Inheritance diagram for libsbml.SBMLLevel1Version1Converter:

Detailed Description

Whole-document SBML Level/Version converter.

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 SBML converter takes an SBML document having one SBML Level+Version combination, and attempts to convert it to an SBML document having a different Level+Version combination. This converter (SBMLLevel1Version1Converter) converts models to SBML Level 1 Version 1, to the extent possible by the limited features of that Level/Version combination of SBML.

Configuration and use of SBMLLevel1Version1Converter

SBMLLevel1Version1Converter is enabled by creating a ConversionProperties object with the option 'convertToL1V1', and passing this properties object to SBMLDocument.convert(). The target SBML Level and Version combination are determined by the value of the SBML namespace set on the ConversionProperties object (using ConversionProperties.setTargetNamespaces()).

In addition, this converter offers the following options:

'changePow': Mathematical expressions for exponentiation of the form pow(s1, 2) will be converted to the expression s1^2.

'inlineCompartmentSizes': Back in the days of SBML Level 1 Version 1, many software tools assumed that the 'kinetic laws' of SBML were written in terms of units of concentration/time. These tools would not expect (and thus not handle) rate expressions such as CompartmentOfS1 * k * S1. When the option 'inlineCompartmentSizes' is enabled, libSBML will replace the references to compartments (such as 'CompartmentOfS1' in this example) with their initial sizes. This is not strictly correct in all cases; in particular, if the compartment volume varies during simulation, this conversion will not reflect the expected behavior. However, many models do not have time-varying compartment sizes, so this option makes it easy to get modern SBML rate expressions into a form that old software tools may better understand.

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:

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 SBMLLevel1Version1Converter 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.SBMLLevel1Version1Converter.__init__	(	self,
		args
	)

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

__init__()   SBMLLevel1Version1Converter
__init__(SBMLLevel1Version1Converter obj)   SBMLLevel1Version1Converter

Each variant is described separately below.

Method variant with the following signature:

SBMLLevel1Version1Converter()

Creates a new SBMLLevel1Version1Converter object.

Method variant with the following signature:

SBMLLevel1Version1Converter(SBMLLevel1Version1Converter obj)

Copy constructor; creates a copy of an SBMLLevel1Version1Converter object.

Parameters

obj	the SBMLLevel1Version1Converter object to copy.

Member Function Documentation

def libsbml.SBMLLevel1Version1Converter.clone ( self )

Creates and returns a deep copy of this SBMLLevel1Version1Converter object.

clone()   SBMLLevel1Version1Converter

Returns: a (deep) copy of this converter.

def libsbml.SBMLLevel1Version1Converter.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:

def libsbml.SBMLLevel1Version1Converter.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.SBMLLevel1Version1Converter.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 SBMLLevel1Version1Converter 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:

See also: getProperties(); matchesProperties()

Detailed Description

Configuration and use of SBMLLevel1Version1Converter

General information about the use of SBML converters

Example of invoking an SBML converter

Available SBML converters in libSBML

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation