package kappa-library

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in-package search v0.2.0

kappa-library.generic
- Kappa_data_structures
  - Base64
  - Bigbuffer
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    Buffers
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    Cache
    
    O
    
    OO
  - Circular_buffers
  - Color
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  - 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
    
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    String2SetMap
    
    Map
    
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    StringSetMap
    
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  - NamedDecls
  - Nbr
  - Operator
    
    DepSet
  - Option_util
  - Pp
  - Pp_html
  - Random_tree
  - Renaming
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  - SetMap
    
    Make
    
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    A
    
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    S
    
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  - Stop
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kappa-library.mixtures
- Kappa_site_graphs
  - Agent
    
    SetMap
    
    Map
    
    Set
  - Counters_info
  - Edges
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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

Legend:
Library
Module
Module type
Parameter
Class
Class type

Event loop module

type t

Abstract state

val empty : with_delta_activities:bool -> Counter.t -> Kappa_terms.Model.t -> t

empty ~with_delta_activities env

val initialize : 
  bind:('a -> ((bool * Rule_interpreter.t * t) -> 'a) -> 'a) ->
  return:((bool * Rule_interpreter.t * t) -> 'a) ->
  debug_mode:bool ->
  outputs:(Data.t -> unit) ->
  Kappa_terms.Model.t ->
  Counter.t ->
  Rule_interpreter.t ->
  t ->
  (Kappa_terms.Primitives.alg_expr * Kappa_terms.Primitives.elementary_rule)
    list ->
  'a

initial env counter graph state builds up the initial state

val observables_values : 
  Kappa_terms.Model.t ->
  Rule_interpreter.t ->
  Counter.t ->
  Kappa_data_structures.Nbr.t array

Returns (the current biological time, an array of the current values of observables)

val do_modifications : 
  debug_mode:bool ->
  outputs:(Data.t -> unit) ->
  Kappa_terms.Model.t ->
  Counter.t ->
  Rule_interpreter.t ->
  t ->
  Kappa_terms.Primitives.modification list ->
  bool * Rule_interpreter.t * t * bool

val a_loop : 
  debug_mode:bool ->
  outputs:(Data.t -> unit) ->
  dumpIfDeadlocked:bool ->
  maxConsecutiveClash:int ->
  Kappa_terms.Model.t ->
  Counter.t ->
  Rule_interpreter.t ->
  t ->
  bool * Rule_interpreter.t * t

One event loop

val end_of_simulation : 
  outputs:(Data.t -> unit) ->
  Kappa_terms.Model.t ->
  Counter.t ->
  Rule_interpreter.t ->
  t ->
  unit

What to do after stopping simulation.