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Simulation configuration

Source: R/SimulationConfiguration.R
SimulationConfiguration.Rd

Configuration of a simulation. Contains description of the modules used for the simulation, selected Parameter Values (PV) and Initial Conditions (IC), and molecule calculation methods.

Value

A new SimulationConfiguration object.

Active bindings

individual

A building block of type "Individual" used in the configuration. Can be NULL if no Individual should be applied.

expressionProfiles

A list of building blocks of type "Expression Profile" used in the configuration. Only one profile per protein is allowed.

modules

A named list of MoBiModule objects from which to create the simulation. The order of modules defines the order in which the modules will be combined to a simulation! When setting the modules, the selection of Initial Conditions and Parameter Values is reset to the first available ones in the modules.

selectedInitialConditions

A named list with names being the names of the modules, and the values the names of Initial Conditions Building Blocks

selectedParameterValues

A named list with names being the names of the modules, and the values the names of Parameter Values Building Blocks If the modules for which the PV selection is provided are not in the configuration, throw an error.

partitionCoefficientOverrides

A named list of partition coefficient method overrides. Names are molecule names, values are the full calculation method names. Read-only; use setPartitionCoefficientMethods() to modify.

cellularPermeabilityOverrides

A named list of cellular permeability method overrides. Names are molecule names, values are the full calculation method names. Read-only; use setCellularPermeabilityMethods() to modify.

settings

A SimulationSettings object defining the simulation settings. If no settings are provided, default settings will be used upon simulation creation. Individual properties within the SimulationSettings object are read-only, but the entire settings object can be replaced with another SimulationSettings instance (or set to NULL to use defaults). Setting the solver settings, output intervals, and output selections must be done after creating the simulation from the configuration.

Methods

Public methods

Method new()

Initialize a new instance of the class

Usage

SimulationConfiguration$new(
  modules,
  individual = NULL,
  expressionProfiles = NULL,
  selectedInitialConditions = NULL,
  selectedParameterValues = NULL,
  settings = NULL
)

Arguments

modules

A list of MoBiModule objects from which to create in simulation. The order of modules defines the order in which the modules will be combined to a simulation!

individual

Optional, an individual building block

expressionProfiles

Optional, a list of expression profiles to apply to the simulation.

selectedInitialConditions

By default, the first Initial Conditions (IC) building block (BB) of each module will be selected. If a module has multiple IC BBs, it is possible to specify which IC BB to apply by providing a named list, where the name should be the name of the module and the value the name of the IC BB. By explicitly setting the value for a specific module to NULL, no IC BB from the specified module will be applied. If the list contains a module name that is not part of the provided modules, it will be ignored.

selectedParameterValues

By default, the first Parameter Values (PV) building block (BB) of each module will be selected. If a module has multiple PV BBs, it is possible to specify which PV BB to apply by providing a named list, where the name should be the name of the module and the value the name of the PV BB. By explicitly setting the value for a specific module to NULL, no PV BB from the specified module will be applied. If the list contains a module name that is not part of the provided modules, it will be ignored.

settings

Optional, a SimulationSettings object defining the simulation settings. If no settings are provided, default settings will be used upon simulation creation.

Method setPartitionCoefficientMethods()

Sets the method used for calculation of partition coefficients. This method can be used to specify the partition coefficient method for each molecule used in the modules. If not specified, the method set in the Molecules Building Block of the last module in which the molecule is present will be used.

Usage

SimulationConfiguration$setPartitionCoefficientMethods(
  moleculeName,
  methodName
)

Arguments

moleculeName

The name of the molecule for which to set the partition coefficient method.

methodName

The name of the method to use for calculation of partition coefficients for the specified molecule. Should be one of the PartitionCoefficientMethods enum values. Use NULL to remove an existing override.

Method setCellularPermeabilityMethods()

Sets the method used for calculation of cellular permeabilities. This method can be used to specify the cellular permeability method for each molecule used in the modules. If not specified, the method set in the Molecules Building Block of the last module in which the molecule is present will be used.

Usage

SimulationConfiguration$setCellularPermeabilityMethods(
  moleculeName,
  methodName
)

Arguments

moleculeName

The name of the molecule for which to set the cellular permeability method.

methodName

The name of the method to use for calculation of cellular permeabilities for the specified molecule. Should be one of the CellularPermeabilityMethods enum values. Use NULL to remove an existing override.

Method print()

Print the object to the console

Usage

SimulationConfiguration$print(...)

Arguments

...

Rest arguments.