MathSBML

MathSBML Model Builder: compartmentToSBML

compartmentToSBML[options] returns a <compartment .../> definition.

compartmentToSBML[{{options},{options},...}] returns a <listOfCompartments.../> where each option list corresponds to a single <compartment .../> definition.

compartmentToSymbolicSBML[options] returns Symbolic SBML for a <compartment .../> definition.

New in version 2.1.5. Modified in 2.3.0, 2.6.0.

Options

Options are identical to their SBML fields in the <compartment.../> definition.

Option	Default	Description
compartmentType	No default	compartmentType that this compartment represents (Starting in Level 2, Version 2).
id	generated*	Value of compartment id. *If not specified, an id of the form compartmentn, where n is an integer, is generated.
name	Value of id	Gives compartment name.
spatialDimensions	3	Gives compartment spatialDimension. Must be 0, 1, 2, or 3.
size	No default	Gives compartment size. Unless constant->false then the size of the compartment is fixed.
units	No default	Gives compartment units.
outside	No default	Gives compartment outside of this compartment.
constant	true	If true then compartment size is fixed. If false then compartment size may vary as a variable.
metaid	No default	metaid for this compartmentType
notes	No default	notes for this compartmentType
annotation	No default	annotation for this compartmentType

Experimental Options

If Arrays->True is set by an call to newModel[]: ArrayDimensions->{i->{min,max},j->{min,max},...} or {} (default).

Example 1: Single compartment definition:

compartmentToSBML[id-> c1,name->"boundary_layer", spatialDimension->2]

returns the string

<compartment id="c1" name="boundarylayer" spatialDimension="2"/>

Example 2: list of compartment definitions:

The input string:

compartmentToSBML[{{id->"c1", size-> 5},
                   {id->"c2", spatialDimension-> 2},
                   {id->"c3",name-> "unsized_compartment_3"}}]

returns

<listOfCompartments>
 <compartment id="c1" name="c1" size="5"/>
 <compartment id="c2" name="c2" spatialDimension="2"/>
 <compartment id="c3" name="unsized_compartment_3"/>
</listOfCompartments>"

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