libsbml.Model Class Reference

Inheritance diagram for libsbml.Model:

Detailed Description

LibSBML implementation of SBML's Model construct.

In an SBML model definition, a single object of class Model serves as the overall container for the lists of the various model components. All of the lists are optional, but if a given list container is present within the model, the list must not be empty; that is, it must have length one or more. The following are the components and lists permitted in different Levels and Versions of SBML in version 5.3.0 of libSBML:

In SBML Level 1, the components are: UnitDefinition, Compartment, Species, Parameter, Rule, and Reaction. Instances of the classes are placed inside instances of classes ListOfUnitDefinitions, ListOfCompartments, ListOfSpecies, ListOfParameters, ListOfRules, and ListOfReactions.
In SBML Level 2 Version 1, the components are: FunctionDefinition, UnitDefinition, Compartment, Species, Parameter, Rule, Reaction and Event. Instances of the classes are placed inside instances of classes ListOfFunctionDefinitions, ListOfUnitDefinitions, ListOfCompartments, ListOfSpecies, ListOfParameters, ListOfRules, ListOfReactions, and ListOfEvents.
In SBML Level 2 Versions 2, 3 and 4, the components are: FunctionDefinition, UnitDefinition, CompartmentType, SpeciesType, Compartment, Species, Parameter, InitialAssignment, Rule, Constraint, Reaction and Event. Instances of the classes are placed inside instances of classes ListOfFunctionDefinitions, ListOfUnitDefinitions, ListOfCompartmentTypes, ListOfSpeciesTypes, ListOfCompartments, ListOfSpecies, ListOfParameters, ListOfInitialAssignments, ListOfRules, ListOfConstraints, ListOfReactions, and ListOfEvents.
In SBML Level 3 Version 1, the components are: FunctionDefinition, UnitDefinition, Compartment, Species, Parameter, InitialAssignment, Rule, Constraint, Reaction and Event. Instances of the classes are placed inside instances of classes ListOfFunctionDefinitions, ListOfUnitDefinitions, ListOfCompartments, ListOfSpecies, ListOfParameters, ListOfInitialAssignments, ListOfRules, ListOfConstraints, ListOfReactions, and ListOfEvents.

Although all the lists are optional, there are dependencies between SBML components such that defining some components requires defining others. An example is that defining a species requires defining a compartment, and defining a reaction requires defining a species. The dependencies are explained in more detail in the SBML specifications.

In addition to the above lists and attributes, the Model class in both SBML Level 2 and Level 3 has the usual two attributes of 'id' and 'name', and both are optional. As is the case for other SBML components with 'id' and 'name' attributes, they must be used according to the guidelines described in the SBML specifications. (Within the frameworks of SBML Level 2 and Level 3 Version 1 Core, a Model object identifier has no assigned meaning, but extension packages planned for SBML Level 3 are likely to make use of this identifier.)

Finally, SBML Level 3 has introduced a number of additional Model attributes. They are discussed in a separate section below.

Approaches to creating objects using the libSBML API

LibSBML provides two main mechanisms for creating objects: class constructors (e.g., Species.Species() ), and createObject() methods (such as Model.createSpecies()) provided by certain Object classes such as Model. These multiple mechanisms are provided by libSBML for flexibility and to support different use-cases, but they also have different implications for the overall model structure.

In general, the recommended approach is to use the createObject() methods. These methods both create an object and link it to the parent in one step. Here is an example:

 # Create an SBMLDocument object in Level 3 Version 1 format:

 sbmlDoc = SBMLDocument(3, 1)

 # Create a Model object inside the SBMLDocument object and set
 # its identifier.  The call to setId() returns a status code
 # to indicate whether the assignment was successful.  Code 0
 # means success; see the documentation for Model's setId() for 
 # more information.

 model = sbmlDoc.createModel()
 model.setId(&#34;BestModelEver&#34;)

 # Create a Species object inside the Model and set its identifier.
 # Again, the setId() returns a status code to indicate whether the
 # assignment was successful.  Code 0 means success; see the
 # documentation for Specie's setId() for more information.

 sp = model.createSpecies()
 sp.setId(&#34;BestSpeciesEver&#34;)

The createObject() methods return a pointer to the object created, but they also add the object to the relevant list of object instances contained in the parent. (These lists become the <listOfObjects> elements in the finished XML rendition of SBML.) In the example above, Model.createSpecies() adds the created species directly to the <listOfSpecies> list in the model. Subsequently, methods called on the species change the species in the model (which is what is expected in most situations).

Consistency and adherence to SBML specifications

To make it easier for applications to do whatever they need, libSBML version 5.3.0 is relatively lax when it comes to enforcing correctness and completeness of models during model construction and editing. Essentially, libSBML will not in most cases check automatically that a model's components have valid attribute values, or that the overall model is consistent and free of errors—even obvious errors such as duplication of identifiers. This allows applications great leeway in how they build their models, but it means that software authors must take deliberate steps to ensure that the model will be, in the end, valid SBML. These steps include such things as keeping track of the identifiers used in a model, manually performing updates in certain situations where an entity is referenced in more than one place (e.g., a species that is referenced by multiple SpeciesReference objects), and so on.

That said, libSBML does provide powerful features for deliberately performing validation of SBML when an application decides it is time to do so. The interfaces to these facilities are on the SBMLDocument class, in the form of SBMLDocument.checkInternalConsistency() and SBMLDocument.checkConsistency(). Please refer to the documentation for SBMLDocument for more information about this.

While applications may play fast and loose and live like free spirits during the construction and editing of SBML models, they should always make sure to call SBMLDocument.checkInternalConsistency() and/or SBMLDocument.checkConsistency() before writing out the final version of an SBML model.

Model attributes introduced in SBML Level 3

As mentioned above, the Model class has a number of optional attributes in SBML Level 3 Version 1 Core. These are 'substanceUnits', 'timeUnits', 'volumeUnits', 'areaUnits', 'lengthUnits', 'extentUnits', and 'conversionFactor. The following provide more information about them.

The 'substanceUnits' attribute

The 'substanceUnits' attribute is used to specify the unit of measurement associated with substance quantities of Species objects that do not specify units explicitly. If a given Species object definition does not specify its unit of substance quantity via the 'substanceUnits' attribute on the Species object instance, then that species inherits the value of the Model 'substanceUnits' attribute. If the Model does not define a value for this attribute, then there is no unit to inherit, and all species that do not specify individual 'substanceUnits' attribute values then have no declared units for their quantities. The SBML Level 3 Version 1 Core specification provides more details.

Note that when the identifier of a species appears in a model's mathematical expressions, the unit of measurement associated with that identifier is not solely determined by setting 'substanceUnits' on Model or Species. Please see the discussion about units given in the documentation for the Species class.

The 'timeUnits' attribute

The 'timeUnits' attribute on SBML Level 3's Model object is used to specify the unit in which time is measured in the model. This attribute on Model is the only way to specify a unit for time in a model. It is a global attribute; time is measured in the model everywhere in the same way. This is particularly relevant to Reaction and RateRule objects in a model: all Reaction and RateRule objects in SBML define per-time values, and the unit of time is given by the 'timeUnits' attribute on the Model object instance. If the Model 'timeUnits' attribute has no value, it means that the unit of time is not defined for the model's reactions and rate rules. Leaving it unspecified in an SBML model does not result in an invalid model in SBML Level 3; however, as a matter of best practice, we strongly recommend that all models specify units of measurement for time.

The 'volumeUnits', 'areaUnits', and 'lengthUnits' attributes

The attributes 'volumeUnits', 'areaUnits' and 'lengthUnits' together are used to set the units of measurements for the sizes of Compartment objects in an SBML Level 3 model when those objects do not otherwise specify units. The three attributes correspond to the most common cases of compartment dimensions: 'volumeUnits' for compartments having a 'spatialDimensions' attribute value of '3', 'areaUnits' for compartments having a 'spatialDimensions' attribute value of '2', and 'lengthUnits' for compartments having a 'spatialDimensions' attribute value of '1'. The attributes are not applicable to compartments whose 'spatialDimensions' attribute values are not one of '1', '2' or '3'.

If a given Compartment object instance does not provide a value for its 'units' attribute, then the unit of measurement of that compartment's size is inherited from the value specified by the Model 'volumeUnits', 'areaUnits' or 'lengthUnits' attribute, as appropriate based on the Compartment object's 'spatialDimensions' attribute value. If the Model object does not define the relevant attribute, then there are no units to inherit, and all Compartment objects that do not set a value for their 'units' attribute then have no units associated with their compartment sizes.

The use of three separate attributes is a carry-over from SBML Level 2. Note that it is entirely possible for a model to define a value for two or more of the attributes 'volumeUnits', 'areaUnits' and 'lengthUnits' simultaneously, because SBML models may contain compartments with different numbers of dimensions.

The 'extentUnits' attribute

Reactions are processes that occur over time. These processes involve events of some sort, where a single ``reaction event'' is one in which some set of entities (known as reactants, products and modifiers in SBML) interact, once. The extent of a reaction is a measure of how many times the reaction has occurred, while the time derivative of the extent gives the instantaneous rate at which the reaction is occurring. Thus, what is colloquially referred to as the 'rate of the reaction' is in fact equal to the rate of change of reaction extent.

In SBML Level 3, the combination of 'extentUnits' and 'timeUnits' defines the units of kinetic laws in SBML and establishes how the numerical value of each KineticLaw object's mathematical formula is meant to be interpreted in a model. The units of the kinetic laws are taken to be 'extentUnits' divided by 'timeUnits'.

Note that this embodies an important principle in SBML Level 3 models: all reactions in an SBML model must have the same units for the rate of change of extent. In other words, the units of all reaction rates in the model must be the same. There is only one global value for 'extentUnits' and one global value for 'timeUnits'.

The 'conversionFactor' attribute

The attribute 'conversionFactor' in SBML Level 3's Model object defines a global value inherited by all Species object instances that do not define separate values for their 'conversionFactor' attributes. The value of this attribute must refer to a Parameter object instance defined in the model. The Parameter object in question must be a constant; ie it must have its 'constant' attribute value set to 'true'.

If a given Species object definition does not specify a conversion factor via the 'conversionFactor' attribute on Species, then the species inherits the conversion factor specified by the Model 'conversionFactor' attribute. If the Model does not define a value for this attribute, then there is no conversion factor to inherit. More information about conversion factors is provided in the SBML Level 3 Version 1 specification.

Public Member Functions
def	addCompartment
def	addCompartmentType
def	addConstraint
def	addCVTerm
def	addEvent
def	addFunctionDefinition
def	addInitialAssignment
def	addParameter
def	addReaction
def	addRule
def	addSpecies
def	addSpeciesType
def	addUnitDefinition
def	appendAnnotation
def	appendFrom
def	appendNotes
def	clone
def	createAlgebraicRule
def	createAssignmentRule
def	createCompartment
def	createCompartmentType
def	createConstraint
def	createDelay
def	createEvent
def	createEventAssignment
def	createFunctionDefinition
def	createInitialAssignment
def	createKineticLaw
def	createKineticLawLocalParameter
def	createKineticLawParameter
def	createModifier
def	createParameter
def	createProduct
def	createRateRule
def	createReactant
def	createReaction
def	createSpecies
def	createSpeciesType
def	createTrigger
def	createUnit
def	createUnitDefinition
def	disablePackage
def	enablePackage
def	getAncestorOfType
def	getAnnotation
def	getAnnotationString
def	getAreaUnits
def	getColumn
def	getCompartment
def	getCompartmentType
def	getConstraint
def	getConversionFactor
def	getCVTerm
def	getCVTerms
def	getElementByMetaId
def	getElementBySId
def	getElementName
def	getEvent
def	getExtentUnits
def	getFunctionDefinition
def	getId
def	getInitialAssignment
def	getLengthUnits
def	getLevel
def	getLine
def	getListOfAllElements
def	getListOfAllElementsFromPlugins
def	getListOfCompartments
def	getListOfCompartmentTypes
def	getListOfConstraints
def	getListOfEvents
def	getListOfFunctionDefinitions
def	getListOfInitialAssignments
def	getListOfParameters
def	getListOfReactions
def	getListOfRules
def	getListOfSpecies
def	getListOfSpeciesTypes
def	getListOfUnitDefinitions
def	getMetaId
def	getModel
def	getModelHistory
def	getName
def	getNamespaces
def	getNotes
def	getNotesString
def	getNumCompartments
def	getNumCompartmentTypes
def	getNumConstraints
def	getNumCVTerms
def	getNumEvents
def	getNumFunctionDefinitions
def	getNumInitialAssignments
def	getNumParameters
def	getNumPlugins
def	getNumReactions
def	getNumRules
def	getNumSpecies
def	getNumSpeciesTypes
def	getNumSpeciesWithBoundaryCondition
def	getNumUnitDefinitions
def	getPackageName
def	getPackageVersion
def	getParameter
def	getParentSBMLObject
def	getPlugin
def	getReaction
def	getResourceBiologicalQualifier
def	getResourceModelQualifier
def	getRule
def	getSBMLDocument
def	getSBOTerm
def	getSBOTermID
def	getSpecies
def	getSpeciesReference
def	getSpeciesType
def	getSubstanceUnits
def	getTimeUnits
def	getTypeCode
def	getUnitDefinition
def	getVersion
def	getVolumeUnits
def	hasRequiredElements
def	hasValidLevelVersionNamespaceCombination
def	isPackageEnabled
def	isPackageURIEnabled
def	isPkgEnabled
def	isPkgURIEnabled
def	isPopulatedListFormulaUnitsData
def	isSetAnnotation
def	isSetAreaUnits
def	isSetConversionFactor
def	isSetExtentUnits
def	isSetId
def	isSetLengthUnits
def	isSetMetaId
def	isSetModelHistory
def	isSetName
def	isSetNotes
def	isSetSBOTerm
def	isSetSubstanceUnits
def	isSetTimeUnits
def	isSetVolumeUnits
def	matchesSBMLNamespaces
def	populateListFormulaUnitsData
def	removeCompartment
def	removeCompartmentType
def	removeConstraint
def	removeEvent
def	removeFromParentAndDelete
def	removeFunctionDefinition
def	removeInitialAssignment
def	removeParameter
def	removeReaction
def	removeRule
def	removeSpecies
def	removeSpeciesType
def	removeUnitDefinition
def	renameMetaIdRefs
def	renameSIdRefs
def	renameUnitSIdRefs
def	setAnnotation
def	setAreaUnits
def	setConversionFactor
def	setExtentUnits
def	setId
def	setLengthUnits
def	setMetaId
def	setModelHistory
def	setName
def	setNamespaces
def	setNotes
def	setSBOTerm
def	setSubstanceUnits
def	setTimeUnits
def	setVolumeUnits
def	toSBML
def	unsetAnnotation
def	unsetAreaUnits
def	unsetConversionFactor
def	unsetCVTerms
def	unsetExtentUnits
def	unsetId
def	unsetLengthUnits
def	unsetMetaId
def	unsetModelHistory
def	unsetName
def	unsetNotes
def	unsetSBOTerm
def	unsetSubstanceUnits
def	unsetTimeUnits
def	unsetVolumeUnits

Member Function Documentation

def libsbml.Model.addCompartment	(	self,
		args
	)

Python method signature(s):

addCompartment(Compartment c)    int

Adds a copy of the given Compartment object to this Model.

Parameters:

c

the Compartment object to add

Returns:

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

Note:: This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Model.createCompartment() for a method that does not lead to these issues.

See also:: createCompartment()

def libsbml.Model.addCompartmentType	(	self,
		args
	)

Python method signature(s):

addCompartmentType(CompartmentType ct)    int

Adds a copy of the given CompartmentType object to this Model.

Parameters:

ct

the CompartmentType object to add

Returns:

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

Note:: This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Model.createCompartmentType() for a method that does not lead to these issues.; The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.

See also:: createCompartmentType()

def libsbml.Model.addConstraint	(	self,
		args
	)

Python method signature(s):

addConstraint(Constraint c)    int

Adds a copy of the given Constraint object to this Model.

Parameters:

c

the Constraint object to add

Returns:

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

Note:: This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Model.createConstraint() for a method that does not lead to these issues.

See also:: createConstraint()

def libsbml.SBase.addCVTerm	(	self,
		args
	)		`[inherited]`

Python method signature(s):

addCVTerm(CVTerm term, bool newBag = False)    int
addCVTerm(CVTerm term)    int

Adds a copy of the given CVTerm object to this SBML object.

Parameters:

	term	the CVTerm to assign
	newBag	if `true`, creates a new RDF bag with the same identifier as a previous bag, and if `false`, adds the term to an existing RDF bag with the same type of qualifier as the term being added.

Returns:

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

LIBSBML_OPERATION_SUCCESS
LIBSBML_OPERATION_FAILED
LIBSBML_UNEXPECTED_ATTRIBUTE , if this object lacks a 'metaid' attribute
LIBSBML_INVALID_OBJECT

Note:: Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.

Warning:: The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance added here. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result.

Documentation note:: The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.

def libsbml.Model.addEvent	(	self,
		args
	)

Python method signature(s):

addEvent(Event e)    int

Adds a copy of the given Event object to this Model.

Parameters:

e

the Event object to add

Returns:

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

Note:: This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Model.createEvent() for a method that does not lead to these issues.

See also:: createEvent()

def libsbml.Model.addFunctionDefinition	(	self,
		args
	)

Python method signature(s):

addFunctionDefinition(FunctionDefinition fd)    int

Adds a copy of the given FunctionDefinition object to this Model.

Parameters:

fd

the FunctionDefinition to add

Returns:

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

Note:: This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Model.createFunctionDefinition() for a method that does not lead to these issues.

See also:: createFunctionDefinition()

def libsbml.Model.addInitialAssignment	(	self,
		args
	)

Python method signature(s):

addInitialAssignment(InitialAssignment ia)    int

Adds a copy of the given InitialAssignment object to this Model.

Parameters:

ia

the InitialAssignment object to add

Returns:

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

Note:: This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Model.createInitialAssignment() for a method that does not lead to these issues.

See also:: createInitialAssignment()

def libsbml.Model.addParameter	(	self,
		args
	)

Python method signature(s):

addParameter(Parameter p)    int

Adds a copy of the given Parameter object to this Model.

Parameters:

p

the Parameter object to add

Returns:

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

Note:: This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Model.createParameter() for a method that does not lead to these issues.

See also:: createParameter()

def libsbml.Model.addReaction	(	self,
		args
	)

Python method signature(s):

addReaction(Reaction r)    int

Adds a copy of the given Reaction object to this Model.

Parameters:

r

the Reaction object to add

Returns:

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

Note:: This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Model.createReaction() for a method that does not lead to these issues.

See also:: createReaction()

def libsbml.Model.addRule	(	self,
		args
	)

Python method signature(s):

addRule(Rule r)    int

Adds a copy of the given Rule object to this Model.

Parameters:

r

the Rule object to add

Returns:

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

Note:: This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see the methods Model.createAlgebraicRule(), Model.createAssignmentRule() and Model.createRateRule() for methods that do not lead to these issues.

See also:: createAlgebraicRule(); createAssignmentRule(); createRateRule()

def libsbml.Model.addSpecies	(	self,
		args
	)

Python method signature(s):

addSpecies(Species s)    int

Adds a copy of the given Species object to this Model.

Parameters:

s

the Species object to add

Returns:

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

Note:: This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Model.createSpecies() for a method that does not lead to these issues.

See also:: createSpecies()

def libsbml.Model.addSpeciesType	(	self,
		args
	)

Python method signature(s):

addSpeciesType(SpeciesType st)    int

Adds a copy of the given SpeciesType object to this Model.

Parameters:

st

the SpeciesType object to add

Returns:

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

Note:: This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Model.createSpeciesType() for a method that does not lead to these issues.; The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.

See also:: createSpeciesType()

def libsbml.Model.addUnitDefinition	(	self,
		args
	)

Python method signature(s):

addUnitDefinition(UnitDefinition ud)    int

Adds a copy of the given UnitDefinition object to this Model.

Parameters:

ud

the UnitDefinition object to add

Returns:

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

Note:: This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this Model. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the Model. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see Model.createUnitDefinition() for a method that does not lead to these issues.

See also:: createUnitDefinition()

def libsbml.Model.appendAnnotation	(	self,
		args
	)

Python method signature(s):

appendAnnotation(XMLNode annotation)    int
appendAnnotation(string annotation)    int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

appendAnnotation(XMLNode annotation)

Appends annotation content to any existing content in the 'annotation' subelement of this object.

The content in annotation is copied. Unlike setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.

Parameters:

annotation

an XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object

Returns:

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

See also:: setAnnotation()

Method variant with the following signature:

appendAnnotation(string annotation)

Appends annotation content to any existing content in the 'annotation' subelement of this object.

The content in annotation is copied. Unlike setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.

Parameters:

annotation

an XML string that is to be copied and appended to the content of the 'annotation' subelement of this object

Returns:

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

See also:: setAnnotation()

Reimplemented from libsbml.SBase.

def libsbml.Model.appendFrom	(	self,
		args
	)

Python method signature(s):

appendFrom(Model model)    int

Takes the contents of the passed-in Model, makes copies of everything, and appends those copies to the appropriate places in this Model. Also calls 'appendFrom' on all plugin objects.

Parameters:

model

the Model to merge with this one.

def libsbml.SBase.appendNotes	(	self,
		args
	)		`[inherited]`

Python method signature(s):

appendNotes(XMLNode notes)    int
appendNotes(string notes)    int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

appendNotes(string notes)

Appends the given notes to the 'notes' subelement of this object.

The content of the parameter notes is copied.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters:

notes

an XML string that is to appended to the content of the 'notes' subelement of this object

Returns:

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

See also:: getNotesString(); isSetNotes(); setNotes(); setNotes(); appendNotes(); unsetNotes(); SyntaxChecker.hasExpectedXHTMLSyntax()

Method variant with the following signature:

appendNotes(XMLNode notes)

Appends the given notes to the 'notes' subelement of this object.

The content of notes is copied.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters:

notes

an XML node structure that is to appended to the content of the 'notes' subelement of this object

Returns:

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

See also:: getNotesString(); isSetNotes(); setNotes(); setNotes(); appendNotes(); unsetNotes(); SyntaxChecker.hasExpectedXHTMLSyntax()

def libsbml.Model.clone ( self )

Python method signature(s):

clone()    Model

Creates and returns a deep copy of this Model object.

Returns:: a (deep) copy of this Model.

Reimplemented from libsbml.SBase.

def libsbml.Model.createAlgebraicRule ( self )

Python method signature(s):

createAlgebraicRule()    AlgebraicRule

Creates a new AlgebraicRule inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns:: the AlgebraicRule object created

See also:: addRule()

def libsbml.Model.createAssignmentRule ( self )

Python method signature(s):

createAssignmentRule()    AssignmentRule

Creates a new AssignmentRule inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns:: the AssignmentRule object created

See also:: addRule()

def libsbml.Model.createCompartment ( self )

Python method signature(s):

createCompartment()    Compartment

Creates a new Compartment inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns:: the Compartment object created

See also:: addCompartment()

def libsbml.Model.createCompartmentType ( self )

Python method signature(s):

createCompartmentType()    CompartmentType

Creates a new CompartmentType inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns:: the CompartmentType object created

Note:: The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.

See also:: addCompartmentType()

def libsbml.Model.createConstraint ( self )

Python method signature(s):

createConstraint()    Constraint

Creates a new Constraint inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns:: the Constraint object created

See also:: addConstraint()

def libsbml.Model.createDelay ( self )

Python method signature(s):

createDelay()    Delay

Creates a new Delay inside the last Event object created in this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the last Event object in this model was created is not significant. It could have been created in a variety of ways, for example by using createEvent(). If no Event object exists in this Model object, a new Delay is not created and None is returned instead.

Returns:: the Delay object created

def libsbml.Model.createEvent ( self )

Python method signature(s):

createEvent()    Event

Creates a new Event inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns:: the Event object created

def libsbml.Model.createEventAssignment ( self )

Python method signature(s):

createEventAssignment()    EventAssignment

Creates a new EventAssignment inside the last Event object created in this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the last Event object in this model was created is not significant. It could have been created in a variety of ways, for example by using createEvent(). If no Event object exists in this Model object, a new EventAssignment is not created and None is returned instead.

Returns:: the EventAssignment object created

def libsbml.Model.createFunctionDefinition ( self )

Python method signature(s):

createFunctionDefinition()    FunctionDefinition

Creates a new FunctionDefinition inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns:: the FunctionDefinition object created

See also:: addFunctionDefinition()

def libsbml.Model.createInitialAssignment ( self )

Python method signature(s):

createInitialAssignment()    InitialAssignment

Creates a new InitialAssignment inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns:: the InitialAssignment object created

See also:: addInitialAssignment()

def libsbml.Model.createKineticLaw ( self )

Python method signature(s):

createKineticLaw()    KineticLaw

Creates a new KineticLaw inside the last Reaction object created in this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, or a Reaction exists but already has a KineticLaw, a new KineticLaw is not created and None is returned instead.

Returns:: the KineticLaw object created

def libsbml.Model.createKineticLawLocalParameter ( self )

Python method signature(s):

createKineticLawLocalParameter()    LocalParameter

Creates a new LocalParameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The last KineticLaw object in this Model could have been created in a variety of ways. For example, it could have been added using createKineticLaw(), or it could be the result of using Reaction.createKineticLaw() on the Reaction object created by a createReaction(). If a Reaction does not exist for this model, or the last Reaction does not contain a KineticLaw object, a new Parameter is not created and None is returned instead.

Returns:: the Parameter object created

def libsbml.Model.createKineticLawParameter ( self )

Python method signature(s):

createKineticLawParameter()    Parameter

Creates a new local Parameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The last KineticLaw object in this Model could have been created in a variety of ways. For example, it could have been added using createKineticLaw(), or it could be the result of using Reaction.createKineticLaw() on the Reaction object created by a createReaction(). If a Reaction does not exist for this model, or the last Reaction does not contain a KineticLaw object, a new Parameter is not created and None is returned instead.

Returns:: the Parameter object created

def libsbml.Model.createModifier ( self )

Python method signature(s):

createModifier()    ModifierSpeciesReference

Creates a new ModifierSpeciesReference object for a modifier species inside the last Reaction object in this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, a new ModifierSpeciesReference is not created and None is returned instead.

Returns:: the SpeciesReference object created

def libsbml.Model.createParameter ( self )

Python method signature(s):

createParameter()    Parameter

Creates a new Parameter inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns:: the Parameter object created

See also:: addParameter()

def libsbml.Model.createProduct ( self )

Python method signature(s):

createProduct()    SpeciesReference

Creates a new SpeciesReference object for a product inside the last Reaction object in this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, a new SpeciesReference is not created and None is returned instead.

Returns:: the SpeciesReference object created

def libsbml.Model.createRateRule ( self )

Python method signature(s):

createRateRule()    RateRule

Creates a new RateRule inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns:: the RateRule object created

See also:: addRule()

def libsbml.Model.createReactant ( self )

Python method signature(s):

createReactant()    SpeciesReference

Creates a new SpeciesReference object for a reactant inside the last Reaction object in this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, a new SpeciesReference is not created and None is returned instead.

Returns:: the SpeciesReference object created

def libsbml.Model.createReaction ( self )

Python method signature(s):

createReaction()    Reaction

Creates a new Reaction inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns:: the Reaction object created

See also:: addReaction()

def libsbml.Model.createSpecies ( self )

Python method signature(s):

createSpecies()    Species

Creates a new Species inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns:: the Species object created

See also:: addSpecies()

def libsbml.Model.createSpeciesType ( self )

Python method signature(s):

createSpeciesType()    SpeciesType

Creates a new SpeciesType inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns:: the SpeciesType object created

Note:: The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.

See also:: addSpeciesType()

def libsbml.Model.createTrigger ( self )

Python method signature(s):

createTrigger()    Trigger

Creates a new Trigger inside the last Event object created in this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the last Event object in this model was created is not significant. It could have been created in a variety of ways, for example by using createEvent(). If no Event object exists in this Model object, a new Trigger is not created and None is returned instead.

Returns:: the Trigger object created

def libsbml.Model.createUnit ( self )

Python method signature(s):

createUnit()    Unit

Creates a new Unit object within the last UnitDefinition object created in this model and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the UnitDefinition was created is not significant. If a UnitDefinition object does not exist in this model, a new Unit is not created and None is returned instead.

Returns:: the Unit object created

See also:: addUnitDefinition()

def libsbml.Model.createUnitDefinition ( self )

Python method signature(s):

createUnitDefinition()    UnitDefinition

Creates a new UnitDefinition inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns:: the UnitDefinition object created

See also:: addUnitDefinition()

def libsbml.SBase.disablePackage	(	self,
		args
	)		`[inherited]`

Python method signature(s):

disablePackage(string pkgURI, string pkgPrefix)    int

Disables the given SBML Level 3 package

This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.

Parameters:

	pkgURI	the URI of the package
	pkgPrefix	the XML prefix of the package

Returns:

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

def libsbml.SBase.enablePackage	(	self,
		args
	)		`[inherited]`

Python method signature(s):

enablePackage(string pkgURI, string pkgPrefix, bool flag)    int

Enables or disables the given SBML Level 3 package

This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.

Parameters:

	pkgURI	the URI of the package
	pkgPrefix	the XML prefix of the package
	flag	whether to enable (`true`) or disable (`false`) the package

Returns:

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

def libsbml.SBase.getAncestorOfType	(	self,
		args
	)		`[inherited]`

Python method signature(s):

getAncestorOfType(int type, string pkgName = "core")    SBase
getAncestorOfType(int type)    SBase
getAncestorOfType(int type, string pkgName = "core")    SBase
getAncestorOfType(int type)    SBase

Returns the first ancestor object that has the given SBML type code.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_.

This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName is given, it will cause the search to be limited to the SBML Level 3 package given.

Parameters:

	type	the SBML type code of the object sought
	pkgName	(optional) the short name of an SBML Level 3 package to which the sought-after object must belong

Returns:: the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or None if no ancestor exists.

Documentation note:: The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.

def libsbml.SBase.getAnnotation ( self ) [inherited]

Python method signature(s):

getAnnotation()    XMLNode

Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.

Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.

Returns:: the annotation of this SBML object as a tree of XMLNode objects.

See also:: getAnnotationString(); isSetAnnotation(); setAnnotation(); setAnnotation(); appendAnnotation(); appendAnnotation(); unsetAnnotation()

def libsbml.SBase.getAnnotationString ( self ) [inherited]

Python method signature(s):

getAnnotationString()    string

Returns the content of the 'annotation' subelement of this object as a character string.

Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in string form.

Returns:: the annotation of this SBML object as a character string.

See also:: getAnnotation(); isSetAnnotation(); setAnnotation(); setAnnotation(); appendAnnotation(); appendAnnotation(); unsetAnnotation()

def libsbml.Model.getAreaUnits ( self )

Python method signature(s):

getAreaUnits()    string

Returns the value of the 'areaUnits' attribute of this Model.

Returns:: the areaUnits of this Model.

Note:: The 'areaUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.SBase.getColumn ( self ) [inherited]

Python method signature(s):

getColumn()    long

Returns the column number on which this object first appears in the XML representation of the SBML document.

Returns:: the column number of this SBML object.

Note:: The column number for each construct in an SBML model is set upon reading the model. The accuracy of the column number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real column number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)

See also:: getLine()

def libsbml.Model.getCompartment	(	self,
		args
	)

Python method signature(s):

getCompartment(long n)    Compartment
getCompartment(long n)    Compartment
getCompartment(string sid)    Compartment
getCompartment(string sid)    Compartment

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

getCompartment(long n)

Get the nth Compartment object in this Model.

Returns:: the nth Compartment of this Model.

Method variant with the following signature:

getCompartment(string sid)

Get a Compartment object based on its identifier.

Returns:: the Compartment in this Model with the identifier sid or None if no such Compartment exists.

def libsbml.Model.getCompartmentType	(	self,
		args
	)

Python method signature(s):

getCompartmentType(long n)    CompartmentType
getCompartmentType(long n)    CompartmentType
getCompartmentType(string sid)    CompartmentType
getCompartmentType(string sid)    CompartmentType

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

getCompartmentType(long n)

Get the nth CompartmentType object in this Model.

Returns:: the nth CompartmentType of this Model.

Note:: The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.

Method variant with the following signature:

getCompartmentType(string sid)

Get a CompartmentType object based on its identifier.

Returns:: the CompartmentType in this Model with the identifier sid or None if no such CompartmentType exists.

Note:: The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.

def libsbml.Model.getConstraint	(	self,
		args
	)

Python method signature(s):

getConstraint(long n)    Constraint
getConstraint(long n)    Constraint

Get the nth Constraint object in this Model.

Returns:: the nth Constraint of this Model.

def libsbml.Model.getConversionFactor ( self )

Python method signature(s):

getConversionFactor()    string

Returns the value of the 'conversionFactor' attribute of this Model.

Returns:: the conversionFactor of this Model.

Note:: The 'conversionFactor' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.SBase.getCVTerm	(	self,
		args
	)		`[inherited]`

Python method signature(s):

getCVTerm(long n)    CVTerm

Returns the nth CVTerm in the list of CVTerms of this SBML object.

Parameters:

n

long the index of the CVTerm to retrieve

Returns:: the nth CVTerm in the list of CVTerms for this SBML object.

def libsbml.SBase.getCVTerms ( self ) [inherited]

Python method signature(s):

getCVTerms()    CVTermList

Get the CVTermList of CVTerm objects in this SBase.

Returns:: the CVTermList for this SBase.

def libsbml.Model.getElementByMetaId	(	self,
		args
	)

Python method signature(s):

getElementByMetaId(string metaid)    SBase

Returns the first child element it can find with the given metaid, or None if no such object is found.

Parameters:

metaid

string representing the metaid of objects to find

Returns:: pointer to the first element found with the given metaid.

Reimplemented from libsbml.SBase.

def libsbml.Model.getElementBySId	(	self,
		args
	)

Python method signature(s):

getElementBySId(string id)    SBase

Returns the first child element found that has the given id in the model-wide SId namespace, or None if no such object is found.

Parameters:

id

string representing the id of objects to find.

Returns:: pointer to the first element found with the given id.

Reimplemented from libsbml.SBase.

def libsbml.Model.getElementName ( self )

Python method signature(s):

getElementName()    string

Returns the XML element name of this object, which for Model, is always 'model'.

Returns:: the name of this element, i.e., 'model'.

Reimplemented from libsbml.SBase.

def libsbml.Model.getEvent	(	self,
		args
	)

Python method signature(s):

getEvent(long n)    Event
getEvent(long n)    Event
getEvent(string sid)    Event
getEvent(string sid)    Event

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

getEvent(long n)

Get the nth Event object in this Model.

Returns:: the nth Event of this Model.

Method variant with the following signature:

getEvent(string sid)

Get an Event object based on its identifier.

Returns:: the Event in this Model with the identifier sid or None if no such Event exists.

def libsbml.Model.getExtentUnits ( self )

Python method signature(s):

getExtentUnits()    string

Returns the value of the 'extentUnits' attribute of this Model.

Returns:: the extentUnits of this Model.

Note:: The 'extentUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.Model.getFunctionDefinition	(	self,
		args
	)

Python method signature(s):

getFunctionDefinition(long n)    FunctionDefinition
getFunctionDefinition(long n)    FunctionDefinition
getFunctionDefinition(string sid)    FunctionDefinition
getFunctionDefinition(string sid)    FunctionDefinition

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

getFunctionDefinition(long n)

Get the nth FunctionDefinitions object in this Model.

Returns:: the nth FunctionDefinition of this Model.

Method variant with the following signature:

getFunctionDefinition(string sid)

Get a FunctionDefinition object based on its identifier.

Returns:: the FunctionDefinition in this Model with the identifier sid or None if no such FunctionDefinition exists.

def libsbml.Model.getId ( self )

Python method signature(s):

getId()    string

Returns the value of the 'id' attribute of this Model.

Returns:: the id of this Model.

def libsbml.Model.getInitialAssignment	(	self,
		args
	)

Python method signature(s):

getInitialAssignment(long n)    InitialAssignment
getInitialAssignment(long n)    InitialAssignment
getInitialAssignment(string symbol)    InitialAssignment
getInitialAssignment(string symbol)    InitialAssignment

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

getInitialAssignment(string symbol)

Get an InitialAssignment object based on the symbol to which it assigns a value.

Returns:: the InitialAssignment in this Model with the given 'symbol' attribute value or None if no such InitialAssignment exists.

Method variant with the following signature:

getInitialAssignment(long n)

Get the nth InitialAssignment object in this Model.

Returns:: the nth InitialAssignment of this Model.

def libsbml.Model.getLengthUnits ( self )

Python method signature(s):

getLengthUnits()    string

Returns the value of the 'lengthUnits' attribute of this Model.

Returns:: the lengthUnits of this Model.

Note:: The 'lengthUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.SBase.getLevel ( self ) [inherited]

Python method signature(s):

getLevel()    long

Returns the SBML Level of the SBMLDocument object containing this object.

Returns:: the SBML level of this SBML object.

See also:: getVersion(); getNamespaces(); getPackageVersion()

def libsbml.SBase.getLine ( self ) [inherited]

Python method signature(s):

getLine()    long

Returns the line number on which this object first appears in the XML representation of the SBML document.

Returns:: the line number of this SBML object.

Note:: The line number for each construct in an SBML model is set upon reading the model. The accuracy of the line number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real line number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)

See also:: getColumn()

def libsbml.SBase.getListOfAllElements ( self ) [inherited]

Python method signature(s):

getListOfAllElements()    SBaseList

def libsbml.SBase.getListOfAllElementsFromPlugins ( self ) [inherited]

Python method signature(s):

getListOfAllElementsFromPlugins()    SBaseList

def libsbml.Model.getListOfCompartments	(	self,
		args
	)

Python method signature(s):

getListOfCompartments()    ListOfCompartments
getListOfCompartments()    ListOfCompartments

Get the ListOfCompartments object in this Model.

Returns:: the list of Compartments for this Model.

def libsbml.Model.getListOfCompartmentTypes	(	self,
		args
	)

Python method signature(s):

getListOfCompartmentTypes()    ListOfCompartmentTypes
getListOfCompartmentTypes()    ListOfCompartmentTypes

Get the ListOfCompartmentTypes object in this Model.

Returns:: the list of CompartmentTypes for this Model.

Note:: The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.

def libsbml.Model.getListOfConstraints	(	self,
		args
	)

Python method signature(s):

getListOfConstraints()    ListOfConstraints
getListOfConstraints()    ListOfConstraints

Get the ListOfConstraints object in this Model.

Returns:: the list of Constraints for this Model.

def libsbml.Model.getListOfEvents	(	self,
		args
	)

Python method signature(s):

getListOfEvents()    ListOfEvents
getListOfEvents()    ListOfEvents

Get the ListOfEvents object in this Model.

Returns:: the list of Events for this Model.

def libsbml.Model.getListOfFunctionDefinitions	(	self,
		args
	)

Python method signature(s):

getListOfFunctionDefinitions()    ListOfFunctionDefinitions
getListOfFunctionDefinitions()    ListOfFunctionDefinitions

Get the ListOfFunctionDefinitions object in this Model.

Returns:: the list of FunctionDefinitions for this Model.

def libsbml.Model.getListOfInitialAssignments	(	self,
		args
	)

Python method signature(s):

getListOfInitialAssignments()    ListOfInitialAssignments
getListOfInitialAssignments()    ListOfInitialAssignments

Get the ListOfInitialAssignments object in this Model.

Returns:: the list of InitialAssignments for this Model.

def libsbml.Model.getListOfParameters	(	self,
		args
	)

Python method signature(s):

getListOfParameters()    ListOfParameters
getListOfParameters()    ListOfParameters

Get the ListOfParameters object in this Model.

Returns:: the list of Parameters for this Model.

def libsbml.Model.getListOfReactions	(	self,
		args
	)

Python method signature(s):

getListOfReactions()    ListOfReactions
getListOfReactions()    ListOfReactions

Get the ListOfReactions object in this Model.

Returns:: the list of Reactions for this Model.

def libsbml.Model.getListOfRules	(	self,
		args
	)

Python method signature(s):

getListOfRules()    ListOfRules
getListOfRules()    ListOfRules

Get the ListOfRules object in this Model.

Returns:: the list of Rules for this Model.

def libsbml.Model.getListOfSpecies	(	self,
		args
	)

Python method signature(s):

getListOfSpecies()    ListOfSpecies
getListOfSpecies()    ListOfSpecies

Get the ListOfSpecies object in this Model.

Returns:: the list of Species for this Model.

def libsbml.Model.getListOfSpeciesTypes	(	self,
		args
	)

Python method signature(s):

getListOfSpeciesTypes()    ListOfSpeciesTypes
getListOfSpeciesTypes()    ListOfSpeciesTypes

Get the ListOfSpeciesTypes object in this Model.

Returns:: the list of SpeciesTypes for this Model.

Note:: The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.

def libsbml.Model.getListOfUnitDefinitions	(	self,
		args
	)

Python method signature(s):

getListOfUnitDefinitions()    ListOfUnitDefinitions
getListOfUnitDefinitions()    ListOfUnitDefinitions

Get the ListOfUnitDefinitions object in this Model.

Returns:: the list of UnitDefinitions for this Model.

def libsbml.SBase.getMetaId ( self ) [inherited]

Python method signature(s):

getMetaId()    string

Returns the value of the 'metaid' attribute of this object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns:: the metaid of this SBML object.

See also:: isSetMetaId(); setMetaId()

def libsbml.SBase.getModel ( self ) [inherited]

Python method signature(s):

getModel()    Model

Returns the Model object in which the current object is located.

Returns:: the parent Model of this SBML object.

See also:: getParentSBMLObject(); getSBMLDocument()

def libsbml.SBase.getModelHistory	(	self,
		args
	)		`[inherited]`

Python method signature(s):

getModelHistory()    ModelHistory
getModelHistory()    ModelHistory

Returns the ModelHistory object, if any, attached to this object.

Returns:: the ModelHistory object attached to this object, or None if none exist.

Note:: In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.

def libsbml.Model.getName ( self )

Python method signature(s):

getName()    string

Returns the value of the 'name' attribute of this Model.

Returns:: the name of this Model.

def libsbml.SBase.getNamespaces ( self ) [inherited]

Python method signature(s):

getNamespaces()    XMLNamespaces

Returns a list of the XML Namespaces declared on this SBML document.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in SBML Level 3) packages used in addition to SBML Level 3 Core.

Returns:: the XML Namespaces associated with this SBML object

See also:: getLevel(); getVersion()

Reimplemented in libsbml.SBMLDocument.

def libsbml.SBase.getNotes ( self ) [inherited]

Python method signature(s):

getNotes()    XMLNode

Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

The 'notes' element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().

Returns:: the content of the 'notes' subelement of this SBML object as a tree structure composed of XMLNode objects.

See also:: getNotesString(); isSetNotes(); setNotes(); setNotes(); appendNotes(); appendNotes(); unsetNotes(); SyntaxChecker.hasExpectedXHTMLSyntax()

def libsbml.SBase.getNotesString ( self ) [inherited]

Python method signature(s):

getNotesString()    string

Returns the content of the 'notes' subelement of this object as a string.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.

Returns:: the content of the 'notes' subelement of this SBML object as a string.

See also:: getNotes(); isSetNotes(); setNotes(); setNotes(); appendNotes(); appendNotes(); unsetNotes(); SyntaxChecker.hasExpectedXHTMLSyntax()

def libsbml.Model.getNumCompartments ( self )

Python method signature(s):

getNumCompartments()    long

Get the number of Compartment objects in this Model.

Returns:: the number of Compartments in this Model.

def libsbml.Model.getNumCompartmentTypes ( self )

Python method signature(s):

getNumCompartmentTypes()    long

Get the number of CompartmentType objects in this Model.

Returns:: the number of CompartmentTypes in this Model.

Note:: The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.

def libsbml.Model.getNumConstraints ( self )

Python method signature(s):

getNumConstraints()    long

Get the number of Constraint objects in this Model.

Returns:: the number of Constraints in this Model.

def libsbml.SBase.getNumCVTerms ( self ) [inherited]

Python method signature(s):

getNumCVTerms()    long

Returns the number of CVTerm objects in the annotations of this SBML object.

Returns:: the number of CVTerms for this SBML object.

def libsbml.Model.getNumEvents ( self )

Python method signature(s):

getNumEvents()    long

Get the number of Event objects in this Model.

Returns:: the number of Events in this Model.

def libsbml.Model.getNumFunctionDefinitions ( self )

Python method signature(s):

getNumFunctionDefinitions()    long

Get the number of FunctionDefinition objects in this Model.

Returns:: the number of FunctionDefinitions in this Model.

def libsbml.Model.getNumInitialAssignments ( self )

Python method signature(s):

getNumInitialAssignments()    long

Get the number of InitialAssignment objects in this Model.

Returns:: the number of InitialAssignments in this Model.

def libsbml.Model.getNumParameters ( self )

Python method signature(s):

getNumParameters()    long

Get the number of Parameter objects in this Model.

Returns:: the number of Parameters in this Model. Parameters defined in KineticLaws are not included.

def libsbml.SBase.getNumPlugins ( self ) [inherited]

Python method signature(s):

getNumPlugins()    long

Returns the number of plugin objects (extenstion interfaces) for SBML Level 3 package extensions known.

Returns:: the number of plugin objects (extension interfaces) of package extensions known by this instance of libSBML.

def libsbml.Model.getNumReactions ( self )

Python method signature(s):

getNumReactions()    long

Get the number of Reaction objects in this Model.

Returns:: the number of Reactions in this Model.

def libsbml.Model.getNumRules ( self )

Python method signature(s):

getNumRules()    long

Get the number of Rule objects in this Model.

Returns:: the number of Rules in this Model.

def libsbml.Model.getNumSpecies ( self )

Python method signature(s):

getNumSpecies()    long

Get the number of Specie objects in this Model.

Returns:: the number of Species in this Model.

def libsbml.Model.getNumSpeciesTypes ( self )

Python method signature(s):

getNumSpeciesTypes()    long

Get the number of SpeciesType objects in this Model.

Returns:: the number of SpeciesTypes in this Model.

Note:: The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.

def libsbml.Model.getNumSpeciesWithBoundaryCondition ( self )

Python method signature(s):

getNumSpeciesWithBoundaryCondition()    long

Get the number of Species in this Model having their 'boundaryCondition' attribute value set to true.

Returns:: the number of Species in this Model with boundaryCondition set to true.

def libsbml.Model.getNumUnitDefinitions ( self )

Python method signature(s):

getNumUnitDefinitions()    long

Get the number of UnitDefinition objects in this Model.

Returns:: the number of UnitDefinitions in this Model.

def libsbml.SBase.getPackageName ( self ) [inherited]

Python method signature(s):

getPackageName()    string

Returns the name of the SBML Level 3 package in which this element is defined.

Returns:: the name of the SBML package in which this element is defined. The string "core" will be returned if this element is defined in SBML Level 3 Core. The string "unknown" will be returned if this element is not defined in any SBML package.

def libsbml.SBase.getPackageVersion ( self ) [inherited]

Python method signature(s):

getPackageVersion()    long

Returns the Version of the SBML Level 3 package to which this element belongs to.

Returns:: the version of the SBML Level 3 package to which this element belongs. The value 0 will be returned if this element belongs to the SBML Level 3 Core package.

See also:: getLevel(); getVersion()

def libsbml.Model.getParameter	(	self,
		args
	)

Python method signature(s):

getParameter(long n)    Parameter
getParameter(long n)    Parameter
getParameter(string sid)    Parameter
getParameter(string sid)    Parameter

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

getParameter(long n)

Get the nth Parameter object in this Model.

Returns:: the nth Parameter of this Model.

Method variant with the following signature:

getParameter(string sid)

Get a Parameter object based on its identifier.

Returns:: the Parameter in this Model with the identifier sid or None if no such Parameter exists.

def libsbml.SBase.getParentSBMLObject	(	self,
		args
	)		`[inherited]`

Python method signature(s):

getParentSBMLObject()    SBase
getParentSBMLObject()    SBase

Returns the parent SBML object containing this object.

This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.

Returns:: the parent SBML object of this SBML object.

See also:: getSBMLDocument(); getModel()

def libsbml.SBase.getPlugin	(	self,
		args
	)		`[inherited]`

Python method signature(s):

getPlugin(string package)    SBasePlugin
getPlugin(string package)    SBasePlugin
getPlugin(long n)    SBasePlugin
getPlugin(long n)    SBasePlugin

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

getPlugin(long n)

Returns the nth plugin object (extension interface) for an SBML Level 3 package extension.

Parameters:

n

the index of the plugin to return

Returns:: the plugin object (the libSBML extension interface) of a package extension with the given package name or URI.

Method variant with the following signature:

getPlugin(string package)

Returns a plugin object (extension interface) for an SBML Level 3 package extension with the given package name or URI.

Parameters:

package

the name or URI of the package

Returns:: the plugin object (the libSBML extension interface) of a package extension with the given package name or URI.

def libsbml.Model.getReaction	(	self,
		args
	)

Python method signature(s):

getReaction(long n)    Reaction
getReaction(long n)    Reaction
getReaction(string sid)    Reaction
getReaction(string sid)    Reaction

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

getReaction(long n)

Get the nth Reaction object in this Model.

Returns:: the nth Reaction of this Model.

Method variant with the following signature:

getReaction(string sid)

Get a Reaction object based on its identifier.

Returns:: the Reaction in this Model with the identifier sid or None if no such Reaction exists.

def libsbml.SBase.getResourceBiologicalQualifier	(	self,
		args
	)		`[inherited]`

Python method signature(s):

getResourceBiologicalQualifier(string resource)    long

Returns the MIRIAM biological qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include 'is' and 'has part', but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using values whose names begin with BQB_ in the interface class libsbml.

This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a value whose name begins with BQB_ from the interface class libsbml.

Parameters:

resource string representing the resource; e.g., 'http://www.geneontology.org/GO:0005892'.

Returns:: the qualifier associated with the resource, or BQB_UNKNOWN if the resource does not exist.

Note:: The set of MIRIAM biological qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQB_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.

def libsbml.SBase.getResourceModelQualifier	(	self,
		args
	)		`[inherited]`

Python method signature(s):

getResourceModelQualifier(string resource)    long

Returns the MIRIAM model qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is 'isDerivedFrom', to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using values whose names begin with BQM_ in the interface class libsbml.

This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a value whose name begins with BQM_ from the interface class libsbml.

Parameters:

resource string representing the resource; e.g., 'http://www.geneontology.org/GO:0005892'.

Returns:: the model qualifier typeassociated with the resource, or BQM_UNKNOWN if the resource does not exist.

Note:: The set of MIRIAM model qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQM_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.

def libsbml.Model.getRule	(	self,
		args
	)

Python method signature(s):

getRule(long n)    Rule
getRule(long n)    Rule
getRule(string variable)    Rule
getRule(string variable)    Rule

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

getRule(string variable)

Get a Rule object based on the variable to which it assigns a value.

Returns:: the Rule in this Model with the given 'variable' attribute value or None if no such Rule exists.

Method variant with the following signature:

getRule(long n)

Get the nth Rule object in this Model.

Returns:: the nth Rule of this Model.

def libsbml.SBase.getSBMLDocument	(	self,
		args
	)		`[inherited]`

Python method signature(s):

getSBMLDocument()    SBMLDocument
getSBMLDocument()    SBMLDocument

Returns the SBMLDocument object containing this object instance.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns:: the parent SBMLDocument object of this SBML object.

See also:: getParentSBMLObject(); getModel()

def libsbml.SBase.getSBOTerm ( self ) [inherited]

Python method signature(s):

getSBOTerm()    int

Returns the integer portion of the value of the 'sboTerm' attribute of this object.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. (For convenience, libSBML offers methods for returning both the integer form and a text-string form of the SBO identifier.)

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns:: the value of the 'sboTerm' attribute as an integer, or -1 if the value is not set.

def libsbml.SBase.getSBOTermID ( self ) [inherited]

Python method signature(s):

getSBOTermID()    string

Returns the string representation of the 'sboTerm' attribute of this object.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method returns the entire SBO identifier as a text string in the form 'SBO:NNNNNNN'.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns:: the value of the 'sboTerm' attribute as a string (its value will be of the form 'SBO:NNNNNNN'), or an empty string if the value is not set.

def libsbml.Model.getSpecies	(	self,
		args
	)

Python method signature(s):

getSpecies(long n)    Species
getSpecies(long n)    Species
getSpecies(string sid)    Species
getSpecies(string sid)    Species

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

getSpecies(long n)

Get the nth Species object in this Model.

Returns:: the nth Species of this Model.

Method variant with the following signature:

getSpecies(string sid)

Get a Species object based on its identifier.

Returns:: the Species in this Model with the identifier sid or None if no such Species exists.

def libsbml.Model.getSpeciesReference	(	self,
		args
	)

Python method signature(s):

getSpeciesReference(string sid)    SpeciesReference
getSpeciesReference(string sid)    SpeciesReference

Get a SpeciesReference object based on its identifier.

Returns:: the SpeciesReference in this Model with the identifier sid or None if no such SpeciesReference exists.

def libsbml.Model.getSpeciesType	(	self,
		args
	)

Python method signature(s):

getSpeciesType(long n)    SpeciesType
getSpeciesType(long n)    SpeciesType
getSpeciesType(string sid)    SpeciesType
getSpeciesType(string sid)    SpeciesType

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

getSpeciesType(long n)

Get the nth SpeciesType object in this Model.

Returns:: the nth SpeciesType of this Model.

Note:: The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.

Method variant with the following signature:

getSpeciesType(string sid)

Get a SpeciesType object based on its identifier.

Returns:: the SpeciesType in this Model with the identifier sid or None if no such SpeciesType exists.

Note:: The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.

def libsbml.Model.getSubstanceUnits ( self )

Python method signature(s):

getSubstanceUnits()    string

Returns the value of the 'substanceUnits' attribute of this Model.

Returns:: the substanceUnits of this Model.

Note:: The 'substanceUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.Model.getTimeUnits ( self )

Python method signature(s):

getTimeUnits()    string

Returns the value of the 'timeUnits' attribute of this Model.

Returns:: the timeUnits of this Model.

Note:: The 'timeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.Model.getTypeCode ( self )

Python method signature(s):

getTypeCode()    int

Returns the libSBML type code for this SBML object.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_.

Returns:: the SBML type code for this object, or SBML_UNKNOWN (default).

See also:: getElementName()

Reimplemented from libsbml.SBase.

def libsbml.Model.getUnitDefinition	(	self,
		args
	)

Python method signature(s):

getUnitDefinition(long n)    UnitDefinition
getUnitDefinition(long n)    UnitDefinition
getUnitDefinition(string sid)    UnitDefinition
getUnitDefinition(string sid)    UnitDefinition

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

getUnitDefinition(long n)

Get the nth UnitDefinition object in this Model.

Returns:: the nth UnitDefinition of this Model.

Method variant with the following signature:

getUnitDefinition(string sid)

Get a UnitDefinition based on its identifier.

Returns:: the UnitDefinition in this Model with the identifier sid or None if no such UnitDefinition exists.

def libsbml.SBase.getVersion ( self ) [inherited]

Python method signature(s):

getVersion()    long

Returns the Version within the SBML Level of the SBMLDocument object containing this object.

Returns:: the SBML version of this SBML object.

See also:: getLevel(); getNamespaces()

def libsbml.Model.getVolumeUnits ( self )

Python method signature(s):

getVolumeUnits()    string

Returns the value of the 'volumeUnits' attribute of this Model.

Returns:: the volumeUnits of this Model.

Note:: The 'volumeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.Model.hasRequiredElements ( self )

Python method signature(s):

hasRequiredElements()    bool

Predicate returning true if all the required elements for this Model object have been set.

Note:: The required elements for a Model object are: listOfCompartments (L1 only); listOfSpecies (L1V1 only); listOfReactions(L1V1 only)

Returns:: a boolean value indicating whether all the required elements for this object have been defined.

def libsbml.SBase.hasValidLevelVersionNamespaceCombination ( self ) [inherited]

Python method signature(s):

hasValidLevelVersionNamespaceCombination()    bool

def libsbml.SBase.isPackageEnabled	(	self,
		args
	)		`[inherited]`

Python method signature(s):

isPackageEnabled(string pkgName)    bool

Predicate returning true if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters:

pkgName

the name of the package

Returns:: true if the given package is enabled within this object, false otherwise.

See also:: isPackageURIEnabled()

def libsbml.SBase.isPackageURIEnabled	(	self,
		args
	)		`[inherited]`

Python method signature(s):

isPackageURIEnabled(string pkgURI)    bool

Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.

Parameters:

pkgURI

the URI of the package

Returns:: true if the given package is enabled within this object, false otherwise.

See also:: isPackageEnabled()

def libsbml.SBase.isPkgEnabled	(	self,
		args
	)		`[inherited]`

Python method signature(s):

isPkgEnabled(string pkgName)    bool

Predicate returning true if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters:

pkgName

the name of the package

Returns:: true if the given package is enabled within this object, false otherwise.

See also:: isPkgURIEnabled()

Deprecated:: Replaced in libSBML 5.2.0 by isPackageEnabled()

def libsbml.SBase.isPkgURIEnabled	(	self,
		args
	)		`[inherited]`

Python method signature(s):

isPkgURIEnabled(string pkgURI)    bool

Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.

Parameters:

pkgURI

the URI of the package

Returns:: true if the given package is enabled within this object, false otherwise.

See also:: isPkgEnabled()

Deprecated:: Replaced in libSBML 5.2.0 by isPackageURIEnabled()

def libsbml.Model.isPopulatedListFormulaUnitsData ( self )

Python method signature(s):

isPopulatedListFormulaUnitsData()    bool

Predicate returning true if the list of FormulaUnitsData is populated.

Returns:: true if the list of FormulaUnitsData is populated, false otherwise.

def libsbml.SBase.isSetAnnotation ( self ) [inherited]

Python method signature(s):

isSetAnnotation()    bool

Predicate returning true if this object's 'annotation' subelement exists and has content.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Returns:: true if a 'annotation' subelement exists, false otherwise.

See also:: getAnnotation(); getAnnotationString(); setAnnotation(); setAnnotation(); appendAnnotation(); appendAnnotation(); unsetAnnotation()

def libsbml.Model.isSetAreaUnits ( self )

Python method signature(s):

isSetAreaUnits()    bool

Predicate returning true if this Model's 'areaUnits' attribute is set.

Returns:: true if the 'areaUnits' attribute of this Model is set, false otherwise.

Note:: The 'areaUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.Model.isSetConversionFactor ( self )

Python method signature(s):

isSetConversionFactor()    bool

Predicate returning true if this Model's 'conversionFactor' attribute is set.

Returns:: true if the 'conversionFactor' attribute of this Model is set, false otherwise.

Note:: The 'conversionFactor' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.Model.isSetExtentUnits ( self )

Python method signature(s):

isSetExtentUnits()    bool

Predicate returning true if this Model's 'extentUnits' attribute is set.

Returns:: true if the 'extentUnits' attribute of this Model is set, false otherwise.

Note:: The 'extentUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.Model.isSetId ( self )

Python method signature(s):

isSetId()    bool

Predicate returning true if this Model's 'id' attribute is set.

Returns:: true if the 'id' attribute of this Model is set, false otherwise.

def libsbml.Model.isSetLengthUnits ( self )

Python method signature(s):

isSetLengthUnits()    bool

Predicate returning true if this Model's 'lengthUnits' attribute is set.

Returns:: true if the 'lengthUnits' attribute of this Model is set, false otherwise.

Note:: The 'lengthUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.SBase.isSetMetaId ( self ) [inherited]

Python method signature(s):

isSetMetaId()    bool

Predicate returning true if this object's 'metaid' attribute is set.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns:: true if the 'metaid' attribute of this SBML object is set, false otherwise.

See also:: getMetaId(); setMetaId()

def libsbml.SBase.isSetModelHistory ( self ) [inherited]

Python method signature(s):

isSetModelHistory()    bool

Predicate returning true if this object has a ModelHistory object attached to it.

Returns:: true if the ModelHistory of this object is set, false otherwise.

Note:: In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.

def libsbml.Model.isSetName ( self )

Python method signature(s):

isSetName()    bool

Predicate returning true if this Model's 'name' attribute is set.

Returns:: true if the 'name' attribute of this Model is set, false otherwise.

def libsbml.SBase.isSetNotes ( self ) [inherited]

Python method signature(s):

isSetNotes()    bool

Predicate returning true if this object's 'notes' subelement exists and has content.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

Returns:: true if a 'notes' subelement exists, false otherwise.

See also:: getNotes(); getNotesString(); setNotes(); setNotes(); appendNotes(); appendNotes(); unsetNotes(); SyntaxChecker.hasExpectedXHTMLSyntax()

def libsbml.SBase.isSetSBOTerm ( self ) [inherited]

Python method signature(s):

isSetSBOTerm()    bool

Predicate returning true if this object's 'sboTerm' attribute is set.

Returns:: true if the 'sboTerm' attribute of this SBML object is set, false otherwise.

def libsbml.Model.isSetSubstanceUnits ( self )

Python method signature(s):

isSetSubstanceUnits()    bool

Predicate returning true if this Model's 'substanceUnits' attribute is set.

Returns:: true if the 'substanceUnits' attribute of this Model is set, false otherwise.

Note:: The 'substanceUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.Model.isSetTimeUnits ( self )

Python method signature(s):

isSetTimeUnits()    bool

Predicate returning true if this Model's 'timeUnits' attribute is set.

Returns:: true if the 'timeUnits' attribute of this Model is set, false otherwise.

Note:: The 'substanceUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.Model.isSetVolumeUnits ( self )

Python method signature(s):

isSetVolumeUnits()    bool

Predicate returning true if this Model's 'volumeUnits' attribute is set.

Returns:: true if the 'volumeUnits' attribute of this Model is set, false otherwise.

Note:: The 'volumeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.SBase.matchesSBMLNamespaces	(	self,
		args
	)		`[inherited]`

Python method signature(s):

matchesSBMLNamespaces(SBase sb)    bool

Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces.

Parameters:

sb

an object to compare with respect to namespaces

Returns:: boolean, true if this object's collection of namespaces is the same as sb's, false otherwise.

def libsbml.Model.populateListFormulaUnitsData ( self )

Python method signature(s):

populateListFormulaUnitsData()

Populates the list of FormulaDataUnits with the units derived for the model. The list contains elements of class FormulaUnitsData.

The first element of the list refers to the default units of 'substance per time' derived from the model and has the unitReferenceId 'subs_per_time'. This facilitates the comparison of units derived from mathematical formula with the expected units.

The next elements of the list record the units of the compartments and species established from either explicitly declared or default units.

The next elements record the units of any parameters.

Subsequent elements of the list record the units derived for each mathematical expression encountered within the model.

Note:: This function is utilised by the Unit Consistency Validator. The list is populated prior to running the validation and thus the consistency of units can be checked by accessing the members of the list and comparing the appropriate data.

def libsbml.Model.removeCompartment	(	self,
		args
	)

Python method signature(s):

removeCompartment(long n)    Compartment
removeCompartment(string sid)    Compartment

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

removeCompartment(long n)

Removes the nth Compartment object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters:

n

the index of the Compartment object to remove

Returns:: the Compartment object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.

Method variant with the following signature:

removeCompartment(string sid)

Removes the Compartment object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. If none of the Compartment objects in this Model object have the identifier sid, then None is returned.

Parameters:

sid

the identifier of the Compartment object to remove

Returns:: the Compartment object removed. As mentioned above, the caller owns the returned object. None is returned if no Compartment object with the identifier exists in this Model object.

def libsbml.Model.removeCompartmentType	(	self,
		args
	)

Python method signature(s):

removeCompartmentType(long n)    CompartmentType
removeCompartmentType(string sid)    CompartmentType

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

removeCompartmentType(long n)

Removes the nth CompartmentType object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters:

n

the index of the CompartmentType object to remove

Returns:: the ComapartmentType object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.

Method variant with the following signature:

removeCompartmentType(string sid)

Removes the CompartmentType object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. If none of the CompartmentType objects in this Model object have the identifier sid, then None is returned.

Parameters:

sid

the identifier of the object to remove

Returns:: the CompartmentType object removed. As mentioned above, the caller owns the returned object. None is returned if no CompartmentType object with the identifier exists in this Model object.

def libsbml.Model.removeConstraint	(	self,
		args
	)

Python method signature(s):

removeConstraint(long n)    Constraint

Removes the nth Constraint object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters:

n

the index of the Constraint object to remove

Returns:: the Constraint object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.

def libsbml.Model.removeEvent	(	self,
		args
	)

Python method signature(s):

removeEvent(long n)    Event
removeEvent(string sid)    Event

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

removeEvent(long n)

Removes the nth Event object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters:

n

the index of the Event object to remove

Returns:: the Event object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.

Method variant with the following signature:

removeEvent(string sid)

Removes the Event object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. If none of the Event objects in this Model object have the identifier sid, then None is returned.

Parameters:

sid

the identifier of the Event object to remove

Returns:: the Event object removed. As mentioned above, the caller owns the returned object. None is returned if no Event object with the identifier exists in this Model object.

def libsbml.Model.removeFromParentAndDelete ( self )

Python method signature(s):

removeFromParentAndDelete()    int

Finds this Model's parent SBMLDocument and calls setModel(None) on it, indirectly deleting itself. Overridden from the SBase function since the parent is not a ListOf.

Returns:

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

Reimplemented from libsbml.SBase.

def libsbml.Model.removeFunctionDefinition	(	self,
		args
	)

Python method signature(s):

removeFunctionDefinition(long n)    FunctionDefinition
removeFunctionDefinition(string sid)    FunctionDefinition

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

removeFunctionDefinition(long n)

Removes the nth FunctionDefinition object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters:

n

the index of the FunctionDefinition object to remove

Returns:: the FunctionDefinition object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.

Method variant with the following signature:

removeFunctionDefinition(string sid)

Removes the FunctionDefinition object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. If none of the FunctionDefinition objects in this Model object have the identifier sid, then None is returned.

Parameters:

sid

the identifier of the FunctionDefinition object to remove

Returns:: the FunctionDefinition object removed. As mentioned above, the caller owns the returned object. None is returned if no FunctionDefinition object with the identifier exists in this Model object.

def libsbml.Model.removeInitialAssignment	(	self,
		args
	)

Python method signature(s):

removeInitialAssignment(long n)    InitialAssignment
removeInitialAssignment(string symbol)    InitialAssignment

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

removeInitialAssignment(string symbol)

Removes the InitialAssignment object with the given 'symbol' attribute from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. If none of the InitialAssignment objects in this Model object have the 'symbol' attribute symbol, then None is returned.

Parameters:

symbol

the 'symbol' attribute of the InitialAssignment object to remove

Returns:: the InitialAssignment object removed. As mentioned above, the caller owns the returned object. None is returned if no InitialAssignment object with the 'symbol' attribute exists in this Model object.

Method variant with the following signature:

removeInitialAssignment(long n)

Removes the nth InitialAssignment object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters:

n

the index of the InitialAssignment object to remove

Returns:: the InitialAssignment object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.

def libsbml.Model.removeParameter	(	self,
		args
	)

Python method signature(s):

removeParameter(long n)    Parameter
removeParameter(string sid)    Parameter

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

removeParameter(long n)

Removes the nth Parameter object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters:

n

the index of the Parameter object to remove

Returns:: the Parameter object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.

Method variant with the following signature:

removeParameter(string sid)

Removes the Parameter object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. If none of the Parameter objects in this Model object have the identifier sid, then None is returned.

Parameters:

sid

the identifier of the Parameter object to remove

Returns:: the Parameter object removed. As mentioned above, the caller owns the returned object. None is returned if no Parameter object with the identifier exists in this Model object.

def libsbml.Model.removeReaction	(	self,
		args
	)

Python method signature(s):

removeReaction(long n)    Reaction
removeReaction(string sid)    Reaction

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

removeReaction(long n)

Removes the nth Reaction object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters:

n

the index of the Reaction object to remove

Returns:: the Reaction object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.

Method variant with the following signature:

removeReaction(string sid)

Removes the Reaction object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. If none of the Reaction objects in this Model object have the identifier sid, then None is returned.

Parameters:

sid

the identifier of the Reaction object to remove

Returns:: the Reaction object removed. As mentioned above, the caller owns the returned object. None is returned if no Reaction object with the identifier exists in this Model object.

def libsbml.Model.removeRule	(	self,
		args
	)

Python method signature(s):

removeRule(long n)    Rule
removeRule(string variable)    Rule

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

removeRule(string variable)

Removes the Rule object with the given 'variable' attribute from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. If none of the Rule objects in this Model object have the 'variable' attribute variable, then None is returned.

Parameters:

variable

the 'variable' attribute of the Rule object to remove

Returns:: the Rule object removed. As mentioned above, the caller owns the returned object. None is returned if no Rule object with the 'variable' attribute exists in this Model object.

Method variant with the following signature:

removeRule(long n)

Removes the nth Rule object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters:

n

the index of the Rule object to remove

Returns:: the Rule object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.

def libsbml.Model.removeSpecies	(	self,
		args
	)

Python method signature(s):

removeSpecies(long n)    Species
removeSpecies(string sid)    Species

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

removeSpecies(long n)

Removes the nth Species object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters:

n

the index of the Species object to remove

Returns:: the Species object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.

Method variant with the following signature:

removeSpecies(string sid)

Removes the Species object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. If none of the Species objects in this Model object have the identifier sid, then None is returned.

Parameters:

sid

the identifier of the Species object to remove

Returns:: the Species object removed. As mentioned above, the caller owns the returned object. None is returned if no Species object with the identifier exists in this Model object.

def libsbml.Model.removeSpeciesType	(	self,
		args
	)

Python method signature(s):

removeSpeciesType(long n)    SpeciesType
removeSpeciesType(string sid)    SpeciesType

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

removeSpeciesType(long n)

Removes the nth SpeciesType object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters:

n

the index of the SpeciesType object to remove

Returns:: the SpeciesType object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.

Method variant with the following signature:

removeSpeciesType(string sid)

Removes the SpeciesType object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. If none of the SpeciesType objects in this Model object have the identifier sid, then None is returned.

Parameters:

sid

the identifier of the SpeciesType object to remove

Returns:: the SpeciesType object removed. As mentioned above, the caller owns the returned object. None is returned if no SpeciesType object with the identifier exists in this Model object.

def libsbml.Model.removeUnitDefinition	(	self,
		args
	)

Python method signature(s):

removeUnitDefinition(long n)    UnitDefinition
removeUnitDefinition(string sid)    UnitDefinition

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

removeUnitDefinition(long n)

Removes the nth UnitDefinition object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters:

n

the index of the UnitDefinition object to remove

Returns:: the UnitDefinition object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.

Method variant with the following signature:

removeUnitDefinition(string sid)

Removes the UnitDefinition object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. If none of the UnitDefinition objects in this Model object have the identifier sid, then None is returned.

Parameters:

sid

the identifier of the UnitDefinition object to remove

Returns:: the UnitDefinition object removed. As mentioned above, the caller owns the returned object. None is returned if no UnitDefinition object with the identifier exists in this Model object.

def libsbml.SBase.renameMetaIdRefs	(	self,
		args
	)		`[inherited]`

Python method signature(s):

renameMetaIdRefs(string oldid, string newid)

Renames all the MetaIdRef attributes on this element.

This method works by looking at all meta-attribute values, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters:

	oldid	the old identifier
	newid	the new identifier

def libsbml.Model.renameSIdRefs	(	self,
		args
	)

Python method signature(s):

renameSIdRefs(string oldid, string newid)

Renames all the SIdRef attributes on this element, including any found in MathML

Reimplemented from libsbml.SBase.

def libsbml.Model.renameUnitSIdRefs	(	self,
		args
	)

Python method signature(s):

renameUnitSIdRefs(string oldid, string newid)

Renames all the UnitSIdRef attributes on this element

Reimplemented from libsbml.SBase.

def libsbml.Model.setAnnotation	(	self,
		args
	)

Python method signature(s):

setAnnotation(XMLNode annotation)    int
setAnnotation(string annotation)    int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

setAnnotation(XMLNode annotation)

Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation.

Any existing content of the 'annotation' subelement is discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use appendAnnotation().

Parameters:

annotation

an XML structure that is to be used as the content of the 'annotation' subelement of this object

Returns:

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

LIBSBML_OPERATION_SUCCESS

See also:: appendAnnotation()

Method variant with the following signature:

setAnnotation(string annotation)

Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation.

Any existing content of the 'annotation' subelement is discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use appendAnnotation().

Parameters:

annotation

an XML string that is to be used as the content of the 'annotation' subelement of this object

Returns:

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

See also:: appendAnnotation()

Reimplemented from libsbml.SBase.

def libsbml.Model.setAreaUnits	(	self,
		args
	)

Python method signature(s):

setAreaUnits(string units)    int

Sets the value of the 'areaUnits' attribute of this Model.

The string in units is copied.

Parameters:

units

the new areaUnits for the Model

Returns:

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

Note:: The 'areaUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.Model.setConversionFactor	(	self,
		args
	)

Python method signature(s):

setConversionFactor(string units)    int

Sets the value of the 'conversionFactor' attribute of this Model.

The string in units is copied.

Parameters:

units

the new conversionFactor for the Model

Returns:

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

Note:: The 'conversionFactor' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.Model.setExtentUnits	(	self,
		args
	)

Python method signature(s):

setExtentUnits(string units)    int

Sets the value of the 'extentUnits' attribute of this Model.

The string in units is copied.

Parameters:

units

the new extentUnits for the Model

Returns:

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

Note:: The 'extentUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.Model.setId	(	self,
		args
	)

Python method signature(s):

setId(string sid)    int

Sets the value of the 'id' attribute of this Model.

The string sid is copied. Note that SBML has strict requirements for the syntax of identifiers. The following is a summary of the definition of the SBML identifier type SId, which defines the permitted syntax of identifiers. We express the syntax using an extended form of BNF notation:

letter ::= 'a'..'z','A'..'Z'
digit ::= '0'..'9'
idChar ::= letter | digit | '_'
SId ::= ( letter | '_' ) idChar*

The characters ( and ) are used for grouping, the character * "zero or more times", and the character | indicates logical "or". The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. In addition, there are a few conditions for the uniqueness of identifiers in an SBML model. Please consult the SBML specifications for the exact formulations.

Parameters:

sid

the string to use as the identifier of this Model

Returns:

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

def libsbml.Model.setLengthUnits	(	self,
		args
	)

Python method signature(s):

setLengthUnits(string units)    int

Sets the value of the 'lengthUnits' attribute of this Model.

The string in units is copied.

Parameters:

units

the new lengthUnits for the Model

Returns:

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

Note:: The 'lengthUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.SBase.setMetaId	(	self,
		args
	)		`[inherited]`

Python method signature(s):

setMetaId(string metaid)    int

Sets the value of the 'metaid' attribute of this object.

The string metaid is copied. The value of metaid must be an identifier conforming to the syntax defined by the XML 1.0 data type ID. Among other things, this type requires that a value is unique among all the values of type XML ID in an SBMLDocument. Although SBML only uses XML ID for the 'metaid' attribute, callers should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement.

Parameters:

metaid

the identifier string to use as the value of the 'metaid' attribute

Returns:

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

See also:: getMetaId(); isSetMetaId()

def libsbml.SBase.setModelHistory	(	self,
		args
	)		`[inherited]`

Python method signature(s):

setModelHistory(ModelHistory history)    int

Sets the ModelHistory of this object.

The content of history is copied, and this object's existing model history content is deleted.

Parameters:

history

ModelHistory of this object.

Returns:

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

Note:: In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.

def libsbml.Model.setName	(	self,
		args
	)

Python method signature(s):

setName(string name)    int

Sets the value of the 'name' attribute of this Model.

The string in name is copied.

Parameters:

name

the new name for the Model

Returns:

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

def libsbml.SBase.setNamespaces	(	self,
		args
	)		`[inherited]`

Python method signature(s):

setNamespaces(XMLNamespaces xmlns)    int

Sets the namespaces relevant of this SBML object.

The content of xmlns is copied, and this object's existing namespace content is deleted.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.

Parameters:

xmlns

the namespaces to set

Returns:

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

LIBSBML_OPERATION_SUCCESS

def libsbml.SBase.setNotes	(	self,
		args
	)		`[inherited]`

Python method signature(s):

setNotes(XMLNode notes)    int
setNotes(string notes)    int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

setNotes(string notes)

Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component.

Parameters:

notes

an XML string that is to be used as the content of the 'notes' subelement of this object

Returns:

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

See also:: getNotesString(); isSetNotes(); setNotes(); appendNotes(); appendNotes(); unsetNotes(); SyntaxChecker.hasExpectedXHTMLSyntax()

Method variant with the following signature:

setNotes(XMLNode notes)

Sets the value of the 'notes' subelement of this SBML object.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters:

notes

an XML structure that is to be used as the content of the 'notes' subelement of this object

Returns:

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

See also:: getNotesString(); isSetNotes(); setNotes(); appendNotes(); appendNotes(); unsetNotes(); SyntaxChecker.hasExpectedXHTMLSyntax()

def libsbml.SBase.setSBOTerm	(	self,
		args
	)		`[inherited]`

Python method signature(s):

setSBOTerm(int value)    int
setSBOTerm(string sboid)    int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.

Method variant with the following signature:

setSBOTerm(int value)

Sets the value of the 'sboTerm' attribute.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Parameters:

value

the NNNNNNN integer portion of the SBO identifier

Returns:

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

See also:: setSBOTerm()

Method variant with the following signature:

setSBOTerm(string &sboid)

Sets the value of the 'sboTerm' attribute by string.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method lets you set the value of 'sboTerm' as a complete string of the form 'SBO:NNNNNNN', whereas setSBOTerm(int value) allows you to set it using the integer form.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Parameters:

sboid

the SBO identifier string of the form 'SBO:NNNNNNN'

Returns:

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

See also:: setSBOTerm()

def libsbml.Model.setSubstanceUnits	(	self,
		args
	)

Python method signature(s):

setSubstanceUnits(string units)    int

Sets the value of the 'substanceUnits' attribute of this Model.

The string in units is copied.

Parameters:

units

the new substanceUnits for the Model

Returns:

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

Note:: The 'substanceUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.Model.setTimeUnits	(	self,
		args
	)

Python method signature(s):

setTimeUnits(string units)    int

Sets the value of the 'timeUnits' attribute of this Model.

The string in units is copied.

Parameters:

units

the new timeUnits for the Model

Returns:

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

Note:: The 'timeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.Model.setVolumeUnits	(	self,
		args
	)

Python method signature(s):

setVolumeUnits(string units)    int

Sets the value of the 'volumeUnits' attribute of this Model.

The string in units is copied.

Parameters:

units

the new volumeUnits for the Model

Returns:

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

Note:: The 'volumeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.SBase.toSBML ( self ) [inherited]

Python method signature(s):

toSBML()    string

Returns a string consisting of a partial SBML corresponding to just this object.

Returns:: the partial SBML that describes this SBML object.

Warning:: This is primarily provided for testing and debugging purposes. It may be removed in a future version of libSBML.

def libsbml.SBase.unsetAnnotation ( self ) [inherited]

Python method signature(s):

unsetAnnotation()    int

Unsets the value of the 'annotation' subelement of this SBML object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Returns:

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

LIBSBML_OPERATION_SUCCESS

See also:: getAnnotation(); getAnnotationString(); isSetAnnotation(); setAnnotation(); setAnnotation(); appendAnnotation(); appendAnnotation()

def libsbml.Model.unsetAreaUnits ( self )

Python method signature(s):

unsetAreaUnits()    int

Unsets the value of the 'areaUnits' attribute of this Model.

Returns:

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

Note:: The 'areaUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.Model.unsetConversionFactor ( self )

Python method signature(s):

unsetConversionFactor()    int

Unsets the value of the 'conversionFactor' attribute of this Model.

Returns:

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

Note:: The 'conversionFactor' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.SBase.unsetCVTerms ( self ) [inherited]

Python method signature(s):

unsetCVTerms()    int

Clears the list of CVTerm objects attached to this SBML object.

Returns:

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

def libsbml.Model.unsetExtentUnits ( self )

Python method signature(s):

unsetExtentUnits()    int

Unsets the value of the 'extentUnits' attribute of this Model.

Returns:

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

Note:: The 'extentUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.Model.unsetId ( self )

Python method signature(s):

unsetId()    int

Unsets the value of the 'id' attribute of this Model.

Returns:

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

Reimplemented from libsbml.SBase.

def libsbml.Model.unsetLengthUnits ( self )

Python method signature(s):

unsetLengthUnits()    int

Unsets the value of the 'lengthUnits' attribute of this Model.

Returns:

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

Note:: The 'lengthUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.SBase.unsetMetaId ( self ) [inherited]

Python method signature(s):

unsetMetaId()    int

Unsets the value of the 'metaid' attribute of this SBML object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns:

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

def libsbml.SBase.unsetModelHistory ( self ) [inherited]

Python method signature(s):

unsetModelHistory()    int

Unsets the ModelHistory object attached to this object.

Returns:

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

Note:: In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.

def libsbml.Model.unsetName ( self )

Python method signature(s):

unsetName()    int

Unsets the value of the 'name' attribute of this Model.

Returns:

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

Reimplemented from libsbml.SBase.

def libsbml.SBase.unsetNotes ( self ) [inherited]

Python method signature(s):

unsetNotes()    int

Unsets the value of the 'notes' subelement of this SBML object.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

Returns:

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

LIBSBML_OPERATION_SUCCESS

See also:: getNotesString(); isSetNotes(); setNotes(); setNotes(); appendNotes(); appendNotes(); SyntaxChecker.hasExpectedXHTMLSyntax()

def libsbml.SBase.unsetSBOTerm ( self ) [inherited]

Python method signature(s):

unsetSBOTerm()    int

Unsets the value of the 'sboTerm' attribute of this SBML object.

Returns:

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

def libsbml.Model.unsetSubstanceUnits ( self )

Python method signature(s):

unsetSubstanceUnits()    int

Unsets the value of the 'substanceUnits' attribute of this Model.

Returns:

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

Note:: The 'substanceUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.Model.unsetTimeUnits ( self )

Python method signature(s):

unsetTimeUnits()    int

Unsets the value of the 'timeUnits' attribute of this Model.

Returns:

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

Note:: The 'timeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

def libsbml.Model.unsetVolumeUnits ( self )

Python method signature(s):

unsetVolumeUnits()    int

Unsets the value of the 'volumeUnits' attribute of this Model.

Returns:

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

Note:: The 'volumeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.

libsbml.Model Class Reference

Detailed Description

Public Member Functions

Member Function Documentation