package kappa-library

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in-package search v0.2.0

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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Utilities to make mixtures from traces

type state = {

graph : Kappa_site_graphs.Edges.t;
time : float;
event : int;
connected_components : Kappa_site_graphs.Agent.SetMap.Set.t Kappa_data_structures.Mods.IntMap.t option;

}

type summary = {

unary_distances : (int * int) option;

}

val init_state : with_connected_components:bool -> state

val do_step : 
  Kappa_site_graphs.Signature.s ->
  state ->
  Trace.step ->
  state * summary

returns
the new state and, if the step was an unary instance of a binary rule, the id of the rule and the distance between its 2 connected patterns.

val is_step_triggerable : state -> Trace.step -> bool

determines whether or not a step can be applied from a given state.

val is_step_triggerable_on_edges : 
  Kappa_site_graphs.Edges.t ->
  Trace.step ->
  bool

same function but takes a graph of type Edges.t directly.

val tests_pass_on : 
  Kappa_site_graphs.Edges.t ->
  Kappa_terms.Instantiation.concrete Kappa_terms.Instantiation.test list list ->
  bool

exported for convenience.

val cc_of_state : 
  debug_mode:bool ->
  state ->
  Kappa_terms.Pattern.PreEnv.t ->
  Kappa_terms.Pattern.PreEnv.t
  * ((int * int) list * Kappa_terms.Pattern.cc * Kappa_terms.Pattern.id) list