MoBi Module — MoBiModule • ospsuite

A MoBi module, either loaded from a project or from a pkml file

Super classes

rSharp::NetObject -> DotNetWrapper -> ObjectBase -> MoBiModule

Active bindings

name: Name of the module (read-only)
isPKSimModule: Whether the module is a PK-Sim module (read-only)
mergeBehavior: Merge behavior of the module. Must be one of "Extend" or "Overwrite".
parameterValuesBBnames: Names of the Parameter Values Building Blocks (PV BBs) in the module (read-only)
initialConditionsBBnames: Names of the Initial Conditions Building Blocks (IC BBs) in the module (read-only)

Methods

Inherited methods

`MoBiModule$new()`

Initialize a new instance of the class

Usage

MoBiModule$new(netObject)

Arguments

netObject: Underlying reference to the MoBi module in the simulation engine.

Returns

A new MoBiModule object.

`MoBiModule$getParameterValuesBBs()`

Get the list of Parameter Values Building Blocks (PV BBs) in the module.

Usage

MoBiModule$getParameterValuesBBs(names = NULL, stopIfNotFound = TRUE)

Arguments

names: Optional names of the Parameter Values Building Block to retrieve. If NULL, returns all PV BBs.
stopIfNotFound: If TRUE (default), an error is thrown if any of the specified parameter values BB is not present in the project.

Returns

A named list of BuildingBlock objects, with names being the names of the PV BBs.

`MoBiModule$getInitialConditionsBBs()`

Get the list of Initial Conditions Building Blocks (IC BBs) in the module.

Usage

MoBiModule$getInitialConditionsBBs(names = NULL, stopIfNotFound = TRUE)

Arguments

names: Optional names of the Initial Conditions Building Block to retrieve. If NULL, returns all IC BBs.
stopIfNotFound: If TRUE (default), an error is thrown if any of the specified initial conditions BB is not present in the project.

Returns

A named list of BuildingBlock objects, with names being the names of the IC BBs.

`MoBiModule$getMoleculesBB()`

Get the Molecules Building Block of the module, if any.

Usage

MoBiModule$getMoleculesBB()

Returns

A MoleculesBuildingBlock object exposing molecule-name queries (e.g. allMoleculeNames(), allMoleculeNamesOfType(), moleculeTypeFor()), or NULL if the module has no Molecules BB.

`MoBiModule$addBuildingBlocks()`

Add one or more building blocks to the module.

Single-type building blocks (Molecules, Reactions, Spatial Structure, Passive Transports, Observers, Event Groups) can appear at most once per module; trying to add a second BB of the same single type raises an error. Initial Conditions and Parameter Values BBs may appear multiple times.

Usage

MoBiModule$addBuildingBlocks(buildingBlocks)

Arguments

buildingBlocks: A BuildingBlock, a list of BuildingBlock objects, or NULL / empty list (no-op).

Returns

The module, invisibly.

`MoBiModule$removeBuildingBlock()`

Remove a building block from the module by its name and type.

Single-type building blocks (Molecules, Reactions, Spatial Structure, Passive Transports, Observers, Event Groups) are matched on type and the lone BB's Name is verified against name. Multi-type building blocks (Initial Conditions, Parameter Values) are looked up by name within their type. Expression Profile and Individual are not module-level and raise an error.

Usage

MoBiModule$removeBuildingBlock(name, type)

Arguments

name: Name of the building block to remove (the BB's Name property).
type: Type of the building block to remove. One of the values defined in BuildingBlockTypes (excluding Expression Profile and Individual).

Returns

The module, invisibly.

`MoBiModule$print()`

Print the object to the console

Usage

MoBiModule$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.