How to bound 3 or more agents?

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Matheus Gimenez Fernandes

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Feb 24, 2021, 12:07:53 PM2/24/21
to kappa-users

Hello,

I'm new to Kappa language, and the simulation I'm trying to do has a rule like that:

'rule' A (x[11]{p}), B(x[11]{a}),C(x1[.]{a}, x2[.]{a}, x3[11]{a}, x4[.]{a}) -> A (x[11]{p}), B(x[11]{a}),  C(x1[.]{i}, x2[.]{i}, x3[.]{i}, x4[.]{i}) @ 'k_rate'


I can't implement this rule apparently because 3 agents have sites bounded, is there anyway to deal with this on kappa?

William Waites

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Feb 24, 2021, 12:41:41 PM2/24/21
to Matheus Gimenez Fernandes, kappa-users
Do you intend that the three sites are bound by the same edge? That is
not something that is possible with KaSim as far as I know (but there
are situations where it would be useful).

You can have three agents bound together, but they need to be bound by
different edges, e.g.

A(x[1]), B(y[2]), C(x[1], y[2])

or even,

A(x[1], y[2]), B(x[2], y[3]), C(x[3], y[1])

Best wishes,
-w
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