@reaction_network macro generates a
ReactionSystem object, which has a number of fields that can be accessed directly or via the Catalyst.jl API (the recommended route). Below we list these components, with the recommended API method listed first:
rn.statesis a vector of all the chemical species within the system, each represented as a
rn.psis a vector of all the parameters within the system, each represented as a
rn.eqsis a vector of all the
Reactions within the system.
rn.ivare the independent variable of the system, usually
tfor time, represented as a
reactions(rn) has a number of subfields. For
Reaction we have:
rx.substrates, a vector of
ModelingToolkit.Terms storing each substrate variable.
rx.products, a vector of
ModelingToolkit.Terms storing each product variable.
rx.substoich, a vector storing the corresponding integer stoichiometry of each substrate species in
rx.prodstoich, a vector storing the corresponding integer stoichiometry of each product species in
representing the reaction rate. E.g., for a reaction likekX, Y –> X+Y
, we'd haverate = kX`.
rx.netstoich, a vector of pairs mapping the
ModelingToolkit.Termfor each species that changes numbers by the reaction to how much it changes. E.g., for
k, X + 2Y --> X + W, we'd have
rx.netstoich = [Y(t) => -2, W(t) => 1].
rx.only_use_rate, a boolean that is
trueif the reaction was made with non-filled arrows and should ignore mass action kinetics.
ReactionSystems can be generated via
@reaction_network with no arguments.
ReactionSystems can be programmatically extended using
@add_reactions, or composed using