Index

A

active_primes() (in module pyboolnet.prime_implicants) activities2animation() (in module pyboolnet.interaction_graphs) add_style_activities() (in module pyboolnet.interaction_graphs) add_style_anonymous() (in module pyboolnet.interaction_graphs) (in module pyboolnet.state_transition_graphs) add_style_constants() (in module pyboolnet.interaction_graphs) add_style_default() (in module pyboolnet.interaction_graphs) (in module pyboolnet.state_transition_graphs) add_style_inputs() (in module pyboolnet.interaction_graphs) add_style_interactionsigns() (in module pyboolnet.interaction_graphs) add_style_mintrapspaces() (in module pyboolnet.state_transition_graphs)

add_style_outputs() (in module pyboolnet.interaction_graphs) add_style_path() (in module pyboolnet.interaction_graphs) (in module pyboolnet.state_transition_graphs) add_style_sccs() (in module pyboolnet.interaction_graphs) (in module pyboolnet.state_transition_graphs) add_style_subgraphs() (in module pyboolnet.interaction_graphs) (in module pyboolnet.state_transition_graphs) add_style_subspaces() (in module pyboolnet.state_transition_graphs) add_style_tendencies() (in module pyboolnet.state_transition_graphs) all_globally_exists_finally_one_of_sub_spaces() (in module pyboolnet.temporal_logic) are_equivalent() (in module pyboolnet.boolean_logic) are_mutually_exclusive() (in module pyboolnet.boolean_logic)

B

balanced_tree() (in module pyboolnet.network_generators) best_first_reachability() (in module pyboolnet.state_transition_graphs)

bit_count() (in module pyboolnet.boolean_normal_forms) bnet2primes() (in module pyboolnet.file_exchange) bounding_box() (in module pyboolnet.state_space)

C

commitment_diagram2image() (in module pyboolnet.commitment_diagrams) commitment_diagrams_are_equivalent() (in module pyboolnet.commitment_diagrams) completeness() (in module pyboolnet.attractors) completeness_naive() (in module pyboolnet.attractors) completeness_naive_with_counterexample() (in module pyboolnet.attractors) completeness_with_counterexample() (in module pyboolnet.attractors) compute_attractors() (in module pyboolnet.attractors) compute_attractors_tarjan() (in module pyboolnet.attractors) compute_basins() (in module pyboolnet.basins_of_attraction) compute_circuits() (in module pyboolnet.trap_spaces) compute_commitment_diagram() (in module pyboolnet.commitment_diagrams) compute_phenotype_diagram() (in module pyboolnet.phenotypes) compute_phenotypes() (in module pyboolnet.phenotypes) compute_smallest_trapspace() (in module pyboolnet.trap_spaces) compute_steady_states() (in module pyboolnet.trap_spaces) compute_steady_states_projected() (in module pyboolnet.trap_spaces) compute_trap_spaces() (in module pyboolnet.trap_spaces) compute_trap_spaces_bounded() (in module pyboolnet.trap_spaces) compute_trapspaces_that_contain_state() (in module pyboolnet.trap_spaces) compute_trapspaces_that_intersect_subspace() (in module pyboolnet.trap_spaces)

compute_trapspaces_within_subspace() (in module pyboolnet.trap_spaces) condensationgraph2dot() (in module pyboolnet.state_transition_graphs) condensationgraph2image() (in module pyboolnet.state_transition_graphs) copy_ig() (in module pyboolnet.interaction_graphs) copy_primes() (in module pyboolnet.prime_implicants) copy_stg() (in module pyboolnet.state_transition_graphs) create_attractor_report() (in module pyboolnet.attractors) create_basins_of_attraction_barplot() (in module pyboolnet.basins_of_attraction) create_basins_piechart() (in module pyboolnet.basins_of_attraction) create_blinkers() (in module pyboolnet.prime_implicants) create_commitment_piechart() (in module pyboolnet.commitment_diagrams) create_constants() (in module pyboolnet.prime_implicants) create_disjoint_union() (in module pyboolnet.prime_implicants) create_empty_igraph() (in module pyboolnet.interaction_graphs) create_image() (in module pyboolnet.interaction_graphs) create_inputs() (in module pyboolnet.prime_implicants) create_phenotypes_piechart() (in module pyboolnet.phenotypes) create_stg_image() (in module pyboolnet.state_transition_graphs) create_variables() (in module pyboolnet.prime_implicants) cycle_free_basin() (in module pyboolnet.basins_of_attraction) cycle_graph() (in module pyboolnet.network_generators)

E

energy() (in module pyboolnet.state_transition_graphs) enumerate_states() (in module pyboolnet.state_space)

exists_finally_nested_reachability() (in module pyboolnet.temporal_logic) exists_finally_one_of_subspaces() (in module pyboolnet.temporal_logic) exists_finally_unsteady_components() (in module pyboolnet.temporal_logic)

F

faithfulness() (in module pyboolnet.attractors) faithfulness_with_counterexample() (in module pyboolnet.attractors) find_attractor_state_by_randomwalk_and_ctl() (in module pyboolnet.attractors) find_constants() (in module pyboolnet.prime_implicants) find_inputs() (in module pyboolnet.prime_implicants) find_minimal_autonomous_nodes() (in module pyboolnet.interaction_graphs)

find_outputs() (in module pyboolnet.prime_implicants) find_predecessors() (in module pyboolnet.prime_implicants) find_successors() (in module pyboolnet.prime_implicants) find_vanham_variables() (in module pyboolnet.state_space) functions2mindnf() (in module pyboolnet.boolean_normal_forms) functions2primes() (in module pyboolnet.boolean_normal_forms)

G

get_constant_primes() (in module pyboolnet.prime_implicants)

get_dnf() (in module pyboolnet.boolean_normal_forms)

H

hamming_distance() (in module pyboolnet.state_space)

htg2dot() (in module pyboolnet.state_transition_graphs) htg2image() (in module pyboolnet.state_transition_graphs)

I

igraph2dot() (in module pyboolnet.interaction_graphs) igraph2image() (in module pyboolnet.interaction_graphs) implies() (in module pyboolnet.boolean_logic) intersection() (in module pyboolnet.attractors)

is_constant() (in module pyboolnet.prime_implicants) is_power_of_two_or_zero() (in module pyboolnet.boolean_normal_forms) is_subspace() (in module pyboolnet.state_space) is_trap_space() (in module pyboolnet.trap_spaces) iterative_completeness_algorithm() (in module pyboolnet.attractors)

L

list_input_combinations() (in module pyboolnet.prime_implicants) list_reachable_states() (in module pyboolnet.state_transition_graphs)

list_states_in_subspace() (in module pyboolnet.state_space) local_igraph_of_state() (in module pyboolnet.interaction_graphs) local_igraph_of_states() (in module pyboolnet.interaction_graphs)

M

merge() (in module pyboolnet.boolean_normal_forms) minimize_espresso() (in module pyboolnet.boolean_logic) model_checking() (in module pyboolnet.model_checking) model_checking_smv_file() (in module pyboolnet.model_checking) module pyboolnet.attractors pyboolnet.basins_of_attraction pyboolnet.boolean_logic pyboolnet.boolean_normal_forms pyboolnet.commitment_diagrams pyboolnet.file_exchange pyboolnet.interaction_graphs pyboolnet.model_checking pyboolnet.network_generators pyboolnet.phenotypes pyboolnet.prime_implicants pyboolnet.state_space pyboolnet.state_transition_graphs pyboolnet.temporal_logic pyboolnet.trap_spaces

O

open_commitment_diagram() (in module pyboolnet.commitment_diagrams)

open_phenotype_diagram() (in module pyboolnet.phenotypes)

P

path_graph() (in module pyboolnet.network_generators) percolate() (in module pyboolnet.prime_implicants) phenotype_diagram2image() (in module pyboolnet.phenotypes) primes2bnet() (in module pyboolnet.file_exchange) primes2bns() (in module pyboolnet.file_exchange) primes2eqn() (in module pyboolnet.file_exchange) primes2genysis() (in module pyboolnet.file_exchange) primes2igraph() (in module pyboolnet.interaction_graphs) primes2mindnf() (in module pyboolnet.boolean_normal_forms) primes2smv() (in module pyboolnet.model_checking) primes2stg() (in module pyboolnet.state_transition_graphs) primes_are_equal() (in module pyboolnet.prime_implicants) print_warning_accepting_states_bug() (in module pyboolnet.model_checking) pyboolnet.attractors module pyboolnet.basins_of_attraction module pyboolnet.boolean_logic module pyboolnet.boolean_normal_forms module

pyboolnet.commitment_diagrams module pyboolnet.file_exchange module pyboolnet.interaction_graphs module pyboolnet.model_checking module pyboolnet.network_generators module pyboolnet.phenotypes module pyboolnet.prime_implicants module pyboolnet.state_space module pyboolnet.state_transition_graphs module pyboolnet.temporal_logic module pyboolnet.trap_spaces module

R

random_boolean_expression() (in module pyboolnet.network_generators) random_regular_network() (in module pyboolnet.network_generators) random_state() (in module pyboolnet.state_space) random_successor_asynchronous() (in module pyboolnet.state_transition_graphs) random_successor_mixed() (in module pyboolnet.state_transition_graphs) random_truth_table_network() (in module pyboolnet.network_generators)

random_walk() (in module pyboolnet.state_transition_graphs) read_attractors_json() (in module pyboolnet.attractors) read_primes() (in module pyboolnet.file_exchange) remove_all_constants() (in module pyboolnet.prime_implicants) remove_all_variables_except() (in module pyboolnet.prime_implicants) remove_variables() (in module pyboolnet.prime_implicants) rename_variable() (in module pyboolnet.prime_implicants)

S

save_commitment_diagram() (in module pyboolnet.commitment_diagrams) save_phenotype_diagram() (in module pyboolnet.phenotypes) sccgraph2dot() (in module pyboolnet.state_transition_graphs) sccgraph2image() (in module pyboolnet.state_transition_graphs) size_state_space() (in module pyboolnet.state_space) state2dict() (in module pyboolnet.state_space) state2str() (in module pyboolnet.state_space) state_is_in_subspace() (in module pyboolnet.state_space) states2dict() (in module pyboolnet.state_space) states2str() (in module pyboolnet.state_space) stg2condensationgraph() (in module pyboolnet.state_transition_graphs)

stg2dot() (in module pyboolnet.state_transition_graphs) stg2htg() (in module pyboolnet.state_transition_graphs) stg2image() (in module pyboolnet.state_transition_graphs) stg2sccgraph() (in module pyboolnet.state_transition_graphs) strong_basin() (in module pyboolnet.basins_of_attraction) subspace2dict() (in module pyboolnet.state_space) subspace2proposition() (in module pyboolnet.temporal_logic) subspace2str() (in module pyboolnet.state_space) successor_synchronous() (in module pyboolnet.state_transition_graphs) successors_asynchronous() (in module pyboolnet.state_transition_graphs) successors_mixed() (in module pyboolnet.state_transition_graphs)

U

univocality() (in module pyboolnet.attractors)

univocality_with_counterexample() (in module pyboolnet.attractors) update_primes() (in module pyboolnet.prime_implicants)

W

weak_basin() (in module pyboolnet.basins_of_attraction)

write_attractors_json() (in module pyboolnet.attractors) write_primes() (in module pyboolnet.file_exchange)