SimBiology^®

sbioabstractkineticlaw - Construct abstract kinetic law object

Syntax

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

Arguments

`Name`	Enter a name for the abstract kinetic law. `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

A SimBiology^® abstract kinetic law defines a reaction rate expression, species variables and parameter variables for a kinetic law. abstkineticlawObj = sbioabstractkineticlaw('Name') creates an abstract kinetic law object, with name Name and returns it to abstkineticlawObj.

The abstract kinetic law provides a mechanism for applying a specific rate law to multiple reactions. It acts as a mapping template for the reaction rate. The abstract kinetic law 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 abstkineticlawObj when constructing a kinetic law object with the method addkineticlaw, abstkineticlawObj must be added to the user-defined library with the sbioaddtolibrary function. To get the abstract kinetic law objects in the user-defined library, use the command get(sbioroot, 'UserDefinedKineticLaws').

abstkineticlawObj = sbioabstractkineticlaw('Name','Expression') constructs a SimBiology abstract kinetic law object, abstkineticlawObj with name, 'Name' and with 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

copyobj (any object)	Copy SimBiology^® object and its children
delete (any object)	Delete SimBiology^® object
display (any object)	Display summary of SimBiology^® object

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 abstract kinetic law
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

Example

Create an abstract kinetic law.

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 abstract kinetic law to the user-defined library.

   sbioaddtolibrary(abstkineticlawObj);

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