SimBiology^®

addspecies (compartment) - Create species object and add to compartment object

Syntax

speciesObj = addspecies(compObj, 'NameValue') speciesObj = addspecies(compObj, 'NameValue', InitialAmountValue) speciesObj = addspecies(...'PropertyName', PropertyValue...)

Arguments

`compObj`	Compartment object.
`NameValue`	Name for a species object. Enter a character string unique within `compObj`. Species objects are identified by name within `Event`, `ReactionRate`, and `Rule` property strings. For information on naming species see `Name`. You can use the function `sbioselect` to find an object with a specific `Name` property value.
`IntialAmountValue`	Initial amount value for the species object. Enter `double.` Positive real number, default = `0`.
`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

speciesObj = addspecies(compObj, 'NameValue') creates a species object and returns the species object (speciesObj). In the species object, this method assigns a value (NameValue) to the property Name, and assigns the compartment object (compObj) to the property Parent. In the compartment object, this method assigns the species object to the property Species.

speciesObj = addspecies(compObj, 'NameValue', InitialAmountValue), in addition to the above, this method assigns an initial amount (InitialAmountValue) for the species.

You can also add a species to a reaction using the methods addreactant and addproduct .

A species object must have a unique name at the level at which it is created. For example, a compartment object cannot contain two species objects named H2O. However, another compartment can have a species named H2O.

View properties for a species object with the get command, and modify properties for a species object with the set command. You can view a summary table of species objects in a compartment (compObj) with get(compObj, 'Species') or the properties of the first species with get(compObj.Species(1)).

speciesObj = addspecies(...'PropertyName', PropertyValue...)defines optional properties. The property name/property value pairs can be in any format supported by the function set (for example, name-value string pairs, structures, and name-value cell array pairs). The property summary on this page shows the list of properties.

If there is more than one compartment object (compObj) in the model, you must qualify the species name with the compartment name. For example cell.glucose denotes that you want to put the species named glucose into a compartment named cell. Additionally, if the compartment named cell does not exist, the process of adding the reaction creates the compartment and names it cell.

If you change the name of a species you must configure all applicable elements, such as events and rules that use the species, any user-specified ReactionRate, or the kinetic law object property SpeciesVariableNames. Use the method setspecies to configure SpeciesVariableNames.

To update species names in the SimBiology^® graphical user interface, access each appropriate pane through the Project Explorer. You can also use the Find feature to locate the names that you want to update. The Output pane opens with the results of Find. Double-click a result row to go to the location of the model component.

Species names are automatically updated for reactions that use MassAction kinetic law.

Method Summary

Methods for species objects

copyobj (any object)	Copy SimBiology^® object and its children
delete (any object)	Delete SimBiology^® object
display (any object)	Display summary of SimBiology^® object

Property Summary

Properties for species objects

Annotation	Store link to URL or file
BoundaryCondition	Indicate species boundary condition
ConstantAmount	Specify variable or constant species amount
InitialAmount	Species initial amount
InitialAmountUnits	Species initial amount units
Name	Specify name of object
Notes	HTML text describing SimBiology^® object
Parent	Indicate parent object
Tag	Specify label for SimBiology^® object
Type	Display top-level SimBiology^® object type
UserData	Specify data to associate with object

Examples

Add two species to a model, one is a reactant and the other is the enzyme catalyzing the reaction.

Create a model object with the name my_model and add a compartment object.

modelObj = sbiomodel ('my_model');
compObj = addcompartment(modelObj, 'comp1');

Add two species objects with the names glucose_6_phosphate and glucose_6_phosphate_dehydrogenase.

speciesObj1 = addspecies (compObj, 'glucose_6_phosphate');
speciesObj2 = addspecies (compObj, ...
                         'glucose_6_phosphate_dehydrogenase');

Set initial amount of glucose_6_phosphate to 100 and verify.

set (speciesObj1, 'InitialAmount',100);
get (speciesObj1, 'InitialAmount')

MATLAB returns

ans =

   100

Use get to note that modelObj contains the species object array.

get(compObj, 'Species')

MATLAB returns,

SimBiology Species Array

   Index:    Name:                                InitialAmount:    InitialAmountUnits:
   1         glucose_6_phosphate                  100               
   2         glucose_6_phosphate_dehydrogenase    0

Retrieve information about the first species in the array.

get(compObj.Species(1))
            Annotation: ''
     BoundaryCondition: 0
        ConstantAmount: 0
         InitialAmount: 100
    InitialAmountUnits: ''
                  Name: 'glucose_6_phosphate'
                 Notes: ''
                Parent: [1x1 SimBiology.Compartment]
                   Tag: ''
                  Type: 'species'
              UserData: []