libsbml.AlgebraicRule Class Reference

Inheritance diagram for libsbml.AlgebraicRule:

Detailed Description

LibSBML implementation of SBML's AlgebraicRule construct.

The rule type AlgebraicRule is derived from the parent class Rule. It is used to express equations that are neither assignments of model variables nor rates of change. AlgebraicRule does not add any attributes to the basic Rule; its role is simply to distinguish this case from the other cases.

In the context of a simulation, algebraic rules are in effect at all times, t >= 0. For purposes of evaluating expressions that involve the delay 'csymbol' (see the SBML specification), algebraic rules are considered to apply also at t <= 0. Please consult the relevant SBML specification for additional information about the semantics of assignments, rules, and entity values for simulation time t <= 0.

An SBML model must not be overdetermined. The ability to define arbitrary algebraic expressions in an SBML model introduces the possibility that a model is mathematically overdetermined by the overall system of equations constructed from its rules, reactions and events. Therefore, if an algebraic rule is introduced in a model, for at least one of the entities referenced in the rule's 'math' element the value of that entity must not be completely determined by other constructs in the model. This means that at least this entity must not have the attribute 'constant'=true and there must also not be a rate rule or assignment rule for it. Furthermore, if the entity is a Species object, its value must not be determined by reactions, which means that it must either have the attribute 'boundaryCondition'=true or else not be involved in any reaction at all. These restrictions are explained in more detail in the SBML specification documents.

In SBML Levels 2 and 3, Reaction object identifiers can be referenced in the 'math' expression of an algebraic rule, but reaction rates can never be determined by algebraic rules. This is true even when a reaction does not contain a KineticLaw element. (In such cases of missing KineticLaw elements, the model is valid but incomplete; the rates of reactions lacking kinetic laws are simply undefined, and not determined by the algebraic rule.)

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.

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. An 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 Version 1 Core 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 in the following table.

Enumerator	Meaning
`RULE_TYPE_RATE`	Indicates the rule is a 'rate' rule.
`RULE_TYPE_SCALAR`	Indicates the rule is a 'scalar' rule.
`RULE_TYPE_INVALID`	Indicates the rule type is unknown or not yet set.

Public Member Functions
def	addCVTerm
def	appendAnnotation
def	appendNotes
def	clone
def	containsUndeclaredUnits
def	disablePackage
def	enablePackage
def	getAncestorOfType
def	getAnnotation
def	getAnnotationString
def	getColumn
def	getCVTerm
def	getCVTerms
def	getDerivedUnitDefinition
def	getElementByMetaId
def	getElementBySId
def	getElementName
def	getFormula
def	getId
def	getL1TypeCode
def	getLevel
def	getLine
def	getListOfAllElements
def	getListOfAllElementsFromPlugins
def	getMath
def	getMetaId
def	getModel
def	getModelHistory
def	getNamespaces
def	getNotes
def	getNotesString
def	getNumCVTerms
def	getNumPlugins
def	getPackageName
def	getPackageVersion
def	getParentSBMLObject
def	getPlugin
def	getResourceBiologicalQualifier
def	getResourceModelQualifier
def	getSBMLDocument
def	getSBOTerm
def	getSBOTermID
def	getType
def	getTypeCode
def	getUnits
def	getVariable
def	getVersion
def	hasRequiredAttributes
def	hasRequiredElements
def	hasValidLevelVersionNamespaceCombination
def	isAlgebraic
def	isAssignment
def	isCompartmentVolume
def	isPackageEnabled
def	isPackageURIEnabled
def	isParameter
def	isPkgEnabled
def	isPkgURIEnabled
def	isRate
def	isScalar
def	isSetAnnotation
def	isSetFormula
def	isSetMath
def	isSetMetaId
def	isSetModelHistory
def	isSetNotes
def	isSetSBOTerm
def	isSetUnits
def	isSetVariable
def	isSpeciesConcentration
def	matchesSBMLNamespaces
def	removeFromParentAndDelete
def	renameMetaIdRefs
def	renameSIdRefs
def	renameUnitSIdRefs
def	setAnnotation
def	setFormula
def	setL1TypeCode
def	setMath
def	setMetaId
def	setModelHistory
def	setNamespaces
def	setNotes
def	setSBOTerm
def	setUnits
def	setVariable
def	toSBML
def	unsetAnnotation
def	unsetCVTerms
def	unsetId
def	unsetMetaId
def	unsetModelHistory
def	unsetName
def	unsetNotes
def	unsetSBOTerm
def	unsetUnits

Member Function Documentation

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

Python method signature(s):

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

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

Parameters:

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

Returns:

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

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

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

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

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

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

Python method signature(s):

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

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

Method variant with the following signature:

appendAnnotation(XMLNode annotation)

Appends 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:

See also:: 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:

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

Reimplemented in libsbml.Model, and libsbml.SpeciesReference.

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

Python method signature(s):

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

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

Method variant with the following signature:

appendNotes(string notes)

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

The content of the parameter notes is copied.

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

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

Parameters:

notes

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

Returns:

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

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

Method variant with the following signature:

appendNotes(XMLNode notes)

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

The content of notes is copied.

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

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

Parameters:

notes

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

Returns:

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

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

def libsbml.AlgebraicRule.clone ( self )

Python method signature(s):

clone()    AlgebraicRule

Creates and returns a deep copy of this Rule.

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

Reimplemented from libsbml.Rule.

def libsbml.Rule.containsUndeclaredUnits	(	self,
		args
	)		`[inherited]`

Python method signature(s):

containsUndeclaredUnits()    bool
containsUndeclaredUnits()    bool

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

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.

See also:: getDerivedUnitDefinition()

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

Python method signature(s):

disablePackage(string pkgURI, string pkgPrefix)    int

Disables the given SBML Level 3 package

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

Parameters:

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

Returns:

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

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

Python method signature(s):

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

Enables or disables the given SBML Level 3 package

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

Parameters:

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

Returns:

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

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

Python method signature(s):

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

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

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

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

Parameters:

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

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

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

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

Python method signature(s):

getAnnotation()    XMLNode

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

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

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

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

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

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

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

Python method signature(s):

getAnnotationString()    string

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

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

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

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

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

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

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

Python method signature(s):

getColumn()    long

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

Returns:: the column number of this SBML object.

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

See also:: getLine()

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

Python method signature(s):

getCVTerm(long n)    CVTerm

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

Parameters:

n

long the index of the CVTerm to retrieve

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

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

Python method signature(s):

getCVTerms()    CVTermList

Get the CVTermList of CVTerm objects in this SBase.

Returns:: the CVTermList for this SBase.

def libsbml.Rule.getDerivedUnitDefinition	(	self,
		args
	)		`[inherited]`

Python method signature(s):

getDerivedUnitDefinition()    UnitDefinition
getDerivedUnitDefinition()    UnitDefinition

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

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 getDerivedUnitDefinition() method returns the calculated units.

Note that 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 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 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.

See also:: containsUndeclaredUnits()

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

Python method signature(s):

getElementByMetaId(string metaid)    SBase

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

Parameters:

metaid

string representing the 'metaid' attribute value of the object to find

Returns:: pointer to the first element found with the given meta-identifier.

Reimplemented in libsbml.ListOf, libsbml.Model, libsbml.SBMLDocument, libsbml.UnitDefinition, libsbml.Reaction, libsbml.KineticLaw, and libsbml.Event.

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

Python method signature(s):

getElementBySId(string id)    SBase

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

Parameters:

id

string representing the 'id' attribute value of the object to find

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

Reimplemented in libsbml.ListOf, libsbml.Model, libsbml.SBMLDocument, libsbml.UnitDefinition, libsbml.ListOfUnitDefinitions, libsbml.ListOfLocalParameters, libsbml.Reaction, libsbml.KineticLaw, and libsbml.Event.

def libsbml.Rule.getElementName ( self ) [inherited]

Python method signature(s):

getElementName()    string

Returns the XML element name of this object

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 5.3.0 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

Reimplemented from libsbml.SBase.

def libsbml.Rule.getFormula ( self ) [inherited]

Python method signature(s):

getFormula()    string

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

The text string is produced by SBML_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.

See also:: getMath()

def libsbml.Rule.getId ( self ) [inherited]

Python method signature(s):

getId()    string

Renames all the UnitSIdRef attributes on this element

def libsbml.Rule.getL1TypeCode ( self ) [inherited]

Python method signature(s):

getL1TypeCode()    int

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

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]

Python method signature(s):

getLevel()    long

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

Returns:: the SBML level of this SBML object.

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

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

Python method signature(s):

getLine()    long

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

Returns:: the line number of this SBML object.

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

See also:: getColumn()

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

Python method signature(s):

getListOfAllElements()    SBaseList

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

Python method signature(s):

getListOfAllElementsFromPlugins()    SBaseList

def libsbml.Rule.getMath ( self ) [inherited]

Python method signature(s):

getMath()    ASTNode

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

Returns:: an ASTNode, the value of the 'math' subelement of this Rule.

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.

See also:: getFormula()

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

Python method signature(s):

getMetaId()    string

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

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

Returns:: the metaid of this SBML object.

See also:: isSetMetaId(); setMetaId()

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

Python method signature(s):

getModel()    Model

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

Returns:: the parent Model of this SBML object.

See also:: getParentSBMLObject(); getSBMLDocument()

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

Python method signature(s):

getModelHistory()    ModelHistory
getModelHistory()    ModelHistory

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

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

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

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

Python method signature(s):

getNamespaces()    XMLNamespaces

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

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

Returns:: the XML Namespaces associated with this SBML object

See also:: getLevel(); getVersion()

Reimplemented in libsbml.SBMLDocument.

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

Python method signature(s):

getNotes()    XMLNode

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

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

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

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

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

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

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

Python method signature(s):

getNotesString()    string

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

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

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

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

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

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

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

Python method signature(s):

getNumCVTerms()    long

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

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

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

Python method signature(s):

getNumPlugins()    long

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

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

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

Python method signature(s):

getPackageName()    string

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

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

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

Python method signature(s):

getPackageVersion()    long

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

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

See also:: getLevel(); getVersion()

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

Python method signature(s):

getParentSBMLObject()    SBase
getParentSBMLObject()    SBase

Returns the parent SBML object containing this object.

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

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

See also:: getSBMLDocument(); getModel()

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

Python method signature(s):

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

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

Method variant with the following signature:

getPlugin(long n)

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

Parameters:

n

the index of the plugin to return

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

Method variant with the following signature:

getPlugin(string package)

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

Parameters:

package

the name or URI of the package

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

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

Python method signature(s):

getResourceBiologicalQualifier(string resource)    long

Returns the MIRIAM biological qualifier associated with the given resource.

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

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

Parameters:

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

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

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

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

Python method signature(s):

getResourceModelQualifier(string resource)    long

Returns the MIRIAM model qualifier associated with the given resource.

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

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

Parameters:

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

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

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

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

Python method signature(s):

getSBMLDocument()    SBMLDocument
getSBMLDocument()    SBMLDocument

Returns the SBMLDocument object containing this object instance.

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

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

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

See also:: getParentSBMLObject(); getModel()

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

Python method signature(s):

getSBOTerm()    int

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

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

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

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

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

Python method signature(s):

getSBOTermID()    string

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

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

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

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

def libsbml.Rule.getType ( self ) [inherited]

Python method signature(s):

getType()    long

Get the type of rule this is.

Returns:: the rule type (a value drawn from the enumeration long) of this Rule. The value will be either RULE_TYPE_RATE or RULE_TYPE_SCALAR.

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 ) [inherited]

Python method signature(s):

getTypeCode()    int

Returns the libSBML type code for this SBML object.

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

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

See also:: getElementName()

Reimplemented from libsbml.SBase.

def libsbml.Rule.getUnits ( self ) [inherited]

Python method signature(s):

getUnits()    string

Returns the units for the mathematical formula of this Rule.

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.Rule.getVariable ( self ) [inherited]

Python method signature(s):

getVariable()    string

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

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 of such attributes, and it is 'variable', regardless of whether Level 1 rules or Level 2–3 rules are being used.

Returns:: the identifier string stored as the 'variable' attribute value in this Rule, or None if this object is an AlgebraicRule object.

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

Python method signature(s):

getVersion()    long

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

Returns:: the SBML version of this SBML object.

See also:: getLevel(); getNamespaces()

def libsbml.AlgebraicRule.hasRequiredAttributes ( self )

Python method signature(s):

hasRequiredAttributes()    bool

Predicate returning true if all the required attributes for this AlgebraicRule object have been set.

Note:: In SBML Levels 2–3, there is no required attribute for an AlgebraicRule object. For Level 1, the only required attribute is 'formula'.

Returns:: true if the required attributes have been set, false otherwise.

Reimplemented from libsbml.Rule.

def libsbml.Rule.hasRequiredElements ( self ) [inherited]

Python method signature(s):

hasRequiredElements()    bool

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

The only required element for a Rule object is the 'math' subelement.

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

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

Python method signature(s):

hasValidLevelVersionNamespaceCombination()    bool

def libsbml.Rule.isAlgebraic ( self ) [inherited]

Python method signature(s):

isAlgebraic()    bool

Predicate returning true if this Rule is an AlgebraicRule.

Returns:: true if this Rule is an AlgebraicRule, false otherwise.

def libsbml.Rule.isAssignment ( self ) [inherited]

Python method signature(s):

isAssignment()    bool

Predicate returning true if this Rule is an AssignmentRule.

Returns:: true if this Rule is an AssignmentRule, false otherwise.

def libsbml.Rule.isCompartmentVolume ( self ) [inherited]

Python method signature(s):

isCompartmentVolume()    bool

Predicate returning true if this Rule is an CompartmentVolumeRule or equivalent.

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,
		args
	)		`[inherited]`

Python method signature(s):

isPackageEnabled(string pkgName)    bool

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

The search ignores the package version.

Parameters:

pkgName

the name of the package

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

See also:: isPackageURIEnabled()

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

Python method signature(s):

isPackageURIEnabled(string pkgURI)    bool

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

Parameters:

pkgURI

the URI of the package

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

See also:: isPackageEnabled()

def libsbml.Rule.isParameter ( self ) [inherited]

Python method signature(s):

isParameter()    bool

Predicate returning true if this Rule is an ParameterRule or equivalent.

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,
		args
	)		`[inherited]`

Python method signature(s):

isPkgEnabled(string pkgName)    bool

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

The search ignores the package version.

Parameters:

pkgName

the name of the package

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

See also:: isPkgURIEnabled()

Deprecated:: Replaced in libSBML 5.2.0 by isPackageEnabled()

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

Python method signature(s):

isPkgURIEnabled(string pkgURI)    bool

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

Parameters:

pkgURI

the URI of the package

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

See also:: isPkgEnabled()

Deprecated:: Replaced in libSBML 5.2.0 by isPackageURIEnabled()

def libsbml.Rule.isRate ( self ) [inherited]

Python method signature(s):

isRate()    bool

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

Returns:: true if this Rule is a RateRule (Level 2) or has type 'rate' (Level 1), false otherwise.

def libsbml.Rule.isScalar ( self ) [inherited]

Python method signature(s):

isScalar()    bool

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

Returns:: true if this Rule is an AssignmentRule (Level 2) or has type 'scalar' (Level 1), false otherwise.

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

Python method signature(s):

isSetAnnotation()    bool

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

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

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

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

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

def libsbml.Rule.isSetFormula ( self ) [inherited]

Python method signature(s):

isSetFormula()    bool

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

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.

See also:: isSetMath()

def libsbml.Rule.isSetMath ( self ) [inherited]

Python method signature(s):

isSetMath()    bool

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

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.

See also:: isSetFormula()

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

Python method signature(s):

isSetMetaId()    bool

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

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

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

See also:: getMetaId(); setMetaId()

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

Python method signature(s):

isSetModelHistory()    bool

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

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

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

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

Python method signature(s):

isSetNotes()    bool

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

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

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

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

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

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

Python method signature(s):

isSetSBOTerm()    bool

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

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

def libsbml.Rule.isSetUnits ( self ) [inherited]

Python method signature(s):

isSetUnits()    bool

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

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.Rule.isSetVariable ( self ) [inherited]

Python method signature(s):

isSetVariable()    bool

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

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 ) [inherited]

Python method signature(s):

isSpeciesConcentration()    bool

Predicate returning true if this Rule is a SpeciesConcentrationRule or equivalent.

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.matchesSBMLNamespaces	(	self,
		args
	)		`[inherited]`

Python method signature(s):

matchesSBMLNamespaces(SBase sb)    bool

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

Parameters:

sb

an object to compare with respect to namespaces

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

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

Python method signature(s):

removeFromParentAndDelete()    int

Removes itself from its parent. If the parent was storing it as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). Pure virutal, 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:

Reimplemented in libsbml.ListOf, libsbml.Model, libsbml.KineticLaw, libsbml.Trigger, libsbml.Delay, libsbml.Priority, and libsbml.StoichiometryMath.

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

Python method signature(s):

renameMetaIdRefs(string oldid, string newid)

Renames all the MetaIdRef attributes on this element.

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

Parameters:

	oldid	the old identifier
	newid	the new identifier

def libsbml.Rule.renameSIdRefs	(	self,
		args
	)		`[inherited]`

Python method signature(s):

renameSIdRefs(string oldid, string newid)

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

Reimplemented from libsbml.SBase.

Reimplemented in libsbml.AssignmentRule, and libsbml.RateRule.

def libsbml.Rule.renameUnitSIdRefs	(	self,
		args
	)		`[inherited]`

Python method signature(s):

renameUnitSIdRefs(string oldid, string newid)

Renames all the UnitSIdRef attributes on this element

Reimplemented from libsbml.SBase.

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

Python method signature(s):

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

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

Method variant with the following signature:

setAnnotation(XMLNode annotation)

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

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. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

See also:: 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:

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

Reimplemented in libsbml.Model, and libsbml.SpeciesReference.

def libsbml.Rule.setFormula	(	self,
		args
	)		`[inherited]`

Python method signature(s):

setFormula(string formula)    int

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

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.

See also:: setMath()

def libsbml.Rule.setL1TypeCode	(	self,
		args
	)		`[inherited]`

Python method signature(s):

setL1TypeCode(int type)    int

Sets the SBML Level 1 type code for this Rule.

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:

LIBSBML_OPERATION_SUCCESS
LIBSBML_INVALID_ATTRIBUTE_VALUE if given type value is not one of the above.

def libsbml.Rule.setMath	(	self,
		args
	)		`[inherited]`

Python method signature(s):

setMath(ASTNode math)    int

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

Parameters:

math

the ASTNode 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.

See also:: setFormula()

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

Python method signature(s):

setMetaId(string metaid)    int

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

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

Parameters:

metaid

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

Returns:

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

See also:: getMetaId(); isSetMetaId()

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

Python method signature(s):

setModelHistory(ModelHistory history)    int

Sets the ModelHistory of this object.

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

Parameters:

history

ModelHistory of this object.

Returns:

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

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

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

Python method signature(s):

setNamespaces(XMLNamespaces xmlns)    int

Sets the namespaces relevant of this SBML object.

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

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

Parameters:

xmlns

the namespaces to set

Returns:

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

LIBSBML_OPERATION_SUCCESS

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

Python method signature(s):

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

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

Method variant with the following signature:

setNotes(string notes)

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

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

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

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

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

Parameters:

notes

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

Returns:

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

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

Method variant with the following signature:

setNotes(XMLNode notes)

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

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

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

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

Parameters:

notes

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

Returns:

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

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

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

Python method signature(s):

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

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

Method variant with the following signature:

setSBOTerm(int value)

Sets the value of the 'sboTerm' attribute.

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

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

Parameters:

value

the NNNNNNN integer portion of the SBO identifier

Returns:

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

See also:: setSBOTerm()

Method variant with the following signature:

setSBOTerm(string &sboid)

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

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

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

Parameters:

sboid

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

Returns:

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

See also:: setSBOTerm()

def libsbml.Rule.setUnits	(	self,
		args
	)		`[inherited]`

Python method signature(s):

setUnits(string sname)    int

Sets the units for this Rule.

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,
		args
	)		`[inherited]`

Python method signature(s):

setVariable(string sid)    int

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

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]

Python method signature(s):

toSBML()    string

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

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

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

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

Python method signature(s):

unsetAnnotation()    int

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

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

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

Returns:

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

LIBSBML_OPERATION_SUCCESS

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

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

Python method signature(s):

unsetCVTerms()    int

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

Returns:

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

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

Python method signature(s):

unsetId()    int

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

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. The data type of 'id' is always either Sid or UnitSId, depending on the object in question. Both data types are defined as follows:

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

The equality of SId and UnitSId type values in SBML is determined by an exact character sequence match; i.e., comparisons of these identifiers must be performed in a case-sensitive manner. This applies to all uses of SId and UnitSId.

Returns:

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

Reimplemented in libsbml.Model, libsbml.SimpleSpeciesReference, and libsbml.Event.

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

Python method signature(s):

unsetMetaId()    int

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

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

Returns:

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

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

Python method signature(s):

unsetModelHistory()    int

Unsets the ModelHistory object attached to this object.

Returns:

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

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

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

Python method signature(s):

unsetName()    int

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

Most (but not all) objects in SBML include two common attributes: 'id' and 'name'. In contrast to the 'id' attribute, 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.

Returns:

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

Reimplemented in libsbml.Model, libsbml.FunctionDefinition, libsbml.UnitDefinition, libsbml.CompartmentType, libsbml.SpeciesType, libsbml.Compartment, libsbml.Species, libsbml.Parameter, libsbml.Reaction, libsbml.SimpleSpeciesReference, and libsbml.Event.

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

Python method signature(s):

unsetNotes()    int

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

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

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

Returns:

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

LIBSBML_OPERATION_SUCCESS

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

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

Python method signature(s):

unsetSBOTerm()    int

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

Returns:

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

def libsbml.Rule.unsetUnits ( self ) [inherited]

Python method signature(s):

unsetUnits()    int

Unsets the 'units' for this Rule.

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.

libsbml.AlgebraicRule Class Reference

Detailed Description

General summary of SBML rules

Additional restrictions on SBML rules

A model must not contain algebraic loops

A model must not be overdetermined

Rule types for SBML Level 1

Public Member Functions

Member Function Documentation