Reaction object

Object containing model reaction information

Description

The reaction object represents a reaction, which describes a transformation, transport, or binding process that changes one or more species. Typically, the change is the amount of a species. For example:

  Creatine + ATP <-> ADP + phosphocreatine

  glucose + 2 ADP + 2 Pi -> 2 lactic acid + 2 ATP + 2 H2O

Spaces are required before and after species names and stoichiometric values.

See Property Summary for links to reaction object property reference pages.

Properties define the characteristics of an object. Use the get and set commands to list object properties and change their values at the command line. You can graphically change object properties in the graphical user interface.

Note

If you create a new reaction at the command line and do not specify its name, the reaction gets an automatic name Reaction_N, where N is a positive integer. N increases monotonically as you add more reactions.

If you copy a reaction using copyobj, the name of the copied reaction is generated by appending _N, where N is the smallest integer not in use by that prefix. For example, GivenName_1 gets copied to GivenName_1_1.

Constructor Summary

addreaction (model)

Create reaction object and add to model object

Method Summary

addkineticlaw (reaction)	Create kinetic law object and add to reaction object
addproduct (reaction)	Add product species object to reaction object
addreactant (reaction)	Add species object as reactant to reaction object
copyobj	Copy SimBiology object and its children
delete	Delete SimBiology object
display	Display summary of SimBiology object
get	Get SimBiology object properties
getadjacencymatrix (model)	Get adjacency matrix from model object
getstoichmatrix (model)	Get stoichiometry matrix from model object
rename	Rename object and update expressions
rmproduct (reaction)	Remove species object from reaction object products
rmreactant (reaction)	Remove species object from reaction object reactants
set	Set SimBiology object properties

Property Summary

Active	Indicate object in use during simulation
KineticLaw	Show kinetic law used for ReactionRate
Name	Specify name of object
Notes	HTML text describing SimBiology object
Parent	Indicate parent object
Products	Array of reaction products
Reactants	Array of reaction reactants
Reaction	Reaction object reaction
ReactionRate	Reaction rate equation in reaction object
Reversible	Specify whether reaction is reversible or irreversible
Stoichiometry	Species coefficients in reaction
Tag	Specify label for SimBiology object
Type	Display SimBiology object type
UserData	Specify data to associate with object