Index

A | B | C | D | E | F | G | I | L | M | N | O | P | Q | R | S | T | U | W

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)