Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
V
|
W
A
activator_required (phievo.Networks.classes_eds2.Network attribute)
add_CorePromoter2Species() (in module phievo.Networks.CorePromoter)
(phievo.Networks.classes_eds2.Network method)
add_edge() (phievo.Networks.PlotGraph.Components.Interaction method)
(phievo.Networks.PlotGraph.Graph.Graph method)
add_Node() (phievo.Networks.classes_eds2.Network method)
add_node() (phievo.Networks.PlotGraph.Graph.Graph method)
add_TFHill() (in module phievo.Networks.TFHill)
(phievo.Networks.classes_eds2.Network method)
add_TModule2CorePromoter() (in module phievo.Networks.CorePromoter)
(phievo.Networks.classes_eds2.Network method)
add_type() (phievo.Networks.classes_eds2.Species method)
all_params2C() (in module phievo.Networks.deriv2)
Arrow (class in phievo.Networks.PlotGraph.Components)
B
BarB (class in phievo.Networks.PlotGraph.Components)
best_fitness (phievo.Populations_Types.evolution_gillespie.Population attribute)
bests_file (phievo.Populations_Types.evolution_gillespie.Population attribute)
Bezier() (in module phievo.Networks.PlotGraph.Components)
build_lists() (in module phievo.Networks.mutation)
build_mutations() (phievo.Networks.mutation.Mutable_Network method)
C
catal_data() (phievo.Networks.classes_eds2.Network method)
Ccompiler (in module phievo.Networks.deriv2)
cfile (in module phievo.Networks.deriv2)
change_type() (phievo.Networks.classes_eds2.Species method)
check_consistency() (in module phievo.Networks.classes_eds2)
check_existing_binary() (phievo.Networks.classes_eds2.Network method)
check_existing_Degradation() (in module phievo.Networks.Degradation)
(phievo.Networks.classes_eds2.Network method)
check_existing_link() (phievo.Networks.classes_eds2.Network method)
check_existing_Phosphorylation() (in module phievo.Networks.Phosphorylation)
(phievo.Networks.classes_eds2.Network method)
check_grammar() (phievo.Networks.classes_eds2.Interaction method)
(phievo.Networks.Degradation.Degradation method)
(phievo.Networks.PPI.PPI method)
(phievo.Networks.Phosphorylation.Phosphorylation method)
check_Node() (phievo.Networks.classes_eds2.Network method)
Circle (class in phievo.Networks.PlotGraph.Components)
clean_Nodes() (phievo.Networks.classes_eds2.Network method)
clean_type() (phievo.Networks.classes_eds2.Species method)
clear_buffer() (phievo.AnalysisTools.Simulation.Simulation method)
color_generate() (in module phievo.AnalysisTools.palette)
compare_node() (in module phievo.Networks.classes_eds2)
compare_ss_wrt_parent() (phievo.AnalysisTools.Simulation.Genealogy method)
compdist() (in module phievo.Populations_Types.pareto_population)
compile_and_integrate() (in module phievo.Networks.deriv2)
compute_best_fitness() (phievo.AnalysisTools.Simulation.Seed method)
compute_center() (phievo.Networks.PlotGraph.Components.Edge method)
compute_Cseed() (phievo.Networks.mutation.Mutable_Network method)
compute_leap() (in module phievo.Networks.deriv2)
compute_next_mutation() (phievo.Networks.mutation.Mutable_Network method)
compute_transcription() (in module phievo.Networks.TFHill)
CorePromoter (class in phievo.Networks.CorePromoter)
Cseed (phievo.Networks.classes_eds2.Network attribute)
custom_plot() (phievo.AnalysisTools.Simulation.Seed method)
(phievo.AnalysisTools.Simulation.Simulation method)
D
data_evolution (phievo.Networks.mutation.Mutable_Network attribute)
data_next_mutation (phievo.Networks.mutation.Mutable_Network attribute)
def_label() (phievo.Networks.classes_eds2.Species method)
default_tags (phievo.Networks.classes_eds2.Species attribute)
degrad_deriv_inC() (in module phievo.Networks.deriv2)
Degradation (class in phievo.Networks.Degradation)
Degradation_deriv_inC() (in module phievo.Networks.Degradation)
delay (phievo.Networks.CorePromoter.CorePromoter attribute)
delete_clean() (phievo.Networks.classes_eds2.Network method)
dephosphorylation (phievo.Networks.Phosphorylation.Phosphorylation attribute)
dict_types (phievo.Networks.classes_eds2.Network attribute)
dlt_fitness (phievo.Networks.mutation.Mutable_Network attribute)
download_example() (in module phievo.AnalysisTools.main_functions)
download_tools() (in module phievo.AnalysisTools.main_functions)
download_zip() (in module phievo.AnalysisTools.main_functions)
draw() (phievo.Networks.classes_eds2.Network method)
(phievo.Networks.PlotGraph.Graph.Graph method)
duplicate_downstream_interactions() (phievo.Networks.classes_eds2.Network method)
duplicate_gene() (in module phievo.Networks.CorePromoter)
(phievo.Networks.classes_eds2.Network method)
duplicate_PPI() (in module phievo.Networks.PPI)
(phievo.Networks.classes_eds2.Network method)
duplicate_species_and_interactions() (phievo.Networks.classes_eds2.Network method)
duplicate_TFHill() (in module phievo.Networks.TFHill)
(phievo.Networks.classes_eds2.Network method)
E
Edge (class in phievo.Networks.PlotGraph.Components)
edge_list() (phievo.Networks.PlotGraph.Graph.Graph method)
evolution() (phievo.Populations_Types.evolution_gillespie.Population method)
F
find_freeAngle() (phievo.Networks.PlotGraph.Components.Node method)
fitness_treatment() (in module phievo.Populations_Types.evolution_gillespie)
fixed_activity_for_TF (phievo.Networks.classes_eds2.Network attribute)
floatrange() (in module phievo.AnalysisTools.palette)
G
Genealogy (class in phievo.AnalysisTools.Simulation)
generate_gradient() (in module phievo.AnalysisTools.palette)
genus (phievo.Populations_Types.evolution_gillespie.Population attribute)
genus_mutate_and_integrate() (phievo.Populations_Types.evolution_gillespie.Population method)
get_autoPatch() (phievo.Networks.PlotGraph.Components.Arrow method)
get_backup_net() (phievo.AnalysisTools.Simulation.Seed method)
(phievo.AnalysisTools.Simulation.Simulation method)
get_backup_pop() (phievo.AnalysisTools.Simulation.Seed method)
(phievo.AnalysisTools.Simulation.Simulation method)
get_best_net() (phievo.AnalysisTools.Simulation.Seed method)
(phievo.AnalysisTools.Simulation.Simulation method)
get_genealogy() (phievo.AnalysisTools.Simulation.Simulation method)
get_network_from_identifier() (phievo.AnalysisTools.Simulation.Genealogy method)
get_networkx() (phievo.Networks.PlotGraph.Graph.Graph method)
get_node() (phievo.Networks.classes_eds2.Network method)
get_patch() (phievo.Networks.PlotGraph.Components.Arrow method)
(phievo.Networks.PlotGraph.Components.Circle method)
(phievo.Networks.PlotGraph.Components.HouseDown method)
(phievo.Networks.PlotGraph.Components.HouseUp method)
(phievo.Networks.PlotGraph.Components.RoundedRectangle method)
(phievo.Networks.PlotGraph.Components.Square method)
(phievo.Networks.PlotGraph.Components.TriangleDown method)
(phievo.Networks.PlotGraph.Components.TriangleUp method)
get_patches() (phievo.Networks.PlotGraph.Components.Interaction method)
get_vector() (phievo.Networks.PlotGraph.Components.Edge method)
get_vector_auto() (phievo.Networks.PlotGraph.Components.Edge method)
gettype() (in module phievo.Networks.lovelyGraph)
Graph (class in phievo.Networks.PlotGraph.Graph)
graph (phievo.Networks.classes_eds2.Network attribute)
H
hash_topology (phievo.Networks.classes_eds2.Network attribute)
hierarchical_layout() (in module phievo.Networks.PlotGraph.Layout)
hill (phievo.Networks.Phosphorylation.Phosphorylation attribute)
HouseDown (class in phievo.Networks.PlotGraph.Components)
HouseUp (class in phievo.Networks.PlotGraph.Components)
HSL_to_RGB() (in module phievo.AnalysisTools.palette)
I
id (phievo.Networks.classes_eds2.Node attribute)
increment_identifier() (phievo.Populations_Types.evolution_gillespie.Population method)
init_network() (in module phievo.Populations_Types.evolution_gillespie)
initialize_identifier() (phievo.Populations_Types.evolution_gillespie.Population method)
input (phievo.Networks.CorePromoter.CorePromoter attribute)
(phievo.Networks.Degradation.Degradation attribute)
(phievo.Networks.Phosphorylation.Phosphorylation attribute)
int_id() (phievo.Networks.classes_eds2.Node method)
Interaction (class in phievo.Networks.classes_eds2)
(class in phievo.Networks.PlotGraph.Components)
isinstance() (phievo.Networks.classes_eds2.Node method)
(phievo.Networks.classes_eds2.Species method)
isremovable() (phievo.Networks.classes_eds2.Node method)
L
label (phievo.Networks.classes_eds2.Species attribute)
(phievo.Networks.CorePromoter.CorePromoter attribute)
(phievo.Networks.Degradation.Degradation attribute)
(phievo.Networks.Phosphorylation.Phosphorylation attribute)
layout() (in module phievo.Networks.PlotGraph.Layout)
(phievo.Networks.PlotGraph.Graph.Graph method)
ligand_fct() (in module phievo.Networks.mutation)
Line (class in phievo.Networks.PlotGraph.Components)
list_possible_Degradation() (in module phievo.Networks.Degradation)
(phievo.Networks.classes_eds2.Network method)
list_types() (phievo.Networks.classes_eds2.Node method)
(phievo.Networks.classes_eds2.Species method)
load_generation_data() (in module phievo.AnalysisTools.main_functions)
load_Profile_data() (phievo.AnalysisTools.Simulation.Simulation method)
load_sort_networks() (phievo.AnalysisTools.Simulation.Genealogy method)
M
make_colormap() (in module phievo.AnalysisTools.palette)
Mutable_Network (class in phievo.Networks.mutation)
mutate_and_integrate() (phievo.Networks.mutation.Mutable_Network method)
mutate_Node() (phievo.Networks.mutation.Mutable_Network method)
N
Network (class in phievo.Networks.classes_eds2)
new_custom_random_gene() (in module phievo.Networks.CorePromoter)
(phievo.Networks.classes_eds2.Network method)
new_Degradation() (in module phievo.Networks.Degradation)
(phievo.Networks.classes_eds2.Network method)
new_enhancer() (in module phievo.Networks.CorePromoter)
(phievo.Networks.classes_eds2.Network method)
new_gene() (in module phievo.Networks.CorePromoter)
(phievo.Networks.classes_eds2.Network method)
new_Phosphorylation() (in module phievo.Networks.Phosphorylation)
(phievo.Networks.classes_eds2.Network method)
new_PPI() (in module phievo.Networks.PPI)
(phievo.Networks.classes_eds2.Network method)
new_random_Degradation() (in module phievo.Networks.Degradation)
(phievo.Networks.mutation.Mutable_Network method)
new_random_Phosphorylation() (in module phievo.Networks.Phosphorylation)
(phievo.Networks.mutation.Mutable_Network method)
new_random_PPI() (in module phievo.Networks.PPI)
(phievo.Networks.mutation.Mutable_Network method)
new_random_TFHill() (in module phievo.Networks.TFHill)
(phievo.Networks.mutation.Mutable_Network method)
new_Species() (phievo.Networks.classes_eds2.Network method)
new_TFHill() (in module phievo.Networks.TFHill)
(phievo.Networks.classes_eds2.Network method)
nfunctions (phievo.Populations_Types.pareto_population.pareto_Population attribute)
Node (class in phievo.Networks.classes_eds2)
(class in phievo.Networks.PlotGraph.Components)
node_list() (phievo.Networks.PlotGraph.Graph.Graph method)
noise_flag (in module phievo.Networks.deriv2)
npopulation (phievo.Populations_Types.evolution_gillespie.Population attribute)
number_Degradation() (in module phievo.Networks.Degradation)
(phievo.Networks.classes_eds2.Network method)
number_nodes() (phievo.Networks.classes_eds2.Network method)
number_Phosphorylation() (in module phievo.Networks.Phosphorylation)
(phievo.Networks.classes_eds2.Network method)
number_PPI() (in module phievo.Networks.PPI)
(phievo.Networks.classes_eds2.Network method)
number_TFHill() (in module phievo.Networks.TFHill)
(phievo.Networks.classes_eds2.Network method)
O
order_node (phievo.Networks.classes_eds2.Network attribute)
output (phievo.Networks.CorePromoter.CorePromoter attribute)
(phievo.Networks.Degradation.Degradation attribute)
(phievo.Networks.Phosphorylation.Phosphorylation attribute)
outputs_to_delete() (phievo.Networks.classes_eds2.Node method)
(phievo.Networks.CorePromoter.CorePromoter method)
(phievo.Networks.Degradation.Degradation method)
(phievo.Networks.PPI.PPI method)
(phievo.Networks.Phosphorylation.Phosphorylation method)
P
parameters (phievo.Networks.classes_eds2.Species attribute)
pareto_generate_fit_dict() (phievo.AnalysisTools.Simulation.Seed_Pareto method)
pareto_Population (class in phievo.Populations_Types.pareto_population)
pareto_thread_Population (class in phievo.Populations_Types.pareto_population)
pcompare() (in module phievo.Populations_Types.pareto_population)
phievo.AnalysisTools.main_functions (module)
phievo.AnalysisTools.palette (module)
phievo.AnalysisTools.Simulation (module)
phievo.Networks.classes_eds2 (module)
phievo.Networks.CorePromoter (module)
phievo.Networks.Degradation (module)
phievo.Networks.deriv2 (module)
phievo.Networks.lovelyGraph (module)
phievo.Networks.mutation (module)
phievo.Networks.Phosphorylation (module)
phievo.Networks.PlotGraph.Components (module)
phievo.Networks.PlotGraph.Graph (module)
phievo.Networks.PlotGraph.Layout (module)
phievo.Networks.PPI (module)
phievo.Networks.TFHill (module)
phievo.Populations_Types.evolution_gillespie (module)
phievo.Populations_Types.pareto_population (module)
Phospho_deriv_inC() (in module phievo.Networks.Phosphorylation)
Phosphorylation (class in phievo.Networks.Phosphorylation)
plot_compare_multiple_networks() (phievo.AnalysisTools.Simulation.Genealogy method)
plot_front_genealogy() (phievo.AnalysisTools.Simulation.Genealogy method)
plot_label() (phievo.Networks.PlotGraph.Components.Node method)
plot_lineage_fitness() (phievo.AnalysisTools.Simulation.Genealogy method)
plot_mutation_fitness_deviation() (phievo.AnalysisTools.Simulation.Genealogy method)
plot_pareto_fronts() (phievo.AnalysisTools.Simulation.Seed_Pareto method)
Plot_Profile() (phievo.AnalysisTools.Simulation.Simulation method)
Plot_TimeCourse() (phievo.AnalysisTools.Simulation.Simulation method)
PlotData() (phievo.AnalysisTools.Simulation.Simulation method)
pop_fitness_share() (phievo.Populations_Types.pareto_population.pareto_Population method)
pop_mutate_and_integrate() (phievo.Populations_Types.evolution_gillespie.Population method)
(phievo.Populations_Types.pareto_population.pareto_thread_Population method)
pop_print_pareto() (phievo.Populations_Types.pareto_population.pareto_Population method)
pop_sort() (phievo.Populations_Types.evolution_gillespie.Population method)
(phievo.Populations_Types.pareto_population.pareto_Population method)
Population (class in phievo.Populations_Types.evolution_gillespie)
PPI (class in phievo.Networks.PPI)
PPI_deriv_inC() (in module phievo.Networks.PPI)
pretty_graph() (in module phievo.Networks.lovelyGraph)
print_node() (phievo.Networks.classes_eds2.Node method)
produce_CorePromoter_name() (in module phievo.Networks.lovelyGraph)
produce_Degradation_name() (in module phievo.Networks.lovelyGraph)
produce_Phospho_name() (in module phievo.Networks.lovelyGraph)
produce_PPI_name() (in module phievo.Networks.lovelyGraph)
produce_species_name() (in module phievo.Networks.lovelyGraph)
produce_TFHill_name() (in module phievo.Networks.lovelyGraph)
produce_TModule_name() (in module phievo.Networks.lovelyGraph)
propagate_activity_TFHill() (in module phievo.Networks.TFHill)
(phievo.Networks.classes_eds2.Network method)
R
radius() (phievo.Networks.PlotGraph.Components.Circle method)
(phievo.Networks.PlotGraph.Components.Edge method)
(phievo.Networks.PlotGraph.Components.HouseDown method)
(phievo.Networks.PlotGraph.Components.HouseUp method)
(phievo.Networks.PlotGraph.Components.RoundedRectangle method)
(phievo.Networks.PlotGraph.Components.Square method)
(phievo.Networks.PlotGraph.Components.TriangleDown method)
(phievo.Networks.PlotGraph.Components.TriangleUp method)
rand_modify() (in module phievo.Networks.mutation)
(phievo.Networks.classes_eds2.Node method)
Random (phievo.Networks.mutation.Mutable_Network attribute)
random_add_output() (phievo.Networks.mutation.Mutable_Network method)
random_change_output() (phievo.Networks.mutation.Mutable_Network method)
random_Degradation() (in module phievo.Networks.Degradation)
(phievo.Networks.mutation.Mutable_Network method)
random_duplicate() (phievo.Networks.mutation.Mutable_Network method)
random_enhancer() (in module phievo.Networks.CorePromoter)
(phievo.Networks.mutation.Mutable_Network method)
random_gene() (in module phievo.Networks.CorePromoter)
(phievo.Networks.mutation.Mutable_Network method)
random_Interaction() (phievo.Networks.mutation.Mutable_Network method)
random_parameters() (in module phievo.Networks.mutation)
random_Phosphorylation() (in module phievo.Networks.Phosphorylation)
(phievo.Networks.mutation.Mutable_Network method)
random_PPI() (in module phievo.Networks.PPI)
(phievo.Networks.mutation.Mutable_Network method)
random_remove_output() (phievo.Networks.mutation.Mutable_Network method)
random_Species() (phievo.Networks.mutation.Mutable_Network method)
random_TFHill() (in module phievo.Networks.TFHill)
(phievo.Networks.mutation.Mutable_Network method)
rate (phievo.Networks.Degradation.Degradation attribute)
(phievo.Networks.Phosphorylation.Phosphorylation attribute)
read_network() (in module phievo.AnalysisTools.main_functions)
record_angle() (phievo.Networks.PlotGraph.Components.Edge method)
(phievo.Networks.PlotGraph.Components.Node method)
remove_Interaction() (phievo.Networks.mutation.Mutable_Network method)
remove_Node() (phievo.Networks.classes_eds2.Network method)
remove_output_when_duplicate (phievo.Networks.classes_eds2.Network attribute)
restart() (in module phievo.Populations_Types.evolution_gillespie)
RoundedRectangle (class in phievo.Networks.PlotGraph.Components)
rshare (phievo.Populations_Types.pareto_population.pareto_Population attribute)
run_dynamics() (phievo.AnalysisTools.Simulation.Simulation method)
S
same_seed (phievo.Populations_Types.evolution_gillespie.Population attribute)
sample_dictionary_ranges() (in module phievo.Networks.mutation)
save_restart_file() (phievo.Populations_Types.evolution_gillespie.Population method)
scatter_pareto_accross_generations() (phievo.AnalysisTools.Simulation.Genealogy method)
search_ancestors() (phievo.AnalysisTools.Simulation.Genealogy method)
Seed (class in phievo.AnalysisTools.Simulation)
Seed_Pareto (class in phievo.AnalysisTools.Simulation)
set_center() (phievo.Networks.PlotGraph.Components.Edge method)
(phievo.Networks.PlotGraph.Components.Node method)
set_node_size() (phievo.Networks.PlotGraph.Graph.Graph method)
setReceiveEdge() (phievo.Networks.PlotGraph.Components.Edge method)
short_label() (in module phievo.Networks.lovelyGraph)
show_fitness() (phievo.AnalysisTools.Simulation.Seed method)
(phievo.AnalysisTools.Simulation.Seed_Pareto method)
(phievo.AnalysisTools.Simulation.Simulation method)
Simulation (class in phievo.AnalysisTools.Simulation)
single_comparison() (in module phievo.Populations_Types.pareto_population)
smoothing() (in module phievo.AnalysisTools.main_functions)
sort_networks() (phievo.AnalysisTools.Simulation.Genealogy method)
Species (class in phievo.Networks.classes_eds2)
Square (class in phievo.Networks.PlotGraph.Components)
store_to_pickle() (phievo.Networks.classes_eds2.Network method)
stored_generation_indexes() (phievo.AnalysisTools.Simulation.Seed method)
(phievo.AnalysisTools.Simulation.Simulation method)
storing() (phievo.Populations_Types.evolution_gillespie.Population method)
string_param() (phievo.Networks.classes_eds2.Node method)
(phievo.Networks.CorePromoter.CorePromoter method)
(phievo.Networks.TFHill.TFHill method)
(phievo.Networks.classes_eds2.TModule method)
T
Tags_Species (phievo.Networks.classes_eds2.Species attribute)
TFHill (class in phievo.Networks.TFHill)
tgeneration (phievo.Populations_Types.evolution_gillespie.Population attribute)
threshold (phievo.Networks.Phosphorylation.Phosphorylation attribute)
title (phievo.Networks.classes_eds2.Network attribute)
TModule (class in phievo.Networks.classes_eds2)
track_changing_variable() (in module phievo.Networks.deriv2)
track_variable() (in module phievo.Networks.deriv2)
transcription_deriv_inC() (in module phievo.Networks.TFHill)
TriangleDown (class in phievo.Networks.PlotGraph.Components)
TriangleUp (class in phievo.Networks.PlotGraph.Components)
U
update_default_colormap() (in module phievo.AnalysisTools.palette)
update_fitness() (phievo.Populations_Types.evolution_gillespie.Population method)
(phievo.Populations_Types.pareto_population.pareto_Population method)
V
verify_IO_numbers() (phievo.Networks.classes_eds2.Network method)
W
workplace_dir (in module phievo.Networks.deriv2)
write_id() (phievo.Networks.classes_eds2.Network method)
write_program() (in module phievo.Networks.deriv2)
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