Simulation

An OSPSuite simulation

Super classes

rSharp::NetObject -> DotNetWrapper -> ObjectBase -> Simulation

Active bindings

root

Root container of the simulation (read-only)

path

Path of the root container of the simulation (read-only)

solver

SimulationSolver object for the simulation (read-only)

outputSchema

outputSchema object for the simulation (read-only)

outputSelections

outputSelections object for the simulation (read-only)

sourceFile

Path to the file the simulation was loaded from (read-only)

name

Name of the simulation

Methods

Public methods

• Simulation$new()

• Simulation$allEndogenousStationaryMoleculeNames()

• Simulation$allXenobioticFloatingMoleculeNames()

• Simulation$allStationaryMoleculeNames()

• Simulation$allFloatingMoleculeNames()

• Simulation$molWeightFor()

• Simulation$allApplicationsFor()

• Simulation$print()

Inherited methods

• rSharp::NetObject$.printClass()
• rSharp::NetObject$.printLine()
• rSharp::NetObject$call()
• rSharp::NetObject$get()
• rSharp::NetObject$getFields()
• rSharp::NetObject$getMemberSignature()
• rSharp::NetObject$getMethods()
• rSharp::NetObject$getProperties()
• rSharp::NetObject$getStaticFields()
• rSharp::NetObject$getStaticMethods()
• rSharp::NetObject$getStaticProperties()
• rSharp::NetObject$set()

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Simulation$new()

Initialize a new instance of the class

Usage

Simulation$new(netObject, sourceFile = NULL)

Arguments

netObject

Reference to NetObject .NET simulation object

sourceFile

(Optional) File used to load the simulation

Returns

A new Simulation object.

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Simulation$allEndogenousStationaryMoleculeNames()

Returns the name of all endogenous stationary molecules defined in the simulation. (e.g. with the flag IsStationary = TRUE) This is a typically a molecule that is individual specific such as en Enzyme, Protein, Transporter, FcRn etc.

Usage

Simulation$allEndogenousStationaryMoleculeNames()

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Simulation$allXenobioticFloatingMoleculeNames()

Returns the name of all xenobiotic floating molecules defined in the simulation. (e.g. with the flag IsStationary = FALSE) This is typically a molecule that is being explicitly simulated such as Compound, Inhibitor, DrugComplex.

Usage

Simulation$allXenobioticFloatingMoleculeNames()

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Simulation$allStationaryMoleculeNames()

Returns the name of all stationary molecules defined in the simulation. (e.g. with the flag IsStationary = TRUE)

Usage

Simulation$allStationaryMoleculeNames()

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Simulation$allFloatingMoleculeNames()

Returns the name of all floating molecules defined in the simulation. (e.g. with the flag IsStationary = FALSE)

Usage

Simulation$allFloatingMoleculeNames()

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Simulation$molWeightFor()

Returns the mol weight value (in core unit) associated to the quantity with given path or NA if not found

Usage

Simulation$molWeightFor(quantityPath)

Arguments

quantityPath

Path of quantity used to retrieve the molecular weight

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Simulation$allApplicationsFor()

Returns the applications ordered by start time associated to the quantity with path quantityPath or an empty list if not found

Usage

Simulation$allApplicationsFor(quantityPath)

Arguments

quantityPath

Path of quantity used to retrieve the applications (e.g. applications resulting in this quantity being applied)

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Simulation$print()

Print the object to the console

Usage

Simulation$print(...)

Arguments

...

Rest arguments.