package kappa-library

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Signature

kappa-library.generic
- Kappa_data_structures
  - Base64
  - Bigbuffer
  - Buffers
    
    Buffers
  - Cache
    
    Cache
    
    O
    
    OO
  - Circular_buffers
  - Color
  - Crc32
  - DynamicArray
    
    DynArray
    
    _
  - ExceptionDefn
  - Fifo
  - Fractions
  - GenArray
    
    GenArray
  - Hashed_list
    
    Hash
    
    Make
    
    A
  - Infinite_buffers
  - IntCollection
  - JsonUtil
  - LargeArray
  - List_util
    
    Infix
  - Loc
  - Mods
    
    CharSetMap
    
    Map
    
    Set
    
    DynArray
    
    Int2SetMap
    
    Map
    
    Set
    
    IntSetMap
    
    Map
    
    Set
    
    String2SetMap
    
    Map
    
    Set
    
    StringSetMap
    
    Map
    
    Set
  - NamedDecls
  - Nbr
  - Operator
    
    DepSet
  - Option_util
  - Pp
  - Pp_html
  - Random_tree
  - Renaming
  - Result_util
  - SetMap
    
    Make
    
    Map
    
    Ord
    
    Set
    
    Map
    
    OrderedType
    
    Proj
    
    A
    
    Map
    
    Set
    
    B
    
    Map
    
    Set
    
    Proj2
    
    A
    
    Map
    
    Set
    
    B
    
    Map
    
    Set
    
    C
    
    Map
    
    Set
    
    Projection
    
    Projection2
    
    S
    
    Map
    
    Set
    
    Set
  - Stop
  - Tools
  - ValMap
kappa-library.mixtures
- Kappa_site_graphs
  - Agent
    
    SetMap
    
    Map
    
    Set
  - Counters_info
  - Edges
  - Navigation
  - Signature
  - Snapshot
  - User_graph
kappa-library.runtime
- Kappa_runtime
  - Counter
    
    Efficiency
  - Data
  - Expr_interpreter
  - Fluxmap
  - Generic_rule_interpreter
    
    Make
    
    Instances
  - Instances
  - Instances_sig
    
    S
  - Replay
  - Resource_strings
  - Roots
  - Rule_interpreter
  - State_interpreter
  - Trace
    
    Simulation_info
kappa-library.terms
- Kappa_terms
  - Alg_expr
  - Alg_expr_extra
  - Configuration
  - Contact_map
  - Instantiation
  - Kappa_printer
  - LKappa
  - Matching
    
    Agent
  - Model
  - Pattern
    
    Env
    
    Map
    
    ObsMap
    
    PreEnv
    
    Set
  - Pattern_compiler
  - Pattern_decompiler
  - Primitives
    
    Transformation
  - Raw_mixture
kappa-library.utils
- Kappa_utils
  - Utils

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Module
Module type
Parameter
Class
Class type

Parameters

module Instances : Instances_sig.S

Signature

type t

Abstract graph

type instance

type result =

| Clash
| Corrected
| Blocked
| Success of t
(*
Clash means rectangular approximation failure Corrected means molecular ambiguity failure
*)

Initialisation

val empty : 
  outputs:(Data.t -> unit) ->
  with_trace:bool ->
  Random.State.t ->
  Kappa_terms.Model.t ->
  Counter.t ->
  t

algebraic expression computation

get_alg is by default Model.get_alg but it is not hard wired because perturbations can redefined alg_expr.

val value_alg : 
  Counter.t ->
  t ->
  Kappa_terms.Primitives.alg_expr ->
  Kappa_data_structures.Nbr.t

val value_bool : 
  Counter.t ->
  t ->
  (Kappa_terms.Pattern.id array list, int) Kappa_terms.Alg_expr.bool ->
  bool

val activity : t -> float

val get_edges : t -> Kappa_site_graphs.Edges.t

Core

val apply_given_rule : 
  debug_mode:bool ->
  outputs:(Data.t -> unit) ->
  ?rule_id:int ->
  Kappa_terms.Model.t ->
  Counter.t ->
  t ->
  Trace.event_kind ->
  Kappa_terms.Primitives.elementary_rule ->
  result

Returns the graph obtained by applying the rule. rule_id is mandatory if the rule has an unary rate.

val pick_an_instance : debug_mode:bool -> Kappa_terms.Model.t -> t -> instance

val is_correct_instance : Kappa_terms.Model.t -> t -> instance -> bool

val apply_instance : 
  debug_mode:bool ->
  outputs:(Data.t -> unit) ->
  ?maxConsecutiveBlocked:int ->
  maxConsecutiveClash:int ->
  Kappa_terms.Model.t ->
  Counter.t ->
  t ->
  instance ->
  int option * bool * t

apply_rule ~outputs ~maxConsecutiveClash ?is_blocked model counter st Returns (corresponding_syntactic_rule, is_final_step, new_state). is_final_step is determined by the counter. corresponding_syntactic_rule is equal to None if and only if a null event occured

val force_rule : 
  debug_mode:bool ->
  outputs:(Data.t -> unit) ->
  Kappa_terms.Model.t ->
  Counter.t ->
  t ->
  Trace.event_kind ->
  ?rule_id:int ->
  Kappa_terms.Primitives.elementary_rule ->
  t option

Apply the rule for sure if it is possible. Try apply_rule but in case of null_event, it computes the exact injections of the left hand side to do apply the rule and returns the remaining exact injections.

val incorporate_extra_pattern : 
  debug_mode:bool ->
  Kappa_terms.Pattern.Env.t ->
  t ->
  Kappa_terms.Pattern.id ->
  t

val overwrite_var : 
  int ->
  Counter.t ->
  t ->
  Kappa_terms.Primitives.alg_expr ->
  t

val update_outdated_activities : 
  debug_mode:bool ->
  (int -> float -> float -> unit) ->
  Kappa_terms.Model.t ->
  Counter.t ->
  t ->
  int list ->
  t * int list

Resynchronize the state after a rule application.

It takes the function to store the new activities as an argument whose signature is store rule_id syntactic_rule_id new_activity.

As long as you don't use any algebraic variable (that include don't pick a rule randomly), you can apply several rules in row before resynchronizing. (This is what initial state does.)

takes the list of perturbations to be tried and returns it updated

val snapshot : 
  debug_mode:bool ->
  raw:bool ->
  Kappa_terms.Model.t ->
  Counter.t ->
  t ->
  Data.snapshot

val print : Kappa_terms.Model.t -> Format.formatter -> t -> unit

val get_random_state : t -> Random.State.t

val update_edges_from_actions : 
  debug_mode:bool ->
  outputs:(Data.t -> unit) ->
  Kappa_site_graphs.Signature.s ->
  Counter.t ->
  Kappa_terms.Pattern.Env.t ->
  t ->
  (Kappa_terms.Instantiation.concrete Kappa_terms.Instantiation.action list
   * Kappa_terms.Instantiation.concrete Kappa_terms.Instantiation.site list) ->
  t

val send_instances_message : Instances.message -> t -> t

Blocking events

type event_predicate =
  int option ->
  Kappa_terms.Matching.t ->
  Kappa_terms.Instantiation.concrete Kappa_terms.Instantiation.test list ->
  Kappa_terms.Instantiation.concrete Kappa_terms.Instantiation.action list ->
  bool

val set_events_to_block : event_predicate option -> t -> t

Stories

val add_tracked : 
  outputs:(Data.t -> unit) ->
  Kappa_terms.Pattern.id array ->
  string ->
  Kappa_terms.Instantiation.abstract Kappa_terms.Instantiation.test list list ->
  t ->
  t

val remove_tracked : Kappa_terms.Pattern.id array -> string option -> t -> t

Species

val add_tracked_species : 
  Kappa_terms.Pattern.id array ->
  string ->
  Kappa_terms.Instantiation.abstract Kappa_terms.Instantiation.test list list ->
  t ->
  t

val remove_tracked_species : string -> t -> t

Debugging

type stats = {

mixture_stats : Kappa_site_graphs.Edges.stats;

}

val stats : t -> stats

val print_stats : Format.formatter -> t -> unit

val debug_print : Format.formatter -> t -> unit

val apply_negative_transformation : 
  ?mod_connectivity_store:Roots.mod_ccs_cache ->
  Instances.t ->
  (Kappa_terms.Instantiation.concrete Kappa_terms.Instantiation.site list
   * Kappa_site_graphs.Edges.t) ->
  Kappa_terms.Instantiation.concrete Kappa_terms.Primitives.Transformation.t ->
  Kappa_terms.Instantiation.concrete Kappa_terms.Instantiation.site list
  * Kappa_site_graphs.Edges.t

Internals

val apply_positive_transformation : 
  debug_mode:bool ->
  Kappa_site_graphs.Signature.s ->
  ?mod_connectivity_store:Roots.mod_ccs_cache ->
  Instances.t ->
  ((Kappa_terms.Matching.t * int Kappa_data_structures.Mods.IntMap.t)
   * Kappa_terms.Instantiation.concrete Kappa_terms.Instantiation.site list
   * Kappa_site_graphs.Edges.t) ->
  Kappa_terms.Instantiation.abstract Kappa_terms.Primitives.Transformation.t ->
  ((Kappa_terms.Matching.t * int Kappa_data_structures.Mods.IntMap.t)
   * Kappa_terms.Instantiation.concrete Kappa_terms.Instantiation.site list
   * Kappa_site_graphs.Edges.t)
  * Kappa_terms.Instantiation.concrete Kappa_terms.Primitives.Transformation.t

val apply_concrete_positive_transformation : 
  Kappa_site_graphs.Signature.s ->
  ?mod_connectivity_store:Roots.mod_ccs_cache ->
  Instances.t ->
  Kappa_site_graphs.Edges.t ->
  Kappa_terms.Instantiation.concrete Kappa_terms.Primitives.Transformation.t ->
  Kappa_site_graphs.Edges.t

val obs_from_transformations : 
  debug_mode:bool ->
  Kappa_terms.Pattern.Env.t ->
  Kappa_site_graphs.Edges.t ->
  Kappa_terms.Instantiation.concrete Kappa_terms.Primitives.Transformation.t
    list ->
  (Kappa_terms.Pattern.id * Kappa_site_graphs.Agent.t) list
  * Kappa_data_structures.Operator.DepSet.t

obs_from_transformations domain state transformations

returns
(obs, deps)

val add_outdated_dependencies : 
  Kappa_data_structures.Operator.DepSet.t ->
  t ->
  t

val debug_print_instances : Format.formatter -> t -> unit