2020-11-29 17:43:20 +01:00
|
|
|
#lang scribble/manual
|
2023-08-08 17:22:03 +02:00
|
|
|
@(require scribble/example racket/sandbox
|
|
|
|
(for-label typed/racket/base
|
|
|
|
(submod "../rs.rkt" typed)))
|
|
|
|
|
|
|
|
@(define rs-evaluator
|
|
|
|
(parameterize ([sandbox-output 'string]
|
|
|
|
[sandbox-error-output 'string]
|
|
|
|
[sandbox-memory-limit 500])
|
|
|
|
(make-evaluator 'typed/racket #:requires '((submod "rs.rkt" typed)))))
|
|
|
|
|
|
|
|
@(define-syntax-rule (ex . args)
|
|
|
|
(examples #:eval rs-evaluator . args))
|
|
|
|
|
|
|
|
@(define-syntax-rule (deftypeform . args)
|
|
|
|
(defform #:kind "type" . args))
|
|
|
|
|
|
|
|
@(define-syntax-rule (deftype . args)
|
|
|
|
(defidform #:kind "type" . args))
|
2020-11-29 17:43:20 +01:00
|
|
|
|
|
|
|
@title[#:tag "rs"]{dds/rs: Reaction Systems}
|
|
|
|
|
2023-08-08 17:22:03 +02:00
|
|
|
@defmodule[(submod dds/rs typed)]
|
2020-11-29 22:12:01 +01:00
|
|
|
|
|
|
|
This module defines reaction systems and various tools for working with them.
|
|
|
|
|
|
|
|
@section[#:tag "rs-basics"]{Basic definitions}
|
|
|
|
|
2023-08-08 17:22:03 +02:00
|
|
|
@deftype[Species]{
|
|
|
|
|
|
|
|
A synonym of @racket[Symbol].
|
|
|
|
|
|
|
|
}
|
|
|
|
|
2023-08-08 17:40:44 +02:00
|
|
|
@defstruct*[reaction ([reactants (Setof Species)]
|
|
|
|
[inhibitors (Setof Species)]
|
|
|
|
[products (Setof Species)])]{
|
|
|
|
|
|
|
|
A reaction is a triple of sets, giving the reactants, the inhibitors,
|
|
|
|
and the products, respectively.
|
|
|
|
|
|
|
|
}
|
|
|
|
|
|
|
|
@deftype[Reaction]{
|
|
|
|
|
|
|
|
The type of the instances of @racket[reaction].
|
|
|
|
|
|
|
|
}
|
|
|
|
|
2023-08-08 18:09:24 +02:00
|
|
|
@defproc[(make-reaction [r (Listof Reaction)]
|
|
|
|
[i (Listof Reaction)]
|
|
|
|
[p (Listof Reaction)])
|
|
|
|
Reaction]{
|
|
|
|
|
|
|
|
A shortcut for constructing @racket[Reaction]s using list syntax
|
|
|
|
instead of set syntax.
|
|
|
|
|
|
|
|
@ex[
|
|
|
|
(make-reaction '(a b) '(c d) '(e f))
|
|
|
|
]}
|
|
|
|
|
2023-08-08 18:28:25 +02:00
|
|
|
@defproc[(enabled? [r Reaction] [s (Setof Species)]) Boolean]{
|
|
|
|
|
|
|
|
A @racket[Reaction] is enabled on a set of species if all of its
|
|
|
|
reactants are in the set and none of its inhibitors are.
|
|
|
|
|
|
|
|
@ex[
|
|
|
|
(enabled? (make-reaction '(a b) '(c d) '())
|
|
|
|
(set 'a 'b 'e))
|
|
|
|
(enabled? (make-reaction '(a b) '(c d) '())
|
|
|
|
(set 'a 'b 'c))
|
|
|
|
(enabled? (make-reaction '(a b) '(c d) '())
|
|
|
|
(set 'b 'e))
|
|
|
|
]}
|
|
|
|
|
2023-08-08 18:34:40 +02:00
|
|
|
@deftype[ReactionSystem]{
|
|
|
|
|
|
|
|
A reaction system is a dictionary mapping reaction names
|
|
|
|
(@racket[Symbol]s) to @racket[Reaction]s.
|
|
|
|
|
|
|
|
}
|
|
|
|
|
|
|
|
|
2020-11-29 22:12:01 +01:00
|
|
|
@section{Org-mode interaction}
|
|
|
|
|
|
|
|
This section contains some useful primitives for
|
|
|
|
@hyperlink["https://orgmode.org/"]{Org-mode} interoperability.
|
|
|
|
|
|
|
|
@section{Dynamics of reaction systems}
|
|
|
|
|
|
|
|
The dynamics of reaction systems is typically defined as @emph{interaction
|
|
|
|
processes}. An interactive process of a reaction system is a sequence of
|
|
|
|
states driven by a sequence of contexts in the following way. The reaction
|
|
|
|
system starts with the initial context. Then, at every step, the result of
|
|
|
|
applying the reaction system is merged with the next element of the context
|
|
|
|
sequence, and the reaction system is then applied to the result of the union.
|
|
|
|
If the sequence of contexts is empty, the reaction system cannot evolve.
|