryote.sim.genome)

D

delete_gene() (in module pykaryote.sim.genome) delete_probability (built-in variable) details() (pykaryote.sim.simulation.Simulation method) diffuse() (pykaryote.sim.environment.Environment method) diffusion (built-in variable)

diffusion_coefficient (built-in variable) diffusion_step (built-in variable) dim (pykaryote.sim.environment.Environment attribute) double_probability (built-in variable) draw_environment() (pykaryote.utils.comparison.Grapher method)

E

Environment (class in pykaryote.sim.environment) environment (pykaryote.sim.families.Family attribute) (pykaryote.sim.organism.Organism attribute)

export_all_as_csv() (pykaryote.utils.analysis.Analyzer method) export_varialble_as_csv() (pykaryote.utils.analysis.Analyzer method)

F

failed_builds (pykaryote.sim.organism.Organism attribute) families (pykaryote.sim.environment.Environment attribute) Family (class in pykaryote.sim.families) family (pykaryote.sim.complexes.Complex attribute) family_binding_chance (built-in variable) family_bindings (pykaryote.sim.families.FamilyTracker attribute) family_lookup (pykaryote.sim.families.FamilyTracker attribute) FamilyTracker (class in pykaryote.sim.families)

finished_yet() (pykaryote.sim.simulation.Simulation method) fit_scale (pykaryote.sim.organism.Organism attribute) fitness() (pykaryote.sim.organism.Organism method) fitness_scale (built-in variable) function (pykaryote.sim.complexes.Complex attribute) (pykaryote.sim.organism.Organism attribute) function_string() (in module pykaryote.sim.complexes) function_vector (pykaryote.sim.families.Family attribute)

G

gather_proportion (built-in variable) gathers (pykaryote.sim.organism.Organism attribute) gaussians (built-in variable) (pykaryote.sim.environment.Environment attribute) gaussians_at_location() (pykaryote.sim.environment.Environment method) generate_function_vector() (in module pykaryote.sim.families) generate_genome() (in module pykaryote.sim.genome) generation_length (built-in variable) generation_limit (built-in variable) genome (pykaryote.sim.organism.Organism attribute)

genome_cap_ratio (built-in variable) genome_fitness_cost (built-in variable) get_complex() (pykaryote.sim.complexes.ComplexTracker method) get_config() (in module pykaryote.utils.comparison) get_metrics_files() (in module pykaryote.utils.comparison) graph_comparison() (pykaryote.petri.worker.Worker method) Grapher (class in pykaryote.utils.comparison) grid (pykaryote.sim.environment.Environment attribute) grid_type (built-in variable) (pykaryote.sim.environment.Environment attribute)

I

id (pykaryote.sim.families.Family attribute) (pykaryote.sim.organism.Organism attribute) initial_genome_creation (built-in variable) initial_genome_length (built-in variable)

is_functional (pykaryote.sim.complexes.Complex attribute) iterate() (pykaryote.sim.simulation.Simulation method)

L

len (pykaryote.sim.organism.Organism attribute) length (pykaryote.sim.complexes.Complex attribute) (pykaryote.sim.families.Family attribute) load_sim() (in module pykaryote.sim.simulation)

log() (pykaryote.petri.master.Master method) (pykaryote.sim.simulation.Simulation method) log_step (built-in variable)

M

make_cfg() (in module pykaryote.utils.comparison) Master (class in pykaryote.petri.master) max_binding_affinity (built-in variable) max_complex_length (built-in variable) max_cut_del (built-in variable) max_moves (built-in variable) max_protein_length (built-in variable) max_relation_distance (built-in variable) maximum_bound (built-in variable) mean_to_aggregate (built-in variable) metrics (built-in variable) min_binding_affinity (built-in variable)

min_genome_length (built-in variable) min_protein_length (built-in variable) mode (pykaryote.sim.organism.Organism attribute) mode_switch_probability (built-in variable) move_count (pykaryote.sim.organism.Organism attribute) move_speed (built-in variable) moves (pykaryote.sim.organism.Organism attribute) mutate_factor (built-in variable) mutate_family_vector() (in module pykaryote.sim.complexes) mutate_function_vector() (in module pykaryote.sim.complexes) mutate_genome() (in module pykaryote.sim.genome)

N

name (pykaryote.sim.complexes.Complex attribute) (pykaryote.sim.families.Family attribute) new_generation() (pykaryote.sim.simulation.Simulation method) num_gather (built-in variable)

num_move (built-in variable) num_organisms (built-in variable) num_protein (built-in variable)

O

org_step (built-in variable)

Organism (class in pykaryote.sim.organism)

P

plot() (pykaryote.utils.comparison.Grapher method) plot_ancestry() (pykaryote.utils.analysis.Analyzer method) plot_avg_time_spent() (pykaryote.utils.analysis.Analyzer method) plot_chemical_complexity() (pykaryote.utils.analysis.Analyzer method) plot_chemicals() (pykaryote.utils.analysis.Analyzer method) plot_complex_diversity() (pykaryote.utils.analysis.Analyzer method) plot_complexes() (pykaryote.utils.analysis.Analyzer method) plot_complexity() (pykaryote.utils.analysis.Analyzer method) plot_complexity_and_fitness() (pykaryote.utils.analysis.Analyzer method) plot_component_percent_functional() (pykaryote.utils.analysis.Analyzer method) plot_failed_builds() (pykaryote.utils.analysis.Analyzer method) plot_family_lengths() (pykaryote.utils.analysis.Analyzer method) plot_family_sizes() (pykaryote.utils.analysis.Analyzer method) plot_final_values() (pykaryote.utils.comparison.Grapher method) plot_fitness() (pykaryote.utils.analysis.Analyzer method) plot_gen_time() (pykaryote.utils.analysis.Analyzer method) plot_genome_length() (pykaryote.utils.analysis.Analyzer method) plot_invented_complexes() (pykaryote.utils.analysis.Analyzer method) plot_num_distinct() (pykaryote.utils.analysis.Analyzer method) plot_percent_functional() (pykaryote.utils.analysis.Analyzer method) plot_threshold() (pykaryote.utils.comparison.Grapher method)

plot_time_spent_in_gaussian() (pykaryote.utils.analysis.Analyzer method) point_mutate() (in module pykaryote.sim.genome) point_mutate_chance (built-in variable) poison_chance (built-in variable) poison_factor (built-in variable) pos (pykaryote.sim.organism.Organism attribute) protein_cost (built-in variable) pykaryote.petri.master (module) pykaryote.petri.tags (module) pykaryote.petri.worker (module) pykaryote.sim.complexes (module) pykaryote.sim.environment (module) pykaryote.sim.families (module) pykaryote.sim.genome (module) pykaryote.sim.organism (module) pykaryote.sim.simulation (module) pykaryote.test.test (module) pykaryote.utils.analysis (module) pykaryote.utils.comparison (module) pykaryote.utils.globals (module)

Q

quick_append() (pykaryote.utils.analysis.CreativeAnalyzer method)

quick_read() (pykaryote.utils.analysis.Analyzer method)

R

randint() (in module pykaryote.sim.genome) random() (in module pykaryote.sim.complexes) (in module pykaryote.sim.families) (in module pykaryote.sim.genome) random_location() (pykaryote.sim.environment.Environment method) randomseed (built-in variable) range_factor (built-in variable) read_genome() (pykaryote.sim.organism.Organism method)

recorded_actions (built-in variable) row (pykaryote.sim.organism.Organism attribute) rows (built-in variable) run() (in module pykaryote.test.test) (pykaryote.petri.worker.Worker method) (pykaryote.sim.simulation.Simulation method) (pykaryote.utils.comparison.Comparer method) run_generation() (pykaryote.sim.simulation.Simulation method) runtime_limit (built-in variable)

S

save() (pykaryote.sim.simulation.Simulation method) save_all() (pykaryote.utils.analysis.Analyzer method) (pykaryote.utils.comparison.Grapher method) save_as_data() (pykaryote.utils.analysis.CreativeAnalyzer method) save_environment_drawing() (pykaryote.utils.analysis.Analyzer method) save_step (built-in variable) save_time_spent_in_gaussian() (pykaryote.utils.comparison.Grapher method) selection_exponent (built-in variable) separation_chance (built-in variable) shutdown() (pykaryote.petri.master.Master method) sibling_distance (built-in variable)

Simulation (class in pykaryote.sim.simulation) size (pykaryote.sim.families.Family attribute) string_from_set() (in module pykaryote.sim.families) strong_chance (built-in variable) strong_factor (built-in variable) summary() (pykaryote.sim.simulation.Simulation method) swap() (pykaryote.sim.organism.Organism method) swap_gene() (in module pykaryote.sim.genome) swap_probability (built-in variable)

T

tearDown() (pykaryote.test.test.TestTimeSpentInGaussian method) termination_size (built-in variable) test_blanks() (pykaryote.test.test.TestAnalyzerQuickRead method) test_complexity() (pykaryote.test.test.TestAnalyzerQuickRead method) test_flat_environment() (pykaryote.test.test.TestTimeSpentInGaussian method) test_get_config() (pykaryote.test.test.TestReadComparison method) test_make_flat_grid() (pykaryote.test.test.TestEnvironment method) test_make_gaussian_grid() (pykaryote.test.test.TestEnvironment method) test_means() (pykaryote.test.test.TestAnalyzerQuickRead method) test_plot_time_spent_in_gaussian() (pykaryote.test.test.TestTimeSpentInGaussian method)

test_shape() (pykaryote.test.test.TestAnalyzerQuickRead method) test_time_spent_in_gaussian() (pykaryote.test.test.TestTimeSpentInGaussian method) test_variable_length_data() (pykaryote.test.test.TestAnalyzerQuickRead method) TestAnalyzerQuickRead (class in pykaryote.test.test) TestEnvironment (class in pykaryote.test.test) TestEnvironmentDraw (class in pykaryote.test.test) TestReadComparison (class in pykaryote.test.test) TestTimeSpentInGaussian (class in pykaryote.test.test) thresholds (built-in variable) tracked_ancestors (built-in variable)

U

update() (pykaryote.utils.analysis.CreativeAnalyzer method)

W

wait_and_log() (pykaryote.petri.master.Master method) weak_factor (built-in variable)

Worker (class in pykaryote.petri.worker) wrap (built-in variable)