Is it possible to deactivate all reactions within a compartment in SimBiology?

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emjey
emjey 2022-12-6
回答： Arthur Goldsipe 2022-12-7
I would like to test a selected submodule of my model, which amounts to switching off other unwanted compartments which contain computational heavy model parts. Additionally, I would like to be able to do it from command line (without manual deactivating reaction).
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emjey
emjey 2022-12-7
I might underestimate the complexity of this, but would not be possible to deactivate compartment-wide those reactions which are placed within the boundary of this compartment? The products/reactants might be elsewhere, they would not 'see' that particular reaction rate.
Setting Active property is an option but how to do it programatically for all reactions located within a given compartment? I can do it manualy but that not very practical.
The background: I have a compartmental PK model coupled with a PD compartment - I would like to test the PK part only, the PD being computationally heavy and makes it difficult to test/work with PK.
Arthur Goldsipe
Arthur Goldsipe 2022-12-7
I think it will be straightforward but perhaps a little tedious to write a function do do this. So I didn't want to go into all the details until I made sure I was going to answer the question you were actually asking. :-)

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采纳的回答

Arthur Goldsipe
Arthur Goldsipe 2022-12-7
I think the getBlock function will give you the information you need to determine whether a reaction is inside a compartment. It will return the position of blocks. In pseudocode, it might look something like this:
  • Make sure the model is open in the Model Builder app.
  • Use getBlock to find the boundaries of all compartments you want to disable the reaction in.
  • For each reaction in the model
  • Use getBlock to determine the boundaries of the reaction.
  • See if those boundaries are within the boundaries of any compartment (perhaps using inpolygon).
  • If so, set the reaction's Active property to false.

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