Index of values


($$) [List_util.Infix]
cons_option

A
a_loop [State_interpreter]
One event loop
above_average [Priority]
action_of_json [Instantiation]
action_to_json [Instantiation]
actions_of_step [Trace]
add [Communication.PathMap]
add [Ode_interface_sig.Interface.ObsMap]
add [Alg_expr]
add [Fractions]
add [Nbr]
add [Loggers.FormatMap]
add [Buffers.Buffers]
add [ValMap]
add [IntCollection]
add [SetMap.Map]
add [SetMap.Set]
add_agent [Build_graph]
add_agent [Ckappa_sig]
add_agent [Edges]
add_agent ?id sigs agent_type graph
add_agent_id [Ckappa_sig]
add_binding_type [Ckappa_sig]
add_bound [Ckappa_sig]
add_cc [Matching]
add_dep [Alg_expr]
depend in time, depend in event number, depend in given var
add_dep_bool [Alg_expr]
add_edge [Loggers]
add_free [Ckappa_sig]
add_free [Edges]
add_free agent_id site graph
add_initial_state [Static_contact_map_domain.Domain]
add_initial_state [Composite_domain.Composite_domain]
add_initial_state [Analyzer_domain_sig.Domain]
add_internal [Edges]
add_internal agent_id site internal_state graph
add_internal_state [Ckappa_sig]
add_link [Build_graph]
add_link [Ckappa_sig]
add_link [Edges]
add_link ag1 s1 ag2 s2 t Some (i,j) as second returned element means cc j is now merged into cc i
add_node [Loggers]
add_oriented_relation [Static_contact_map_domain.Domain]
add_plot_line [Data]
add_relation [Static_contact_map_domain.Domain]
add_rule [Communication]
add_rule_id [Ckappa_sig]
add_site [Communication]
add_site [Build_graph]
add_site [Ckappa_sig]
add_wake_up_relation [Analyzer_headers]
add_while_testing_freshness [SetMap.Map]
add_while_testing_freshness [SetMap.Set]
add_with_logs [SetMap.Map]
add_with_logs [SetMap.Set]
agent_id_of_int [Ckappa_sig]
agent_name_of_int [Ckappa_sig]
agent_of_num [Signature]
alg_expr [Kappa_printer]
algs_finder [Model]
all_agents_where [Edges]
all_dependencies [Model]
allocate [Loggers]
allocate_fresh_name [Loggers]
allowed_link [Signature]
allowed_link ag1 s1 ag2 s2 sigs
annot_of_yojson [Locality]
annot_to_yojson [Locality]
append [DynamicArray.DynArray]
append [GenArray.GenArray]
apply [Ode_interface_sig.Interface]
apply_event_list [Static_contact_map_domain.Domain]
apply_event_list [Analyzer_domain_sig.Domain]
apply_rule [Static_contact_map_domain.Domain]
apply_rule [Composite_domain.Composite_domain]
apply_rule [Analyzer_domain_sig.Domain]
are_connected [Edges]
are_connected ?max_distance graph nodes_x nodes_y
arity [Signature]
arity sigs agent_id
array [Pp]
array_compare [Tools]
array_filter [Tools]
array_fold_left2i [Tools]
array_fold_left_mapi [Tools]
array_fold_lefti [Tools]
array_fold_righti [Tools]
array_map_of_list [Tools]
array_min_equal_not_null [Tools]
array_of_list_rule_id [Ckappa_sig]
array_rev_map_of_list [Tools]
array_rev_of_list [Tools]
associate [Ode_loggers]
associate_nonnegative [Ode_loggers]
associate_nrows [Ode_loggers]
associate_t [Ode_loggers]
automorphisms [Pattern]
average [Priority]

B
begin_new [Pattern]
Starts creation
bellow_average [Priority]
bin_alg_op_of_json [Operator]
bin_alg_op_to_json [Operator]
bin_bool_op_of_json [Operator]
bin_bool_op_to_json [Operator]
bind [Option_util]
bindings [SetMap.Map]
black_list [Utilities]
blit [DynamicArray.DynArray]
blit [GenArray.GenArray]
bool_expr [Kappa_printer]
bool_of_yojson [Alg_expr]
bool_to_yojson [Alg_expr]
bottom [Pp]
build_address [Cckappa_sig]
build_association_list [Mvbdu_wrapper.Internalized_mvbdu]
build_association_list [Mvbdu_wrapper.Mvbdu]
build_initial_state [Eval]
build_parameter [Compression_main]
build_range_list [Mvbdu_wrapper.Internalized_mvbdu]
build_range_list [Mvbdu_wrapper.Mvbdu]
build_renaming_list [Mvbdu_wrapper.Internalized_mvbdu]
build_renaming_list [Mvbdu_wrapper.Mvbdu]
build_reverse_sorted_association_list [Mvbdu_wrapper.Internalized_mvbdu]
build_reverse_sorted_association_list [Mvbdu_wrapper.Mvbdu]
build_reverse_sorted_range_list [Mvbdu_wrapper.Internalized_mvbdu]
build_reverse_sorted_range_list [Mvbdu_wrapper.Mvbdu]
build_reverse_sorted_renaming_list [Mvbdu_wrapper.Internalized_mvbdu]
build_reverse_sorted_renaming_list [Mvbdu_wrapper.Mvbdu]
build_reverse_sorted_variables_list [Mvbdu_wrapper.Internalized_mvbdu]
build_reverse_sorted_variables_list [Mvbdu_wrapper.Mvbdu]
build_snapshot [Edges]
build_sorted_association_list [Mvbdu_wrapper.Internalized_mvbdu]
build_sorted_association_list [Mvbdu_wrapper.Mvbdu]
build_sorted_range_list [Mvbdu_wrapper.Internalized_mvbdu]
build_sorted_range_list [Mvbdu_wrapper.Mvbdu]
build_sorted_renaming_list [Mvbdu_wrapper.Internalized_mvbdu]
build_sorted_renaming_list [Mvbdu_wrapper.Mvbdu]
build_sorted_variables_list [Mvbdu_wrapper.Internalized_mvbdu]
build_sorted_variables_list [Mvbdu_wrapper.Mvbdu]
build_variables_list [Mvbdu_wrapper.Internalized_mvbdu]
build_variables_list [Mvbdu_wrapper.Mvbdu]

C
c_rule_id_of_string [Ckappa_sig]
canonic_form [Ode_interface_sig.Interface]
capitalize [Tools]
causal [Priority]
causal_prefix_of_an_observable_hit [Utilities]
cc_mixture_is_reachable [Static_contact_map_domain.Domain]
cc_of_state [Replay]
channel_of_logger [Loggers]
check_edge [Navigation]
check_if_counter_is_filled_enough [Model]
check_orbit_binding_state_permutation [LKappa_group_action]
check_orbit_full_permutation [LKappa_group_action]
check_orbit_internal_state_permutation [LKappa_group_action]
choose [SetMap.Set]
clean [Symmetries_sig]
clean [Buffers.Buffers]
clear_sites_working_list [Communication]
close [Outputs]
close_asso [Graph_loggers]
close_logger [Loggers]
close_procedure [Ode_loggers]
close_row [Loggers]
colon [Pp]
comma [Pp]
compact_comma [Pp]
compare [Agent]
compare [Nbr]
compare [SetMap.OrderedType]
compare [SetMap.Map]
compare [SetMap.Set]
compare_agent_id [Ckappa_sig]
compare_agent_name [Ckappa_sig]
compare_by_story_id [Trace.Simulation_info]
compare_canonical_form [Utilities]
compare_canonicals [Pattern]
compare_connected_component [Ode_interface_sig.Interface]
compare_op_of_json [Operator]
compare_op_to_json [Operator]
compare_rule_id [Ckappa_sig]
compare_site_name [Ckappa_sig]
compare_state_index [Ckappa_sig]
compare_unit [Ckappa_sig]
compare_unit_agent_name [Ckappa_sig]
compare_unit_agent_site [Ckappa_sig]
compare_unit_site_name [Ckappa_sig]
compare_unit_state_index [Ckappa_sig]
compatible_fresh_point [Navigation]
Retuns the extension of the given injections so that the second edge is the image of the first
compil_of_json [Ast]
compil_to_json [Ast]
compile [Eval]
compile_bool [Eval]
compile_inits [Eval]
compile_modifications_no_track [Eval]
complete_progress_bar [Counter]
complete_progress_bar [Progress_report]
complete_wake_up_relation [Static_contact_map_domain.Domain]
complete_wake_up_relation [Analyzer_domain_sig.Domain]
compose_embeddings_unary_binary [Ode_interface_sig.Interface]
compress [Utilities]
compress a trace with the level of abstraction defined in the argument parameter.
compress_and_print [Compression_main]
computation_steps_to_json [Utilities]
compute_canonical_form [Utilities]
compute_initial_state [Analyzer_headers]
compute_symmetries_from_model [Odes.Make]
concat [DynamicArray.DynArray]
concat [GenArray.GenArray]
concretize [Navigation]
concretize [Primitives.Transformation]
concretize [Matching.Agent]
concretize_action [Instantiation]
concretize_event [Instantiation]
concretize_test [Instantiation]
connected_component_of_string [User_graph]
Deserialize JSON data of type User_graph.connected_component.
connected_components_of_mixture [Ode_interface_sig.Interface]
connected_components_of_patterns [Ode_interface_sig.Interface]
connected_components_sum_of_ambiguous_mixture [Snip]
connected_components_sum_of_ambiguous_rule [Snip]
cons_option [List_util]
consecutive_null_event [Counter]
const [Alg_expr]
Smart constructor
consume [Ode_loggers]
consume_jac [Ode_loggers]
contact_map [Model]
content [Pattern.Env]
convert_trace_into_grid [Utilities]
convert_trace_into_musical_notation [Utilities]
copy [Edges]
You'd better NOT use that on the state of a simulation
copy [DynamicArray.DynArray]
copy [GenArray.GenArray]
copy_agent_in_lkappa [Patterns_extra]
copy_agent_in_raw_mixture [Patterns_extra]
copy_log_info [Utilities]
copy_rule_agent [LKappa]
cos [Alg_expr]
count_stories [Utilities]
Give the number of stories (up to isomorphism classes) stored in a table
counter_of_site [Signature]
create [Counter]
create [Progress_report]
create [Raw_mixture]
create [Signature]
create [NamedDecls]
create [Buffers.Buffers]
create [Int_storage.Storage]
create [IntCollection]
create initial_guess_size
create [DynamicArray.DynArray]
create [GenArray.GenArray]
create_biggest_key [Int_storage.Storage]
create_black_list [Utilities]
create_story_table [Utilities]
Initialization
creation_of_actions [Trace]
creation_of_step [Trace]
current_event [Counter]
current_simulation_info [Counter]
current_story [Counter]
current_time [Counter]
cut [Utilities]
cut performs partial order reduction and remove orthogonal events
cut [Pp]
cut_rev_trace [Utilities]

D
debug_print [Edges]
debug_print [Matching]
debug_print [Pattern.PreEnv]
debug_print [NamedDecls]
debug_print_id [Pattern]
declare_global [Ode_loggers]
declare_init [Ode_loggers]
default_internal_state [Signature]
default_message_delimter [Tools]
default_progress [Counter]
dep [Alg_expr_extra]
deps [Pattern.Env]
depset_of_yojson [Operator]
depset_to_yojson [Operator]
detect_symmetries [Symmetries]
detect_symmetries [Ode_interface_sig.Interface]
diff [SetMap.Map]
diff [SetMap.Set]
diff a b = minus (union a b) (inter a b)
diff_mixture [Alg_expr_extra]
diff_pred [SetMap.Map]
diff_pred_with_logs [SetMap.Map]
diff_token [Alg_expr_extra]
diff_with_logs [SetMap.Map]
diff_with_logs [SetMap.Set]
dimension [Int_storage.Storage]
disjoint_union [Ode_interface_sig.Interface]
disjoint_union [SetMap.Set]
disjoint_union_with_logs [SetMap.Set]
div [Alg_expr]
div [Fractions]
div_scal [Affine_combinations]
divide_expr_by_int [Alg_expr_extra]
divide_rule_rate_by [Ode_interface_sig.Interface]
do_modifications [State_interpreter]
do_step [Replay]
do_we_count_in_embeddings [Ode_interface_sig.Interface]
do_we_prompt_reactions [Ode_interface_sig.Interface]
domain [Model]
dot [Pp]
dummy [Pattern.ObsMap]
dummy [Locality]
dummy_agent_id [Ckappa_sig]
dummy_agent_name [Ckappa_sig]
dummy_annot [Locality]
dummy_chemical_species [Ode_interface_sig.Interface]
dummy_dead_rules [Analyzer_headers]
dummy_html_logger [Loggers]
dummy_init [Cckappa_sig]
dummy_link_value [Ckappa_sig]
dummy_precondition [Communication]
dummy_rule_id [Ckappa_sig]
dummy_site_name [Ckappa_sig]
dummy_site_name_1 [Ckappa_sig]
dummy_site_name_minus1 [Ckappa_sig]
dummy_state_index [Ckappa_sig]
dummy_state_index_1 [Ckappa_sig]
dummy_step [Trace]
dummy_txt_logger [Loggers]
dump_c_compil [Export_to_KaSa.Type]
dump_contact_map [Export_to_KaSa.Type]
dump_errors_light [Export_to_KaSim.Type]
dump_json [Loggers]

E
e_of_yojson [Alg_expr]
e_to_yojson [Alg_expr]
elementary_rule [Kappa_printer]
elements [SetMap.Set]
elements_with_types [Matching]
elt_id [NamedDecls]
elt_name [NamedDecls]
embeddings_to_fully_specified [Pattern]
empty [Symmetries_sig]
empty [Communication.PathMap]
empty [Ode_interface_sig.Interface.ObsMap]
empty [State_interpreter]
empty ~with_delta_activities env stopping_times
empty [Edges]
empty [Matching]
empty [Pattern.PreEnv]
empty [Loggers.FormatMap]
empty [ValMap]
empty [SetMap.Map]
empty [SetMap.Set]
empty [Pp]
empty_actions [Cckappa_sig]
empty_association_list [Mvbdu_wrapper.Internalized_mvbdu]
empty_association_list [Mvbdu_wrapper.Mvbdu]
empty_cache [Symmetries]
empty_cache [Ode_interface_sig.Interface]
empty_cache [Matching]
empty_cc [Pattern]
empty_compil [Ast]
empty_constraints_list [Export_to_KaSa.Type]
empty_event [Instantiation]
empty_path [Edges]
empty_range_list [Mvbdu_wrapper.Internalized_mvbdu]
empty_range_list [Mvbdu_wrapper.Mvbdu]
empty_renaming_list [Mvbdu_wrapper.Internalized_mvbdu]
empty_renaming_list [Mvbdu_wrapper.Mvbdu]
empty_set [Pp]
empty_variables_list [Mvbdu_wrapper.Internalized_mvbdu]
empty_variables_list [Mvbdu_wrapper.Mvbdu]
end_of_simulation [State_interpreter]
What to do after stopping simulation.
enrich_grid_with_transitive_past_of_each_node_without_a_progress_bar [Utilities]
enrich_grid_with_transitive_past_of_observables_with_a_progress_bar [Utilities]
compute transitive closure with different parameters (progress_bar, gc)
enrich_grid_with_transitive_past_of_observables_without_a_progress_bar [Utilities]
env [Kappa_printer]
env_kappa [Kappa_printer]
equal [Mvbdu_wrapper.Internalized_mvbdu]
equal [Mvbdu_wrapper.Mvbdu]
equal [Option_util]
equal [SetMap.Map]
equal [SetMap.Set]
equal_with_logs [Mvbdu_wrapper.Mvbdu]
equiv_class [Symmetries]
equiv_class [LKappa_group_action]
equiv_class_of_a_pattern [Pattern_group_action]
equiv_class_of_a_species [Pattern_group_action]
equiv_class_of_pattern [Ode_interface_sig.Interface]
error [Pp]
error_init [Utilities]
error_init is an empty log of errors
error_list_to_json [Utilities]
event [Trace.Simulation_info]
event_of_json [Instantiation]
event_percentage [Counter]
event_to_json [Instantiation]
exists [SetMap.Set]
exists_fresh [Edges]
exists_fresh ag1 site1 type_of_ag2 site2 graph
exists_modification [Primitives]
exists_uniq [List_util]
expand [DynamicArray.DynArray]
expand_and_copy [Int_storage.Storage]
export [Static_contact_map_domain.Domain]
export [Composite_domain.Composite_domain]
export [Analyzer_domain_sig.Domain]
export [Analyzer.Analyzer]
export [Build_graph]
export_handler [Mvbdu_wrapper.Internalized_mvbdu]
export_musical_grid_to_xls [Utilities]
Show the current status of the branch and cut assumptions in a libreoffice macro file
export_network [Odes.Make]
export_plot [Data]
export_story_table [Utilities]
convert a table into a list of grid (with runtime information)
extensional_of_association_list [Mvbdu_wrapper.Internalized_mvbdu]
extensional_of_association_list [Mvbdu_wrapper.Mvbdu]
extensional_of_mvbdu [Mvbdu_wrapper.Internalized_mvbdu]
extensional_of_mvbdu [Mvbdu_wrapper.Mvbdu]
extensional_of_range_list [Mvbdu_wrapper.Mvbdu]
extensional_of_variables_list [Mvbdu_wrapper.Internalized_mvbdu]
extensional_of_variables_list [Mvbdu_wrapper.Mvbdu]
extract_abstract_event [Primitives]
extract_cc_ids [Primitives]
extract_connected_components [Alg_expr]
extract_connected_components_bool [Primitives]
extract_connected_components_bool [Alg_expr]
extract_connected_components_modifications [Primitives]
extract_observable_hit_from_musical_notation [Utilities]
extract_observable_hits_from_musical_notation [Utilities]

F
fact [Tools]
fill [Counter]
fill [DynamicArray.DynArray]
fill [GenArray.GenArray]
fill_siphon [Utilities]
fill_siphon adds spurious init event, to break causal dependences; Currently, it inserts an init event when an agent return to its initial state; other heuristics may be considered; The output has to be disanbiguated, otherwise it is useless (compression will remove the ficitious init events) It should work in quasi linear time (I think)
filter [SetMap.Set]
filter_one [SetMap.Map]
filter_with_logs [SetMap.Set]
finalize [Pattern]
find [Communication.PathMap]
find [Raw_mixture]
find [Loggers.FormatMap]
find_all_embeddings [Ode_interface_sig.Interface]
find_default [SetMap.Map]
find_default_with_logs [SetMap.Map]
find_embeddings [Ode_interface_sig.Interface]
find_option [List_util]
find_option [SetMap.Map]
find_option_with_logs [SetMap.Map]
find_ty [Pattern]
Abstraction leak, please do not use
finish_new [Pattern]
flag_dangerous [Loggers]
flatten_story_table [Utilities]
put together the stories having the same canonic form, this has do be done explicitely on the moment, I will improve this soon
flip_label [Ast]
float [Alg_expr]
float_is_zero [Tools]
flush_and_clean [Loggers]
flush_buffer [Loggers]
flush_errors [Export_to_KaSim.Type]
flush_logger [Loggers]
flux_kind_of_string [Primitives]
Deserialize JSON data of type Primitives.flux_kind.
flux_kind_of_yojson [Primitives]
flux_kind_to_yojson [Primitives]
flux_map_of_string [Data]
Deserialize JSON data of type Data.flux_map.
fold [Pattern]
fold [Signature]
fold [NamedDecls]
fold [Int_storage.Storage]
fold [IntCollection]
fold [SetMap.Map]
fold [SetMap.Set]
fold2_common [Int_storage.Storage]
fold2_sparse_with_logs [SetMap.Map]
fold2_with_logs [SetMap.Map]
fold2z_with_logs [SetMap.Map]
fold_ast_rules [Model]
fold_inv [SetMap.Set]
fold_left2 [List_util]
fold_left_with_progress_bar [Utilities]
fold_lefti [Pattern.ObsMap]
fold_lefti [DynamicArray.DynArray]
fold_lefti [GenArray.GenArray]
fold_over_mixtures_in_alg_exprs [Alg_expr_extra]
fold_over_permutations [Tools]
fold_over_potential_partners [Communication]
fold_over_the_causal_past_of_observables_with_a_progress_bar [Utilities]
fold over the causal past of each observable in a given trace, the first argument indicates whether we display the current steps on the err output; the second arfument indicated whether the function is launched in debug mode or not
fold_perturbations [Model]
fold_restriction_with_logs [SetMap.Map]
fold_restriction_with_missing_associations_with_logs [SetMap.Map]
fold_right_map [List_util]
fold_righti [DynamicArray.DynArray]
fold_righti [GenArray.GenArray]
fold_rules [Model]
fold_sites [Communication]
fold_story_table_with_progress_bar [Utilities]
fold_story_table_without_progress_bar [Utilities]
Apply a function on each trace (and each list of runtime information associated to this trace), the string contains the message to display in case of faillure of one call of the ternary function
fold_trace_file [Trace]
fold_with_interruption [Int_storage.Storage]
fold_with_interruption [SetMap.Map]
follow_path_inside_cc [Communication]
for_all [SetMap.Map]
for_all [SetMap.Set]
forbid_modification [LKappa]
formatter_of_logger [Loggers]
fprintf [Loggers]
free [Int_storage.Storage]
free_all [Int_storage.Storage]
fst_site [Ckappa_sig]

G
gcd_2 [Tools]
get [Ode_interface_sig.Interface.ObsMap]
get [Matching]
get [Pattern.Env]
get [Pattern.ObsMap]
get [Signature]
get sigs agent_id
get [Int_storage.Storage]
get [DynamicArray.DynArray]
get [GenArray.GenArray]
get_action_binding [Analyzer_headers]
get_agent_color [Ckappa_sig]
get_agent_id [Communication]
get_agent_name [Analyzer_headers]
get_agent_name_from_pattern [Analyzer_headers]
get_agent_shape [Ckappa_sig]
get_alg [Model]
get_alg_reverse_dependencies [Model]
get_algs [Model]
get_ast [Odes.Make]
get_ast [Ode_interface_sig.Interface]
get_ast_rule [Model]
get_ast_rule_rate_pos [Model]
get_bond_lhs [Static_contact_map_domain.Domain]
get_bond_rhs [Static_contact_map_domain.Domain]
get_bonds_lhs [Analyzer_headers]
get_bonds_rhs [Analyzer_headers]
get_c_compilation [Export_to_KaSa.Type]
get_cc_code [Analyzer_headers]
get_cflow [Kappa_files]
get_comment [Odes.Make]
get_common_views [Analyzer_headers]
get_compil [Static_contact_map_domain.Domain]
get_compil [Odes.Make]
get_compil [Ode_interface_sig.Interface]
get_compilation_information [Analyzer_headers]
get_connected_component [Edges]
get_constraints_list [Export_to_json.Type]
get_constraints_list [Export_to_KaSa.Type]
get_contact_map [Export_to_KaDE.Type]
get_contact_map [Export_to_json.Type]
get_contact_map [Export_to_KaSa.Type]
get_contact_map [Export_to_KaSim.Type]
get_corrected_rate [Alg_expr_extra]
get_counter [Utilities]
get_covering_classes [Analyzer_headers]
get_covering_classes_id [Analyzer_headers]
get_ctmc_flow [Export_to_KaSa.Type]
get_data [Export_to_KaSa.Type]
get_data [Odes.Make]
get_dead_rules [Export_to_json.Type]
get_dead_rules [Export_to_KaSim.Type]
get_dead_rules [Static_contact_map_domain.Domain]
get_dead_rules [Analyzer_domain_sig.Domain]
get_defined_in [Communication]
get_dir [Kappa_files]
get_divide_rate_by [Odes.Make]
get_edge_map [Loggers]
get_efficiency [Counter]
get_elementary [Pattern.Env]
get_encoding_format [Loggers]
get_env [Export_to_KaSa.Type]
get_errors [Export_to_KaDE.Type]
get_errors [Export_to_json.Type]
get_errors [Export_to_KaSa.Type]
get_errors_json [Export_to_json.Type]
get_expr [Loggers]
get_fresh_meta_id [Loggers]
get_fresh_obs_id [Loggers]
get_fresh_reaction_id [Loggers]
get_global_dynamic_information [Static_contact_map_domain.Domain]
get_global_dynamic_information [Composite_domain.Composite_domain]
get_global_dynamic_information [Analyzer_domain_sig.Domain]
get_global_static_information [Static_contact_map_domain.Domain]
get_handler [Export_to_KaDE.Type]
get_handler [Export_to_KaSa.Type]
get_handler [Mvbdu_wrapper.Mvbdu]
get_id [Matching.Agent]
get_id_of_event [Utilities]
get the id of an event in the simulation (only proper events have an id)
get_id_of_global_parameter [Loggers]
get_influence_map [Export_to_json.Type]
get_influence_map [Export_to_KaSa.Type]
get_init [Ode_interface_sig.Interface]
get_internal [Edges]
get_internal ag site graph
get_internal_contact_map [Export_to_KaSa.Type]
get_interval_list [Tools]
get_kappa_handler [Static_contact_map_domain.Domain]
get_kappa_handler [Analyzer_headers]
get_lhs [Odes.Make]
get_lhs_cc [Odes.Make]
get_list_of_site_type_in_covering_classes [Analyzer_headers]
get_local_influence_map [Export_to_json.Type]
get_local_influence_map [Export_to_KaSa.Type]
get_log_info [Analyzer_headers]
get_logger [Compression_main]
Use
get_modified_map [Analyzer_headers]
get_mvbdu_handler [Analyzer_headers]
get_nodes [Loggers]
get_obs [Ode_interface_sig.Interface]
get_obs [Model]
get_obs_titles [Ode_interface_sig.Interface]
get_ode [Kappa_files]
get_ode_flow [Export_to_KaSa.Type]
get_parameter [Static_contact_map_domain.Domain]
get_parameter [Analyzer_domain_sig.Domain]
get_parameter [Analyzer_headers]
get_parameters [Export_to_KaDE.Type]
get_parameters [Export_to_KaSa.Type]
get_perturbation [Model]
get_potential_partner [Communication]
get_potential_side_effects [Analyzer_headers]
get_potential_side_effects_per_rule [Analyzer_headers]
get_preprocessed_ast [Odes.Make]
get_preprocessed_ast [Ode_interface_sig.Interface]
get_pretrace_of_trace [Utilities]
conversely, convert a trace in a list of refined steps
get_product_image_occ [Tools]
get_product_image_occ_2 [Tools]
get_project_modified_map [Analyzer_headers]
get_reachability_analysis [Export_to_KaSa.Type]
get_reactions [Odes.Make]
get_relative_address [Communication]
get_remanent_triple [Analyzer_headers]
get_representative [Ode_interface_sig.Interface]
get_rule [Odes.Make]
get_rule [Model]
get_rule_cache [Ode_interface_sig.Interface]
get_rule_id_with_mode [Odes.Make]
get_rules [Ode_interface_sig.Interface]
get_rules [Model]
get_runtime_info_from_observable_hit [Utilities]
Musical processing
get_scc_decomposition [Export_to_json.Type]
get_scc_decomposition [Export_to_KaSa.Type]
get_side_effects [Analyzer_headers]
get_simulation_time_of_event [Utilities]
get the date of an event in the simulation (only proper events have a time)
get_single_agent [Pattern.Env]
get_site [Communication]
get_sites [Edges]
get_sort [Edges]
get_state_of_site [Communication]
get_state_of_site_in_postcondition [Communication]
get_state_of_site_in_precondition [Communication]
get_symmetric_sites [Export_to_KaSa.Type]
get_test_modif_map [Analyzer_headers]
get_token_reverse_dependencies [Model]
get_type [Matching.Agent]
get_variables [Ode_interface_sig.Interface]
get_views_lhs [Analyzer_headers]
get_views_rhs [Analyzer_headers]
get_wake_up_relation [Analyzer_headers]
glb_list [Usual_domains]
go [Outputs]
graph_of_logger [Loggers]
graph_page [Pp_html]
graph_page title deps header core f

H
has_counter [Signature]
has_creation_of_step [Trace]
has_dummy_annot [Locality]
has_forbidden_char [Loggers]
has_mix [Alg_expr]
has_obs [Utilities]
check wether there is an observable in a trace
hash_of_association_list [Mvbdu_wrapper.Internalized_mvbdu]
hash_of_association_list [Mvbdu_wrapper.Mvbdu]
hash_of_range_list [Mvbdu_wrapper.Mvbdu]
hash_of_variables_list [Mvbdu_wrapper.Internalized_mvbdu]
hash_of_variables_list [Mvbdu_wrapper.Mvbdu]
hashtbl [Pp]
high [Priority]
higher [Priority]
highest [Priority]

I
id [Agent]
id_of_internal_state [Signature]
id_of_internal_state agent_type site_name state_name sigs
id_of_site [Signature]
id_of_site agent_type site_name sigs
id_of_yojson [Pattern]
id_to_yojson [Pattern]
imperative_edge_is_valid [Navigation]
implicit_signature [Ast]
Infer agent signatures and tokens from init, rules and perturbations
import_handler [Mvbdu_wrapper.Internalized_mvbdu]
in_same_connected_component [Edges]
inc_stories [Counter]
incr_agent [Signature]
id, arity, before, after
increment [Ode_loggers]
infs [Pattern]
init [Export_to_KaDE.Type]
init [Export_to_json.Type]
init [Export_to_KaSa.Type]
init [Export_to_KaSim.Type]
init [Build_graph]
init [Mvbdu_wrapper.Internalized_mvbdu]
init [Mvbdu_wrapper.Mvbdu]
init [Odes.Make]
init [Model]
init sigs tokens algs dependencies (ast_rules,rules) obs perts
init [Int_storage.Storage]
init [DynamicArray.DynArray]
init [GenArray.GenArray]
init_bwd_bisim_info [Odes.Make]
init_bwd_bisim_info [Ode_interface_sig.Interface]
init_plot [Data]
init_secret_log_info [Compression_main]
init_sites_working_list [Communication]
init_state [Replay]
init_time [Counter]
init_time [Ode_loggers]
init_trace_file [Trace]
initial_inputs [Outputs]
initialize [Static_contact_map_domain.Domain]
initialize [Composite_domain.Composite_domain]
initialize [Analyzer_domain_sig.Domain]
initialize [Outputs]
initialize [State_interpreter]
initial env counter graph state builds up the initial state
initialize [Ode_loggers]
initialize_global_information [Analyzer_headers]
injection_for_one_more_edge [Navigation]
input_modifications [Outputs]
int [Alg_expr]
int_compare [Mods]
int_of_agent_id [Ckappa_sig]
int_of_agent_name [Ckappa_sig]
int_of_rule_id [Ckappa_sig]
int_of_site_name [Ckappa_sig]
int_of_state_index [Ckappa_sig]
int_of_string_id [Loggers]
int_pair_compare [Mods]
inter [SetMap.Set]
inter_with_logs [SetMap.Set]
internal_div [Nbr]
euler division when only int are involved, float div else
internal_state_of_num [Signature]
internal_states_number [Signature]
internal_state_number agent_id site_id sigs
introduceable_species_in_pertubation [Ckappa_sig]
inv [Fractions]
is_agent [Edges]
is_agent agent graph
is_const [Loggers]
is_counter_agent [Signature]
is_dangerous_ode_variable [Loggers]
is_empty [ValMap]
is_empty [IntCollection]
is_empty [SetMap.Map]
is_empty [SetMap.Set]
is_enabled [Static_contact_map_domain.Domain]
is_enabled [Composite_domain.Composite_domain]
is_enabled [Analyzer_domain_sig.Domain]
is_equal [Fractions]
is_equal [Nbr]
is_equal_canonicals [Pattern]
is_equality_test_time [Alg_expr]
is_free [Edges]
is_free agent_id site graph
is_fresh [Matching.Agent]
is_greater [Nbr]
is_init [Mvbdu_wrapper.Internalized_mvbdu]
is_init [Mvbdu_wrapper.Mvbdu]
is_internal [Edges]
is_internal internal_state agent_id site graph
is_invariant_binding_states_permutation [LKappa_group_action]
is_invariant_full_states_permutation [LKappa_group_action]
is_invariant_internal_states_permutation [LKappa_group_action]
is_pattern_invariant_binding_states_permutation [Pattern_group_action]
is_pattern_invariant_full_states_permutation [Pattern_group_action]
is_pattern_invariant_internal_states_permutation [Pattern_group_action]
is_root_of [Matching]
is_singleton [SetMap.Set]
is_smaller [Nbr]
is_step_triggerable [Replay]
determines whether or not a step can be applied from a given state.
is_step_triggerable_on_edges [Replay]
same function but takes a graph of type Edges.t directly.
is_strictly_positive [Nbr]
is_subnavigation [Navigation]
is_subnavigation inj_nav2sub nav subpart
is_the_rule_applied_for_the_first_time [Communication]
is_time [Ode_loggers]
is_zero [Fractions]
is_zero [Nbr]
iter [Buffers.Buffers]
iter [Int_storage.Storage]
iter [SetMap.Map]
iter [SetMap.Set]
iter [DynamicArray.DynArray]
iter [GenArray.GenArray]
iter2_sparse_with_logs [SetMap.Map]
iteri [Nbr]
iteri f x n
iteri [Tools]
iteri [DynamicArray.DynArray]
iteri [GenArray.GenArray]

J
join_link [Ckappa_sig]
join_mixture [Cckappa_sig]
join_mixture [Ckappa_sig]
join_with_logs [SetMap.Map]

K
key_list [Int_storage.Storage]

L
last [List_util]
last_eid_in_pretrace [Utilities]
last_entry [Mvbdu_wrapper.Mvbdu]
launch_main [Ode_loggers]
lcm [Tools]
length [Pattern]
length [DynamicArray.DynArray]
length [GenArray.GenArray]
lhs [Ode_interface_sig.Interface]
lift [Static_contact_map_domain.Domain]
lift_embedding [Ode_interface_sig.Interface]
linearise [Affine_combinations]
link_destination [Edges]
link_destination ag site graph
link_exists [Edges]
link_exists ag1_id site1 ag2_id site2 graph
link_of_json [Ast]
link_only_one_occurence [LKappa]
link_to_json [Ast]
Fragile: the list MUST NOT be a singleton
list [Pp]
list_to_string [Pp]
listi [Pp]
lkappa_mixture_is_reachable [Static_contact_map_domain.Domain]
ln [Alg_expr]
lnk_value_of_int [Ckappa_sig]
local_trace [Static_contact_map_domain]
low [Priority]
lower [Priority]
lowercase [Tools]
lowest [Priority]
lub [Usual_domains]

M
main [Analyzer.Analyzer]
make [DynamicArray.DynArray]
make [GenArray.GenArray]
make_unambiguous [Utilities]
reallocate agent id to avoid conflict (implicitly called by cut and fill_siphon)
map [Symmetries_sig]
map [Pattern.ObsMap]
map [Option_util]
map [SetMap.Map]
map [DynamicArray.DynArray]
map [GenArray.GenArray]
map2 [SetMap.Map]
map2_with_logs [SetMap.Map]
map2z_with_logs [SetMap.Map]
map_agent [Cckappa_sig]
map_expr_perturbation [Primitives]
map_expr_rule [Primitives]
map_flatten [List_util]
map_observables [Model]
map_option [List_util]
mapi [NamedDecls]
mapi [List_util]
mapi [SetMap.Map]
matching_abstract_concrete [Instantiation]
matchings [Pattern]
max [Nbr]
max_arity [Signature]
max_arity sigs returns max
max_elt [SetMap.Set]
max_events [Counter]
max_key [SetMap.Map]
max_pos_int_not_zero [Tools]
max_state_index [Cckappa_sig]
max_time [Counter]
maybe_iteri [Nbr]
maybe_iteri f x n
maybe_reachable [Static_contact_map_domain.Domain]
maybe_reachable [Composite_domain.Composite_domain]
maybe_reachable [Analyzer_domain_sig.Domain]
maybe_reachable [Analyzer.Analyzer]
mem [ValMap]
mem [SetMap.Map]
mem [SetMap.Set]
merge [SetMap.Map]
merge_on_inf [Pattern]
merge_uniq [List_util]
Set union of 2 sorted list When l1 is included in l2: merge_uniq l1 l2 == merge_uniq l2 l1 == l2
merge_variables_lists [Mvbdu_wrapper.Internalized_mvbdu]
merge_variables_lists [Mvbdu_wrapper.Mvbdu]
merge_version [Ast]
merge_with_logs [SetMap.Map]
min [Nbr]
min_elt [SetMap.Map]
min_elt [SetMap.Set]
min_level [Priority]
min_pos_int_not_zero [Tools]
min_state_index [Cckappa_sig]
minus [Alg_expr]
minus [SetMap.Set]
minus a b contains elements of a that are not in b
minus_with_logs [SetMap.Set]
mixture_of_init [Ode_interface_sig.Interface]
mixture_to_pattern [Patterns_extra]
mk_dir_r [Kappa_files]
modification [Kappa_printer]
monadic_fold2 [SetMap.Map]
monadic_fold2_sparse [SetMap.Map]
monadic_fold_restriction [SetMap.Map]
monadic_iter2_sparse [SetMap.Map]
mul_scal [Affine_combinations]
mult [Alg_expr]
mult [Fractions]
mult [Nbr]
mvbdu_and [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_and [Mvbdu_wrapper.Mvbdu]
mvbdu_bi_false [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_bi_false [Mvbdu_wrapper.Mvbdu]
mvbdu_bi_true [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_bi_true [Mvbdu_wrapper.Mvbdu]
mvbdu_cartesian_abstraction [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_cartesian_abstraction [Mvbdu_wrapper.Mvbdu]
mvbdu_cartesian_decomposition_depth [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_cartesian_decomposition_depth [Mvbdu_wrapper.Mvbdu]
mvbdu_equiv [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_equiv [Mvbdu_wrapper.Mvbdu]
mvbdu_false [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_false [Mvbdu_wrapper.Mvbdu]
mvbdu_fst [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_fst [Mvbdu_wrapper.Mvbdu]
mvbdu_full_cartesian_decomposition [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_full_cartesian_decomposition [Mvbdu_wrapper.Mvbdu]
mvbdu_id [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_id [Mvbdu_wrapper.Mvbdu]
mvbdu_imply [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_imply [Mvbdu_wrapper.Mvbdu]
mvbdu_nand [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_nand [Mvbdu_wrapper.Mvbdu]
mvbdu_nfst [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_nfst [Mvbdu_wrapper.Mvbdu]
mvbdu_nimply [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_nimply [Mvbdu_wrapper.Mvbdu]
mvbdu_nor [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_nor [Mvbdu_wrapper.Mvbdu]
mvbdu_not [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_not [Mvbdu_wrapper.Mvbdu]
mvbdu_nrev_imply [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_nrev_imply [Mvbdu_wrapper.Mvbdu]
mvbdu_nsnd [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_nsnd [Mvbdu_wrapper.Mvbdu]
mvbdu_of_association_list [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_of_association_list [Mvbdu_wrapper.Mvbdu]
mvbdu_of_hconsed_asso [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_of_hconsed_asso [Mvbdu_wrapper.Mvbdu]
mvbdu_of_hconsed_range [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_of_hconsed_range [Mvbdu_wrapper.Mvbdu]
mvbdu_of_range_list [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_of_range_list [Mvbdu_wrapper.Mvbdu]
mvbdu_of_reverse_sorted_association_list [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_of_reverse_sorted_association_list [Mvbdu_wrapper.Mvbdu]
mvbdu_of_reverse_sorted_range_list [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_of_reverse_sorted_range_list [Mvbdu_wrapper.Mvbdu]
mvbdu_of_sorted_association_list [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_of_sorted_association_list [Mvbdu_wrapper.Mvbdu]
mvbdu_of_sorted_range_list [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_of_sorted_range_list [Mvbdu_wrapper.Mvbdu]
mvbdu_or [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_or [Mvbdu_wrapper.Mvbdu]
mvbdu_project_abstract_away [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_project_abstract_away [Mvbdu_wrapper.Mvbdu]
mvbdu_project_keep_only [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_project_keep_only [Mvbdu_wrapper.Mvbdu]
mvbdu_redefine [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_redefine [Mvbdu_wrapper.Mvbdu]
mvbdu_redefine_range [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_redefine_range [Mvbdu_wrapper.Mvbdu]
mvbdu_rename [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_rename [Mvbdu_wrapper.Mvbdu]
mvbdu_rev_imply [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_rev_imply [Mvbdu_wrapper.Mvbdu]
mvbdu_snd [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_snd [Mvbdu_wrapper.Mvbdu]
mvbdu_subseteq [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_subseteq [Mvbdu_wrapper.Mvbdu]
mvbdu_true [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_true [Mvbdu_wrapper.Mvbdu]
mvbdu_unary_false [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_unary_false [Mvbdu_wrapper.Mvbdu]
mvbdu_unary_true [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_unary_true [Mvbdu_wrapper.Mvbdu]
mvbdu_xor [Mvbdu_wrapper.Internalized_mvbdu]
mvbdu_xor [Mvbdu_wrapper.Mvbdu]

N
n_branch [Priority]
n_story [Priority]
nb_algs [Model]
nb_null_event [Counter]
nb_perturbations [Model]
nb_rules [Model]
nb_syntactic_rules [Model]
nb_tokens [Ode_interface_sig.Interface]
nb_tokens [Model]
nbr_automorphisms_in_chemical_species [Ode_interface_sig.Interface]
nbr_variables [Mvbdu_wrapper.Internalized_mvbdu]
nbr_variables [Mvbdu_wrapper.Mvbdu]
necessarily_equal [Alg_expr_extra]
necessarily_equal [Affine_combinations]
neg [Nbr]
negative_transformations_of_actions [Primitives.Transformation]
network_from_compil [Odes.Make]
new_domain [Model]
new_free [Pattern]
new_internal_state [Pattern]
new_link_type work (node,site) type
new_link [Pattern]
new_link wk (node, site_id) (node', site_id')
new_node [Pattern]
new_node wk node_type
new_obs_map [Pattern.Env]
next_agent_id [Ckappa_sig]
next_agent_name [Ckappa_sig]
next_lnk_value [Ckappa_sig]
next_node_in_influence_map [Export_to_json.Type]
next_rule [Composite_domain.Composite_domain]
next_rule_id [Ckappa_sig]
next_site_name [Ckappa_sig]
next_state_index [Ckappa_sig]
next_story [Counter]
no_more_site_on_right [Ast]
normalize_species [Pattern_group_action]
not_an_id [Tools]
not_enough_specified [LKappa]
nu [Pp]
num_of_agent [Model]
num_of_agent [Signature]
num_of_alg [Model]
num_of_internal_state [Signature]
num_of_internal_state site_id state_name sign
num_of_site [Signature]
num_of_token [Model]
nums_of_rule [Model]

O
observables_from_agent [Matching]
observables_from_free domain graph sort agent the int * int in the return list and the following ones is a Instantiation.concrete
observables_from_free [Matching]
observables_from_free domain graph sort agent site
observables_from_internal [Matching]
observables_from_internal domain graph sort agent site internal_state
observables_from_link [Matching]
observables_from_link domain graph sort ag site sort' ag' site'
observables_values [State_interpreter]
Returns (the current biological time, an array of the current values of observables)
of_bin_alg_op [Nbr]
of_compare_op [Nbr]
of_env [Pattern.PreEnv]
of_int [Affine_combinations]
of_int [Fractions]
of_json [Export_to_json.Type]
of_json [Trace.Simulation_info]
of_json [Raw_mixture]
of_json [Signature]
of_json [Agent]
of_json [NamedDecls]
of_json [Graph_json]
of_json [Loggers]
of_json [SetMap.Map]
of_list [DynamicArray.DynArray]
of_list [GenArray.GenArray]
of_pos [Locality]
of_string [Nbr]
of_un_alg_op [Nbr]
of_yojson [Trace]
of_yojson [Navigation]
of_yojson [Model]
of_yojson [Matching.Agent]
of_yojson [Pattern.Env]
of_yojson [Contact_map]
of_yojson [Nbr]
on_the_fly_cut_finalize [Utilities]
on_the_fly_cut_init [Utilities]
on_the_fly_cut_step [Utilities]
one [Fractions]
one [Nbr]
one_clashing_instance_event [Counter]
one_constructive_event [Counter]
one_no_more_binary_event [Counter]
one_no_more_unary_event [Counter]
one_time_advance [Counter]
one_time_correction_event [Counter]
open_asso [Graph_loggers]
open_branch_and_cut_engine_profiling [Kappa_files]
open_circular_buffer [Loggers]
open_infinite_buffer [Loggers]
open_logger_from_channel [Loggers]
open_logger_from_formatter [Loggers]
open_out [Kappa_files]
open_out_fresh [Kappa_files]
open_out_fresh base facultative ext
open_procedure [Ode_loggers]
open_row [Loggers]
open_tasks_profiling [Kappa_files]
option [Pp]
origin_of_influence_map [Export_to_json.Type]
output_constraints_list [Export_to_KaSa.Type]
output_influence_map [Export_to_KaSa.Type]
output_internal_contact_map [Export_to_KaSa.Type]
output_local_influence_map [Export_to_KaSa.Type]
output_scc_decomposition [Export_to_KaSa.Type]
output_symmetries [Export_to_KaSa.Type]
overwrite_association_lists [Mvbdu_wrapper.Internalized_mvbdu]
overwrite_association_lists [Mvbdu_wrapper.Mvbdu]
overwrite_potential_partners_map [Communication]
overwrite_vars [Model]

P
pair [Pp]
parse [Configuration]
partition [SetMap.Set]
partition_set [SetMap.Projection]
partition_set f set is the map mapping any element b with an antecedent for f in the set set, into the set of its antecedents, ie to the set {a\in set | f(a)=b}.
partition_set_monadic [SetMap.Projection]
partition_with_logs [SetMap.Set]
path [Kappa_files]
pattern_id_to_cc [Patterns_extra]
pattern_id_to_lkappa_rule [Patterns_extra]
pattern_id_to_lkappa_rule_and_unspec [Patterns_extra]
pattern_id_to_mixture [Patterns_extra]
pattern_to_lkappa_rule [Patterns_extra]
pattern_to_mixture [Patterns_extra]
patterns_of_mixture [Snip]
perturbation [Kappa_printer]
perturbation_of_yojson [Primitives]
perturbation_to_yojson [Primitives]
plain_array [Pp]
plot_of_string [Data]
Deserialize JSON data of type Data.plot.
plot_period [Counter]
pop [SetMap.Map]
pop_json [Utilities]
ports_if_counter_agent [Signature]
positive_plot_period [Counter]
positive_transformations_of_actions [Primitives.Transformation]
positive_transformations_of_actions signature side_effect_dsts actions
pow [Alg_expr]
pow [Nbr]
pow [Tools]
pow64 [Tools]
pred [Nbr]
pred_agent_name [Ckappa_sig]
pred_site_name [Ckappa_sig]
pred_state_index [Ckappa_sig]
preprocess [Odes.Make]
preprocess [Ode_interface_sig.Interface]
pretty_print [Nbr]
Floats are compactly printed
previous_node_in_influence_map [Export_to_json.Type]
print [Symmetries_sig]
print [Static_contact_map_domain.Domain]
print [Composite_domain.Composite_domain]
print [Analyzer_domain_sig.Domain]
print [Analyzer.Analyzer]
print [Mvbdu_wrapper.Internalized_mvbdu]
print [Mvbdu_wrapper.Mvbdu]
print [Navigation]
print signatures find_existing_type nav
print [Configuration]
print [Model]
print [Primitives.Transformation]
print [Raw_mixture]
print [Alg_expr_extra]
print [Alg_expr]
print [Matching.Agent]
print [Pattern.Env]
print [Pattern.ObsMap]
print [Pattern]
print ~domain ?with_id:None form cc
print [Signature]
print [Agent]
print [Locality]
print [NamedDecls]
print [Nbr]
print [ValMap]
print [Int_storage.Storage]
print [IntCollection]
print [SetMap.OrderedType]
print [SetMap.Map]
print [SetMap.Set]
print [DynamicArray.DynArray]
print [GenArray.GenArray]
print_agent [Model]
print_agent [Signature]
print_alg [Model]
print_alg_expr_few_parenthesis [Ode_loggers]
print_annot [Locality]
print_as_logger [Loggers]
print_asso [Graph_loggers]
print_association_list [Mvbdu_wrapper.Internalized_mvbdu]
print_association_list [Mvbdu_wrapper.Mvbdu]
print_ast_mix [Ast]
print_ast_rule [Ast]
print_ast_rule [Model]
The int is the ast_rule_id
print_bin_alg_op [Operator]
print_bin_bool_op [Operator]
print_bool [Alg_expr]
print_breakable_hint [Loggers]
print_breakable_space [Loggers]
print_canonic_species [Ode_interface_sig.Interface]
print_cc [User_graph]
print_cc [Pattern]
print_cell [Loggers]
print_chemical_species [Ode_interface_sig.Interface]
print_comment [Ode_loggers]
print_comment [Graph_loggers]
print_compare_op [Operator]
print_concrete_action [Instantiation]
print_concrete_binding_state [Instantiation]
print_concrete_test [Instantiation]
print_connected_component [Ode_interface_sig.Interface]
print_counter [Ast]
print_counter [Signature]
print_cycles [Contact_map]
print_dot_cc [User_graph]
print_dot_flux_map [Data]
print_dot_snapshot [Data]
print_dump_plots [Ode_loggers]
print_edge [Graph_loggers]
print_efficiency [Counter]
print_event_kind [Trace]
print_event_kind_dot_annot [Trace]
print_expr_of_yojson [Primitives]
print_expr_to_yojson [Primitives]
print_expr_val [Kappa_printer]
print_graph_foot [Graph_loggers]
print_graph_preamble [Graph_loggers]
print_html_flux_map [Data]
print_integrate [Ode_loggers]
print_internal [Matching.Agent]
print_internal [Agent]
print_internal_state [Signature]
print_interpolate [Ode_loggers]
print_kappa [Model]
print_kappa [Contact_map]
print_label_of_step [Trace]
print_license_check [Ode_loggers]
print_link [Ast]
print_musical_grid [Utilities]
print_newline [Ode_loggers]
print_newline [Loggers]
print_node [Graph_loggers]
print_ode_preamble [Ode_loggers]
print_one_to_n_relation [Graph_loggers]
print_option [Nbr]
Prints nothing in case of infinity or Not a Number
print_options [Ode_loggers]
print_path [Edges]
print_plot_legend [Data]
print_plot_line [Data]
print_rates [LKappa]
print_rev_dep [Operator]
print_rule [Ode_interface_sig.Interface]
print_rule [LKappa]
print_rule [Model]
Same as above but the int is this time the rule_id
print_rule_content [Ast]
print_rule_id [Ode_interface_sig.Interface]
print_rule_mixture [LKappa]
print_rule_name [Ode_interface_sig.Interface]
print_site [Matching.Agent]
print_site [Signature]
print_site [Agent]
print_site_internal_state [Signature]
print_site_internal_state sigs agent_type site_id f state_id prints both the site and its internal state if it is not None.
print_snapshot [Data]
print_state_alg_op [Operator]
print_step [Trace]
print_symmetries [Symmetries]
print_symmetries [Odes.Make]
print_symmetries [Ode_interface_sig.Interface]
print_token [Ode_interface_sig.Interface]
print_token [Model]
print_trace [Utilities]
print_un_alg_op [Operator]
print_un_bool_op [Operator]
print_variables_list [Mvbdu_wrapper.Internalized_mvbdu]
print_variables_list [Mvbdu_wrapper.Mvbdu]
produce [Ode_loggers]
produce_jac [Ode_loggers]
profiling_state_to_json [Utilities]
proj2 [SetMap.Projection2]
proj2_monadic [SetMap.Projection2]
proj_map [SetMap.Projection]
proj_map f init merge map is a map mapping each element b to the result of the itteration of the function merge over the image in map of the element a in f such that f(a)=b, starting with the element init.
proj_map_monadic [SetMap.Projection]
proj_set [SetMap.Projection]
proj_set f set is the set {f(a) | a\in S}
proj_set_monadic [SetMap.Projection]
propagate_constant [Model]
propagate_constant updated_vars overwrite_vars env
propagate_constant [Alg_expr]
propagate_constant_bool [Alg_expr]

R
random [ValMap]
random [IntCollection]
random [List_util]
random [SetMap.Set]
range_of_string [Locality]
Deserialize JSON data of type Locality.t.
rate [Ode_interface_sig.Interface]
rate_name [Ode_interface_sig.Interface]
raw_mixture_of_fresh [Primitives.Transformation]
raw_mixture_to_lkappa_rule [Patterns_extra]
raw_mixture_to_species [Patterns_extra]
reaction_rate_convention [Ode_interface_sig.Interface]
read_c_rule_id [Ckappa_sig]
read_connected_component [User_graph]
Input JSON data of type User_graph.connected_component.
read_flux_kind [Primitives]
Input JSON data of type Primitives.flux_kind.
read_flux_map [Data]
Input JSON data of type Data.flux_map.
read_input [Tools]
read_plot [Data]
Input JSON data of type Data.plot.
read_range [Locality]
Input JSON data of type Locality.t.
read_snapshot [Data]
Input JSON data of type Data.snapshot.
read_step [Trace]
Input JSON data of type Trace.step.
read_t [Counter.Efficiency]
Input JSON data of type Counter.Efficiency.t.
read_t [Nbr]
Input JSON data of type Nbr.t.
reconstruct [Matching]
reconstruct domain graph matching_of_previous_cc cc_id_in_rule cc root
reconstruct_renaming [Matching]
reconstruct_renaming domain graph cc root
reconstruction_navigation [Pattern]
recti [Tools]
recti f x n = f (f (f ..
redirect [Loggers]
refine_information_about_state_of_sites_in_precondition [Communication]
refine_partitioned_contact_map_in_lkappa_representation [Symmetries]
refresh_id [Loggers]
reinitialize [Counter]
rem [Nbr]
remove [ValMap]
remove [IntCollection]
remove [SetMap.Map]
remove [SetMap.Set]
remove_agent [Edges]
remove_blacklisted_event [Utilities]
remove_consecutive_double [List_util]
remove_events_after_last_obs [Utilities]
remove the events after the last observable
remove_free [Edges]
remove_internal [Edges]
remove_link [Edges]
Some (i,j) as second returned element means separate "new" cc j from cc i
remove_obs_before [Utilities]
remove_obs_before removes the observable_hits before the simulation info prodided as a first argument
remove_pseudo_inverse_events [Utilities]
remove_pseudo_inverse_events removes pseudo inverse events
remove_suffix_after_last_occurrence [List_util]
remove_while_testing_existence [SetMap.Map]
remove_while_testing_existence [SetMap.Set]
remove_with_logs [SetMap.Map]
remove_with_logs [SetMap.Set]
rename [Navigation]
rename [Primitives.Transformation]
rename [Matching.Agent]
rename [Agent]
rename_abstract_action [Instantiation]
rename_abstract_event [Instantiation]
rename_abstract_side_effect [Instantiation]
rename_abstract_test [Instantiation]
rename_link [Ckappa_sig]
rename_mixture [Cckappa_sig]
rename_mixture [Ckappa_sig]
representative [Symmetries]
reset [Mvbdu_wrapper.Mvbdu]
reset [Odes.Make]
reset [Ode_interface_sig.Interface.ObsMap]
return [Ode_loggers]
rev_dep_of_yojson [Operator]
rev_dep_to_yojson [Operator]
rev_map_append [List_util]
rev_path [Edges]
root [SetMap.Map]
roots [Pattern.Env]
(ids,ty)
roots_of [Matching]
rule_id_of_int [Ckappa_sig]
rule_id_of_json [Ckappa_sig]
rule_id_to_json [Ckappa_sig]
rule_of_json [LKappa]
rule_of_yojson [Primitives]
rule_rate_convention [Ode_interface_sig.Interface]
rule_to_json [LKappa]
rule_to_yojson [Primitives]

S
same_connected_component [Matching.Agent]
saturate_domain_with_symmetric_patterns [LKappa_group_action]
set [Pattern.ObsMap]
set [Int_storage.Storage]
set [DynamicArray.DynArray]
set [GenArray.GenArray]
set [Pp]
setCheckFileExists [Kappa_files]
setCheckFileExistsODE [Kappa_files]
set_action_binding [Analyzer_headers]
set_agent_name [Analyzer_headers]
set_agent_name_from_pattern [Analyzer_headers]
set_bonds_lhs [Analyzer_headers]
set_bonds_rhs [Analyzer_headers]
set_cflow [Kappa_files]
set_common_views [Analyzer_headers]
set_covering_classes [Analyzer_headers]
set_covering_classes_id [Analyzer_headers]
set_dir [Kappa_files]
set_errors [Export_to_KaSa.Type]
set_expr [Loggers]
set_flux [Kappa_files]
set_global_dynamic_information [Static_contact_map_domain.Domain]
set_global_dynamic_information [Composite_domain.Composite_domain]
set_global_dynamic_information [Analyzer_domain_sig.Domain]
set_id_of_global_parameter [Loggers]
set_list_of_site_type_in_covering_classes [Analyzer_headers]
set_log_info [Analyzer_headers]
set_marshalized [Kappa_files]
set_max_events [Counter]
set_max_time [Counter]
set_modified_map [Analyzer_headers]
set_mvbdu_handler [Analyzer_headers]
set_ode [Kappa_files]
set_parameters [Export_to_KaDE.Type]
set_parameters [Export_to_KaSa.Type]
set_plot_period [Counter]
set_potential_side_effects [Analyzer_headers]
set_potential_side_effects_per_rule [Analyzer_headers]
set_project_modified_map [Analyzer_headers]
set_remanent_triple [Analyzer_headers]
set_rule_cache [Ode_interface_sig.Interface]
set_side_effects [Analyzer_headers]
set_test_modif_map [Analyzer_headers]
set_to_backward_symmetries_from_model [Odes.Make]
set_to_forward_symmetries_from_model [Odes.Make]
set_to_string [Pp]
set_views_lhs [Analyzer_headers]
set_views_rhs [Analyzer_headers]
setup_alg_vars_rev_dep [Alg_expr]
several_internal_states [LKappa]
several_occurence_of_site [LKappa]
show_time_advance [Ode_loggers]
side_effects_of_step [Trace]
signatures [Model]
signatures [Pattern.Env]
sigs [Pattern.PreEnv]
simplify [Alg_expr_extra]
simulation_info_of_step [Trace]
sin [Alg_expr]
singleton [SetMap.Set]
singleton_path [Edges]
site_is_counter [Signature]
site_name_of_int [Ckappa_sig]
site_of_num [Signature]
size [Signature]
size [NamedDecls]
size [IntCollection]
size [SetMap.Map]
size [SetMap.Set]
size_of_cc [Pattern]
size_of_pretrace [Utilities]
smart_filter [List_util]
not tail rec but don't allocate if unecessary
smart_map [List_util]
smash_duplicate_in_ordered_list [Tools]
smash_reactions [Ode_loggers]
snapshot_of_string [Data]
Deserialize JSON data of type Data.snapshot.
snd_site [Ckappa_sig]
sons [Pattern.Env]
sort [Agent]
space [Pp]
species [Edges]
species_of_initial_state [Ode_interface_sig.Interface]
species_of_initial_state_env [Ode_interface_sig.Interface]
species_to_lkappa_rule [Patterns_extra]
species_to_lkappa_rule_and_unspec [Patterns_extra]
species_to_raw_mixture [Patterns_extra]
split [SetMap.Set]
split_init [Utilities]
split_init split init event agent-wise
split_mixture [Ast]
split_with_logs [SetMap.Map]
sqrt [Alg_expr]
stabilize [Static_contact_map_domain.Domain]
stabilize [Composite_domain.Composite_domain]
stabilize [Analyzer_domain_sig.Domain]
start_time [Ode_loggers]
state_alg_op_of_json [Operator]
state_alg_op_to_json [Operator]
state_index_of_int [Ckappa_sig]
stats [Edges]
step_is_init [Trace]
step_is_obs [Trace]
step_is_pert [Trace]
step_is_rule [Trace]
step_is_subs [Trace]
step_of_string [Trace]
Deserialize JSON data of type Trace.step.
step_of_yojson [Trace]
step_of_yojson [Navigation]
step_to_yojson [Trace]
step_to_yojson [Navigation]
stops_of_perturbation [Primitives]
store_by_mvbdu [Mvbdu_wrapper.Mvbdu]
store_by_variables_list [Mvbdu_wrapper.Mvbdu]
store_trace [Utilities]
Store trace in story table
story_id [Trace.Simulation_info]
string_of_agent_id [Ckappa_sig]
string_of_agent_name [Ckappa_sig]
string_of_c_link_value [Ckappa_sig]
string_of_c_rule_id [Ckappa_sig]
string_of_connected_component [User_graph]
Serialize a value of type User_graph.connected_component into a JSON string.
string_of_flux_kind [Primitives]
Serialize a value of type Primitives.flux_kind into a JSON string.
string_of_flux_map [Data]
Serialize a value of type Data.flux_map into a JSON string.
string_of_level [Priority]
string_of_plot [Data]
Serialize a value of type Data.plot into a JSON string.
string_of_range [Locality]
Serialize a value of type Locality.t into a JSON string.
string_of_rule_id [Ckappa_sig]
string_of_site_name [Ckappa_sig]
string_of_snapshot [Data]
Serialize a value of type Data.snapshot into a JSON string.
string_of_state_index [Ckappa_sig]
string_of_step [Trace]
Serialize a value of type Trace.step into a JSON string.
string_of_t [Counter.Efficiency]
Serialize a value of type Counter.Efficiency.t into a JSON string.
string_of_t [Nbr]
Serialize a value of type Nbr.t into a JSON string.
string_of_var_id [Ode_interface_sig.Interface]
string_of_variable [Ode_loggers]
strong [Priority]
strongly_compress [Utilities]
compute the strong compression of a given trace, if parameter.compute_all_stories, then each minimal stories is computed, otherwise, only the first found one is provided; the optional argument heuristic can be used to redefined the heuristic that select which event to try to discard first.
sub [Fractions]
sub [Nbr]
sub [DynamicArray.DynArray]
sub [GenArray.GenArray]
sub_rule_id [Ckappa_sig]
subs_step [Trace]
subset [SetMap.Set]
subst_agent_in_concrete_action [Instantiation]
subst_agent_in_concrete_event [Instantiation]
subst_agent_in_concrete_side_effect [Instantiation]
subst_agent_in_concrete_test [Instantiation]
subst_map2_agent_in_concrete_event [Instantiation]
subst_map_agent_in_concrete_action [Instantiation]
subst_map_agent_in_concrete_event [Instantiation]
subst_map_agent_in_concrete_side_effect [Instantiation]
subst_map_agent_in_concrete_test [Instantiation]
succ [Nbr]
sum [Affine_combinations]
sum_map [Rule_modes]
swap_binding_state_created [LKappa_group_action]
swap_binding_state_regular [LKappa_group_action]
swap_full_created [LKappa_group_action]
swap_full_regular [LKappa_group_action]
swap_internal_state_created [LKappa_group_action]
swap_internal_state_regular [LKappa_group_action]

T
t_of_string [Counter.Efficiency]
Deserialize JSON data of type Counter.Efficiency.t.
t_of_string [Nbr]
Deserialize JSON data of type Nbr.t.
test_of_json [Instantiation]
test_to_json [Instantiation]
tests_of_step [Trace]
tests_pass_on [Replay]
exported for convenience.
the_rule_is_applied_for_the_first_time [Communication]
the_rule_is_not_applied_for_the_first_time [Communication]
tick [Counter]
Output on stdout
tick [Progress_report]
time_percentage [Counter]
to_ast [Odes.Make]
to_ast [Ode_interface_sig.Interface]
to_erased [LKappa]
to_file [Pp_svg]
to_float [Nbr]
None when infinity or Not a Number
to_int [Nbr]
to_json [Export_to_json.Type]
to_json [Trace.Simulation_info]
to_json [Raw_mixture]
to_json [Signature]
to_json [Agent]
to_json [NamedDecls]
to_json [Graph_json]
to_json [Loggers]
to_json [SetMap.Map]
to_maintained [LKappa]
to_navigation [Pattern.Env]
to_raw_mixture [LKappa]
to_string [Locality]
to_string [Nbr]
to_string [Pp_svg]
to_yojson [Trace]
to_yojson [Navigation]
to_yojson [Model]
to_yojson [Matching.Agent]
to_yojson [Pattern.Env]
to_yojson [Contact_map]
to_yojson [Nbr]
token_vector [Ode_interface_sig.Interface]
token_vector_of_init [Ode_interface_sig.Interface]
tokens_finder [Model]
total [ValMap]
trace_of_pretrace [Utilities]
convert a list of refined steps into a trace
tracked_events [Counter]
try_concretize_action [Instantiation]
Same than concretize_action, except that it returns None if the provided injection's domain does not contain a fresh agent that is involved in the action that is being concretized.

U
uminus [Alg_expr]
un_alg_op_of_json [Operator]
un_alg_op_to_json [Operator]
un_bool_op_of_json [Operator]
un_bool_op_to_json [Operator]
unary_patterns [Model]
union [Raw_mixture]
union [SetMap.Map]
union [SetMap.Set]
union_find_counters [Raw_mixture]
union_with_logs [SetMap.Map]
union_with_logs [SetMap.Set]
unit [Pp]
unsafe_get [Int_storage.Storage]
unsome [Option_util]
update [SetMap.Map]
update_profiling_info [Trace.Simulation_info]
update_token [Ode_loggers]
update_token_jac [Ode_loggers]
update_with_logs [SetMap.Map]
upgrade_interface [Cckappa_sig]
upgrade_some_interface [Cckappa_sig]

V
valid_mixture [Ode_interface_sig.Interface]
valid_modes [Ode_interface_sig.Interface]
value_alg [Expr_interpreter]
value_alg c ?t get_alg get_mix get_tok expr_alg with get_mix [interp1;...;interpn]
value_bool [Expr_interpreter]
variable_of_derived_variable [Ode_loggers]
variables_list_of_mvbdu [Mvbdu_wrapper.Internalized_mvbdu]
variables_list_of_mvbdu [Mvbdu_wrapper.Mvbdu]

W
weak [Priority]
weakly_compress [Utilities]
compute the weak compression of a given trace, if parameter.compute_all_stories, then each minimal stories is computed, otherwise, only the first found one is provided; the optional argument heuristic can be used to redefined the heuristic that select which event to try to discard first.
what_do_we_count [Ode_interface_sig.Interface]
with_cflow_file [Kappa_files]
with_channel [Kappa_files]
with_channel path f
with_flux [Kappa_files]
with_marshalized [Kappa_files]
with_snapshot [Kappa_files]
wrap_formatter [Kappa_files]
write_c_rule_id [Ckappa_sig]
write_connected_component [User_graph]
Output a JSON value of type User_graph.connected_component.
write_flux_kind [Primitives]
Output a JSON value of type Primitives.flux_kind.
write_flux_map [Data]
Output a JSON value of type Data.flux_map.
write_plot [Data]
Output a JSON value of type Data.plot.
write_range [Locality]
Output a JSON value of type Locality.t.
write_snapshot [Data]
Output a JSON value of type Data.snapshot.
write_step [Trace]
Output a JSON value of type Trace.step.
write_t [Counter.Efficiency]
Output a JSON value of type Counter.Efficiency.t.
write_t [Nbr]
Output a JSON value of type Nbr.t.

Z
zero [Fractions]
zero [Nbr]