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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` 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.

In order to use the kinetic law definition, it must be added to the user-defined library with the sbioaddtolibrary function. To get the kinetic law definitions in the user-defined library, use the command get(sbioroot, 'UserDefinedKineticLaws').

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 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).

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

Method Summary

delete (any object)	Delete SimBiology object
display (any object)	Display summary of SimBiology object
get (any object)	Get object properties
set (any object)	Set object properties

Property Summary

Annotation	Store link to URL or file
Expression	Expression to determine reaction rate equation
Name	Specify name of object
Notes	HTML text describing SimBiology object
ParameterVariables	Parameters in kinetic law definition
Parent	Indicate parent object
SpeciesVariables	Species in abstract kinetic law
Tag	Specify label for SimBiology object
Type	Display top-level 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');
```