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

configuration

An object of the type SimulationConfiguration, describing the modules used for the simulation, selected Parameter Values (PV) and Initial Conditions (IC).

isPopulation

TRUE if a population is currently assigned to the simulation, meaning it will be run as a population simulation; FALSE if it will be run for a single individual. To change this, assign a population (or NULL) to the population field. (read-only)

population

The Population assigned to the simulation, or NULL if the simulation is run for a single individual.

Assigning a Population turns the simulation into a population simulation, so that a subsequent runSimulations(simulation) runs it for the whole population. Assigning NULL removes the population and switches the simulation back to an individual simulation.

Any aging data previously set on the simulation is cleared whenever the population is (re)assigned or removed, since aging data only applies to the population it was generated for.

Methods

Public methods

• Simulation$new()

• Simulation$allEndogenousStationaryMoleculeNames()

• Simulation$allXenobioticFloatingMoleculeNames()

• Simulation$allStationaryMoleculeNames()

• Simulation$allFloatingMoleculeNames()

• Simulation$molWeightFor()

• Simulation$calculationMethodFor()

• 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$calculationMethodFor()

Returns the calculation method name used for the given molecule and category, or NULL if no override is set.

Usage

Simulation$calculationMethodFor(moleculeName, category)

Arguments

moleculeName

Name of the molecule.

category

One of the CalculationMethodCategories enum values (e.g. CalculationMethodCategories$PartitionCoefficient).

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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(printClassProperties = FALSE, ...)

Arguments

printClassProperties

Logical, whether to print class properties (default: FALSE). If TRUE, calls first the print method of the parent class. Useful for debugging.

...

Rest arguments.