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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
copyobjCopy SimBiology object and its children
deleteDelete SimBiology object
displayDisplay summary of SimBiology object
getGet SimBiology object properties
getadjacencymatrix (model)Get adjacency matrix from model object
getstoichmatrix (model)Get stoichiometry matrix from model object
renameRename object and update expressions
rmproduct (reaction)Remove species object from reaction object products
rmreactant (reaction)Remove species object from reaction object reactants
setSet SimBiology object properties

Property Summary

ActiveIndicate object in use during simulation
KineticLawShow kinetic law used for ReactionRate
NameSpecify name of object
NotesHTML text describing SimBiology object
ParentIndicate parent object
ProductsArray of reaction products
ReactantsArray of reaction reactants
ReactionReaction object reaction
ReactionRateReaction rate equation in reaction object
ReversibleSpecify whether reaction is reversible or irreversible
StoichiometrySpecies coefficients in reaction
TagSpecify label for SimBiology object
TypeDisplay SimBiology object type
UserDataSpecify data to associate with object
Introduced in R2006b