This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. It is a class used in the implementation of extra functionality provided by libSBML.

This is an SBML converter for replacing InitialAssignment objects, when possible, by setting the initial value attributes on the model objects being assigned. In other words, for every object that is the target of an initial assignment in the model, the converter evaluates the mathematical expression of the assignment to get a numerical value, and then sets the corresponding attribute of the object to the value. The effects for different kinds of SBML components are as follows:

Configuration and use of SBMLInitialAssignmentConverter

SBMLInitialAssignmentConverter is enabled by creating a ConversionProperties object with the option 'expandInitialAssignments', and passing this properties object to SBMLDocument.convert(ConversionProperties). The converter offers no other options.

General information about the use of SBML converters

The use of all the converters follows a similar approach. First, one creates a ConversionProperties object and calls ConversionProperties.addOption(ConversionOption) on this object with one arguments: a text string that identifies the desired converter. (The text string is specific to each converter consult the documentation for a given converter to find out how it should be enabled.)

Next, for some converters, the caller can optionally set some converter-specific properties using additional calls to ConversionProperties.addOption(ConversionOption). Many converters provide the ability to configure their behavior to some extent this is realized through the use of properties that offer different options. The default property values for each converter can be interrogated using the method SBMLConverter.getDefaultProperties() on the converter class in question .

Finally, the caller should invoke the method SBMLDocument.convert(ConversionProperties) with the ConversionProperties object as an argument.

Example of invoking an SBML converter

The following code fragment illustrates an example using SBMLReactionConverter, which is invoked using the option string 'replaceReactions':

ConversionProperties props = new ConversionProperties()
if (props != null) {
  props.addOption('replaceReactions')
} else {
  // Deal with error.
}

In the case of SBMLReactionConverter, there are no options to affect its behavior, so the next step is simply to invoke the converter on an SBMLDocument object. Continuing the example code:

  // Assume that the variable 'document' has been set to an SBMLDocument object.
  status = document.convert(config)
  if (status != libsbml.LIBSBML_OPERATION_SUCCESS)
  {
    // Handle error somehow.
    System.out.println('Error: conversion failed due to the following:')
    document.printErrors()
  }

Here is an example of using a converter that offers an option. The following code invokes SBMLStripPackageConverter to remove the SBML Level 3 Layout package from a model. It sets the name of the package to be removed by adding a value for the option named 'package' defined by that converter:

ConversionProperties config = new ConversionProperties()
if (config != None) {
  config.addOption('stripPackage')
  config.addOption('package', 'layout')
  status = document.convert(config)
  if (status != LIBSBML_OPERATION_SUCCESS) {
    // Handle error somehow.
    System.out.println('Error: unable to strip the Layout package')
    document.printErrors()
  }
} else {
  // Handle error somehow.
  System.out.println('Error: unable to create ConversionProperties object')
}

Available SBML converters in libSBML

LibSBML provides a number of built-in converters by convention, their names end in Converter. The following are the built-in converters provided by libSBML 5.12.0 :

• CobraToFbcConverter
• CompFlatteningConverter
• FbcToCobraConverter
• FbcV1ToV2Converter
• FbcV2ToV1Converter
• SBMLFunctionDefinitionConverter
• SBMLIdConverter
• SBMLInferUnitsConverter
• SBMLInitialAssignmentConverter
• SBMLLevel1Version1Converter
• SBMLLevelVersionConverter
• SBMLLocalParameterConverter
• SBMLReactionConverter
• SBMLRuleConverter
• SBMLStripPackageConverter
• SBMLUnitsConverter