MathSBML

MathSBML Model Builder: functionToSBML

functionToSBML[options] returns a single SBML <functionDefinition.../>;

functionToSBML[{{options},{options},...}] returns an SBML <listOfFunctionDefinitions.../>;

functionToSymbolicSBML[arguments] returns Symbolic SBML for a single <functionDefinition.../>;

New in version 2.1.4. Revised in 2.6.0.

Options

Option	Default	Description
arguments	generated*	Single argument or list of arguments, as in arguments->x or arguments->{x, y, z}. If not specified, a dummy variable is generated.
id	generated*	Value of SBML id. *If not specified, an id of the form functionn, where n is an integer, is generated.
math	1	Expression giving function value in terms of the arguments.
name	Uses id*	Value of SBML name. *If not specified, the value of the id is used.
sboTerm	No default	sboTerm for this function
metaid	No default	metaid for this function
notes	No default	notes for this function
annotation	No default	annotation for this function

Example 1: Single function, <function .. /> definition

The following input expression (optional line-feeds added to emphasize syntactical nesting):

	functionToSBML[id->alfafa,
	               arguments->{horse, grass},
	               math->(1/(horse*grass))]

will produce the following output:

	<functionDefinition id="alfafa"
	    name="alfafa">
	 <math xmlns="http://www.w3.org/1998/Math/MathML">
	  <lambda>
	   <bvar>
	    <ci>horse</ci>
	   </bvar>
	   <bvar>
	    <ci>grass</ci>
	   </bvar>
	   <apply>
	    <times/>
	    <cn type="integer">1</cn>
	    <apply>
	     <power/>
	     <apply>
	      <times/>
	      <ci>grass</ci>
	      <ci>horse</ci>
	     </apply>
	     <cn type="integer">-1</cn>
	    </apply>
	   </apply>
	  </lambda>
	 </math>
	</functionDefinition>

Example 2: Multiple functions, <listOfFunctionDefinitions .. /> definition

The following input expression (optional line-feeds added to emphasize syntactical nesting):

	functionToSBML[
	  { {id->QRT, arguments->{x}, math->x^(1/4)},
	    {id->sinc, arguments->{x}, math->Sin[x]/x}
	  }]

will produce the following output:


	<listOfFunctionDefinitions>
	 <functionDefinition id=\"QRT\"
	     name=\"QRT\">
	  <math xmlns=\"http://www.w3.org/1998/Math/MathML\">
	   <lambda>
	    <bvar>
	     <ci>x</ci>
	    </bvar>
	    <apply>
	     <power/>
	     <ci>x</ci>
	     <cn type=\"rational\">1<sep/>4</cn>
	    </apply>
	   </lambda>
	  </math>
	 </functionDefinition>
	 <functionDefinition id=\"sinc\"
	     name=\"sinc\">
	  <math xmlns=\"http://www.w3.org/1998/Math/MathML\">
	   <lambda>
	    <bvar>
	     <ci>x</ci>
	    </bvar>
	    <apply>
	     <times/>
	     <apply>
	      <sin/>
	      <ci>x</ci>
	     </apply>
	     <apply>
	      <power/>
	      <ci>x</ci>
	      <cn type=\"integer\">-1</cn>
	     </apply>
	    </apply>
	   </lambda>
	  </math>
	 </functionDefinition>
	</listOfFunctionDefinitions>

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