reversible reaction

[metma99]

Quick question if I may:
I tried to use <>, <->, and <--> for representing reversible reactions without success. Errors are ">" is not a unary operator, invalid identifier name "->".
Because of technical reasons I cannot use the double arrow used in the examples.
Is the double arrow in the examples the only way to represent equilibrium reactions?
Markus

[ChrisRackauckas]

inside of the macro?

[metma99]

That is what I am trying:
rxn = #reaction_network begin
2.0, X + Y <> XY
end

[ChrisRackauckas]

rxn = @reaction_network begin
2.0, X + Y <> XY
end

?

[metma99]

It does not work. I showed to you the code, and the error messages.
I tried <> because you mention that > is ok for irreversible reaction.
Not sure what else to tell you.

[metma99]

Go you. My mistake. It is a typo.
I of course used @. Sorry

[ChrisRackauckas]

Does

rxn = @reaction_network begin
2.0, X + Y <-> XY
end

work? I think it might need a - in there. I know that the unicode ↔ works. Pinging @TorkelE @isaacsas

[metma99]

This throws the error:
syntax: invalid identifier name "->"

[ChrisRackauckas]

What version of Julia? v1.4.2 with DiffEqBio v4.3?

[metma99]

Juliav1.4.2
DiffEqBiov4.3.0

[isaacsas]

These seem to be the valid arrow symbols:

double_arrows = Set{Symbol}([:↔, :⟷, :⇄, :⇆, :⇔, :⟺])

I’m not sure about the text representation of some of them, maybe you need <—>? (I.e. using two dashes?) I’ve never used a non-Unicode reversible arrow.

[isaacsas]

Never mind, I see that didn’t work either for you.

You may have to just define it as two separate reactions. Internally it should lead to no changes in the models that are generated.

[ChrisRackauckas]

Let's move this issue over to DEBio, but not address it until after the change to MTK (which is almost done!)

[TorkelE]

This basically has to do with the parsing of expressions in Julia. When creating expressions I think neither one of

rxn = @reaction_network begin
2.0, X + Y <--> XY
2.0, X + Y <-> XY
2.0, X + Y <> XY
end

yields working code. Similar limitations for how expressions are parsed makes it so we cannot use X + Y -> XY, but have to use X + Y --> XY.

This leaves us with only various one character symbols as possible separators for reversible reactions (↔, ⟷, ⇄, ⇆, ⇔, ⟺ added currently). If someone came up with a way of using <-->, <->, <> that would be good. But I simply don't think this is possible, given the current way expressions work in julia.

For your problem specifically, it would be interesting to know why you cannot use those arrows? And what alternative symbols you have available? More practically, what you will have to do here, is to simply write out both reactions:

rxn = @reaction_network begin
2.0, X + Y --> XY
2.0, XY --> X + Y
end

[ChrisRackauckas]

This leaves us with only various one character symbols as possible separators for reversible reactions (↔, ⟷, ⇄, ⇆, ⇔, ⟺ added currently). If someone came up with a way of using <-->, <->, <> that would be good. But I simply don't think this is possible, given the current way expressions work in julia.

Some of the arrows parse in the parser, like -->. I thought bidirectional arrows were in the list?

[TorkelE]

--> is the only exception we have currently. Basically everything that is just counted as a symbol makes
X ... Y and vector with the elements X, ... and Y. Here ... can be one of all the different arrows we have added to our list (⟷, etc.).

I'm not really sure what kind of operation --> is, but X --> Y is a valid expression, and since it is a natural way to write things we have a special check to parse this. If you, however, try to write something like

ex = :(X <> Y)
ex = :(X <-> Y)
ex = :(X <--> Y)

you will get an error (syntax: invalid identifier name "->"), so we cannot even create some kind of exception to handle them specifically. I think these are interpreted as X, followed by a <, followed by a >, or ->, or -->, and Julia don't know how to make sense of that.

[isaacsas]

@metma99 So Julia will add the ability to parse reversible reaction arrows, which in turn will (eventually) allow us to use them here. I assume this won't be available until at least 1.6 though. See JuliaLang/julia#36666

[metma99]

Thank you very much!

[isaacsas]

This works now with version 6.11 and Julia 1.6!