package kappa-library
Public internals of the Kappa tool suite. Use this package to use kappa as a lib
Install
Dune Dependency
Authors
Maintainers
Sources
v4.1.3.tar.gz
md5=1c9a8a0d79f085757817f90834e166f5
sha512=13ac40442940ba6e72d7dc5bf952e67443872f7bff63e9c76a3a699a6904c88696047fe04519b7ec6546371642f6ee7b0983117be302694aca15500b0df40de3
doc/kappa-library.runtime/Kappa_runtime/Rule_interpreter/index.html
Module Kappa_runtime.Rule_interpreter
Source
Source
val value_alg :
Counter.t ->
t ->
Kappa_terms.Primitives.alg_expr ->
Kappa_data_structures.Nbr.t
Source
val empty :
outputs:(Data.t -> unit) ->
with_trace:bool ->
Random.State.t ->
Kappa_terms.Model.t ->
Counter.t ->
t
Source
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
Source
val update_outdated_activities :
debug_mode:bool ->
(int -> float -> float -> unit) ->
Kappa_terms.Model.t ->
Counter.t ->
t ->
int list ->
t * int list
Source
val snapshot :
debug_mode:bool ->
raw:bool ->
Kappa_terms.Model.t ->
Counter.t ->
t ->
Data.snapshot
Source
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
Source
val add_tracked_species :
Kappa_terms.Pattern.id array ->
string ->
Kappa_terms.Instantiation.abstract Kappa_terms.Instantiation.test list list ->
t ->
t
Source
val value_bool :
Counter.t ->
t ->
(Kappa_terms.Pattern.id array list, int) Kappa_terms.Alg_expr.bool ->
bool
Source
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
Source
val incorporate_extra_pattern :
debug_mode:bool ->
Kappa_terms.Pattern.Env.t ->
t ->
Kappa_terms.Pattern.id ->
t
Source
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
Source
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_terms.Instantiation.concrete) list
* Kappa_data_structures.Operator.DepSet.t
Source
val apply_negative_transformation :
?mod_connectivity_store:Roots.mod_ccs_cache ->
Instances.t ->
(Kappa_site_graphs.Agent.t Kappa_terms.Instantiation.site list
* Kappa_site_graphs.Edges.t) ->
Kappa_site_graphs.Agent.t Kappa_terms.Primitives.Transformation.t ->
Kappa_site_graphs.Agent.t Kappa_terms.Instantiation.site list
* Kappa_site_graphs.Edges.t
Source
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_site_graphs.Agent.t 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_site_graphs.Agent.t Kappa_terms.Instantiation.site list
* Kappa_site_graphs.Edges.t)
* Kappa_site_graphs.Agent.t Kappa_terms.Primitives.Transformation.t
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