State mapping in reaction rules?

Hi, BNGL supports state mapping using “%” in reaction rules, e.g. A(a%x) -> B(a%x), to indicate that the state of A is transferred to B. I was wondering if there exists anything comparable in pysb? I see that it is straightforward to generate all the rules programmatically, but it would be convenient if that could be avoided.

[lh64]

@FFroehlich The basic reason is that the syntax for molecule and complex tags isn’t consistent with the syntax for component state tags, that’s all. A tag is conceptually like a pointer to an object. They can be used to map reactants to products (needed for extracting base operations from the rules, e.g., bind, change state, etc.) and for defining the context for performing pattern matching in Observables. Observables produce numbers (the number of matches to a molecule or complex) but the tag itself is not a number.

In the state-mapping example, the tag in A(a%x) -> B(a%x) represents a number, which is the problem. We thought about modifying the syntax so the rule would look something like A(a~?%x) -> B(a~valueOf(x)), where %x would point to the state (as an object) of a and then a new builtin function (that we’d have to implement) valueOf would extract the value of the state from the tag x. But we never came to an agreement on exactly how to do this so it didn’t happen. For example, should we tag the state, like I did above, or the component, as in something like A(a%x) -> B(a~x.getState())?

Anyway, we threw around ideas like this for a while but nothing ever came of it. So the original state-mapping syntax is still in there if it’s useful but I’d be careful about using it because it could change at some point in a new BNG release.

[FFroehlich]

@lh64 Thank you for the detailed explanation, that definitely makes sense.