Reaction expression parser

[thevolatilebit]

It'd be nice to isolate the reaction expression parser for use in, e.g., loading reactions from a file. This is simple to do: One can overload get_reactions as in get_reactions(exs::Vector{Expr}, reactions = Vector{ReactionStruct}(undef,0)) (where the exs are the reaction expressions as supplied in @reaction_network.).

I'd be grateful to know if there's a more generic / elegant approach / you've some ideas on this that I'd implement and push.

[isaacsas]

If you want to put in a PR that makes the parsing code more modular that would be great and appreciated! It would need some work to generate Reactions from one reaction line I think since the parser needs to know and define parameter and species variables too before making a reaction.

You could always also just build a string with the macro wrapping the reactions, and then eval it. While that’s not recommended for loading other people’s code it would be fine for your own files.

[Leticia-maria]

Could I submit a PR for it? I did something that would fit.

[isaacsas]

Certainly! Making it more modular would be great. We've also recently discussed adding a

rx = @reaction k, A --> B

type macro, so having a standalone parser for such expressions would be good. The plan was to make it default to having k be a parameter and anything in the reaction part (i.e. A --> B) be a species, with users being able to override this default behavior by predeclaring a symbol with ModelingToolkit's @parameters and @variables macros.

[isaacsas]

We support serialization now, so I think that should cover this.