libSBML Python API  5.18.0
libsbml.Rule Class Reference
Inheritance diagram for libsbml.Rule:
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## Detailed Description

Parent class for SBML rules in libSBML.

In SBML, rules provide additional ways to define the values of variables in a model, their relationships, and the dynamical behaviors of those variables. They enable encoding relationships that cannot be expressed using Reaction nor InitialAssignment objects alone.

The libSBML implementation of rules mirrors the SBML Level 3 definition (which is in turn is very similar to the Level 2 Version 4 definition), with Rule being the parent class of three subclasses as explained below. The Rule class itself cannot be instantiated by user programs and has no constructor; only the subclasses AssignmentRule, AlgebraicRule and RateRule can be instantiated directly.

# General summary of SBML rules

In SBML Level 3 as well as Level 2, rules are separated into three subclasses for the benefit of model analysis software. The three subclasses are based on the following three different possible functional forms (where x is a variable, f is some arbitrary function returning a numerical result, V is a vector of variables that does not include x, and W is a vector of variables that may include x):

 Algebraic: left-hand side is zero 0 = f(W) Assignment: left-hand side is a scalar: x = f(V) Rate: left-hand side is a rate-of-change: dx/dt = f(W)

In their general form given above, there is little to distinguish between assignment and algebraic rules. They are treated as separate cases for the following reasons:

• Assignment rules can simply be evaluated to calculate intermediate values for use in numerical methods. They are statements of equality that hold at all times. (For assignments that are only performed once, see InitialAssignment.)
• SBML needs to place restrictions on assignment rules, for example the restriction that assignment rules cannot contain algebraic loops.
• Some simulators do not contain numerical solvers capable of solving unconstrained algebraic equations, and providing more direct forms such as assignment rules may enable those simulators to process models they could not process if the same assignments were put in the form of general algebraic equations;
• Those simulators that can solve these algebraic equations make a distinction between the different categories listed above; and
• Some specialized numerical analyses of models may only be applicable to models that do not contain algebraic rules.

The approach taken to covering these cases in SBML is to define an abstract Rule structure containing a subelement, 'math', to hold the right-hand side expression, then to derive subtypes of Rule that add attributes to distinguish the cases of algebraic, assignment and rate rules. The 'math' subelement must contain a MathML expression defining the mathematical formula of the rule. This MathML formula must return a numerical value. The formula can be an arbitrary expression referencing the variables and other entities in an SBML model.

Each of the three subclasses of Rule (AssignmentRule, AlgebraicRule, RateRule) inherit the the 'math' subelement and other fields from SBase. The AssignmentRule and RateRule classes add an additional attribute, 'variable'. See the definitions of AssignmentRule, AlgebraicRule and RateRule for details about the structure and interpretation of each one.

# Additional restrictions on SBML rules

An important design goal of SBML rule semantics is to ensure that a model's simulation and analysis results will not be dependent on when or how often rules are evaluated. To achieve this, SBML needs to place two restrictions on rule use. The first concerns algebraic loops in the system of assignments in a model, and the second concerns overdetermined systems.

## A model must not contain algebraic loops

The combined set of InitialAssignment, AssignmentRule and KineticLaw objects in a model constitute a set of assignment statements that should be considered as a whole. (A KineticLaw object is counted as an assignment because it assigns a value to the symbol contained in the 'id' attribute of the Reaction object in which it is defined.) This combined set of assignment statements must not contain algebraic loops—dependency chains between these statements must terminate. To put this more formally, consider a directed graph in which nodes are assignment statements and directed arcs exist for each occurrence of an SBML species, compartment or parameter symbol in an assignment statement's 'math' subelement. Let the directed arcs point from the statement assigning the symbol to the statements that contain the symbol in their 'math' subelement expressions. This graph must be acyclic.

Similarly, the combined set of RateRule and Reaction objects constitute a set of definitions for the rates of change of various model entities (namely, the objects identified by the values of the 'variable' attributes of the RateRule objects, and the 'species' attributes of the SpeciesReference objects in each Reaction). In SBML Level 3 Version 2, these rates of change may be referenced directly using the rateOf csymbol, but may not thereby contain algebraic loops—dependency chains between these statements must terminate. More formally, consider a directed graph in which the nodes are the definitions of different variables' rates of change, and directed arcs exist for each occurrence of a variable referenced by a rateOf csymbol from any RateRule or KineticLaw object in the model. Let the directed arcs point from the variable referenced by the rateOf csymbol (call it x) to the variable(s) determined by the 'math' expression in which x appears. This graph must be acyclic.

SBML does not specify when or how often rules should be evaluated. Eliminating algebraic loops ensures that assignment statements can be evaluated any number of times without the result of those evaluations changing. As an example, consider the set of equations x = x + 1, y = z + 200 and z = y + 100. If this set of equations were interpreted as a set of assignment statements, it would be invalid because the rule for x refers to x (exhibiting one type of loop), and the rule for y refers to z while the rule for z refers back to y (exhibiting another type of loop). Conversely, the following set of equations would constitute a valid set of assignment statements: x = 10, y = z + 200, and z = x + 100.

## A model must not be overdetermined

An SBML model must not be overdetermined; that is, a model must not define more equations than there are unknowns in a model. A valid SBML model that does not contain AlgebraicRule structures cannot be overdetermined.

LibSBML implements the static analysis procedure described in Appendix B of the SBML Level 3 specification for assessing whether a model is overdetermined.

(In summary, assessing whether a given continuous, deterministic, mathematical model is overdetermined does not require dynamic analysis; it can be done by analyzing the system of equations created from the model. One approach is to construct a bipartite graph in which one set of vertices represents the variables and the other the set of vertices represents the equations. Place edges between vertices such that variables in the system are linked to the equations that determine them. For algebraic equations, there will be edges between the equation and each variable occurring in the equation. For ordinary differential equations (such as those defined by rate rules or implied by the reaction rate definitions), there will be a single edge between the equation and the variable determined by that differential equation. A mathematical model is overdetermined if the maximal matchings of the bipartite graph contain disconnected vertexes representing equations. If one maximal matching has this property, then all the maximal matchings will have this property; i.e., it is only necessary to find one maximal matching.)

# Rule types for SBML Level 1

SBML Level 1 uses a different scheme than SBML Level 2 and Level 3 for distinguishing rules; specifically, it uses an attribute whose value is drawn from an enumeration of 3 values. LibSBML supports this using methods that work with the enumeration values listed below.

## Public Member Functions

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

def appendAnnotation (self, args)
This method has multiple variants; they differ in the arguments they accept. More...

def appendNotes (self, args)
This method has multiple variants; they differ in the arguments they accept. More...

def clone (self)
Creates and returns a deep copy of this Rule object. More...

def connectToChild (self)

def containsUndeclaredUnits (self, args)
Predicate returning `True` if the math expression of this Rule contains parameters/numbers with undeclared units. More...

def deleteDisabledPlugins (self, recursive=True)
Deletes all information stored in disabled plugins. More...

def disablePackage (self, pkgURI, pkgPrefix)
Disables the given SBML Level 3 package on this object. More...

def enablePackage (self, pkgURI, pkgPrefix, flag)
Enables or disables the given SBML Level 3 package on this object. More...

def getAncestorOfType (self, args)
This method has multiple variants; they differ in the arguments they accept. More...

def getAnnotation (self, args)
Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects. More...

def getAnnotationString (self, args)
Returns the content of the 'annotation' subelement of this object as a character string. More...

def getColumn (self)
Returns the column number where this object first appears in the XML representation of the SBML document. More...

def getCVTerm (self, n)
Returns the nth CVTerm in the list of CVTerms of this SBML object. More...

def getCVTerms (self, args)
Returns a list of CVTerm objects in the annotations of this SBML object. More...

def getDerivedUnitDefinition (self, args)
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the 'math' expression of this Rule. More...

def getDisabledPlugin (self, args)
Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More...

def getElementByMetaId (self, args)
Returns the first child element it can find with a specific 'metaid' attribute value, or `None` if no such object is found. More...

def getElementBySId (self, args)
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. More...

def getElementName (self)
Returns the XML element name of this object. More...

def getFormula (self)
Returns the mathematical expression of this Rule in text-string form. More...

def getId (self)
Returns the value of the 'variable' attribute of this Rule (NOT the 'id'). More...

def getIdAttribute (self)
Returns the value of the 'id' attribute of this SBML object. More...

def getL1TypeCode (self)
Returns the SBML Level 1 type code for this Rule object. More...

def getLevel (self)
Returns the SBML Level of the SBMLDocument object containing this object. More...

def getLine (self)
Returns the line number where this object first appears in the XML representation of the SBML document. More...

def getListOfAllElements (self, filter=None)
Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth. More...

def getListOfAllElementsFromPlugins (self, filter=None)
Returns a List of all child SBase objects contained in SBML package plug-ins. More...

def getMath (self)
Get the mathematical formula of this Rule as an ASTNode tree. More...

def getMetaId (self)
Returns the value of the 'metaid' attribute of this SBML object. More...

def getModel (self)
Returns the Model object for the SBML Document in which the current object is located. More...

def getModelHistory (self, args)
Returns the ModelHistory object, if any, attached to this object. More...

def getName (self)
Returns the value of the 'name' attribute of this SBML object. More...

def getNamespaces (self)
Returns a list of the XML Namespaces declared on the SBML document owning this object. More...

def getNotes (self, args)
Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects. More...

def getNotesString (self, args)
Returns the content of the 'notes' subelement of this object as a string. More...

def getNumCVTerms (self)
Returns the number of CVTerm objects in the annotations of this SBML object. More...

def getNumDisabledPlugins (self)
Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known. More...

def getNumPlugins (self)
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More...

def getPackageCoreVersion (self)
Returns the SBML Core Version within the SBML Level of the actual object. More...

def getPackageName (self)
Returns the name of the SBML Level 3 package in which this element is defined. More...

def getPackageVersion (self)
Returns the Version of the SBML Level 3 package to which this element belongs to. More...

def getParentSBMLObject (self, args)
Returns the parent SBML object containing this object. More...

def getPlugin (self, args)
This method has multiple variants; they differ in the arguments they accept. More...

def getPrefix (self)
Returns the XML namespace prefix of this element. More...

def getResourceBiologicalQualifier (self, resource)
Returns the MIRIAM biological qualifier associated with the given resource. More...

def getResourceModelQualifier (self, resource)
Returns the MIRIAM model qualifier associated with the given resource. More...

def getSBMLDocument (self, args)
Returns the SBMLDocument object containing this object instance. More...

def getSBOTerm (self)
Returns the integer portion of the value of the 'sboTerm' attribute of this object. More...

def getSBOTermAsURL (self)
Returns the URL representation of the 'sboTerm' attribute of this object. More...

def getSBOTermID (self)
Returns the string representation of the 'sboTerm' attribute of this object. More...

def getType (self)
Returns a code representing the type of rule this is. More...

def getTypeCode (self)
Returns the libSBML type code for this SBML object. More...

def getUnits (self)
Returns the units for the mathematical formula of this Rule. More...

def getURI (self)
Gets the namespace URI to which this element belongs to. More...

def getVariable (self)
Get the value of the 'variable' attribute of this Rule object. More...

def getVersion (self)
Returns the Version within the SBML Level of the SBMLDocument object containing this object. More...

def hasRequiredAttributes (self)
Predicate returning `True` if all the required attributes for this Rule object have been set. More...

def hasRequiredElements (self)
Predicate returning `True` if all the required elements for this Rule object have been set. More...

def hasValidLevelVersionNamespaceCombination (self)
Predicate returning `true` if this object's level/version and namespace values correspond to a valid SBML specification. More...

def isAlgebraic (self)
Predicate returning `True` if this Rule is an AlgebraicRule. More...

def isAssignment (self)
Predicate returning `True` if this Rule is an AssignmentRule. More...

def isCompartmentVolume (self)
Predicate returning `True` if this Rule is an CompartmentVolumeRule or equivalent. More...

def isPackageEnabled (self, pkgName)
Predicate returning `True` if the given SBML Level 3 package is enabled with this object. More...

def isPackageURIEnabled (self, pkgURI)
Predicate returning `True` if an SBML Level 3 package with the given URI is enabled with this object. More...

def isParameter (self)
Predicate returning `True` if this Rule is an ParameterRule or equivalent. More...

def isPkgEnabled (self, pkgName)
Predicate returning `True` if the given SBML Level 3 package is enabled with this object. More...

def isPkgURIEnabled (self, pkgURI)
Predicate returning `True` if an SBML Level 3 package with the given URI is enabled with this object. More...

def isRate (self)
Predicate returning `True` if this Rule is a RateRule (SBML Levels 2–3) or has a 'type' attribute value of `'rate'` (SBML Level 1). More...

def isScalar (self)
Predicate returning `True` if this Rule is an AssignmentRule (SBML Levels 2–3) or has a 'type' attribute value of `'scalar'` (SBML Level 1). More...

def isSetAnnotation (self)
Predicate returning `True` if this object's 'annotation' subelement exists and has content. More...

def isSetFormula (self)
Predicate returning `True` if this Rule's mathematical expression is set. More...

def isSetId (self)
Predicate returning `True` if a call to getId() returns a non-empty string. More...

def isSetIdAttribute (self)
Predicate returning `True` if this object's 'id' attribute is set. More...

def isSetMath (self)
Predicate returning `True` if this Rule's mathematical expression is set. More...

def isSetMetaId (self)
Predicate returning `True` if this object's 'metaid' attribute is set. More...

def isSetModelHistory (self)
Predicate returning `True` if this object has a ModelHistory object attached to it. More...

def isSetName (self)
Predicate returning `True` if this object's 'name' attribute is set. More...

def isSetNotes (self)
Predicate returning `True` if this object's 'notes' subelement exists and has content. More...

def isSetSBOTerm (self)
Predicate returning `True` if this object's 'sboTerm' attribute is set. More...

def isSetUnits (self)
Predicate returning `True` if this Rule's 'units' attribute is set. More...

def isSetUserData (self)
Predicate returning true or false depending on whether the user data of this element has been set. More...

def isSetVariable (self)
Predicate returning `True` if this Rule's 'variable' attribute is set. More...

def isSpeciesConcentration (self)
Predicate returning `True` if this Rule is a SpeciesConcentrationRule or equivalent. More...

Returns `True` if this object's set of XML namespaces are a subset of the given object's XML namespaces. More...

def matchesSBMLNamespaces (self, args)
Returns `True` if this object's set of XML namespaces are the same as the given object's XML namespaces. More...

def removeFromParentAndDelete (self)
Removes this object from its parent. More...

def removeTopLevelAnnotationElement (self, args)
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More...

def renameMetaIdRefs (self, oldid, newid)
Replaces all uses of a given meta identifier attribute value with another value. More...

def renameSIdRefs (self, oldid, newid)
Replaces all uses of a given `SIdRef` type attribute value with another value. More...

def renameUnitSIdRefs (self, oldid, newid)
Replaces all uses of a given `UnitSIdRef` type attribute value with another value. More...

def replaceTopLevelAnnotationElement (self, args)
This method has multiple variants; they differ in the arguments they accept. More...

def setAnnotation (self, args)
This method has multiple variants; they differ in the arguments they accept. More...

def setFormula (self, formula)
Sets the 'math' subelement of this Rule to an expression in text-string form. More...

def setId (self, sid)
Sets the value of the 'id' attribute of this SBML object. More...

def setIdAttribute (self, sid)
Sets the value of the 'id' attribute of this SBML object. More...

def setL1TypeCode (self, type)
Sets the SBML Level 1 type code for this Rule. More...

def setMath (self, math)
Sets the 'math' subelement of this Rule to a copy of the given ASTNode. More...

def setMetaId (self, metaid)
Sets the value of the meta-identifier attribute of this SBML object. More...

def setModelHistory (self, history)
Sets the ModelHistory of this object. More...

def setName (self, name)
Sets the value of the 'name' attribute of this SBML object. More...

def setNamespaces (self, xmlns)
Sets the namespaces relevant of this SBML object. More...

def setNotes (self, args)
This method has multiple variants; they differ in the arguments they accept. More...

def setSBOTerm (self, args)
This method has multiple variants; they differ in the arguments they accept. More...

def setUnits (self, sname)
Sets the units for this Rule. More...

def setVariable (self, sid)
Sets the 'variable' attribute value of this Rule object. More...

def toSBML (self)
Returns a string consisting of a partial SBML corresponding to just this object. More...

def toXMLNode (self)
Returns this element as an XMLNode. More...

def unsetAnnotation (self)
Unsets the value of the 'annotation' subelement of this SBML object. More...

def unsetCVTerms (self)
Clears the list of CVTerm objects attached to this SBML object. More...

def unsetId (self)
Unsets the value of the 'id' attribute of this SBML object. More...

def unsetIdAttribute (self)
Unsets the value of the 'id' attribute of this SBML object. More...

def unsetMetaId (self)
Unsets the value of the 'metaid' attribute of this SBML object. More...

def unsetModelHistory (self)
Unsets the ModelHistory object attached to this object. More...

def unsetName (self)
Unsets the value of the 'name' attribute of this SBML object. More...

def unsetNotes (self)
Unsets the value of the 'notes' subelement of this SBML object. More...

def unsetSBOTerm (self)
Unsets the value of the 'sboTerm' attribute of this SBML object. More...

def unsetUnits (self)
Unsets the 'units' for this Rule. More...

def unsetUserData (self)
Unsets the user data of this element. More...

def unsetVariable (self)
Unsets the value of the 'variable' attribute of this Rule object. More...

## Member Function Documentation

 def libsbml.SBase.addCVTerm ( self, term, newBag = `False` )
inherited

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

```addCVTerm(CVTerm term, bool newBag)   int
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:
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.
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 inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. 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 other methods on this class (particularly a corresponding method whose name begins with the word `create`) for alternatives that do not lead to these issues.
Owing to the way that language interfaces are created in libSBML, this documentation may show methods that define default values for parameters with text that has the form `parameter` = `value`. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.
 def libsbml.SBase.appendAnnotation ( self, args )
inherited

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

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

Each variant is described separately below.

Method variant with the following signature:
`appendAnnotation(XMLNode annotation)`

Appends the given `annotation` to the 'annotation' subelement of this 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.

Unlike SBase.setAnnotation() or SBase.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:
getAnnotationString()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
unsetAnnotation()

Method variant with the following signature:
`appendAnnotation(string annotation)`

Appends the given `annotation` to the 'annotation' subelement of this 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.

Unlike SBase.setAnnotation() or SBase.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:
getAnnotationString()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
unsetAnnotation()
 def libsbml.SBase.appendNotes ( self, args )
inherited

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

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

Each variant 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:
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:
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
 def libsbml.Rule.clone ( self )

Creates and returns a deep copy of this Rule object.

`clone()   Rule`
Returns
the (deep) copy of this Rule object.
 def libsbml.SBase.connectToChild ( self )
inherited
`connectToChild()`
 def libsbml.Rule.containsUndeclaredUnits ( self, args )

Predicate returning `True` if the math expression of this Rule contains parameters/numbers with undeclared units.

`containsUndeclaredUnits()   bool`
Returns
`True` if the math expression of this Rule includes parameters/numbers with undeclared units, `False` otherwise.
Note
A return value of `True` indicates that the UnitDefinition returned by getDerivedUnitDefinition() may not accurately represent the units of the expression.
getDerivedUnitDefinition()
 def libsbml.SBase.deleteDisabledPlugins ( self, recursive = `True` )
inherited

Deletes all information stored in disabled plugins.

```deleteDisabledPlugins(bool recursive)
deleteDisabledPlugins()```

If the plugin is re-enabled later, it will then not have any previously-stored information.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
Parameters
 recursive if `True`, the disabled information will be deleted also from all child elements, otherwise only from this SBase element.
getNumDisabledPlugins()
 def libsbml.SBase.disablePackage ( self, pkgURI, pkgPrefix )
inherited

Disables the given SBML Level 3 package on this object.

`disablePackage(string pkgURI, string pkgPrefix)   int`

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

An example of when this may be useful is during construction of model components when mixing existing and new models. Suppose your application read an SBML document containing a model that used the SBML Hierarchical Model Composition (“comp”) package, and extracted parts of that model in order to construct a new model in memory. The new, in-memory model will not accept a component drawn from an other SBMLDocument with different package namespace declarations. You could reconstruct the same namespaces in the in-memory model first, but as a shortcut, you could also disable the package namespace on the object being added. Here is a code example to help clarify this:

1 import sys
2 import os.path
3 from libsbml import *
4
5 # We read an SBML L3V1 model that uses the 'comp' package.
6
8 if doc.getNumErrors() > 0:
10  doc.printErrors()
11  sys.exit(1)
12
13 # We extract one of the species from the model.
14
15 model = doc.getModel()
16 if model == None:
17  print('Unable to retrieve Model object')
18  sys.exit(1)
19
20 s1 = model.getSpecies(0)
21 if s1 == None:
22  print('Unable to retrieve Species object')
23  sys.exit(1)
24
25 # We construct a new model.
26 # This model does not use the 'comp' package.
27
28 try:
29  newDoc = SBMLDocument(3, 1)
30 except ValueError:
31  print('Could not create SBMLDocument object')
32  sys.exit(1)
33
34 newModel = newDoc.createModel()
35 if newModel == None:
36  print('Unable to create new Model object')
37  sys.exit(1)
38
39 # The following would normally fail with an error, because
40 # addSpecies() would first check that the parent of the given
41 # object has namespaces declared, and will discover that s1
42 # does but newModel does not.
43
45
46 # However, if we disable the 'comp' package on s1, then the
47 # call to addSpecies will work.
48
49 compNS = 'http://www.sbml.org/sbml/level3/version1/comp/version1'
50 status = s1.disablePackage(compNS, 'comp')
51 if status != LIBSBML_OPERATION_SUCCESS:
52  print('Unable to disable package.')
53  sys.exit(1)
54
55 newSpecies = newModel.addSpecies(s1) # This will work now.
56 if newSpecies == None:
57  print('Could not add Species') # (This will not happen,
58  sys.exit(1) # but always check errors.)
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:
enablePackage()
 def libsbml.SBase.enablePackage ( self, pkgURI, pkgPrefix, flag )
inherited

Enables or disables the given SBML Level 3 package on this object.

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

This method enables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object. This method is the converse of SBase.disablePackage().

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:
disablePackage()
 def libsbml.SBase.getAncestorOfType ( self, args )
inherited

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

```getAncestorOfType(int type, string pkgName)   SBase
getAncestorOfType(int type)   SBase```

Each variant is described separately below.

Method variant with the following signature:
`getAncestorOfType(int type, string pkgName = 'core')`

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

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 from the given `pkgName`.

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.
Warning
The optional argument `pkgName` must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the 'core' namespace alone, not find any corresponding elements, and return None.
Note
Owing to the way that language interfaces are created in libSBML, this documentation may show methods that define default values for parameters with text that has the form `parameter` = `value`. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.

Method variant with the following signature:
`getAncestorOfType(int type, string pkgName = 'core')`

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

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 from the given `pkgName`.

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.
Warning
The optional argument `pkgName` must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the 'core' namespace alone, not find any corresponding elements, and return None.
Note
Owing to the way that language interfaces are created in libSBML, this documentation may show methods that define default values for parameters with text that has the form `parameter` = `value`. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.
 def libsbml.SBase.getAnnotation ( self, args )
inherited

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

`getAnnotation()   XMLNode`
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.
getAnnotationString()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
 def libsbml.SBase.getAnnotationString ( self, args )
inherited

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

`getAnnotationString()   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. See the method getAnnotation() for a version that returns annotations in XML form.

Returns
the annotation of this SBML object as a character string.
getAnnotation()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
 def libsbml.SBase.getColumn ( self )
inherited

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

`getColumn()   long`
Returns
the column number of this SBML object. If this object was created programmatically and not read from a file, this method will return the value `0`.
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.)
getLine()
 def libsbml.SBase.getCVTerm ( self, n )
inherited

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

`getCVTerm(long  n)   CVTerm`
Parameters
 n long the index of the CVTerm to retrieve.
Returns
the nth CVTerm in the list of CVTerms for this SBML object. If the index `n` is invalid, `None` is returned.
 def libsbml.SBase.getCVTerms ( self, args )
inherited

Returns a list of CVTerm objects in the annotations of this SBML object.

`getCVTerms()   List *`
Returns
the list of CVTerms for this SBML object.
 def libsbml.Rule.getDerivedUnitDefinition ( self, args )

Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the 'math' expression of this Rule.

`getDerivedUnitDefinition()   UnitDefinition`
The units are calculated based on the mathematical expression in the Rule and the model quantities referenced by `<ci>` elements used within that expression. The method Rule.getDerivedUnitDefinition() returns the calculated units, to the extent that libSBML can compute them.
Note
The functionality that facilitates unit analysis depends on the model as a whole. Thus, in cases where the object has not been added to a model or the model itself is incomplete, unit analysis is not possible and this method will return `None`.
Warning
Note that it is possible the 'math' expression in the Rule contains pure numbers or parameters with undeclared units. In those cases, it is not possible to calculate the units of the overall expression without making assumptions. LibSBML does not make assumptions about the units, and Rule.getDerivedUnitDefinition() only returns the units as far as it is able to determine them. For example, in an expression X + Y, if X has unambiguously-defined units and Y does not, it will return the units of X. It is important that callers also invoke the method Rule.containsUndeclaredUnits() to determine whether this situation holds. Callers may wish to take suitable actions in those scenarios.
Returns
a UnitDefinition that expresses the units of the math expression of this Rule, or `None` if one cannot be constructed.
containsUndeclaredUnits()
 def libsbml.SBase.getDisabledPlugin ( self, args )
inherited

Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension.

`getDisabledPlugin(long  n)   SBasePlugin`

If no such plugin exists, None is returned.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
Parameters
 n the index of the disabled plug-in to return.
Returns
the nth disabled plug-in object (the libSBML extension interface) of a package extension. If the index `n` is invalid, `None` is returned.
getNumDisabledPlugins()
getPlugin()
 def libsbml.SBase.getElementByMetaId ( self, args )
inherited

Returns the first child element it can find with a specific 'metaid' attribute value, or `None` if no such object is found.

`getElementByMetaId(string metaid)   SBase`
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. The latter point is important, because the uniqueness criterion applies across any attribute with type `ID` anywhere in the file, 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 the XML `ID` type. Although SBML itself specifies the use of XML `ID` only for the 'metaid' attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML `ID` data type; it uses ordinary character strings, which is easier for applications to support.
Parameters
 metaid string representing the 'metaid' attribute value of the object to find.
Returns
pointer to the first element found with the given meta-identifier.
 def libsbml.SBase.getElementBySId ( self, args )
inherited

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.

`getElementBySId(string id)   SBase`
Parameters
 id string representing the 'id' attribute value of the object to find.
Returns
pointer to the first element found with the given identifier.
 def libsbml.Rule.getElementName ( self )

Returns the XML element name of this object.

`getElementName()   string`

The returned value can be any of a number of different strings, depending on the SBML Level in use and the kind of Rule object this is. The rules as of libSBML version 5.18.0 are the following:

• (Level 2 and 3) RateRule: returns `'rateRule'`
• (Level 2 and 3) AssignmentRule: returns `'assignmentRule'`
• (Level 2 and 3) AlgebraicRule: returns `'algebraicRule'`
• (Level 1 Version 1) SpecieConcentrationRule: returns `'specieConcentrationRule'`
• (Level 1 Version 2) SpeciesConcentrationRule: returns `'speciesConcentrationRule'`
• (Level 1) CompartmentVolumeRule: returns `'compartmentVolumeRule'`
• (Level 1) ParameterRule: returns `'parameterRule'`
• Unknown rule type: returns `'unknownRule'`

Beware that the last (`'unknownRule'`) is not a valid SBML element name.

Returns
the name of this element.
 def libsbml.Rule.getFormula ( self )

Returns the mathematical expression of this Rule in text-string form.

`getFormula()   string`

The text string is produced by formulaToString(); please consult the documentation for that function to find out more about the format of the text-string formula.

Returns
the formula text string for this Rule.
Note
The attribute 'formula' is specific to SBML Level 1; in higher Levels of SBML, it has been replaced with a subelement named 'math'. However, libSBML provides a unified interface to the underlying math expression and this method can be used for models of all Levels of SBML.
getMath()
 def libsbml.Rule.getId ( self )

Returns the value of the 'variable' attribute of this Rule (NOT the 'id').

`getId()   string`
Note
Because of the inconsistent behavior of this function with respect to assignments and rules, it is now recommended to use the getIdAttribute() or the getVariable() function instead.

The 'variable' attribute of a Rule indicates the element which the results of the 'math' are to be applied. An AlgebraicRule has no 'variable', and will always return an empty string.

Returns
the variable of this Rule.
getIdAttribute()
setIdAttribute()
isSetIdAttribute()
unsetIdAttribute()
getVariable()
 def libsbml.SBase.getIdAttribute ( self )
inherited

Returns the value of the 'id' attribute of this SBML object.

`getIdAttribute()   string`
The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always `SId` or a type derived from that, such as `UnitSId`, depending on the object in question. All data types are defined as follows:
```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. This applies to all uses of `SId`, `SIdRef`, and derived types.

Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return `False` for objects of these classes.

With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.

Returns
the id of this SBML object, if set and valid for this level and version of SBML; an empty string otherwise.
Note
Because of the inconsistent behavior of this function with respect to assignments and rules, callers should use getIdAttribute() instead.
setIdAttribute()
isSetIdAttribute()
unsetIdAttribute()
 def libsbml.Rule.getL1TypeCode ( self )

Returns the SBML Level 1 type code for this Rule object.

`getL1TypeCode()   int`

This method only applies to SBML Level 1 model objects. If this is not an SBML Level 1 rule object, this method will return SBML_UNKNOWN.

Returns
the SBML Level 1 type code for this Rule (namely, SBML_COMPARTMENT_VOLUME_RULE, SBML_PARAMETER_RULE, SBML_SPECIES_CONCENTRATION_RULE, or SBML_UNKNOWN).
 def libsbml.SBase.getLevel ( self )
inherited

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

`getLevel()   long`
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.)
Returns
the SBML level of this SBML object.
getVersion()
getNamespaces()
getPackageVersion()
 def libsbml.SBase.getLine ( self )
inherited

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

`getLine()   long`
Returns
the line number of this SBML object. If this object was created programmatically and not read from a file, this method will return the value `0`.
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.)
getColumn()
 def libsbml.SBase.getListOfAllElements ( self, filter = `None` )
inherited

Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth.

```getListOfAllElements(ElementFilter filter)   SBaseList
getListOfAllElements()   SBaseList```
Returns
a list of all objects that are children of this object.
 def libsbml.SBase.getListOfAllElementsFromPlugins ( self, filter = `None` )
inherited

Returns a List of all child SBase objects contained in SBML package plug-ins.

```getListOfAllElementsFromPlugins(ElementFilter filter)   SBaseList
getListOfAllElementsFromPlugins()   SBaseList```
SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.

This method walks down the list of all SBML Level 3 packages used by this object and returns all child objects defined by those packages.

Returns
a pointer to a List of pointers to all children objects from plug-ins.
 def libsbml.Rule.getMath ( self )

Get the mathematical formula of this Rule as an ASTNode tree.

`getMath()   ASTNode`
Returns
an ASTNode, the value of the 'math' subelement of this Rule, or `None` if the math is not set.
Note
The subelement 'math' is present in SBML Levels 2 and 3. In SBML Level 1, the equivalent construct is the attribute named 'formula'. LibSBML provides a unified interface to the underlying math expression and this method can be used for models of all Levels of SBML.
getFormula()
 def libsbml.SBase.getMetaId ( self )
inherited

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

`getMetaId()   string`
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. The latter point is important, because the uniqueness criterion applies across any attribute with type `ID` anywhere in the file, 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 the XML `ID` type. Although SBML itself specifies the use of XML `ID` only for the 'metaid' attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML `ID` data type; it uses ordinary character strings, which is easier for applications to support.
Returns
the meta-identifier of this SBML object.
isSetMetaId()
setMetaId()
 def libsbml.SBase.getModel ( self )
inherited

Returns the Model object for the SBML Document in which the current object is located.

`getModel()   Model`
Returns
the Model object for the SBML Document of this SBML object.
getParentSBMLObject()
getSBMLDocument()
 def libsbml.SBase.getModelHistory ( self, args )
inherited

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

`getModelHistory()   ModelHistory`
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.SBase.getName ( self )
inherited

Returns the value of the 'name' attribute of this SBML object.

`getName()   string`
In SBML Level 3 Version 2, the 'id' and 'name' attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. LibSBML has for a long time provided functions defined on SBase itself to get, set, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.

The 'name' attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of 'name' is the type `string` defined in XML Schema. SBML imposes no restrictions as to the content of 'name' attributes beyond those restrictions defined by the `string` type in XML Schema.

The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)

As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.

An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.

Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a 'name' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write 'name' attributes for those objects.

Returns
the name of this SBML object, or the empty string if not set or unsettable.
getIdAttribute()
isSetName()
setName()
unsetName()
 def libsbml.SBase.getNamespaces ( self )
inherited

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

`getNamespaces()   XMLNamespaces`

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.

Returns
the XML Namespaces associated with this SBML object, or `None` in certain very usual circumstances where a namespace is not set.
getLevel()
getVersion()
 def libsbml.SBase.getNotes ( self, args )
inherited

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

`getNotes()   XMLNode`
The optional SBML element named 'notes', present on every major SBML component type (and in SBML Level 3, the 'message' subelement of Constraint), 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 conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. 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.
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
 def libsbml.SBase.getNotesString ( self, args )
inherited

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

`getNotesString()   string`
The optional SBML element named 'notes', present on every major SBML component type (and in SBML Level 3, the 'message' subelement of Constraint), 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 conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. 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.
getNotes()
isSetNotes()
setNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
 def libsbml.SBase.getNumCVTerms ( self )
inherited

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

`getNumCVTerms()   long`
Returns
the number of CVTerms for this SBML object.
 def libsbml.SBase.getNumDisabledPlugins ( self )
inherited

Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known.

`getNumDisabledPlugins()   long`
SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.
Returns
the number of disabled plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.
 def libsbml.SBase.getNumPlugins ( self )
inherited

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

`getNumPlugins()   long`
SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Returns
the number of plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.
getPlugin()
 def libsbml.SBase.getPackageCoreVersion ( self )
inherited

Returns the SBML Core Version within the SBML Level of the actual object.

`getPackageCoreVersion()   long`
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.)
Returns
the SBML core version of this SBML object.
 def libsbml.SBase.getPackageName ( self )
inherited

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

`getPackageName()   string`
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

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

`getPackageVersion()   long`
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.
getLevel()
getVersion()
 def libsbml.SBase.getParentSBMLObject ( self, args )
inherited

Returns the parent SBML object containing this object.

`getParentSBMLObject()   SBase`

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.
getSBMLDocument()
getModel()
 def libsbml.SBase.getPlugin ( self, args )
inherited

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

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

Each variant is described separately below.

Method variant with the following signature:
`getPlugin(long n)`

Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. The returned plug-in will be the appropriate type of plugin requested: calling Model.getPlugin() will return an FbcModelPlugin; calling Parameter.getPlugin() will return CompSBasePlugin, etc.

If no such plugin exists, None is returned.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
 n the index of the plug-in to return.
Returns
the nth plug-in object (the libSBML extension interface) of a package extension. If the index `n` is invalid, `None` is returned.
getNumPlugins()
getPlugin()

Method variant with the following signature:
`getPlugin(string package)`

Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. The returned plug-in will be the appropriate type of plugin requested: calling Model.getPlugin() will return an FbcModelPlugin; calling Parameter.getPlugin() will return CompSBasePlugin, etc.

If no such plugin exists, None is returned.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
 package the name or URI of the package.
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
getPlugin()
 def libsbml.SBase.getPrefix ( self )
inherited

Returns the XML namespace prefix of this element.

`getPrefix()   string`

This reports the XML namespace prefix chosen for this class of object in the current SBML document. This may be an empty string if the component has no explicit prefix (for instance, if it is a core SBML object placed in the default SBML namespace of the document). If it is not empty, then it corresponds to the XML namespace prefix used set the object, whatever that may be in a given SBML document.

Returns
a text string representing the XML namespace prefix.
 def libsbml.SBase.getResourceBiologicalQualifier ( self, resource )
inherited

Returns the MIRIAM biological qualifier associated with the given resource.

`getResourceBiologicalQualifier(string resource)   long`

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 valueswhose 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 valuewhose 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, resource )
inherited

Returns the MIRIAM model qualifier associated with the given resource.

`getResourceModelQualifier(string resource)   long`

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 valueswhose 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 valuewhose 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 type associated 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.SBase.getSBMLDocument ( self, args )
inherited

Returns the SBMLDocument object containing this object instance.

`getSBMLDocument()   SBMLDocument`
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.
getParentSBMLObject()
getModel()
 def libsbml.SBase.getSBOTerm ( self )
inherited

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

`getSBOTerm()   int`
Beginning with SBML Level 2 Version 2, 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'. More details can be found in SBML specifications for Level 2 Version 2 and above.
Returns
the value of the 'sboTerm' attribute as an integer, or `-1` if the value is not set.
 def libsbml.SBase.getSBOTermAsURL ( self )
inherited

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

`getSBOTermAsURL()   string`

This method returns the entire SBO identifier as a text string in the form `http``://identifiers.org/biomodels.sbo/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'. More details can be found in SBML specifications for Level 2 Version 2 and above.
Returns
the value of the 'sboTerm' attribute as an identifiers.org URL, or an empty string if the value is not set.
 def libsbml.SBase.getSBOTermID ( self )
inherited

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

`getSBOTermID()   string`
Beginning with SBML Level 2 Version 2, 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'. More details can be found in SBML specifications for Level 2 Version 2 and above.
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.Rule.getType ( self )

Returns a code representing the type of rule this is.

`getType()   long`
Returns
the rule type, which will be one of the following three possible values:
Note
The attribute 'type' on Rule objects is present only in SBML Level 1. In SBML Level 2 and later, the type has been replaced by subclassing the Rule object.
 def libsbml.Rule.getTypeCode ( self )

Returns the libSBML type code for this SBML object.

`getTypeCode()   int`
LibSBML attaches an identifying code to every kind of SBML object. These are integer constants known as SBML type codes. The names of all the codes begin with the characters `SBML_`. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the `SBase.getPackageName() ` method on the object.

The exception to this is lists: all SBML-style list elements have the type SBML_LIST_OF, regardless of what package they are from.

Returns
the SBML type code for this object, either SBML_ASSIGNMENT_RULE, SBML_RATE_RULE, or SBML_ALGEBRAIC_RULE for SBML Core.
Warning
The specific integer values of the possible type codes may be reused by different libSBML plug-ins for SBML Level 3. packages, To fully identify the correct code, it is necessary to invoke both getPackageName() and getTypeCode() (or ListOf.getItemTypeCode()).
getElementName()
getPackageName()
 def libsbml.Rule.getUnits ( self )

Returns the units for the mathematical formula of this Rule.

`getUnits()   string`
Returns
the identifier of the units for the expression of this Rule.
Note
The attribute 'units' exists on SBML Level 1 ParameterRule objects only. It is not present in SBML Levels 2 and 3.
 def libsbml.SBase.getURI ( self )
inherited

Gets the namespace URI to which this element belongs to.

`getURI()   string`

For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI `'http://www.sbml.org/sbml/level3/version1/core'`; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI `'http://www.sbml.org/sbml/level3/version1/layout/version1'`.

This function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found, it will then look for the namespace associated with the element itself.

Returns
the URI of this element, as a text string.
getSBMLDocument()
getPackageName()
 def libsbml.Rule.getVariable ( self )

Get the value of the 'variable' attribute of this Rule object.

`getVariable()   string`
In SBML Level 1, the different rule types each have a different name for the attribute holding the reference to the object constituting the left-hand side of the rule. (E.g., for SBML Level 1's SpeciesConcentrationRule the attribute is 'species', for CompartmentVolumeRule it is 'compartment', etc.) In SBML Levels 2 and 3, the only two types of Rule objects with a left-hand side object reference are AssignmentRule and RateRule, and both of them use the same name for attribute: 'variable'. In order to make it easier for application developers to work with all Levels of SBML, libSBML uses a uniform name for all such attributes, and it is 'variable', regardless of whether Level 1 rules or Level 2–3 rules are being used.

The 'variable' attribute of a Rule indicates the element which the results of the 'math' are to be applied. An AlgebraicRule has no 'variable', and will always return an empty string.

Returns
the identifier string stored as the 'variable' attribute value in this Rule, or `None` if this object is an AlgebraicRule object, or if the attribute is unset.
 def libsbml.SBase.getVersion ( self )
inherited

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

`getVersion()   long`
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.)
Returns
the SBML version of this SBML object.
getLevel()
getNamespaces()
 def libsbml.Rule.hasRequiredAttributes ( self )

Predicate returning `True` if all the required attributes for this Rule object have been set.

`hasRequiredAttributes()   bool`

The required attributes for a Rule object depend on the type of Rule it is. For AssignmentRule and RateRule objects (and SBML Level 1's SpeciesConcentrationRule, CompartmentVolumeRule, and ParameterRule objects), the required attribute is 'variable'; for AlgebraicRule objects, there is no required attribute.

Returns
`True` if the required attributes have been set, `False` otherwise.
 def libsbml.Rule.hasRequiredElements ( self )

Predicate returning `True` if all the required elements for this Rule object have been set.

`hasRequiredElements()   bool`

The only required element for a Rule object is the 'math' subelement in SBML Level 2 and Level 3 Version 1. In SBML Level 3 Version 2+, it is no longer required.

Returns
a boolean value indicating whether all the required elements for this object have been defined.
 def libsbml.SBase.hasValidLevelVersionNamespaceCombination ( self )
inherited

Predicate returning `true` if this object's level/version and namespace values correspond to a valid SBML specification.

`hasValidLevelVersionNamespaceCombination()   bool`

The valid combinations of SBML Level, Version and Namespace as of this release of libSBML are the following:

• Level 1 Version 2: `http``://www.sbml.org/sbml/level1`
• Level 2 Version 1: `http``://www.sbml.org/sbml/level2`
• Level 2 Version 2: `http``://www.sbml.org/sbml/level2/version2`
• Level 2 Version 3: `http``://www.sbml.org/sbml/level2/version3`
• Level 2 Version 4: `http``://www.sbml.org/sbml/level2/version4`
• Level 3 Version 1 Core: `http``://www.sbml.org/sbml/level3/version1/core`
Returns
`true` if the level, version and namespace values of this SBML object correspond to a valid set of values, `false` otherwise.
 def libsbml.Rule.isAlgebraic ( self )

Predicate returning `True` if this Rule is an AlgebraicRule.

`isAlgebraic()   bool`
Returns
`True` if this Rule is an AlgebraicRule, `False` otherwise.
 def libsbml.Rule.isAssignment ( self )

Predicate returning `True` if this Rule is an AssignmentRule.

`isAssignment()   bool`
Returns
`True` if this Rule is an AssignmentRule, `False` otherwise.
 def libsbml.Rule.isCompartmentVolume ( self )

Predicate returning `True` if this Rule is an CompartmentVolumeRule or equivalent.

`isCompartmentVolume()   bool`

This libSBML method works for SBML Level 1 models (where there is such a thing as an explicit CompartmentVolumeRule), as well as other Levels of SBML. For Levels above Level 1, this method checks the symbol being affected by the rule, and returns `True` if the symbol is the identifier of a Compartment object defined in the model.

Returns
`True` if this Rule is a CompartmentVolumeRule, `False` otherwise.
 def libsbml.SBase.isPackageEnabled ( self, pkgName )
inherited

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

`isPackageEnabled(string pkgName)   bool`

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.
isPackageURIEnabled()
 def libsbml.SBase.isPackageURIEnabled ( self, pkgURI )
inherited

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

`isPackageURIEnabled(string pkgURI)   bool`
Parameters
 pkgURI the URI of the package.
Returns
`True` if the given package is enabled within this object, `False` otherwise.
isPackageEnabled()
 def libsbml.Rule.isParameter ( self )

Predicate returning `True` if this Rule is an ParameterRule or equivalent.

`isParameter()   bool`

This libSBML method works for SBML Level 1 models (where there is such a thing as an explicit ParameterRule), as well as other Levels of SBML. For Levels above Level 1, this method checks the symbol being affected by the rule, and returns `True` if the symbol is the identifier of a Parameter object defined in the model.

Returns
`True` if this Rule is a ParameterRule, `False` otherwise.
 def libsbml.SBase.isPkgEnabled ( self, pkgName )
inherited

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

`isPkgEnabled(string pkgName)   bool`

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.
isPkgURIEnabled()
 def libsbml.SBase.isPkgURIEnabled ( self, pkgURI )
inherited

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

`isPkgURIEnabled(string pkgURI)   bool`
Parameters
 pkgURI the URI of the package.
Returns
`True` if the given package is enabled within this object, `False` otherwise.
isPkgEnabled()
 def libsbml.Rule.isRate ( self )

Predicate returning `True` if this Rule is a RateRule (SBML Levels 2–3) or has a 'type' attribute value of `'rate'` (SBML Level 1).

`isRate()   bool`
Returns
`True` if this Rule is a RateRule (Level 2) or has type 'rate' (Level 1), `False` otherwise.
 def libsbml.Rule.isScalar ( self )

Predicate returning `True` if this Rule is an AssignmentRule (SBML Levels 2–3) or has a 'type' attribute value of `'scalar'` (SBML Level 1).

`isScalar()   bool`
Returns
`True` if this Rule is an AssignmentRule (Level 2) or has type 'scalar' (Level 1), `False` otherwise.
 def libsbml.SBase.isSetAnnotation ( self )
inherited

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

`isSetAnnotation()   bool`

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.
getAnnotation()
getAnnotationString()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
 def libsbml.Rule.isSetFormula ( self )

Predicate returning `True` if this Rule's mathematical expression is set.

`isSetFormula()   bool`

This method is equivalent to isSetMath(). This version is present for easier compatibility with SBML Level 1, in which mathematical formulas were written in text-string form.

Returns
`True` if the mathematical formula for this Rule is set, `False` otherwise.
Note
The attribute 'formula' is specific to SBML Level 1; in higher Levels of SBML, it has been replaced with a subelement named 'math'. However, libSBML provides a unified interface to the underlying math expression and this method can be used for models of all Levels of SBML.
isSetMath()
 def libsbml.SBase.isSetId ( self )
inherited

Predicate returning `True` if a call to getId() returns a non-empty string.

`isSetId()   bool`

For most objects, this function will return `True` if its 'id' attribute is set, and `False` if it is not, or if the object has no 'id' attribute at all. However, for an EventAssignment or a Rule, isSetId() checks whether the 'variable' attribute is set, and for an InitialAssignment, it checks whether the 'symbol' attribute is set. Because those elements will also have an 'id' attribute in SBML Level 3 Version 2 which isSetId() will not check, the function itself is deprecated, and it is recommended to use isSetIdAttribute() in all cases where one needs to know whether the 'id' attribute is set, and to use EventAssignment.isSetVariable(), Rule.isSetVariable() and InitialAssignment.isSetSymbol() when the status of the 'variable' or 'symbol' attributes need to be checked.

The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always `SId` or a type derived from that, such as `UnitSId`, depending on the object in question. All data types are defined as follows:
```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. This applies to all uses of `SId`, `SIdRef`, and derived types.

Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return `False` for objects of these classes.

With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.

Returns
`True` if the 'id' attribute of this SBML object is set, `False` otherwise.
Note
Because of the inconsistent behavior of this function with respect to assignments and rules, it is recommended that callers use isSetIdAttribute() instead.
getIdAttribute()
setIdAttribute()
unsetIdAttribute()
isSetIdAttribute()
 def libsbml.SBase.isSetIdAttribute ( self )
inherited

Predicate returning `True` if this object's 'id' attribute is set.

`isSetIdAttribute()   bool`
The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always `SId` or a type derived from that, such as `UnitSId`, depending on the object in question. All data types are defined as follows:
```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. This applies to all uses of `SId`, `SIdRef`, and derived types.

Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return `False` for objects of these classes.

With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.

Returns
`True` if the 'id' attribute of this SBML object is set, `False` otherwise.
getIdAttribute()
setIdAttribute()
unsetIdAttribute()
 def libsbml.Rule.isSetMath ( self )

Predicate returning `True` if this Rule's mathematical expression is set.

`isSetMath()   bool`

This method is equivalent to isSetFormula().

Returns
`True` if the formula (or equivalently the math) for this Rule is set, `False` otherwise.
Note
The subelement 'math' is present in SBML Levels 2 and 3. In SBML Level 1, the equivalent construct is the attribute named 'formula'. LibSBML provides a unified interface to the underlying math expression and this method can be used for models of all Levels of SBML.
isSetFormula()
 def libsbml.SBase.isSetMetaId ( self )
inherited

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

`isSetMetaId()   bool`
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. The latter point is important, because the uniqueness criterion applies across any attribute with type `ID` anywhere in the file, 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 the XML `ID` type. Although SBML itself specifies the use of XML `ID` only for the 'metaid' attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML `ID` data type; it uses ordinary character strings, which is easier for applications to support.
Returns
`True` if the 'metaid' attribute of this SBML object is set, `False` otherwise.
getMetaId()
setMetaId()
 def libsbml.SBase.isSetModelHistory ( self )
inherited

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

`isSetModelHistory()   bool`
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.SBase.isSetName ( self )
inherited

Predicate returning `True` if this object's 'name' attribute is set.

`isSetName()   bool`
In SBML Level 3 Version 2, the 'id' and 'name' attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. LibSBML has for a long time provided functions defined on SBase itself to get, set, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.

The 'name' attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of 'name' is the type `string` defined in XML Schema. SBML imposes no restrictions as to the content of 'name' attributes beyond those restrictions defined by the `string` type in XML Schema.

The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)

As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.

An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.

Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a 'name' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write 'name' attributes for those objects.

Returns
`True` if the 'name' attribute of this SBML object is set, `False` otherwise.
getName()
setName()
unsetName()
 def libsbml.SBase.isSetNotes ( self )
inherited

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

`isSetNotes()   bool`

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.
getNotes()
getNotesString()
setNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
 def libsbml.SBase.isSetSBOTerm ( self )
inherited

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

`isSetSBOTerm()   bool`
Returns
`True` if the 'sboTerm' attribute of this SBML object is set, `False` otherwise.
 def libsbml.Rule.isSetUnits ( self )

Predicate returning `True` if this Rule's 'units' attribute is set.

`isSetUnits()   bool`
Returns
`True` if the units for this Rule is set, `False` otherwise.
Note
The attribute 'units' exists on SBML Level 1 ParameterRule objects only. It is not present in SBML Levels 2 and 3.
 def libsbml.SBase.isSetUserData ( self )
inherited

Predicate returning true or false depending on whether the user data of this element has been set.

`isSetUserData()   bool`
The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.
Returns
boolean, `True` if this object's user data has been set, `False` otherwise.
 def libsbml.Rule.isSetVariable ( self )

Predicate returning `True` if this Rule's 'variable' attribute is set.

`isSetVariable()   bool`
In SBML Level 1, the different rule types each have a different name for the attribute holding the reference to the object constituting the left-hand side of the rule. (E.g., for SBML Level 1's SpeciesConcentrationRule the attribute is 'species', for CompartmentVolumeRule it is 'compartment', etc.) In SBML Levels 2 and 3, the only two types of Rule objects with a left-hand side object reference are AssignmentRule and RateRule, and both of them use the same name for attribute: 'variable'. In order to make it easier for application developers to work with all Levels of SBML, libSBML uses a uniform name for all such attributes, and it is 'variable', regardless of whether Level 1 rules or Level 2–3 rules are being used.
Returns
`True` if the 'variable' attribute value of this Rule is set, `False` otherwise.
 def libsbml.Rule.isSpeciesConcentration ( self )

Predicate returning `True` if this Rule is a SpeciesConcentrationRule or equivalent.

`isSpeciesConcentration()   bool`

This libSBML method works for SBML Level 1 models (where there is such a thing as an explicit SpeciesConcentrationRule), as well as other Levels of SBML. For Levels above Level 1, this method checks the symbol being affected by the rule, and returns `True` if the symbol is the identifier of a Species object defined in the model.

Returns
`True` if this Rule is a SpeciesConcentrationRule, `False` otherwise.
 def libsbml.SBase.matchesRequiredSBMLNamespacesForAddition ( self, args )
inherited

Returns `True` if this object's set of XML namespaces are a subset of the given object's XML namespaces.

`matchesRequiredSBMLNamespacesForAddition(SBase sb)   bool`
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. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
 sb an object to compare with respect to namespaces.
Returns
boolean, `True` if this object's collection of namespaces is a subset of `sb's`, `False` otherwise.
 def libsbml.SBase.matchesSBMLNamespaces ( self, args )
inherited

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

`matchesSBMLNamespaces(SBase sb)   bool`
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. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
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.SBase.removeFromParentAndDelete ( self )
inherited

Removes this object from its parent.

`removeFromParentAndDelete()   int`

If the parent was storing this object as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). This is a pure virtual method, as every SBase element has different parents, and therefore different methods of removing itself. Will fail (and not delete itself) if it has no parent object. This function is designed to be overridden, but for all objects whose parent is of the class ListOf, the default implementation will work.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
 def libsbml.SBase.removeTopLevelAnnotationElement ( self, args )
inherited

Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.

```removeTopLevelAnnotationElement(string elementName, string elementURI, bool removeEmpty)   int
removeTopLevelAnnotationElement(string elementName, string elementURI)   int
removeTopLevelAnnotationElement(string elementName)   int```

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.

Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.

Parameters
 elementName a string representing the name of the top level annotation element that is to be removed. elementURI an optional string that is used to check both the name and URI of the top level element to be removed. removeEmpty if after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default).
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
replaceTopLevelAnnotationElement()
replaceTopLevelAnnotationElement()
Note
Owing to the way that language interfaces are created in libSBML, this documentation may show methods that define default values for parameters with text that has the form `parameter` = `value`. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.
 def libsbml.SBase.renameMetaIdRefs ( self, oldid, newid )
inherited

Replaces all uses of a given meta identifier attribute value with another value.

`renameMetaIdRefs(string oldid, string newid)`
In SBML, object 'meta' identifiers are of the XML data type `ID`; the SBML object attribute itself is typically named `metaid`. All attributes that hold values referring to values of type `ID` are of the XML data type `IDREF`. They are also sometimes informally referred to as 'metaid refs', in analogy to the SBML-defined type `SIdRef`.

This method works by looking at all meta-identifier 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.Rule.renameSIdRefs ( self, oldid, newid )

Replaces all uses of a given `SIdRef` type attribute value with another value.

`renameSIdRefs(string oldid, string newid)`
In SBML, object identifiers are of a data type called `SId`. In SBML Level 3, an explicit data type called `SIdRef` was introduced for attribute values that refer to `SId` values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to an identifier', but the effective data type was the same as `SIdRef` in Level 3. These and other methods of libSBML refer to the type `SIdRef` for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

This method works by looking at all attributes and (if appropriate) mathematical formulas in MathML content, comparing the referenced identifiers to the value of `oldid`. If any matches are found, the matching values are replaced with `newid`. The method does not descend into child elements.

Parameters
 oldid the old identifier. newid the new identifier.
 def libsbml.Rule.renameUnitSIdRefs ( self, oldid, newid )

Replaces all uses of a given `UnitSIdRef` type attribute value with another value.

`renameUnitSIdRefs(string oldid, string newid)`
In SBML, unit definitions have identifiers of type `UnitSId`. In SBML Level 3, an explicit data type called `UnitSIdRef` was introduced for attribute values that refer to `UnitSId` values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to a unit identifier', but the effective data type was the same as `UnitSIdRef` in Level 3. These and other methods of libSBML refer to the type `UnitSIdRef` for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the referenced unit identifiers to the value of `oldid`. If any matches are found, the matching values are replaced with `newid`. The method does not descend into child elements.

Parameters
 oldid the old identifier. newid the new identifier.
 def libsbml.SBase.replaceTopLevelAnnotationElement ( self, args )
inherited

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

```replaceTopLevelAnnotationElement(XMLNode annotation)   int
replaceTopLevelAnnotationElement(string annotation)   int```

Each variant is described separately below.

Method variant with the following signature:
`replaceTopLevelAnnotationElement(XMLNode annotation)`

Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.

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.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling ` removeTopLevelAnnotationElement(name)` followed by calling `appendAnnotation(annotation_with_name)`, with the exception that the placement of the annotation element remains the same.

Parameters
 annotation XMLNode representing the replacement top level annotation.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
removeTopLevelAnnotationElement()
replaceTopLevelAnnotationElement()

Method variant with the following signature:
`replaceTopLevelAnnotationElement(string annotation)`

Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.

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.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling ` removeTopLevelAnnotationElement(name)` followed by calling `appendAnnotation(annotation_with_name)`, with the exception that the placement of the annotation element remains the same.

Parameters
 annotation string representing the replacement top level annotation.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
removeTopLevelAnnotationElement()
replaceTopLevelAnnotationElement()
 def libsbml.SBase.setAnnotation ( self, args )
inherited

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

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

Each variant is described separately below.

Method variant with the following signature:
`setAnnotation(XMLNode annotation)`

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

The content of `annotation` is copied, and any previous content of this object's 'annotation' subelement is deleted.

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.

Call this method will result in any existing content of the 'annotation' subelement to be 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 SBase.appendAnnotation() or SBase.appendAnnotation().

Parameters
 annotation an XML structure that is to be used as the new content of the 'annotation' subelement of this object.
Returns
integer value indicating success/failure of the function. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:
getAnnotationString()
isSetAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()

Method variant with the following signature:
`setAnnotation(string annotation)`

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

The content of `annotation` is copied, and any previous content of this object's 'annotation' subelement is deleted.

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.

Call this method will result in any existing content of the 'annotation' subelement to be 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 SBase.appendAnnotation() or SBase.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:
getAnnotationString()
isSetAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
 def libsbml.Rule.setFormula ( self, formula )

Sets the 'math' subelement of this Rule to an expression in text-string form.

`setFormula(string formula)   int`

This is equivalent to setMath(ASTNode math). The provision of using text-string formulas is retained for easier SBML Level 1 compatibility. The formula is converted to an ASTNode internally.

Parameters
 formula a mathematical formula in text-string form.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The attribute 'formula' is specific to SBML Level 1; in higher Levels of SBML, it has been replaced with a subelement named 'math'. However, libSBML provides a unified interface to the underlying math expression and this method can be used for models of all Levels of SBML.
setMath()
 def libsbml.SBase.setId ( self, sid )
inherited

Sets the value of the 'id' attribute of this SBML object.

`setId(string sid)   int`
The string `sid` is copied.
The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always `SId` or a type derived from that, such as `UnitSId`, depending on the object in question. All data types are defined as follows:
```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. This applies to all uses of `SId`, `SIdRef`, and derived types.

Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return `False` for objects of these classes.

With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.

Parameters
 sid the string to use as the identifier of this object.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
getIdAttribute()
setIdAttribute()
isSetIdAttribute()
unsetIdAttribute()
 def libsbml.SBase.setIdAttribute ( self, sid )
inherited

Sets the value of the 'id' attribute of this SBML object.

`setIdAttribute(string sid)   int`
The string `sid` is copied.
The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always `SId` or a type derived from that, such as `UnitSId`, depending on the object in question. All data types are defined as follows:
```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. This applies to all uses of `SId`, `SIdRef`, and derived types.

Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return `False` for objects of these classes.

With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.

Parameters
 sid the string to use as the identifier of this object.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
getIdAttribute()
setIdAttribute()
isSetIdAttribute()
unsetIdAttribute()
 def libsbml.Rule.setL1TypeCode ( self, type )

Sets the SBML Level 1 type code for this Rule.

`setL1TypeCode(int type)   int`
Parameters
 type the SBML Level 1 type code for this Rule. The allowable values are SBML_COMPARTMENT_VOLUME_RULE, SBML_PARAMETER_RULE, and SBML_SPECIES_CONCENTRATION_RULE.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
 def libsbml.Rule.setMath ( self, math )

Sets the 'math' subelement of this Rule to a copy of the given ASTNode.

`setMath(ASTNode math)   int`
Parameters
 math the AST structure of the mathematical formula.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The subelement 'math' is present in SBML Levels 2 and 3. In SBML Level 1, the equivalent construct is the attribute named 'formula'. LibSBML provides a unified interface to the underlying math expression and this method can be used for models of all Levels of SBML.
setFormula()
 def libsbml.SBase.setMetaId ( self, metaid )
inherited

Sets the value of the meta-identifier attribute of this SBML object.

`setMetaId(string metaid)   int`
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. The latter point is important, because the uniqueness criterion applies across any attribute with type `ID` anywhere in the file, 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 the XML `ID` type. Although SBML itself specifies the use of XML `ID` only for the 'metaid' attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML `ID` data type; it uses ordinary character strings, which is easier for applications to support.

The string `metaid` is copied.

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:
getMetaId()
isSetMetaId()
 def libsbml.SBase.setModelHistory ( self, history )
inherited

Sets the ModelHistory of this object.

`setModelHistory(ModelHistory history)   int`

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.SBase.setName ( self, name )
inherited

Sets the value of the 'name' attribute of this SBML object.

`setName(string name)   int`

The string in `name` is copied.

Parameters
 name the new name for the SBML object.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
 def libsbml.SBase.setNamespaces ( self, xmlns )
inherited

Sets the namespaces relevant of this SBML object.

`setNamespaces(XMLNamespaces xmlns)   int`

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:
 def libsbml.SBase.setNotes ( self, args )
inherited

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

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

Each variant is described separately below.

Method variant with the following signature:
`setNotes(string notes, bool addXHTMLMarkup = false)`

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.

1 try:
2  sbmlDoc = SBMLDocument(3, 1)
3 except ValueError:
4  print('Could not create SBMLDocument object')
5  sys.exit(1)
6
7 note = '<body xmlns='http://www.w3.org/1999/xhtml'><p>here is my note</p></body>'
8
9 status = sbmlDoc.setNotes(note)
10 if status != LIBSBML_OPERATION_SUCCESS:
11  # Do something to handle the error here.
12  print('Unable to set notes on the SBML document object')
13  sys.exit(1)
Parameters
 notes an XML string that is to be used as the content of the 'notes' subelement of this object. addXHTMLMarkup a boolean indicating whether to wrap the contents of the `notes` argument with XHTML paragraph (`

`) tags. This is appropriate when the string in `notes` does not already containg the appropriate XHTML markup.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
getNotesString()
isSetNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
Note
Owing to the way that language interfaces are created in libSBML, this documentation may show methods that define default values for parameters with text that has the form `parameter` = `value`. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.

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:
getNotesString()
isSetNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
 def libsbml.SBase.setSBOTerm ( self, args )
inherited

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

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

Each variant 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 2, 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'. More details can be found in SBML specifications for Level 2 Version 2 and above.
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:
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 2, 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'. More details can be found in SBML specifications for Level 2 Version 2 and above.
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:
setSBOTerm()
 def libsbml.Rule.setUnits ( self, sname )

Sets the units for this Rule.

`setUnits(string sname)   int`
Parameters
 sname the identifier of the units.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The attribute 'units' exists on SBML Level 1 ParameterRule objects only. It is not present in SBML Levels 2 and 3.
 def libsbml.Rule.setVariable ( self, sid )

Sets the 'variable' attribute value of this Rule object.

`setVariable(string sid)   int`
In SBML Level 1, the different rule types each have a different name for the attribute holding the reference to the object constituting the left-hand side of the rule. (E.g., for SBML Level 1's SpeciesConcentrationRule the attribute is 'species', for CompartmentVolumeRule it is 'compartment', etc.) In SBML Levels 2 and 3, the only two types of Rule objects with a left-hand side object reference are AssignmentRule and RateRule, and both of them use the same name for attribute: 'variable'. In order to make it easier for application developers to work with all Levels of SBML, libSBML uses a uniform name for all such attributes, and it is 'variable', regardless of whether Level 1 rules or Level 2–3 rules are being used.
Parameters
 sid the identifier of a Compartment, Species or Parameter elsewhere in the enclosing Model object.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
 def libsbml.SBase.toSBML ( self )
inherited

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

`toSBML()   string`
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.toXMLNode ( self )
inherited

Returns this element as an XMLNode.

`toXMLNode()   XMLNode`
Returns
this element as an XMLNode.
Warning
This operation is computationally expensive, because the element has to be fully serialized to a string and then parsed into the XMLNode structure. Attempting to convert a large tree structure (e.g., a large Model) may consume significant computer memory and time.
 def libsbml.SBase.unsetAnnotation ( self )
inherited

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

`unsetAnnotation()   int`

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. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:
getAnnotation()
getAnnotationString()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
 def libsbml.SBase.unsetCVTerms ( self )
inherited

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

`unsetCVTerms()   int`
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
 def libsbml.SBase.unsetId ( self )
inherited

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

`unsetId()   int`
The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always `SId` or a type derived from that, such as `UnitSId`, depending on the object in question. All data types are defined as follows:
```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. This applies to all uses of `SId`, `SIdRef`, and derived types.

Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return `False` for objects of these classes.

With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods unless the old behavior is somehow necessary. Regardless of the Level and Version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
getIdAttribute()
setIdAttribute()
isSetIdAttribute()
unsetIdAttribute()
 def libsbml.SBase.unsetIdAttribute ( self )
inherited

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

`unsetIdAttribute()   int`

Most (but not all) objects in SBML include two common attributes: 'id' and 'name'. The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
getIdAttribute()
setIdAttribute()
isSetIdAttribute()
 def libsbml.SBase.unsetMetaId ( self )
inherited

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

`unsetMetaId()   int`
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. The latter point is important, because the uniqueness criterion applies across any attribute with type `ID` anywhere in the file, 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 the XML `ID` type. Although SBML itself specifies the use of XML `ID` only for the 'metaid' attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML `ID` data type; it uses ordinary character strings, which is easier for applications to support.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
 def libsbml.SBase.unsetModelHistory ( self )
inherited

Unsets the ModelHistory object attached to this object.

`unsetModelHistory()   int`
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.SBase.unsetName ( self )
inherited

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

`unsetName()   int`
In SBML Level 3 Version 2, the 'id' and 'name' attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. LibSBML has for a long time provided functions defined on SBase itself to get, set, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.

The 'name' attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of 'name' is the type `string` defined in XML Schema. SBML imposes no restrictions as to the content of 'name' attributes beyond those restrictions defined by the `string` type in XML Schema.

The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)

As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.

An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.

Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a 'name' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write 'name' attributes for those objects.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
getName()
setName()
isSetName()
 def libsbml.SBase.unsetNotes ( self )
inherited

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

`unsetNotes()   int`

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. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
appendNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
 def libsbml.SBase.unsetSBOTerm ( self )
inherited

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

`unsetSBOTerm()   int`
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
 def libsbml.Rule.unsetUnits ( self )

Unsets the 'units' for this Rule.

`unsetUnits()   int`
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The attribute 'units' exists on SBML Level 1 ParameterRule objects only. It is not present in SBML Levels 2 and 3.
 def libsbml.SBase.unsetUserData ( self )
inherited

Unsets the user data of this element.

`unsetUserData()   int`
The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
 def libsbml.Rule.unsetVariable ( self )

Unsets the value of the 'variable' attribute of this Rule object.

`unsetVariable()   int`
Returns
integer value indicating success/failure of the function. The possible values returned by this function are: