libSBML Python API  5.11.0
libsbml.Event Class Reference
Inheritance diagram for libsbml.Event:
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Detailed Description

A discontinuous SBML event.

An SBML Event object defines when the event can occur, the variables that are affected by it, how the variables are affected, and the event's relationship to other events. The effect of the event can optionally be delayed after the occurrence of the condition which invokes it.

The operation of Event is divided into two phases (even when the event is not delayed): one when the event is triggered, and the other when the event is executed. Trigger objects define the conditions for triggering an event, Delay objects define when the event is actually executed, EventAssignment objects define the effects of executing the event, and (in SBML Level 3) Priority objects influence the order of EventAssignment performance in cases of simultaneous events. Please consult the descriptions of Trigger, Delay, EventAssignment and Priority for more information.

SBML Level/Version differences

SBML Level 3

SBML Level 3 introduces several changes to the structure and components of Events compared to SBML Level 2. These changes fall into two main categories: changes to what is optional or required, and additions of new attributes and elements.

  • The attribute 'useValuesFromTriggerTime' on Event is mandatory (it was optional in Level 2);
  • Event's 'listOfEventAssignments' element (of class ListOfEventAssignments) is optional (it was mandatory in Level 2);
  • Event's 'priority' element (of class Priority) is new in Level 3; and
  • The Trigger object gains new mandatory attributes (described as part of the definition of Trigger).

The changes to the attributes of Event are described below; the changes to Trigger and Priority are described in their respective sections.

SBML Level 2

In SBML Level 2 versions before Version 4, the semantics of Event time delays were defined such that the expressions in the event's assignments were always evaluated at the time the event was triggered. This definition made it difficult to define an event whose assignment formulas were meant to be evaluated at the time the event was executed (i.e., after the time period defined by the value of the Delay element). In SBML Level 2 Version 4 and in Level 3, the attribute 'useValuesFromTriggerTime' on Event allows a model to indicate the time at which the event's assignments are intended the values of the assignment formulas are computed at the moment the event is triggered, not after the delay. If 'useValuesFromTriggerTime'=False, it means that the formulas in the event's assignments are to be computed after the delay, at the time the event is executed.

The definition of Event in SBML Level 2 Versions 1 and 2 includes an additional attribute called 'timeUnits', which allowed the time units of the Delay to be set explicitly. Later Versions of SBML Level 2 as well as SBML Level 3 do not define this attribute. LibSBML supports this attribute for compatibility with previous versions of SBML Level 2; however, if a model in SBML Level 3 or Level 2 Versions 3–4 format sets the attribute, the consistency-checking method SBMLDocument.checkConsistency() will report an error.

The attribute 'useValuesFromTriggerTime' was introduced in SBML Level 2 Version 4. Models defined in prior Versions of SBML Level 2 cannot use this attribute, and SBMLDocument.checkConsistency() will report an error if they do.

Semantics of events in SBML Level 3 VersionĀ 1

The detailed semantics of events are described in the specification documents for each SBML Level/Version. Here we include the description from the SBML Level 1 Version 1. Any transition of a Trigger object's 'math' formula from the value False to True will cause the enclosing Event object to trigger. Such a transition is not possible at the very start of a simulation (i.e., at time t = 0) unless the Trigger object's 'initialValue' attribute has a value of False; this defines the value of the trigger formula to be False immediately prior to the start of simulation, thereby giving it the potential to change in value from False to True when the formula is evaluated at t = 0. If 'initialValue'=True, then the trigger expression cannot transition from False to True at t = 0 but may do so at some time t > 0.

Consider an Event object definition E with delay d in which the Trigger object's 'math' formula makes a transition in value from False to True at times t1 and t2. The EventAssignment within the Event object will have effect at t1 + d and t2 + d irrespective of the relative times of t1 and t2. For example, events can 'overlap' so that t1 < t2 < t1 + d still causes an event assignments to occur at t1 + d and t2 + d.

It is entirely possible for two events to be executed simultaneously, and it is possible for events to trigger other events (i.e., an event assignment can cause an event to trigger). This leads to several points:

  • A software package should retest all event triggers after executing an event assignment in order to account for the possibility that the assignment causes another event trigger to transition from False to True. This check should be made after each individual Event object's execution, even when several events are to be executed simultaneously.

  • Any Event object whose Trigger 'persistent' attribute has the value False must have its trigger expression reevaluated continuously between when the event is triggered and when it is executed. If its trigger expression ever evaluates to False, it must be removed from the queue of events pending execution and treated as any other event whose trigger expression evaluates to False.

  • Although the precise time at which events are executed is not resolved beyond the given execution point in simulated time, it is assumed that the order in which the events occur is resolved. This order can be significant in determining the overall outcome of a given simulation. When an event X triggers another event Y and event Y has zero delay, then event Y is added to the existing set of simultaneous events that are pending execution. Events X and Y form a cascade of events at the same point in simulation time. An event such as Y may have a special priority if it contains a Priority subobject.

  • All events in a model are open to being in a cascade. The position of an event in the event queue does not affect whether it can be in the cascade: event Y can be triggered whether it is before or after X in the queue of events pending execution. A cascade of events can be potentially infinite (never terminate); when this occurs a simulator should indicate this has occurred—it is incorrect for a simulator to break a cascade arbitrarily and continue the simulation without at least indicating that the infinite cascade occurred.

  • Simultaneous events having no defined priorities are executed in an undefined order. This does not mean that the behavior of the simulation is completely undefined; merely that the order of execution of these particular events is undefined. A given simulator may use any algorithm to choose an order as long as every event is executed exactly once.

  • Events with defined priorities are executed in the order implied by their Priority 'math' formula values, with events having higher priorities being executed ahead of events with lower priorities, and events with identical priorities being executed in a random order with respect to one another (as determined at run-time by some random algorithm equivalent to coin-flipping). Newly-triggered events that are to be executed immediately (i.e., if they define no delays) should be inserted into the queue of events pending execution according to their priorities: events with higher priority values value must be inserted ahead of events with lower priority values and after any pending events with even higher priorities, and inserted randomly among pending events with the same priority values. Events without Priority objects must be inserted into the queue in some fashion, but the algorithm used to place it in the queue is undefined. Similarly, there is no restriction on the order of a newly-inserted event with a defined Priority with respect to any other pending Event without a defined Priority.

  • A model variable that is the target of one or more event assignments can change more than once when simultaneous events are processed at some time point t. The model's behavior (output) for such a variable is the value of the variable at the end of processing all the simultaneous events at time t.

See also
Trigger
Priority
Delay
EventAssignment

Public Member Functions

def __init__ (self, args)
  A discontinuous SBML event. More...
 
def addCVTerm
 Adds a copy of the given CVTerm object to this SBML object. More...
 
def addEventAssignment (self, ea)
 Appends a copy of the given EventAssignment to this Event. More...
 
def appendAnnotation (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def appendNotes (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def clone (self)
 Creates and returns a deep copy of this Event object. More...
 
def connectToChild (self)
 
def createDelay (self)
 Creates a new, empty Delay, adds it to this Event and returns the Delay. More...
 
def createEventAssignment (self)
 Creates a new, empty EventAssignment, adds it to this Event's list of event assignments and returns the EventAssignment. More...
 
def createPriority (self)
 
def createTrigger (self)
 Creates a new, empty Trigger, adds it to this Event and returns the Trigger. More...
 
def deleteDisabledPlugins
 Deletes all information stored in disabled plugins. More...
 
def disablePackage (self, pkgURI, pkgPrefix)
 Disables the given SBML Level 3 package on this object. More...
 
def enablePackage (self, pkgURI, pkgPrefix, flag)
 Enables or disables the given SBML Level 3 package on this object. More...
 
def getAncestorOfType (self, args)
 Returns the first ancestor object that has the given SBML type code from the given package. More...
 
def getAnnotation (self, args)
 Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects. More...
 
def getAnnotationString (self, args)
 Returns the content of the 'annotation' subelement of this object as a character string. More...
 
def getColumn (self)
 Returns the column number on which this object first appears in the XML representation of the SBML document. More...
 
def getCVTerm (self, n)
 Returns the nth CVTerm in the list of CVTerms of this SBML object. More...
 
def getCVTerms (self, args)
 Returns a list of CVTerm objects in the annotations of this SBML object. More...
 
def getDelay (self, args)
 Get the assignment delay portion of this Event, if there is one. More...
 
def getDisabledPlugin (self, args)
 Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More...
 
def getElementByMetaId (self, metaid)
 Returns the first child element it can find with the given metaid, or None if no such object is found. More...
 
def getElementBySId (self, id)
 Returns the first child element found that has the given id in the model-wide SId namespace, or None if no such object is found. More...
 
def getElementName (self)
 Returns the XML element name of this object, which for Event, is always 'event'. More...
 
def getEventAssignment (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def getId (self)
 Returns the value of the 'id' attribute of this Event. More...
 
def getLevel (self)
 Returns the SBML Level of the SBMLDocument object containing this object. More...
 
def getLine (self)
 Returns the line number on which this object first appears in the XML representation of the SBML document. More...
 
def getListOfAllElements
 Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth. More...
 
def getListOfAllElementsFromPlugins
 Returns a List of all child SBase objects contained in SBML package plug-ins. More...
 
def getListOfEventAssignments (self, args)
 Returns the list of event assignments for this Event. More...
 
def getMetaId (self)
 Returns the value of the 'metaid' attribute of this object. More...
 
def getModel (self)
 Returns the Model object for the SBML Document in which the current object is located. More...
 
def getModelHistory (self, args)
 Returns the ModelHistory object, if any, attached to this object. More...
 
def getName (self)
 Returns the value of the 'name' attribute of this Event. More...
 
def getNamespaces (self)
 Returns a list of the XML Namespaces declared on the SBML document owning this object. More...
 
def getNotes (self, args)
 Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects. More...
 
def getNotesString (self, args)
 Returns the content of the 'notes' subelement of this object as a string. More...
 
def getNumCVTerms (self)
 Returns the number of CVTerm objects in the annotations of this SBML object. More...
 
def getNumDisabledPlugins (self)
 Returns the number of disabled plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More...
 
def getNumEventAssignments (self)
 Returns the number of EventAssignment objects attached to this Event. More...
 
def getNumPlugins (self)
 Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More...
 
def getPackageName (self)
 Returns the name of the SBML Level 3 package in which this element is defined. More...
 
def getPackageVersion (self)
 Returns the Version of the SBML Level 3 package to which this element belongs to. More...
 
def getParentSBMLObject (self, args)
 Returns the parent SBML object containing this object. More...
 
def getPlugin (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def getPrefix (self)
 Returns the namespace prefix of this element. More...
 
def getPriority (self, args)
 
def getResourceBiologicalQualifier (self, resource)
 Returns the MIRIAM biological qualifier associated with the given resource. More...
 
def getResourceModelQualifier (self, resource)
 Returns the MIRIAM model qualifier associated with the given resource. More...
 
def getSBMLDocument (self, args)
 Returns the SBMLDocument object containing this object instance. More...
 
def getSBOTerm (self)
 Returns the integer portion of the value of the 'sboTerm' attribute of this object. More...
 
def getSBOTermAsURL (self)
 Returns the URL representation of the 'sboTerm' attribute of this object. More...
 
def getSBOTermID (self)
 Returns the string representation of the 'sboTerm' attribute of this object. More...
 
def getTimeUnits (self)
 Get the value of the 'timeUnits' attribute of this Event, if it has one. More...
 
def getTrigger (self, args)
 Get the event trigger portion of this Event. More...
 
def getTypeCode (self)
 Returns the libSBML type code of this object instance. More...
 
def getURI (self)
 Gets the namespace URI to which this element belongs to. More...
 
def getUseValuesFromTriggerTime (self)
 Get the value of the 'useValuesFromTriggerTime' attribute of this Event. More...
 
def getVersion (self)
 Returns the Version within the SBML Level of the SBMLDocument object containing this object. More...
 
def hasRequiredAttributes (self)
 Predicate returning True if all the required attributes for this Event object have been set. More...
 
def hasRequiredElements (self)
 Predicate returning True if all the required elements for this Event object have been set. More...
 
def hasValidLevelVersionNamespaceCombination (self)
 Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More...
 
def isPackageEnabled (self, pkgName)
 Predicate returning True if the given SBML Level 3 package is enabled with this object. More...
 
def isPackageURIEnabled (self, pkgURI)
 Predicate returning True if an SBML Level 3 package with the given URI is enabled with this object. More...
 
def isPkgEnabled (self, pkgName)
 Predicate returning True if the given SBML Level 3 package is enabled with this object. More...
 
def isPkgURIEnabled (self, pkgURI)
 Predicate returning True if an SBML Level 3 package with the given URI is enabled with this object. More...
 
def isSetAnnotation (self)
 Predicate returning True if this object's 'annotation' subelement exists and has content. More...
 
def isSetDelay (self)
 Predicate for testing whether the delay for this Event is set. More...
 
def isSetId (self)
 Predicate returning True if this Event's 'id' attribute is set. More...
 
def isSetMetaId (self)
 Predicate returning True if this object's 'metaid' attribute is set. More...
 
def isSetModelHistory (self)
 Predicate returning True if this object has a ModelHistory object attached to it. More...
 
def isSetName (self)
 Predicate returning True if this Event's 'name' attribute is set. More...
 
def isSetNotes (self)
 Predicate returning True if this object's 'notes' subelement exists and has content. More...
 
def isSetPriority (self)
 
def isSetSBOTerm (self)
 Predicate returning True if this object's 'sboTerm' attribute is set. More...
 
def isSetTimeUnits (self)
 Predicate for testing whether the 'timeUnits' attribute of this Event is set. More...
 
def isSetTrigger (self)
 Predicate for testing whether the trigger for this Event is set. More...
 
def isSetUseValuesFromTriggerTime (self)
 Predicate for testing whether the 'useValuesFromTriggerTime' attribute of this Event is set. More...
 
def matchesRequiredSBMLNamespacesForAddition (self, args)
 Returns True if this object's set of XML namespaces are a subset of the given object's XML namespaces. More...
 
def matchesSBMLNamespaces (self, args)
 Returns True if this object's set of XML namespaces are the same as the given object's XML namespaces. More...
 
def removeEventAssignment (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def removeFromParentAndDelete (self)
 Removes this object from its parent. More...
 
def removeTopLevelAnnotationElement (self, args)
 Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More...
 
def renameMetaIdRefs (self, oldid, newid)
 Replaces all uses of a given meta identifier attribute value with another value. More...
 
def renameSIdRefs (self, oldid, newid)
 Replaces all uses of a given SIdRef type attribute value with another value. More...
 
def renameUnitSIdRefs (self, oldid, newid)
 Replaces all uses of a given UnitSIdRef type attribute value with another value. More...
 
def replaceTopLevelAnnotationElement (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def setAnnotation (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def setDelay (self, delay)
 Sets the delay definition of this Event to a copy of the given Delay object instance. More...
 
def setId (self, sid)
 Sets the value of the 'id' attribute of this Event. More...
 
def setMetaId (self, metaid)
 Sets the value of the meta-identifier attribute of this object. More...
 
def setModelHistory (self, history)
 Sets the ModelHistory of this object. More...
 
def setName (self, name)
 Sets the value of the 'name' attribute of this Event. More...
 
def setNamespaces (self, xmlns)
 Sets the namespaces relevant of this SBML object. More...
 
def setNotes (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def setPriority (self, priority)
 
def setSBOTerm (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def setTimeUnits (self, sid)
 Sets the 'timeUnits' attribute of this Event to a copy of sid. More...
 
def setTrigger (self, trigger)
 Sets the trigger definition of this Event to a copy of the given Trigger object instance. More...
 
def setUseValuesFromTriggerTime (self, value)
 Sets the 'useValuesFromTriggerTime' attribute of this Event to a value. More...
 
def toSBML (self)
 Returns a string consisting of a partial SBML corresponding to just this object. More...
 
def toXMLNode (self)
 Returns this element as an XMLNode. More...
 
def unsetAnnotation (self)
 Unsets the value of the 'annotation' subelement of this SBML object. More...
 
def unsetCVTerms (self)
 Clears the list of CVTerm objects attached to this SBML object. More...
 
def unsetDelay (self)
 Unsets the Delay of this Event. More...
 
def unsetId (self)
 Unsets the value of the 'id' attribute of this Event. More...
 
def unsetMetaId (self)
 Unsets the value of the 'metaid' attribute of this SBML object. More...
 
def unsetModelHistory (self)
 Unsets the ModelHistory object attached to this object. More...
 
def unsetName (self)
 Unsets the value of the 'name' attribute of this Event. More...
 
def unsetNotes (self)
 Unsets the value of the 'notes' subelement of this SBML object. More...
 
def unsetPriority (self)
 
def unsetSBOTerm (self)
 Unsets the value of the 'sboTerm' attribute of this SBML object. More...
 
def unsetTimeUnits (self)
 Unsets the 'timeUnits' attribute of this Event. More...
 
def unsetTrigger (self)
 Unsets the Trigger of this Event. More...
 

Member Function Documentation

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

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

addCVTerm(CVTerm term, bool newBag=False)   int
addCVTerm(CVTerm term)   int
Parameters
termthe CVTerm to assign.
newBagif True, creates a new RDF bag with the same identifier as a previous bag, and if False, adds the term to an existing RDF bag with the same type of qualifier as the term being added.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
def libsbml.Event.addEventAssignment (   self,
  ea 
)

Appends a copy of the given EventAssignment to this Event.

addEventAssignment(EventAssignment ea)   int
Parameters
eathe EventAssignment object to add.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
See also
createEventAssignment()
def libsbml.SBase.appendAnnotation (   self,
  args 
)
inherited

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

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

Each variant is described separately below.


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

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

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

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

Unlike SBase.setAnnotation() or SBase.setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan 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
annotationan 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()
def libsbml.SBase.appendNotes (   self,
  args 
)
inherited

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

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

Each variant is described separately below.


Method variant with the following signature:
appendNotes(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
notesan 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()

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
notesan 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()
def libsbml.Event.clone (   self)

Creates and returns a deep copy of this Event object.

clone()   Event
Returns
the (deep) copy of this Event object.
def libsbml.Event.connectToChild (   self)
connectToChild()
def libsbml.Event.createDelay (   self)

Creates a new, empty Delay, adds it to this Event and returns the Delay.

createDelay()   Delay
Returns
the newly created Delay object instance
def libsbml.Event.createEventAssignment (   self)

Creates a new, empty EventAssignment, adds it to this Event's list of event assignments and returns the EventAssignment.

createEventAssignment()   EventAssignment
Returns
the newly created EventAssignment object instance
See also
addEventAssignment()
def libsbml.Event.createPriority (   self)
createPriority()   Priority

(SBML Level 3 only) Creates a new, empty Priority, adds it to this Event and returns the Priority.

Returns
the newly created Priority object instance
Note
The element 'priority' is available in SBML Level 3 Version 1 Core, but is not present in lower Levels of SBML.
def libsbml.Event.createTrigger (   self)

Creates a new, empty Trigger, adds it to this Event and returns the Trigger.

createTrigger()   Trigger
Returns
the newly created Trigger object instance
def libsbml.SBase.deleteDisabledPlugins (   self,
  recursive = True 
)
inherited

Deletes all information stored in disabled plugins.

deleteDisabledPlugins(bool recursive=True)
deleteDisabledPlugins()
Parameters
recursiveif True, the disabled information will be deleted also from all child elements, otherwise only from this SBase element.
See also
getNumDisabledPlugins()
def libsbml.SBase.disablePackage (   self,
  pkgURI,
  pkgPrefix 
)
inherited

Disables the given SBML Level 3 package on this object.

disablePackage(string pkgURI, string pkgPrefix)   int

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

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

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

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

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

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

Parameters
pkgURIthe URI of the package.
pkgPrefixthe XML prefix of the package
flagwhether 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:
See also
disablePackage()
def libsbml.SBase.getAncestorOfType (   self,
  args 
)
inherited

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

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

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

This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code from the given pkgName.

Parameters
typethe SBML type code of the object sought
pkgName(optional) the short name of an SBML Level 3 package to which the sought-after object must belong
Returns
the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or None if no ancestor exists.
Warning
The optional argument pkgName must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the 'core' namespace alone, not find any corresponding elements, and return None.
def libsbml.SBase.getAnnotation (   self,
  args 
)
inherited

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

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

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

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

Returns
the annotation of this SBML object as a tree of XMLNode objects.
See also
getAnnotationString()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.SBase.getAnnotationString (   self,
  args 
)
inherited

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

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

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

The annotations returned by this method will be in string form. See the method getAnnotation() for a version that returns annotations in XML form.

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

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

getColumn()   long
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,
  n 
)
inherited

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

getCVTerm(long n)   CVTerm
Parameters
nlong 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,
  args 
)
inherited

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

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

Get the assignment delay portion of this Event, if there is one.

getDelay()   Delay
Returns
the delay of this Event if one is defined, or None if none is defined.
def libsbml.SBase.getDisabledPlugin (   self,
  args 
)
inherited

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

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

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

getElementByMetaId(string metaid)   SBase
Parameters
metaidstring representing the metaid of objects to find
Returns
pointer to the first element found with the given metaid.
def libsbml.Event.getElementBySId (   self,
  id 
)

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

getElementBySId(string id)   SBase
Parameters
idstring representing the id of objects to find
Returns
pointer to the first element found with the given id.
def libsbml.Event.getElementName (   self)

Returns the XML element name of this object, which for Event, is always 'event'.

getElementName()   string
Returns
the name of this element, i.e., 'event'.
def libsbml.Event.getEventAssignment (   self,
  args 
)

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

getEventAssignment(long n)   EventAssignment
getEventAssignment(string variable)   EventAssignment

Each variant is described separately below.


Method variant with the following signature:
getEventAssignment(long n)

Return a specific EventAssignment object of this Event.

Parameters
nan integer, the index of the EventAssignment object to return
Returns
the nth EventAssignment of this Event.

Method variant with the following signature:
getEventAssignment(string variable)

Return the event assignment indicated by the given variable.

Parameters
variablea string, the identifier of the variable whose EventAssignment is being sought.
Returns
the EventAssignment for the given variable, or None if no such EventAssignment exits.
def libsbml.Event.getId (   self)

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

getId()   string
Returns
the id of this Event.
def libsbml.SBase.getLevel (   self)
inherited

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

getLevel()   long
LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
Returns
the SBML level of this SBML object.
See also
getVersion()
getNamespaces()
getPackageVersion()
def libsbml.SBase.getLine (   self)
inherited

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

getLine()   long
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,
  filter = None 
)
inherited

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

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

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

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

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

Returns
a pointer to a List of pointers to all children objects from plug-ins.
def libsbml.Event.getListOfEventAssignments (   self,
  args 
)

Returns the list of event assignments for this Event.

getListOfEventAssignments()   ListOfEventAssignments
Returns
the list of EventAssignments for this Event.
def libsbml.SBase.getMetaId (   self)
inherited

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

getMetaId()   string
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
the meta-identifier of this SBML object.
See also
isSetMetaId()
setMetaId()
def libsbml.SBase.getModel (   self)
inherited

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

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

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

getModelHistory()   ModelHistory
Returns
the ModelHistory object attached to this object, or None if none exist.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
def libsbml.Event.getName (   self)

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

getName()   string
Returns
the name of this Event.
def libsbml.SBase.getNamespaces (   self)
inherited

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

getNamespaces()   XMLNamespaces

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

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

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

getNotes()   XMLNode
The optional SBML element named 'notes', present on every major SBML component type (and in SBML Level 3, the 'message' subelement of Constraint), is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

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

Returns
the content of the 'notes' subelement of this SBML object as a tree structure composed of XMLNode objects.
See also
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBase.getNotesString (   self,
  args 
)
inherited

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

getNotesString()   string
The optional SBML element named 'notes', present on every major SBML component type (and in SBML Level 3, the 'message' subelement of Constraint), is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

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

Returns
the content of the 'notes' subelement of this SBML object as a string.
See also
getNotes()
isSetNotes()
setNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBase.getNumCVTerms (   self)
inherited

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

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

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

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

Returns the number of EventAssignment objects attached to this Event.

getNumEventAssignments()   long
Returns
the number of EventAssignments in this Event.
def libsbml.SBase.getNumPlugins (   self)
inherited

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

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

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

getPackageName()   string
Returns
the name of the SBML package in which this element is defined. The string "core" will be returned if this element is defined in SBML Level 3 Core. The string "unknown" will be returned if this element is not defined in any SBML package.
def libsbml.SBase.getPackageVersion (   self)
inherited

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

getPackageVersion()   long
Returns
the version of the SBML Level 3 package to which this element belongs. The value 0 will be returned if this element belongs to the SBML Level 3 Core package.
See also
getLevel()
getVersion()
def libsbml.SBase.getParentSBMLObject (   self,
  args 
)
inherited

Returns the parent SBML object containing this object.

getParentSBMLObject()   SBase

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

Returns
the parent SBML object of this SBML object.
See also
getSBMLDocument()
getModel()
def libsbml.SBase.getPlugin (   self,
  args 
)
inherited

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

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

Each variant is described separately below.


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

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

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

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

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

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

Returns the namespace prefix of this element.

getPrefix()   string
def libsbml.Event.getPriority (   self,
  args 
)
getPriority()   Priority

(SBML Level 3 only) Get the event priority portion of this Event.

Returns
the Priority object of this Event.
Note
The element 'priority' is available in SBML Level 3 Version 1 Core, but is not present in lower Levels of SBML.
def libsbml.SBase.getResourceBiologicalQualifier (   self,
  resource 
)
inherited

Returns the MIRIAM biological qualifier associated with the given resource.

getResourceBiologicalQualifier(string resource)   long

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

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

Parameters
resourcestring representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.
Returns
the qualifier associated with the resource, or BQB_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM biological qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQB_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
def libsbml.SBase.getResourceModelQualifier (   self,
  resource 
)
inherited

Returns the MIRIAM model qualifier associated with the given resource.

getResourceModelQualifier(string resource)   long

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

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

Parameters
resourcestring representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.
Returns
the model qualifier type associated with the resource, or BQM_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM model qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQM_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
def libsbml.SBase.getSBMLDocument (   self,
  args 
)
inherited

Returns the SBMLDocument object containing this object instance.

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

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

Returns
the parent SBMLDocument object of this SBML object.
See also
getParentSBMLObject()
getModel()
def libsbml.SBase.getSBOTerm (   self)
inherited

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

getSBOTerm()   int

Beginning with SBML Level 2 Version 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.getSBOTermAsURL (   self)
inherited

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

getSBOTermAsURL()   string

This method returns the entire SBO identifier as a text string in the form http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. 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 identifiers.org URL, or an empty string if the value is not set.
def libsbml.SBase.getSBOTermID (   self)
inherited

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

getSBOTermID()   string

Beginning with SBML Level 2 Version 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.Event.getTimeUnits (   self)

Get the value of the 'timeUnits' attribute of this Event, if it has one.

getTimeUnits()   string
Returns
the value of the attribute 'timeUnits' as a string.
Warning
Definitions of Event in SBML Level 2 Versions 1 and 2 included the additional attribute called 'timeUnits', but it was removed in SBML Level 2 Version 3. LibSBML supports this attribute for compatibility with previous versions of SBML Level 2, but its use is discouraged since models in Level 2 Versions 3 and 4 cannot contain it. If a Version 3 or 4 model sets the attribute, the consistency-checking method SBMLDocument.checkConsistency() will report an error.
def libsbml.Event.getTrigger (   self,
  args 
)

Get the event trigger portion of this Event.

getTrigger()   Trigger
Returns
the Trigger object of this Event.
def libsbml.Event.getTypeCode (   self)

Returns the libSBML type code of this object instance.

getTypeCode()   int
LibSBML attaches an identifying code to every kind of SBML object. These are integer constants known as SBML type codes. The names of all the codes begin with the characters SBML_. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the getPackageName() method on the object.
Returns
the SBML type code for this object: SBML_EVENT (default).
Warning
The specific integer values of the possible type codes may be reused by different Level 3 package plug-ins. Thus, to identifiy the correct code, it is necessary to invoke both getTypeCode() and getPackageName().
See also
getElementName()
getPackageName()
def libsbml.SBase.getURI (   self)
inherited

Gets the namespace URI to which this element belongs to.

getURI()   string

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

This function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found, it willreturn the XML namespace to which this element belongs.

Returns
the URI of this element
See also
getSBMLDocument()
getPackageName()
def libsbml.Event.getUseValuesFromTriggerTime (   self)

Get the value of the 'useValuesFromTriggerTime' attribute of this Event.

getUseValuesFromTriggerTime()   bool
The optional Delay on Event means there are two times to consider when computing the results of an event: the time at which the event is triggered, and the time at which assignments are executed. It is also possible to distinguish between the time at which the EventAssignment's expression is calculated, and the time at which the assignment is made: the expression could be evaluated at the same time the assignments are performed, i.e., when the event is executed, but it could also be defined to be evaluated at the time the event is triggered.

In SBML Level 2 versions prior to Version 4, the semantics of Event time delays were defined such that the expressions in the event's assignments were always evaluated at the time the event was triggered. This definition made it difficult to define an event whose assignment formulas were meant to be evaluated at the time the event was executed (i.e., after the time period defined by the value of the Delay element). In SBML Level 2 Version 4, the attribute 'useValuesFromTriggerTime' on Event allows a model to indicate the time at which the event's assignments are intended to be evaluated. In SBML Level 2, the attribute has a default value of True, which corresponds to the interpretation of event assignments prior to Version 4: the values of the assignment formulas are computed at the moment the event is triggered, not after the delay. If 'useValuesFromTriggerTime'=False, it means that the formulas in the event's assignments are to be computed after the delay, at the time the event is executed. In SBML Level 3, the attribute is mandatory, not optional, and all events must specify a value for it.

Returns
the value of the attribute 'useValuesFromTriggerTime' as a boolean.
Warning
The attribute 'useValuesFromTriggerTime' was introduced in SBML Level 2 Version 4. It is not valid in models defined using SBML Level 2 versions prior to Version 4. If a Level 2 Version 1–3 model sets the attribute, the consistency-checking method SBMLDocument.checkConsistency() will report an error.
def libsbml.SBase.getVersion (   self)
inherited

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

getVersion()   long
LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
Returns
the SBML version of this SBML object.
See also
getLevel()
getNamespaces()
def libsbml.Event.hasRequiredAttributes (   self)

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

hasRequiredAttributes()   bool

The required attributes for an Event object are:

  • 'useValuesfromTriggerTime' (required in SBML Level 3)
Returns
True if the required attributes have been set, False otherwise.
def libsbml.Event.hasRequiredElements (   self)

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

hasRequiredElements()   bool
Note
The required elements for an Event object are:
  • 'trigger'
  • 'listOfEventAssignments' (required in SBML Level 2, optional in Level 3)
def libsbml.SBase.hasValidLevelVersionNamespaceCombination (   self)
inherited

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

hasValidLevelVersionNamespaceCombination()   bool

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

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

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

isPackageEnabled(string pkgName)   bool

The search ignores the package version.

Parameters
pkgNamethe 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,
  pkgURI 
)
inherited

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

isPackageURIEnabled(string pkgURI)   bool
Parameters
pkgURIthe 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,
  pkgName 
)
inherited

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

isPkgEnabled(string pkgName)   bool

The search ignores the package version.

Parameters
pkgNamethe name of the package
Returns
True if the given package is enabled within this object, False otherwise.
See also
isPkgURIEnabled()
def libsbml.SBase.isPkgURIEnabled (   self,
  pkgURI 
)
inherited

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

isPkgURIEnabled(string pkgURI)   bool
Parameters
pkgURIthe URI of the package
Returns
True if the given package is enabled within this object, False otherwise.
See also
isPkgEnabled()
def libsbml.SBase.isSetAnnotation (   self)
inherited

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

isSetAnnotation()   bool

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

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

Returns
True if a 'annotation' subelement exists, False otherwise.
See also
getAnnotation()
getAnnotationString()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.Event.isSetDelay (   self)

Predicate for testing whether the delay for this Event is set.

isSetDelay()   bool
Returns
True if the delay of this Event is set, False otherwise.
def libsbml.Event.isSetId (   self)

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

isSetId()   bool
Returns
True if the 'id' attribute of this Event is set, False otherwise.
def libsbml.SBase.isSetMetaId (   self)
inherited

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

isSetMetaId()   bool
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
True if the 'metaid' attribute of this SBML object is set, False otherwise.
See also
getMetaId()
setMetaId()
def libsbml.SBase.isSetModelHistory (   self)
inherited

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

isSetModelHistory()   bool
Returns
True if the ModelHistory of this object is set, False otherwise.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
def libsbml.Event.isSetName (   self)

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

isSetName()   bool
Returns
True if the 'name' attribute of this Event is set, False otherwise.
def libsbml.SBase.isSetNotes (   self)
inherited

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

isSetNotes()   bool

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

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

Returns
True if a 'notes' subelement exists, False otherwise.
See also
getNotes()
getNotesString()
setNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.Event.isSetPriority (   self)
isSetPriority()   bool

(SBML Level 3 only) Predicate for testing whether the priority for this Event is set.

Returns
True if the priority of this Event is set, False otherwise.
Note
The element 'priority' is available in SBML Level 3 Version 1 Core, but is not present in lower Levels of SBML.
def libsbml.SBase.isSetSBOTerm (   self)
inherited

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

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

Predicate for testing whether the 'timeUnits' attribute of this Event is set.

isSetTimeUnits()   bool
Returns
True if the 'timeUnits' attribute of this Event is set, False otherwise.
Warning
Definitions of Event in SBML Level 2 Versions 1 and 2 included the additional attribute called 'timeUnits', but it was removed in SBML Level 2 Version 3. LibSBML supports this attribute for compatibility with previous versions of SBML Level 2, but its use is discouraged since models in Level 2 Versions 3 and 4 cannot contain it. If a Version 3 or 4 model sets the attribute, the consistency-checking method SBMLDocument.checkConsistency() will report an error.
def libsbml.Event.isSetTrigger (   self)

Predicate for testing whether the trigger for this Event is set.

isSetTrigger()   bool
Returns
True if the trigger of this Event is set, False otherwise.
def libsbml.Event.isSetUseValuesFromTriggerTime (   self)

Predicate for testing whether the 'useValuesFromTriggerTime' attribute of this Event is set.

isSetUseValuesFromTriggerTime()   bool
Returns
True if the 'useValuesFromTriggerTime' attribute of this Event is set, False otherwise.
Note
In SBML Level 2, this attribute is optional and has a default value of True, whereas in Level 3 Version 1, this optional is mandatory and has no default value.
def libsbml.SBase.matchesRequiredSBMLNamespacesForAddition (   self,
  args 
)
inherited

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

matchesRequiredSBMLNamespacesForAddition(SBase sb)   bool
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sban object to compare with respect to namespaces
Returns
boolean, True if this object's collection of namespaces is a subset of sb's, False otherwise.
def libsbml.SBase.matchesSBMLNamespaces (   self,
  args 
)
inherited

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

matchesSBMLNamespaces(SBase sb)   bool
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sban 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.Event.removeEventAssignment (   self,
  args 
)

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

removeEventAssignment(long n)   EventAssignment
removeEventAssignment(string variable)   EventAssignment

Each variant is described separately below.


Method variant with the following signature:
removeEventAssignment(long n)

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

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

Parameters
nthe index of the EventAssignment object to remove
Returns
the EventAssignment object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.

Method variant with the following signature:
removeEventAssignment(string variable)

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

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

Parameters
variablethe 'variable' attribute of the EventAssignment object to remove
Returns
the EventAssignment object removed. As mentioned above, the caller owns the returned object. None is returned if no EventAssignment object with the 'variable' attribute exists in this Event object.
def libsbml.SBase.removeFromParentAndDelete (   self)
inherited

Removes this object from its parent.

removeFromParentAndDelete()   int

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

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

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

removeTopLevelAnnotationElement(string elementName, string elementURI, bool removeEmpty=True)   int
removeTopLevelAnnotationElement(string elementName, string elementURI)   int
removeTopLevelAnnotationElement(string elementName)   int

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

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

Parameters
elementNamea string representing the name of the top level annotation element that is to be removed
elementURIan optional string that is used to check both the name and URI of the top level element to be removed
removeEmptyif after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default).
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
replaceTopLevelAnnotationElement()
replaceTopLevelAnnotationElement()
def libsbml.SBase.renameMetaIdRefs (   self,
  oldid,
  newid 
)
inherited

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

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

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

Parameters
oldidthe old identifier
newidthe new identifier
def libsbml.SBase.renameSIdRefs (   self,
  oldid,
  newid 
)
inherited

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

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

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

Parameters
oldidthe old identifier
newidthe new identifier
def libsbml.SBase.renameUnitSIdRefs (   self,
  oldid,
  newid 
)
inherited

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

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

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

Parameters
oldidthe old identifier
newidthe new identifier
def libsbml.SBase.replaceTopLevelAnnotationElement (   self,
  args 
)
inherited

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

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

Each variant is described separately below.


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

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

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

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

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

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

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

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

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

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

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

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

Each variant is described separately below.


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

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

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

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

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

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

Parameters
annotationan 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
annotationan 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()
def libsbml.Event.setDelay (   self,
  delay 
)

Sets the delay definition of this Event to a copy of the given Delay object instance.

setDelay(Delay delay)   int
Parameters
delaythe Delay object instance to use
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.Event.setId (   self,
  sid 
)

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

setId(string sid)   int

The string sid is copied.

SBML has strict requirements for the syntax of identifiers, that is, the values of the 'id' attribute present on most types of SBML objects. The following is a summary of the definition of the SBML identifier type SId, which defines the permitted syntax of identifiers. We express the syntax using an extended form of BNF notation:
letter ::= 'a'..'z','A'..'Z'
digit  ::= '0'..'9'
idChar ::= letter | digit | '_'
SId    ::= ( letter | '_' ) idChar*
The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. In addition, there are a few conditions for the uniqueness of identifiers in an SBML model. Please consult the SBML specifications for the exact details of the uniqueness requirements.
Parameters
sidthe string to use as the identifier of this Event
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.setMetaId (   self,
  metaid 
)
inherited

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

setMetaId(string metaid)   int
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.

The string metaid is copied.

Parameters
metaidthe 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,
  history 
)
inherited

Sets the ModelHistory of this object.

setModelHistory(ModelHistory history)   int

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

Parameters
historyModelHistory 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.Event.setName (   self,
  name 
)

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

setName(string name)   int

The string in name is copied.

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

Sets the namespaces relevant of this SBML object.

setNamespaces(XMLNamespaces xmlns)   int

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

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

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

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

setNotes(XMLNode notes)   int
setNotes(string notes, bool addXHTMLMarkup=False)   int
setNotes(string notes)   int

Each variant is described separately below.


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
notesan 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()

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

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

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

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

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

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

1 try:
2  sbmlDoc = SBMLDocument(3, 1)
3 except ValueError:
4  print('Could not create SBMLDocument object')
5  sys.exit(1)
6 
7 note = '<body xmlns='http://www.w3.org/1999/xhtml'><p>here is my note</p></body>'
8 
9 status = sbmlDoc.setNotes(note)
10 if status != LIBSBML_OPERATION_SUCCESS:
11  # Do something to handle the error here.
12  print('Unable to set notes on the SBML document object')
13  sys.exit(1)
Parameters
notesan XML string that is to be used as the content of the 'notes' subelement of this object
addXHTMLMarkupa boolean indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p>) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.Event.setPriority (   self,
  priority 
)
setPriority(Priority priority)   int

(SBML Level 3 only) Sets the priority definition of this Event to a copy of the given Priority object instance.

Parameters
prioritythe Priority object instance to use
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The element 'priority' is available in SBML Level 3 Version 1 Core, but is not present in lower Levels of SBML.
def libsbml.SBase.setSBOTerm (   self,
  args 
)
inherited

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

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

Each variant is described separately below.


Method variant with the following signature:
setSBOTerm(int value)

Sets the value of the 'sboTerm' attribute.

Beginning with SBML Level 2 Version 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
valuethe 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(stringsboid)

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
sboidthe 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.Event.setTimeUnits (   self,
  sid 
)

Sets the 'timeUnits' attribute of this Event to a copy of sid.

setTimeUnits(string sid)   int
Parameters
sidthe identifier of the time units to use.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Warning
Definitions of Event in SBML Level 2 Versions 1 and 2 included the additional attribute called 'timeUnits', but it was removed in SBML Level 2 Version 3. LibSBML supports this attribute for compatibility with previous versions of SBML Level 2, but its use is discouraged since models in Level 2 Versions 3 and 4 cannot contain it. If a Version 3 or 4 model sets the attribute, the consistency-checking method SBMLDocument.checkConsistency() will report an error.
def libsbml.Event.setTrigger (   self,
  trigger 
)

Sets the trigger definition of this Event to a copy of the given Trigger object instance.

setTrigger(Trigger trigger)   int
Parameters
triggerthe Trigger object instance to use.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.Event.setUseValuesFromTriggerTime (   self,
  value 
)

Sets the 'useValuesFromTriggerTime' attribute of this Event to a value.

setUseValuesFromTriggerTime(bool value)   int
The optional Delay on Event means there are two times to consider when computing the results of an event: the time at which the event is triggered, and the time at which assignments are executed. It is also possible to distinguish between the time at which the EventAssignment's expression is calculated, and the time at which the assignment is made: the expression could be evaluated at the same time the assignments are performed, i.e., when the event is executed, but it could also be defined to be evaluated at the time the event is triggered.

In SBML Level 2 versions prior to Version 4, the semantics of Event time delays were defined such that the expressions in the event's assignments were always evaluated at the time the event was triggered. This definition made it difficult to define an event whose assignment formulas were meant to be evaluated at the time the event was executed (i.e., after the time period defined by the value of the Delay element). In SBML Level 2 Version 4, the attribute 'useValuesFromTriggerTime' on Event allows a model to indicate the time at which the event's assignments are intended to be evaluated. In SBML Level 2, the attribute has a default value of True, which corresponds to the interpretation of event assignments prior to Version 4: the values of the assignment formulas are computed at the moment the event is triggered, not after the delay. If 'useValuesFromTriggerTime'=False, it means that the formulas in the event's assignments are to be computed after the delay, at the time the event is executed. In SBML Level 3, the attribute is mandatory, not optional, and all events must specify a value for it.

Parameters
valuethe value of useValuesFromTriggerTime to use.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Warning
The attribute 'useValuesFromTriggerTime' was introduced in SBML Level 2 Version 4. It is not valid in models defined using SBML Level 2 versions prior to Version 4. If a Level 2 Version 1–3 model sets the attribute, the consistency-checking method SBMLDocument.checkConsistency() will report an error.
def libsbml.SBase.toSBML (   self)
inherited

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

toSBML()   string
Returns
the partial SBML that describes this SBML object.
Warning
This is primarily provided for testing and debugging purposes. It may be removed in a future version of libSBML.
def libsbml.SBase.toXMLNode (   self)
inherited

Returns this element as an XMLNode.

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

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

unsetAnnotation()   int

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

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

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getAnnotation()
getAnnotationString()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
def libsbml.SBase.unsetCVTerms (   self)
inherited

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

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

Unsets the Delay of this Event.

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

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

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

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

unsetMetaId()   int
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.unsetModelHistory (   self)
inherited

Unsets the ModelHistory object attached to this object.

unsetModelHistory()   int
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
def libsbml.Event.unsetName (   self)

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

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

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

unsetNotes()   int

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

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

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
appendNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.Event.unsetPriority (   self)
unsetPriority()   int

(SBML Level 3 only) Unsets the Priority of this Event.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The element 'priority' is available in SBML Level 3 Version 1 Core, but is not present in lower Levels of SBML.
def libsbml.SBase.unsetSBOTerm (   self)
inherited

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

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

Unsets the 'timeUnits' attribute of this Event.

unsetTimeUnits()   int
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Warning
Definitions of Event in SBML Level 2 Versions 1 and 2 included the additional attribute called 'timeUnits', but it was removed in SBML Level 2 Version 3. LibSBML supports this attribute for compatibility with previous versions of SBML Level 2, but its use is discouraged since models in Level 2 Versions 3 and 4 cannot contain it. If a Version 3 or 4 model sets the attribute, the consistency-checking method SBMLDocument.checkConsistency() will report an error.
def libsbml.Event.unsetTrigger (   self)

Unsets the Trigger of this Event.

unsetTrigger()   int
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The element 'priority' is available in SBML Level 3 Version 1 Core, but is not present in lower Levels of SBML.