libsbml.SBMLRuleConverter Class Reference

Inheritance diagram for libsbml.SBMLRuleConverter:

Detailed Description

Converter that sorts SBML rules and assignments.

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 converter reorders assignments in a model. Specifically, it sorts the list of assignment rules (i.e., the AssignmentRule objects contained in the ListOfAssignmentRules within the Model object) and the initial assignments (i.e., the InitialAssignment objects contained in the ListOfInitialAssignments) such that, within each set, assignments that depend on prior values are placed after the values are set. For example, if there is an assignment rule stating a = b + 1, and another rule stating b = 3, the list of rules is sorted and the rules are arranged so that the rule for b = 3 appears before the rule for a = b + 1. Similarly, if dependencies of this sort exist in the list of initial assignments in the model, the initial assignments are sorted as well.

Beginning with SBML Level 2, assignment rules have no ordering required—the order in which the rules appear in an SBML file has no significance. Software tools, however, may need to reorder assignments for purposes of evaluating them. For example, for simulators that use time integration methods, it would be a good idea to reorder assignment rules such as the following,

b = a + 10 seconds
a = time

so that the evaluation of the rules is independent of integrator step sizes. (This is due to the fact that, in this case, the order in which the rules are evaluated changes the result.) SBMLRuleConverter can be used to reorder the SBML objects regardless of whether the input file contained them in the desired order.

Note that the two sets of SBML assignments (list of assignment rules on the one hand, and list of initial assignments on the other hand) are handled independently. In an SBML model, these entities are treated differently and no amount of sorting can deal with inter-dependencies between assignments of the two kinds.

Configuration and use of SBMLRuleConverter

SBMLRuleConverter is enabled by creating a ConversionProperties object with the option 'sortRules', and passing this properties object to SBMLDocument.convert(). This 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() on this object with one argument: 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(). 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() 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':

config = ConversionProperties()
if config != None:
  config.addOption('replaceReactions')

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_OPERATION_SUCCESS:
  # Handle error somehow.
  print('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:

def strip_layout_example(document):
  config = ConversionProperties()
  if config != None:
    config.addOption('stripPackage')
    config.addOption('package', 'layout')
    status = document.convert(config)
    if status != LIBSBML_OPERATION_SUCCESS:
      # Handle error somehow.
      print('Error: unable to strip the Layout package.')
      print('LibSBML returned error: ' + OperationReturnValue_toString(status).strip())
  else:
    # Handle error somehow.
    print('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 5.18.0:

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

Public Member Functions
def	__init__ (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...
def	clone (self)
	Creates and returns a deep copy of this SBMLLevelVersionConverter object. More...
def	convert (self)
	Perform the conversion. More...
def	getDefaultProperties (self)
	Returns the default properties of this converter. More...
def	getDocument (self, args)
	Returns the SBML document that is the subject of the conversions. More...
def	getName (self)
	Returns the name of this converter. More...
def	getProperties (self)
	Returns the current properties in effect for this converter. More...
def	getTargetNamespaces (self)
	Returns the target SBML namespaces of the currently set properties. More...
def	matchesProperties (self, props)
	Returns True if this converter object's properties match the given properties. More...
def	setDocument (self, doc)
	This method has multiple variants; they differ in the arguments they accept. More...
def	setProperties (self, props)
	Sets the configuration properties to be used by this converter. More...

Constructor & Destructor Documentation

def libsbml.SBMLRuleConverter.__init__	(		self,
			args
	)

This method has multiple variants; they differ in the arguments they accept.

__init__()   SBMLRuleConverter
__init__(SBMLRuleConverter obj)   SBMLRuleConverter

Each variant is described separately below.

---

Method variant with the following signature:

SBMLRuleConverter(SBMLRuleConverter obj)

Copy constructor; creates a copy of an SBMLLevelVersionConverter object.

Parameters

obj	the SBMLLevelVersionConverter object to copy.

---

Method variant with the following signature:

SBMLRuleConverter()

Creates a new SBMLLevelVersionConverter object.

Member Function Documentation

def libsbml.SBMLRuleConverter.clone

(

self

)

Creates and returns a deep copy of this SBMLLevelVersionConverter object.

clone()   SBMLRuleConverter

Returns

a (deep) copy of this converter.

def libsbml.SBMLRuleConverter.convert

(

self

)

Perform the conversion.

convert()   int

This method causes the converter to do the actual conversion work, that is, to convert the SBMLDocument object set by SBMLConverter.setDocument() and with the configuration options set by SBMLConverter.setProperties().

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_OBJECT
• LIBSBML_CONV_INVALID_SRC_DOCUMENT

def libsbml.SBMLRuleConverter.getDefaultProperties

(

self

)

Returns the default properties of this converter.

getDefaultProperties()   ConversionProperties

A given converter exposes one or more properties that can be adjusted in order to influence the behavior of the converter. This method returns the default property settings for this converter. It is meant to be called in order to discover all the settings for the converter object.

Returns

the ConversionProperties object describing the default properties for this converter.

def libsbml.SBMLConverter.getDocument (   self,   args  )

inherited

Returns the SBML document that is the subject of the conversions.

getDocument()   SBMLDocument

Returns

the current SBMLDocument object.

def libsbml.SBMLConverter.getName (   self )

inherited

Returns the name of this converter.

getName()   string

Returns

a string, the name of this converter.

def libsbml.SBMLConverter.getProperties (   self )

inherited

Returns the current properties in effect for this converter.

getProperties()   ConversionProperties

A given converter exposes one or more properties that can be adjusted in order to influence the behavior of the converter. This method returns the current properties for this converter; in other words, the settings in effect at this moment. To change the property values, you can use SBMLConverter.setProperties().

Returns

the currently set configuration properties.

See also

setProperties()

matchesProperties()

def libsbml.SBMLConverter.getTargetNamespaces (   self )

inherited

Returns the target SBML namespaces of the currently set properties.

getTargetNamespaces()   SBMLNamespaces

SBML namespaces are used by libSBML to express the Level+Version of the SBML document (and, possibly, any SBML Level 3 packages in use). Some converters' behavior is affected by the SBML namespace configured in the converter. For example, in SBMLLevelVersionConverter (the converter for converting SBML documents from one Level+Version combination to another), the actions are fundamentally dependent on the SBML namespaces targeted.

Returns

the SBMLNamespaces object that describes the SBML namespaces in effect, or None if none are set.

def libsbml.SBMLRuleConverter.matchesProperties	(		self,
			props
	)

Returns True if this converter object's properties match the given properties.

matchesProperties(ConversionProperties props)   bool

A typical use of this method involves creating a ConversionProperties object, setting the options desired, and then calling this method on an SBMLLevelVersionConverter object to find out if the object's property values match the given ones. This method is also used by SBMLConverterRegistry.getConverterFor() to search across all registered converters for one matching particular properties.

Parameters

props

the properties to match.

Returns

True if this converter's properties match, False otherwise.

def libsbml.SBMLConverter.setDocument (   self,   doc  )

inherited

This method has multiple variants; they differ in the arguments they accept.

setDocument(SBMLDocument doc)   int

Each variant is described separately below.

---

Method variant with the following signature:

setDocument(SBMLDocument doc)

Sets the SBML document to be converted.

Parameters

doc	the document to use for this conversion.

Returns

integer value indicating the success/failure of the operation. The set of possible values that may be returned ultimately depends on the specific subclass of SBMLConverter being used, but the default method can return the following:

• LIBSBML_OPERATION_SUCCESS

---

Method variant with the following signature:

setDocument(SBMLDocument doc)

Sets the SBML document to be converted.

Parameters

doc	the document to use for this conversion.

Returns

integer value indicating the success/failure of the operation. The set of possible values that may be returned ultimately depends on the specific subclass of SBMLConverter being used, but the default method can return the following:

• LIBSBML_OPERATION_SUCCESS

def libsbml.SBMLConverter.setProperties (   self,   props  )

inherited

Sets the configuration properties to be used by this converter.

setProperties(ConversionProperties props)   int

Parameters

props

the ConversionProperties object defining the properties to set.

Returns

integer value indicating the success/failure of the operation. The set of possible values that may be returned ultimately depends on the specific subclass of SBMLConverter being used, but the default method can return the following values:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

See also

getProperties()

matchesProperties()