libSBML 5.3.0 Python API

libsbml.InitialAssignment Class Reference

Inheritance diagram for libsbml.InitialAssignment:
Inheritance graph
[legend]

List of all members.

Detailed Description

LibSBML implementation of SBML's InitialAssignment construct.

SBML Level 2 Versions 2–4 and SBML Level 3 provide two ways of assigning initial values to entities in a model. The simplest and most basic is to set the values of the appropriate attributes in the relevant components; for example, the initial value of a model parameter (whether it is a constant or a variable) can be assigned by setting its 'value' attribute directly in the model definition. However, this approach is not suitable when the value must be calculated, because the initial value attributes on different components such as species, compartments, and parameters are single values and not mathematical expressions. In those situations, the InitialAssignment construct can be used; it permits the calculation of the value of a constant or the initial value of a variable from the values of other quantities in a model.

As explained below, the provision of InitialAssignment does not mean that models necessarily must use this construct when defining initial values of quantities in a model. If a value can be set directly using the relevant attribute of a component in a model, then that approach may be more efficient and more portable to other software tools. InitialAssignment should be used when the other mechanism is insufficient for the needs of a particular model.

The InitialAssignment construct has some similarities to AssignmentRule. The main differences are: (a) an InitialAssignment can set the value of a constant whereas an AssignmentRule cannot, and (b) unlike AssignmentRule, an InitialAssignment definition only applies up to and including the beginning of simulation time, i.e., t <= 0, while an AssignmentRule applies at all times.

InitialAssignment has a required attribute, 'symbol', whose value must follow the guidelines for identifiers described in the SBML specification (e.g., Section 3.3 in the Level 2 Version 4 specification). The value of this attribute in an InitialAssignment object can be the identifier of a Compartment, Species or global Parameter elsewhere in the model. The InitialAssignment defines the initial value of the constant or variable referred to by the 'symbol' attribute. (The attribute's name is 'symbol' rather than 'variable' because it may assign values to constants as well as variables in a model.) Note that an initial assignment cannot be made to reaction identifiers, that is, the 'symbol' attribute value of an InitialAssignment cannot be an identifier that is the 'id' attribute value of a Reaction object in the model. This is identical to a restriction placed on rules.

InitialAssignment also has a required 'math' subelement that contains a MathML expression used to calculate the value of the constant or the initial value of the variable. The units of the value computed by the formula in the 'math' subelement should (in SBML Level 2 Version 4 and in SBML Level 3) or must (in previous Versions) be identical to be the units associated with the identifier given in the 'symbol' attribute. (That is, the units are the units of the species, compartment, or parameter, as appropriate for the kind of object identified by the value of 'symbol'.)

InitialAssignment was introduced in SBML Level 2 Version 2. It is not available in SBML Level 2 Version 1 nor in any version of Level 1.

Semantics of Initial Assignments

The value calculated by an InitialAssignment object overrides the value assigned to the given symbol by the object defining that symbol. For example, if a compartment's 'size' attribute is set in its definition, and the model also contains an InitialAssignment having that compartment's identifier as its 'symbol' attribute value, then the interpretation is that the 'size' assigned in the Compartment object should be ignored and the value assigned based on the computation defined in the InitialAssignment. Initial assignments can take place for Compartment, Species and global Parameter objects regardless of the value of their 'constant' attribute.

The actions of all InitialAssignment objects are in general terms the same, but differ in the precise details depending on the type of variable being set:

In the context of a simulation, initial assignments establish values that are in effect prior to and including the start of simulation time, i.e., t <= 0. Section 3.4.8 in the SBML Level 2 Version 4 and SBML Level 3 Version 1 Core specifications provides information about the interpretation of assignments, rules, and entity values for simulation time up to and including the start time t = 0; this is important for establishing the initial conditions of a simulation if the model involves expressions containing the delay 'csymbol'.

There cannot be two initial assignments for the same symbol in a model; that is, a model must not contain two or more InitialAssignment objects that both have the same identifier as their 'symbol' attribute value. A model must also not define initial assignments and assignment rules for the same entity. That is, there cannot be both an InitialAssignment and an AssignmentRule for the same symbol in a model, because both kinds of constructs apply prior to and at the start of simulated time—allowing both to exist for a given symbol would result in indeterminism).

The ordering of InitialAssignment objects is not significant. The combined set of InitialAssignment, AssignmentRule and KineticLaw objects form a set of assignment statements that must be considered as a whole. The combined set of assignment statements should not contain algebraic loops: a chain of dependency between these statements should terminate. (More formally, consider the directed graph of assignment statements where nodes are a model's assignment statements and directed arcs exist for each occurrence of a symbol in an assignment statement 'math' attribute. The directed arcs in this graph start from the statement assigning the symbol and end at the statement that contains the symbol in their math elements. Such a graph must be acyclic.)

Finally, it is worth being explicit about the expected behavior in the following situation. Suppose (1) a given symbol has a value x assigned to it in its definition, and (2) there is an initial assignment having the identifier as its 'symbol' value and reassigning the value to y, and (3) the identifier is also used in the mathematical formula of a second initial assignment. What value should the second initial assignment use? It is y, the value assigned to the symbol by the first initial assignment, not whatever value was given in the symbol's definition. This follows directly from the behavior described above: if an InitialAssignment object exists for a given symbol, then the symbol's value is overridden by that initial assignment.

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 getId
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 getSymbol
def getTypeCode
def getVersion
def hasRequiredAttributes
def hasRequiredElements
def hasValidLevelVersionNamespaceCombination
def isPackageEnabled
def isPackageURIEnabled
def isPkgEnabled
def isPkgURIEnabled
def isSetAnnotation
def isSetMath
def isSetMetaId
def isSetModelHistory
def isSetNotes
def isSetSBOTerm
def isSetSymbol
def matchesSBMLNamespaces
def removeFromParentAndDelete
def renameMetaIdRefs
def renameSIdRefs
def renameUnitSIdRefs
def setAnnotation
def setMath
def setMetaId
def setModelHistory
def setNamespaces
def setNotes
def setSBOTerm
def setSymbol
def toSBML
def unsetAnnotation
def unsetCVTerms
def unsetId
def unsetMetaId
def unsetModelHistory
def unsetName
def unsetNotes
def unsetSBOTerm

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:
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.InitialAssignment.clone (   self  ) 

Python method signature(s): 

clone()    InitialAssignment

Creates and returns a deep copy of this InitialAssignment.

Returns:
a (deep) copy of this InitialAssignment.

Reimplemented from libsbml.SBase.

def libsbml.InitialAssignment.containsUndeclaredUnits (   self,
  args 
)

Python method signature(s): 

containsUndeclaredUnits()    bool
containsUndeclaredUnits()    bool

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

Returns:
true if the math expression of this InitialAssignment 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.InitialAssignment.getDerivedUnitDefinition (   self,
  args 
)

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 InitialAssignment.

The units are calculated based on the mathematical expression in the InitialAssignment 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 InitialAssignment 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 InitialAssignment, 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.InitialAssignment.getElementName (   self  ) 

Python method signature(s): 

getElementName()    string

Returns the XML element name of this object, which for InitialAssignment, is always 'initialAssignment'.

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

Reimplemented from libsbml.SBase.

def libsbml.InitialAssignment.getId (   self  ) 

Python method signature(s): 

getId()    string

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

Note:
The required elements for a InitialAssignment object are:
  • 'math'
Returns:
a boolean value indicating whether all the required elements for this object have been defined.
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.InitialAssignment.getMath (   self  ) 

Python method signature(s): 

getMath()    ASTNode

Get the mathematical formula of this InitialAssignment.

Returns:
an ASTNode, the value of the 'math' subelement of this InitialAssignment
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.InitialAssignment.getSymbol (   self  ) 

Python method signature(s): 

getSymbol()    string

Get the value of the 'symbol' attribute of this InitialAssignment.

Returns:
the identifier string stored as the 'symbol' attribute value in this InitialAssignment.
def libsbml.InitialAssignment.getTypeCode (   self  ) 

Python method signature(s): 

getTypeCode()    int

Returns the libSBML type code for this SBML object.

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

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

Reimplemented from libsbml.SBase.

def libsbml.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.InitialAssignment.hasRequiredAttributes (   self  ) 

Python method signature(s): 

hasRequiredAttributes()    bool

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

Note:
The required attributes for an InitialAssignment object are:
  • 'symbol'
Returns:
a boolean value indicating whether all the required attributes for this object have been defined.
def libsbml.InitialAssignment.hasRequiredElements (   self  ) 

Python method signature(s): 

hasRequiredElements()    bool

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

Note:
The required elements for a InitialAssignment object are:
  • 'math'
Returns:
a boolean value indicating whether all the required elements for this object have been defined.
def libsbml.SBase.hasValidLevelVersionNamespaceCombination (   self  )  [inherited]

Python method signature(s): 

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

Python method signature(s): 

isPackageEnabled(string pkgName)    bool

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

The search ignores the package version.

Parameters:
pkgName the name of the package
Returns:
true if the given package is enabled within this object, false otherwise.
See also:
isPackageURIEnabled()
def libsbml.SBase.isPackageURIEnabled (   self,
  args 
) [inherited]

Python method signature(s): 

isPackageURIEnabled(string pkgURI)    bool

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

Parameters:
pkgURI the URI of the package
Returns:
true if the given package is enabled within this object, false otherwise.
See also:
isPackageEnabled()
def libsbml.SBase.isPkgEnabled (   self,
  args 
) [inherited]

Python method signature(s): 

isPkgEnabled(string pkgName)    bool

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

The search ignores the package version.

Parameters:
pkgName the name of the package
Returns:
true if the given package is enabled within this object, false otherwise.
See also:
isPkgURIEnabled()
Deprecated:
Replaced in libSBML 5.2.0 by isPackageEnabled()
def libsbml.SBase.isPkgURIEnabled (   self,
  args 
) [inherited]

Python method signature(s): 

isPkgURIEnabled(string pkgURI)    bool

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

Parameters:
pkgURI the URI of the package
Returns:
true if the given package is enabled within this object, false otherwise.
See also:
isPkgEnabled()
Deprecated:
Replaced in libSBML 5.2.0 by isPackageURIEnabled()
def libsbml.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.InitialAssignment.isSetMath (   self  ) 

Python method signature(s): 

isSetMath()    bool

Predicate returning true if this InitialAssignment's 'math' subelement contains a value.

Returns:
true if the 'math' for this InitialAssignment is set, false otherwise.
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.InitialAssignment.isSetSymbol (   self  ) 

Python method signature(s): 

isSetSymbol()    bool

Predicate returning true if this InitialAssignment's 'symbol' attribute is set.

Returns:
true if the 'symbol' attribute of this InitialAssignment is set, 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.InitialAssignment.renameSIdRefs (   self,
  args 
)

Python method signature(s): 

renameSIdRefs(string oldid, string newid)

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

Reimplemented from libsbml.SBase.

def libsbml.InitialAssignment.renameUnitSIdRefs (   self,
  args 
)

Python method signature(s): 

renameUnitSIdRefs(string oldid, string newid)

Renames all the UnitSIdRef attributes on this element

Reimplemented from libsbml.SBase.

def libsbml.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:
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.InitialAssignment.setMath (   self,
  args 
)

Python method signature(s): 

setMath(ASTNode math)    int

Sets the 'math' subelement of this InitialAssignment.

The AST passed in math is copied.

Parameters:
math an AST containing the mathematical expression to be used as the formula for this InitialAssignment.
Returns:
integer value indicating success/failure of the function. The possible values returned by this function are:
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:
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.InitialAssignment.setSymbol (   self,
  args 
)

Python method signature(s): 

setSymbol(string sid)    int

Sets the 'symbol' attribute value of this InitialAssignment.

Parameters:
sid the identifier of a Species, Compartment or Parameter object defined elsewhere in this Model.
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:
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:
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:

SBML Team
http://www.sbml.org/
sbml-team@caltech.edu

HTML documentation generated on Tue Dec 20 01:39:50 2011 using Doxygen 1.6.3.