Specifing agent connection distance

[Héctor F]

Hi everyone!
On current Kappa syntax, rules of ambiguous molecularity require a distinction between unimolecular and bimolecular rates. So basically, if I wrote a reaction such as:

Kinase(), Substrate(s1~x) -> Kinase(), Substrate(s1~p) @ 0.0 (1.0)

Then every time Substrate and Kinase are on the same molecule (i.e. connected graph), s1 will be modified. I was wondering if a feature could be added to specify the maximum distance, in agents, between Kinase and Substrate, i.e.:

Kinase(), |x|, Substrate(s1~x) -> Kinase(), |x|, Substrate(s1~p) @ 0.0 (1.0)

Where |x| is the number of separating agents in the complex (e.g. 0 for a direct connection). This could serve to compensate the lack of geometry on agents (either because KaSim is geometry-free, or because the agent is unstructured in the first place). On my current model, there are many heterogenous paths connecting the agents mentioned, and a combinatorial explosion renders writing each rule down extremely cumbersome. I realize this feature would probably come at the expense of run speed (scaling with the network complexity); and yet, it would also mean not writing a very large number of rules (logarithmic impact on run speed if I recall correctly?).

Best,
Héctor

[Jean Krivine]

Hi 

Yes it is possible and I think I actually implemented something along these lines. It is on my todo list anyway

Cheers

J

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