addcompartment

Create compartment object and add to model or compartment

Syntax

compartmentObj = addcompartment(modelCompartmentObj,compName)

compartmentObj = addcompartment(modelCompartmentObj,compName,capacityValue)

compartmentObj = addcompartment(___,Name=Value)

Description

compartmentObj = addcompartment(modelCompartmentObj,compName) creates and returns a Compartment object compartmentObj. The function also assigns

• compName to the Name property of compartmentObj.

• modelCompartmentObj to the Parent property of compartmentObj.

• compartmentObj to the Compartments property of the model object or compartment object modelCompartmentObj.

• A value of 1 to the Value property of compartmentObj.

compartmentObj = addcompartment(modelCompartmentObj,compName,capacityValue) also assigns the Value property of compartmentObj to capacityValue.

compartmentObj = addcompartment(___,Name=Value) also sets the properties of compartmentObj using one or more name-value arguments. Name is the property name and Value is the corresponding value. The Owner property is one exception; you cannot set the Owner property because the function requires the owning model or compartment to be specified as the first argument and uses this information to set the Owner property.

Examples

Add Compartments

This example shows how to add compartments to a SimBiology model.

Create a SimBiology model which is named m1.

model = sbiomodel('m1');

Add two compartments to the model, which are named as Central and Peripheral respectively.

comp1 = addcompartment(model,'Central');
comp2 = addcompartment(model,'Peripheral');

Change the compartment capacities and units.

comp1.Capacity = 2;
comp1.CapacityUnits = 'liter';
comp2.Capacity = 1;
comp2.CapacityUnits = 'liter';

Display all the compartments of the model.

model.Compartments

ans = 
   SimBiology Compartment Array

   Index:    Name:         Value:    Units:
   1         Central       2         liter 
   2         Peripheral    1         liter 

Input Arguments

modelCompartmentObj — SimBiology model or compartment

SimBiology.Model | SimBiology.Compartment

SimBiology model or compartment, specified as a Model or Compartment object.

If you define a reaction within a model object that does not contain any compartments, the process of adding a reaction generates a default compartment object and assigns the reaction species to the compartment. If there is more than one compartment, you must specify which compartment the species should be assigned to using the format CompartmentName.SpeciesName.

If you specify a compartment object as input, the newly-created compartment is then added as a subcompartment. The parent model is the model that contains the owning compartment.

compName — Name of compartment

character vector | string scalar

Name of the compartment object, specified as a character vector or string scalar.

Data Types: char | string

capacityValue — Value of compartment

1 (default) | positive scalar

Value of the compartment, specified as a positive scalar.

Data Types: double

Version History

Introduced in R2007b

R2024a: Having duplicate model component names is no longer allowed

• When you load a model that contains duplicate names, SimBiology^® automatically updates those names. SimBiology disambiguates the duplicate names by adding a suffix "_N", where N is the first positive integer that results in a unique name. If there is an existing suffix, N will be incremented from that suffix. For example, if there are two model components named x_3, the function updates one of the names to x_4. If the existing suffix has leading zeros, the function omits the zeros in the new name. For instance, if x_003 is a duplicate name, it gets renamed to x_4. However, the function assumes that names with leading zeros and without leading zeros are different. For instance, x_005 and x_5 are considered to be different names.

• SimBiology issues an error if multiple model components (model, compartment, species, parameter, reaction, rule, event, observable, dose, and variant) have the same name. Within a single model, these components are required to have unique names even when they are of different types with the following two exceptions:

  • Species in different compartments can have the same name.

  • Parameters can have the same name if they are scoped to different parents. Specifically, you can use the same name for a model-scoped parameter and reaction-scoped parameters, where each reaction-scoped parameter belongs to a different reaction.

  For details on how to reference model component names in expressions, see Guidelines for Referencing Names in Expressions.

R2022b: Having duplicate model component names issues a warning

SimBiology issues a warning if multiple model components have the same name.

R2022a: Having duplicate model component names will not be allowed in a future release

SimBiology will not allow you to have duplicate names for model components within a model.