addcompartment (model, compartment)

Create compartment object

Syntax

compartmentObj = addcompartment(modelObj, 'NameValue')
compartmentObj = addcompartment(owningCompObj, 'NameValue')
compartmentObj = addcompartment(modelObj, 'NameValue', CapacityValue)
compartmentObj = addcompartment(...'PropertyName', PropertyValue...)


Arguments

modelObj	Model object
owningCompObj	Compartment object that contains the newly created compartment object.
NameValue	Name for a compartment object. Enter a character vector unique to the model object. For information on naming compartments, see Name.
CapacityValue	Capacity value for the compartment object. Enter double. Positive real number, default = 1.
PropertyName	Enter the name of a valid property. Valid property names are listed in Property Summary.
PropertyValue	Enter the value for the property specified in PropertyName. Valid property values are listed on each property reference page.

Description

compartmentObj = addcompartment(modelObj, 'NameValue') creates a compartment object and returns the compartment object (compartmentObj). In the compartment object, this method assigns a value (NameValue) to the property Name, and assigns the model object (modelObj) to the property Parent. In the model object, this method assigns the compartment object to the property Compartments.

compartmentObj = addcompartment(owningCompObj, 'NameValue') in addition to the above, adds the newly created compartment within a compartment object (owningCompObj), and assigns this compartment object (owningCompObj) to the Owner property of the newly created compartment object (compartmentObj). The parent model is the model that contains the owning compartment (owningCompObj).

compartmentObj = addcompartment(modelObj, 'NameValue', CapacityValue), in addition to the above, this method assigns capacity (CapacityValue) for the compartment.

If you define a reaction within a model object (modelObj) 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.

compartmentObj = addcompartment(...'PropertyName', PropertyValue...) defines optional properties. Property Summary lists the properties. The Owner property is one exception; you cannot set the Owner property in the addcompartment syntax because, addcompartment requires the owning model or compartment to be specified as the first argument and uses this information to set the Owner property.

Method Summary

Methods for compartment objects

addcompartment (model, compartment)	Create compartment object
addspecies (model, compartment)	Create species object and add to compartment object within model object
copyobj	Copy SimBiology object and its children
delete	Delete SimBiology object
display	Display summary of SimBiology object
findUsages	Find out how a species, parameter, or compartment is used in a model
get	Get SimBiology object properties
move	Move SimBiology compartment object to new owner
rename	Rename object and update expressions
reorder (model, compartment, kinetic law)	Reorder component lists
set	Set SimBiology object properties

Property Summary

Properties for compartment objects

Capacity	Compartment capacity
CapacityUnits	Compartment capacity units
Compartments	Array of compartments in model or compartment
Constant	Specify variable or constant species amount, parameter value, or compartment capacity
ConstantCapacity	Specify variable or constant compartment capacity
Name	Specify name of object
Notes	HTML text describing SimBiology object
Owner	Owning compartment
Parent	Indicate parent object
Species	Array of species in compartment object
Tag	Specify label for SimBiology object
Type	Display SimBiology object type
Units	Units for species amount, parameter value, compartment capacity, observable expression
UserData	Specify data to associate with object
Value	Value of species, compartment, or parameter object

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 

Version History

Introduced in R2007b

R2022b: Having duplicate model component names issues a warning

• SimBiology issues a warning if multiple model components (model, compartment, species, parameter, reaction, rule, event, observable, dose, and variant) have the same name. In a future release, within a single model, these components will be 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.

  The purpose of this naming restriction is to ensure that every model component can be unambiguously referenced by its unique name within a model. For details on how to reference model component names in expressions, see Guidelines for Referencing Names in Expressions.

• To disambiguate duplicate names from your model, use the updateDuplicateNames function at the command line. The function takes in a SimBiology model as an input and updates the component names as necessary. You can also specify optional outputs, such as a logical flag to check whether any update occurred, a list of model changes, and a copy of the original model before any updates were made.

• The updateDuplicateNames function 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.

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.