addproduct

Add product species object to reaction object

Syntax

speciesObj = addproduct(reactionObj, 'NameValue')
speciesObj = addproduct(reactionObj, speciesObj)
speciesObj = addproduct(reactionObj, 'NameValue', Stoichcoefficient)
speciesObj = addproduct(reactionObj, speciesObj, Stoichcoefficient)


Arguments

reactionObj	Reaction object. Enter a name for the reaction object.
NameValue	Names of species objects. Enter a character vector or cell array of character vectors. A species object can be referenced by other objects using its name. You can use the function sbioselect to find an object with a name specified by NameValue.
speciesObj	Species object or vector of species objects.
Stoichcoeffieient	Stoichiometric coefficients for products. Enter a positive scalar or vector of positive doubles. If vector, it must have the same number of elements as the number of species specified by NameValue or speciesObj.

Description

speciesObj = addproduct(reactionObj, 'NameValue') creates a species object (if it does not exist already in the model) and returns the species object (speciesObj). In the species object, this method assigns the value (NameValue) to the property Name. In the reaction object, this method assigns the species object to the property Products, modifies the reaction equation in the property Reaction to include the new species, and adds the stoichiometric coefficient 1 to the property Stoichiometry.

When you define a reaction with a new species:

• If no compartment objects exist in the model, the method creates a compartment object (called 'unnamed') in the model and adds the newly created species to that compartment.

• If only one compartment object (compObj) exists in the model, the method creates a species object in that compartment.

• 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.

Create and add a species object to a compartment object with the method addspecies.

speciesObj = addproduct(reactionObj, speciesObj), in the species object (speciesObj), assigns the parent object of the reactionObj to the species property Parent. In the reaction object (reactionObj), it assigns the species object to the property Products, modifies the reaction equation in the property Reaction to include the new species, and adds the stoichiometric coefficient 1 to the property Stoichiometry.

speciesObj = addproduct(reactionObj, 'NameValue', Stoichcoefficient), in addition to the description above, adds the stoichiometric coefficient (Stoichcoefficient) to the property Stoichiometry. If NameValue is a cell array of species names, then Stoichcoefficient must be a vector of doubles with the same length as NameValue.

speciesObj = addproduct(reactionObj, speciesObj, Stoichcoefficient), in addition to the description above, adds the stoichiometric coefficient (Stoichcoefficient) to the property Stoichiometry.

Species names are referenced by reaction objects, kinetic law objects, and model objects. If you change the Name of a species the reaction also uses the new name. You must however configure all other applicable elements such as rules that use the species, and the kinetic law object.

Examples

1. Create a model object, and then add a reaction object.

   modelObj = sbiomodel('my_model');
   reactionObj = addreaction(modelObj, 'A + C -> U');

2. Modify the reaction of the reactionObj from A + C -> U to A + C -> U + 2 H.

   speciesObj = addproduct(reactionObj, 'H', 2);