Matching `A(), B(s{one/two}) @ 0.0 {1.0}`

[hmedina]

Taking the tangent out of Kappa-Dev/KappaTools#663 (comment)

In A(), B(s{one/two}) @ 0.0 {1.0}, the usage of the unary rule rate requires the agents be connected somehow; I believe that satisfies your rooting requirement, as the two tested agents are connected via an implicit sequence of bonds.

You are right in that:

• A(), B(s{one/two}) @ 1.0 {0.0} is "spooky action at a distance"
• A(), B(s{one/two}) @ 0.0 {1.0} is not
• A(), B(s{one/two}) @ 1.0 may or may not be spooky at all

BNGL arrived at a similar notion via their "A . B" vs. "A + B" notation. Since the Kappa sages refused to alter the syntax, that information got encoded in the "ambiguous molecularity dual rate" annotation. The rate annotation is part of the rule, and contains some mechanism information.

All this to say, A(), B(s{one/two}) is indeed ambiguous, so some metadata / annotation needs to be supplied in order to constrain that into unary-only embedding, and thus be a rooted pattern.

[jonathan-laurent]

Thanks for the info Hector, this is helpful. So would it be useful to have KaTie be able to match A(), B(s{one/two}) or would you say this is low priority?

[hmedina]

For my personal usage, it is not necessary. The traces I have ready to analyze were executed with rulesets that use the idiom I describe (fake sites, explicit bonds, infinite rates), so I do not have a use for that feature. Had it been implemented years ago, I would be using it now though.