Module `Kappa_terms.Primitives`Source

Compiled kappa model unit

Sourcemodule Transformation : sig ... end

Elementary rule transformations

Sourcetype alg_expr = (Pattern.id array list, int) Alg_expr.e

Sourcetype elementary_rule = {

rate : alg_expr Kappa_data_structures.Loc.annoted;
unary_rate : (alg_expr Kappa_data_structures.Loc.annoted * alg_expr option) option;
connected_components : Pattern.id array;
removed : Instantiation.abstract Transformation.t list;
inserted : Instantiation.abstract Transformation.t list;
delta_tokens : (alg_expr Kappa_data_structures.Loc.annoted * int) list;
syntactic_rule : int;
(*
0 means generated for perturbation.
*)
instantiations : Instantiation.abstract Instantiation.event;
(*
In the reverse order on purpose so that we rev_map when we concretize
*)

}

If unary_rate is Some _, rate means binary rate. Else rate is the rate independently of the connectivity

Sourceval extract_cc_ids : elementary_rule -> Pattern.id array

Source

val extract_abstract_event : 
  elementary_rule ->
  Instantiation.abstract Instantiation.event

Source

val rule_to_yojson : 
  filenames:int Kappa_data_structures.Mods.StringMap.t ->
  elementary_rule ->
  Yojson.Basic.t

Source

val rule_of_yojson : 
  filenames:string array ->
  Yojson.Basic.t ->
  elementary_rule

Source

val fully_specified_pattern_to_positive_transformations : 
  Pattern.cc ->
  Instantiation.concrete Transformation.t list

Sourcetype 'alg_expr print_expr =

| Str_pexpr of string Kappa_data_structures.Loc.annoted
| Alg_pexpr of 'alg_expr Kappa_data_structures.Loc.annoted

Source

val print_expr_to_yojson : 
  filenames:int Kappa_data_structures.Mods.StringMap.t ->
  ('a -> Yojson.Basic.t) ->
  ('b -> Yojson.Basic.t) ->
  ('a, 'b) Alg_expr.e print_expr ->
  Yojson.Basic.t

Source

val print_expr_of_yojson : 
  filenames:string array ->
  (Yojson.Basic.t -> 'a) ->
  (Yojson.Basic.t -> 'b) ->
  Yojson.Basic.t ->
  ('a, 'b) Alg_expr.e print_expr

Sourcetype din_kind =

| ABSOLUTE
| RELATIVE
| PROBABILITY

Sourceval din_kind_to_yojson : din_kind -> Yojson.Basic.t

Sourceval din_kind_of_yojson : Yojson.Basic.t -> din_kind

Sourceval write_din_kind : Buffer.t -> din_kind -> unit

Output a JSON value of type din_kind.

Sourceval string_of_din_kind : ?len:int -> din_kind -> string

Serialize a value of type din_kind into a JSON string.

parameter len
specifies the initial length of the buffer used internally. Default: 1024.

Sourceval read_din_kind : Yojson.Safe.lexer_state -> Lexing.lexbuf -> din_kind

Input JSON data of type din_kind.

Sourceval din_kind_of_string : string -> din_kind

Deserialize JSON data of type din_kind.

Sourcetype modification =

| ITER_RULE of alg_expr Kappa_data_structures.Loc.annoted * elementary_rule
| UPDATE of int * alg_expr Kappa_data_structures.Loc.annoted
| SNAPSHOT of bool * alg_expr print_expr list
| STOP of alg_expr print_expr list
| CFLOW of string option * Pattern.id array * Instantiation.abstract Instantiation.test list list
(*
First string is the named used by the user
*)
| DIN of din_kind * alg_expr print_expr list
| DINOFF of alg_expr print_expr list
| CFLOWOFF of string option * Pattern.id array
| PLOTENTRY
| PRINT of alg_expr print_expr list * alg_expr print_expr list
| SPECIES of alg_expr print_expr list * Pattern.id array * Instantiation.abstract Instantiation.test list list
| SPECIES_OFF of alg_expr print_expr list

Sourcetype perturbation = {

alarm : Kappa_data_structures.Nbr.t option;
precondition : (Pattern.id array list, int) Alg_expr.bool Kappa_data_structures.Loc.annoted;
effect : modification list;
repeat : (Pattern.id array list, int) Alg_expr.bool Kappa_data_structures.Loc.annoted;
needs_backtrack : bool;

}

Source

val perturbation_to_yojson : 
  filenames:int Kappa_data_structures.Mods.StringMap.t ->
  perturbation ->
  Yojson.Basic.t

Source

val perturbation_of_yojson : 
  filenames:string array ->
  Yojson.Basic.t ->
  perturbation

Sourceval exists_modification : (modification -> bool) -> perturbation array -> bool

Source

val extract_connected_components_modifications : 
  modification list ->
  Pattern.id list

Source

val extract_connected_components_bool : 
  (Pattern.id array list, int) Alg_expr.bool Kappa_data_structures.Loc.annoted ->
  Pattern.id list

Source

val map_expr_rule : 
  (alg_expr Kappa_data_structures.Loc.annoted ->
    alg_expr Kappa_data_structures.Loc.annoted) ->
  elementary_rule ->
  elementary_rule

Source

val map_expr_perturbation : 
  (alg_expr Kappa_data_structures.Loc.annoted ->
    alg_expr Kappa_data_structures.Loc.annoted) ->
  ((Pattern.id array list, int) Alg_expr.bool Kappa_data_structures.Loc.annoted ->
    (Pattern.id array list, int) Alg_expr.bool
      Kappa_data_structures.Loc.annoted) ->
  perturbation ->
  perturbation

Source

val fold_expr_rule : 
  ('a -> alg_expr Kappa_data_structures.Loc.annoted -> 'a) ->
  'a ->
  elementary_rule ->
  'a

Source

val fold_expr_perturbation : 
  ('a -> alg_expr Kappa_data_structures.Loc.annoted -> 'a) ->
  ('a ->
    (Pattern.id array list, int) Alg_expr.bool
      Kappa_data_structures.Loc.annoted ->
    'a) ->
  'a ->
  perturbation ->
  'a

Install

Dune Dependency

Authors

Maintainers

Sources

doc/kappa-library.terms/Kappa_terms/Primitives/index.html

Module `Kappa_terms.Primitives`Source

package kappa-library

Install

Dune Dependency

Authors

Maintainers

Sources

doc/kappa-library.terms/Kappa_terms/Primitives/index.html

Module Kappa_terms.PrimitivesSource

Module `Kappa_terms.Primitives`Source