Functor Odes.Make

module Make: 
functor (I : Ode_interface_sig.Interface) -> sig .. end

type ode_var_id 

type ('a, 'b) network 

type enriched_rule 

type rule_id 

type connected_component_id 

val get_preprocessed_ast : Run_cli_args.t -> I.preprocessed_ast

val get_ast : Run_cli_args.t -> I.ast

val to_ast : I.ast -> Ast.parsing_compil

val preprocess : Run_cli_args.t -> I.ast -> I.preprocessed_ast

val get_compil : ?bwd_bisim:LKappa_group_action.bwd_bisim_info ->
       rule_rate_convention:Remanent_parameters_sig.rate_convention ->
       ?reaction_rate_convention:Remanent_parameters_sig.rate_convention ->
       show_reactions:bool ->
       count:Ode_args.count ->
       compute_jacobian:bool -> Run_cli_args.t -> I.preprocessed_ast -> I.compil

val init : I.compil ->
       (ode_var_id, Ode_loggers_sig.ode_var_id) network

val reset : I.compil ->
       (ode_var_id, Ode_loggers_sig.ode_var_id) network ->
       (ode_var_id, Ode_loggers_sig.ode_var_id) network

val network_from_compil : ?max_size:int ->
       dotnet:bool ->
       smash_reactions:bool ->
       ignore_obs:bool ->
       Remanent_parameters_sig.parameters ->
       I.compil ->
       (ode_var_id, Ode_loggers_sig.ode_var_id) network ->
       (ode_var_id, Ode_loggers_sig.ode_var_id) network

val get_reactions : ('a, 'b) network ->
       ((ode_var_id list * ode_var_id list *
         ode_var_id Locality.annot list * I.rule) *
        int)
       list

val export_network : command_line:string ->
       command_line_quotes:string ->
       ?data_file:string ->
       ?init_t:float ->
       max_t:float ->
       ?plot_period:float ->
       ?compute_jacobian:bool ->
       ?propagate_constants:bool ->
       ?show_time_advance:bool ->
       ?nonnegative:bool ->
       ?initial_step:float ->
       ?max_step:float ->
       ?abstol:float ->
       ?reltol:float ->
       Remanent_parameters_sig.parameters ->
       Loggers.t ->
       Loggers.t ->
       Loggers.t ->
       I.compil ->
       (ode_var_id, Ode_loggers_sig.ode_var_id) network ->
       (ode_var_id, Ode_loggers_sig.ode_var_id) network

val get_comment : enriched_rule -> string

val get_rule_id_with_mode : enriched_rule ->
       rule_id * Rule_modes.arity * Rule_modes.direction

val get_rule : enriched_rule -> I.rule

val get_lhs : enriched_rule -> I.pattern

val get_lhs_cc : enriched_rule ->
       (connected_component_id * I.connected_component) list

val get_divide_rate_by : enriched_rule -> int

val compute_symmetries_from_model : Remanent_parameters_sig.parameters ->
       I.compil ->
       (ode_var_id, Ode_loggers_sig.ode_var_id) network ->
       Public_data.contact_map ->
       (ode_var_id, Ode_loggers_sig.ode_var_id) network

val set_to_backward_symmetries_from_model : (ode_var_id, Ode_loggers_sig.ode_var_id) network ->
       (ode_var_id, Ode_loggers_sig.ode_var_id) network

val set_to_forward_symmetries_from_model : (ode_var_id, Ode_loggers_sig.ode_var_id) network ->
       (ode_var_id, Ode_loggers_sig.ode_var_id) network

val print_symmetries : Remanent_parameters_sig.parameters ->
       I.compil ->
       (ode_var_id, Ode_loggers_sig.ode_var_id) network -> unit

val get_data : (ode_var_id, Ode_loggers_sig.ode_var_id) network ->
       int * int * int

val init_bwd_bisim_info : I.compil ->
       (ode_var_id, Ode_loggers_sig.ode_var_id) network ->
       LKappa_group_action.bwd_bisim_info option