Index

Symbols

"" # %agent: %def: %mod:

%obs: %var: '' @ @ X(Y) @ X,Y

A

add_model_file() (kappy.kappa_std.KappaStd method) add_model_string() (kappy.kappa_std.KappaStd method) agent_ids_by_type() (kappy.kappa_graph.KappaComplex method) agent_ids_of_type() (kappy.kappa_graph.KappaComplex method)

analyses_constraints_list() (kappy.kappa_std.KappaStd method) analyses_contact_map() (kappy.kappa_std.KappaStd method) analyses_dead_rules() (kappy.kappa_std.KappaStd method) analyses_influence_map() (kappy.kappa_std.KappaStd method) analyses_potential_polymers() (kappy.kappa_std.KappaStd method)

C

complexes (kappy.kappa_graph.KappaSnapshot attribute)

E

event (kappy.kappa_graph.KappaSnapshot attribute)

F

file_create() (kappy.kappa_std.KappaStd method) file_delete() (kappy.kappa_std.KappaStd method) file_get() (kappy.kappa_std.KappaStd method)

file_info() (kappy.kappa_std.KappaStd method) find_pattern() (kappy.kappa_graph.KappaComplex method) from_JSONDecoder() (kappy.kappa_graph.KappaComplex class method) from_string() (kappy.kappa_graph.KappaComplex class method)

G

get_complexes_by_abundance() (kappy.kappa_graph.KappaSnapshot method) get_complexes_by_size() (kappy.kappa_graph.KappaSnapshot method) get_default_sim_param() (kappy.kappa_std.KappaStd method) get_internal_state() (kappy.kappa_graph.KappaSite method) get_is_sim_running() (kappy.kappa_std.KappaStd method) get_largest_complexes() (kappy.kappa_graph.KappaSnapshot method) get_least_abundant_complexes() (kappy.kappa_graph.KappaSnapshot method)

get_most_abundant_complexes() (kappy.kappa_graph.KappaSnapshot method) get_neighbours_in_complex() (kappy.kappa_graph.KappaAgent method) get_node_id() (kappy.kappa_graph.KappaAgent method) get_size_distribution() (kappy.kappa_graph.KappaSnapshot method) get_smallest_complexes() (kappy.kappa_graph.KappaSnapshot method) get_token_abundance() (kappy.kappa_graph.KappaSnapshot method) get_total_mass() (kappy.kappa_graph.KappaSnapshot method) get_type() (kappy.kappa_graph.KappaAgent method)

H

has_link() (kappy.kappa_graph.KappaSite method)

I

items() (kappy.kappa_graph.KappaComplex method)

K

KappaAgent (class in kappy.kappa_graph) KappaComplex (class in kappy.kappa_graph) KappaError KappaSite (class in kappy.kappa_graph) KappaSnapshot (class in kappy.kappa_graph)

KappaStd (class in kappy.kappa_std) KappaSyntaxError kappy.kappa_common (module) kappy.kappa_graph (module) kappy.kappa_std (module)

N

neighbours_in_complex() (kappy.kappa_graph.KappaSite method)

P

PlotLimit (class in kappy.kappa_common)

project_overwrite() (kappy.kappa_std.KappaStd method) project_parse() (kappy.kappa_std.KappaStd method)

S

set_default_sim_param() (kappy.kappa_std.KappaStd method) shutdown() (kappy.kappa_std.KappaStd method) simulation_continue() (kappy.kappa_std.KappaStd method) simulation_delete() (kappy.kappa_std.KappaStd method) simulation_DIN() (kappy.kappa_std.KappaStd method) simulation_DINs() (kappy.kappa_std.KappaStd method) simulation_file_line() (kappy.kappa_std.KappaStd method) simulation_info() (kappy.kappa_std.KappaStd method) simulation_info_file_line() (kappy.kappa_std.KappaStd method)

simulation_intervention() (kappy.kappa_std.KappaStd method) simulation_log_messages() (kappy.kappa_std.KappaStd method) simulation_pause() (kappy.kappa_std.KappaStd method) simulation_plot() (kappy.kappa_std.KappaStd method) simulation_snapshot() (kappy.kappa_std.KappaStd method) simulation_snapshots() (kappy.kappa_std.KappaStd method) simulation_start() (kappy.kappa_std.KappaStd method) SimulationParameter (class in kappy.kappa_common) Smith(foo)

T

time (kappy.kappa_graph.KappaSnapshot attribute)

tokens (kappy.kappa_graph.KappaSnapshot attribute)

W

wait_for_simulation_stop() (kappy.kappa_std.KappaStd method)

Y

Y!_ Y!x

Y? Y~foo