sbioabstractkineticlaw

Create kinetic law definition

Syntax

abstkineticlawObj = sbioabstractkineticlaw('Name') abstkineticlawObj = sbioabstractkineticlaw('Name','Expression') abstkineticlawObj = sbioabstractkineticlaw(...'PropertyName', PropertyValue...)

Arguments

`Name`	Enter a name for the kinetic law definition. `Name` can be a character vector or string. It must be unique in the user-defined kinetic law library. `Name` is referenced by `kineticlawObj`.
`Expression`	The mathematical expression that defines the kinetic law.

Description

abstkineticlawObj = sbioabstractkineticlaw('Name') creates an abstract kinetic law object, with the name Name and returns it to abstkineticlawObj. Use the abstract kinetic law object to specify a kinetic law definition.

The kinetic law definition provides a mechanism for applying a specific rate law to multiple reactions. It acts as a mapping template for the reaction rate. The kinetic law definition defines a reaction rate expression, which is shown in the property Expression, and the species and parameter variables used in the expression. The species variables are defined in the SpeciesVariables property, and the parameter variables are defined in the ParameterVariables property of the abstract kinetic law object.

To use the kinetic law definition, you must add it to the user-defined library with the sbioaddtolibrary function. To retrieve the kinetic law definitions from the user-defined library, first create a root object using sbioroot, then use the command get(rootObj.UserDefinedLibrary, 'KineticLaws').

abstkineticlawObj = sbioabstractkineticlaw('Name','Expression') constructs a SimBiology^® abstract kinetic law object, abstkineticlawObj with the name 'Name' and with the expression 'Expression' and returns it to abstkineticlawObj.

abstkineticlawObj = sbioabstractkineticlaw(...'PropertyName', PropertyValue...) defines optional properties. The name-value pairs can be in any format supported by the function set.

Additional abstkineticlawObj properties can be viewed with the get command. abstkineticlawObj properties can be modified with the set command.

Note

If you use the sbioabstractkineticlaw constructor function to create an object containing a reaction rate expression that is not continuous and differentiable, see Using Events to Address Discontinuities in Rule and Reaction Rate Expressions before simulating your model.

Method Summary

delete	Delete SimBiology object
display	Display summary of SimBiology object
findUsages	Find out how an `AbstractKineticLaw` object is used
get	Get SimBiology object properties
rename	Rename SimBiology model component and update expressions
set	Set SimBiology object properties

Property Summary

Notes	HTML text describing SimBiology object
Type	Display SimBiology object type
UserData	Specify data to associate with object

Examples

Create a kinetic law definition.

abstkineticlawObj = sbioabstractkineticlaw('ex_mylaw1', '(k1*s)/(k2+k1+s)');

Assign the parameter and species variables in the expression.

   set (abstkineticlawObj, 'SpeciesVariables', {'s'});
   set (abstkineticlawObj, 'ParameterVariables', {'k1', 'k2'});

Add the new kinetic law definition to the user-defined library.

   sbioaddtolibrary(abstkineticlawObj);

sbioaddtolibrary adds the kinetic law definition to the user-defined library. You can verify this using sbiowhos.

sbiowhos -kineticlaw -userdefined

SimBiology Abstract Kinetic Law Array

   Index:    Library:       Name:        Expression:
   1         UserDefined    ex_mylaw1    (k1*s)/(k2+k1+s)

Use the new kinetic law definition when defining a reaction's kinetic law.
```
     modelObj = sbiomodel('cell');
     reactionObj = addreaction(modelObj, 'A + B <-> B + C');
     kineticlawObj = addkineticlaw(reactionObj, 'ex_mylaw1');
```
Note
Remember to specify the SpeciesVariableNames and the ParameterVariableNames in kineticlawObj to fully define the ReactionRate of the reaction.

Version History

Introduced in R2006a