libsbml.Layout Class Reference

Inheritance diagram for libsbml.Layout:

Detailed Description

layout The layout of a diagram of an SBML model.

The Layout class stores layout information for some or all elements of the SBML model as well as additional objects that need not be connected to the model. The Layout has two attributes: id and name. Additionally, a Dimensions element specifies the size of the layout. The actual layout elements are contained in several lists, namely: a ListOfCompartmentGlyphs, a ListOfSpeciesGlyphs, a ListOfReactionGlyphs, a ListOfTextGlyphs, and a ListOfAdditionalGraphicalObjects. Each of these lists can only occur once, and, if present, are not allowed to be empty.

Public Member Functions
def	__init__ (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...
def	addAdditionalGraphicalObject (self, glyph)
	Adds a new additional graphical object glyph. More...
def	addCompartmentGlyph (self, glyph)
	Adds a new compartment glyph. More...
def	addCVTerm (self, term, newBag=False)
	Adds a copy of the given CVTerm object to this SBML object. More...
def	addGeneralGlyph (self, glyph)
	Adds a new general glyph. More...
def	addReactionGlyph (self, glyph)
	Adds a new reaction glyph. More...
def	addSpeciesGlyph (self, glyph)
	Adds a new species glyph. More...
def	addTextGlyph (self, glyph)
	Adds a new text glyph. 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 Layout. More...
def	connectToChild (self)
def	createAdditionalGraphicalObject (self)
	Creates a GraphicalObject object, adds it to the end of the additional graphical objects list and returns a pointer to the newly created object. More...
def	createCompartmentGlyph (self)
	Creates a CompartmentGlyph object, adds it to the end of the compartment glyph objects list and returns a pointer to the newly created object. More...
def	createCubicBezier (self)
	Creates a new CubicBezier for the Curve object of the last ReactionGlyph or the last SpeciesReferenceGlyph in the last ReactionGlyph and adds it to its list of SpeciesReferenceGlyph objects. More...
def	createGeneralGlyph (self)
	Creates a GeneralGlyph object, adds it to the end of the additional objects list and returns a reference to the newly created object. More...
def	createLineSegment (self)
	Creates a new LineSegment for the Curve object of the last ReactionGlyph or the last SpeciesReferenceGlyph in the last ReactionGlyph and adds it to its list of SpeciesReferenceGlyph objects. More...
def	createReactionGlyph (self)
	Creates a ReactionGlyph object, adds it to the end of the reaction glyph objects list and returns a pointer to the newly created object. More...
def	createSpeciesGlyph (self)
	Creates a SpeciesGlyph object, adds it to the end of the species glyph objects list and returns a pointer to the newly created object. More...
def	createSpeciesReferenceGlyph (self)
	Creates a new SpeciesReferenceGlyph for the last ReactionGlyph and adds it to its list of SpeciesReferenceGlyph objects. More...
def	createTextGlyph (self)
	Creates a TextGlyph object, adds it to the end of the text glyph objects list and returns a pointer to the newly created object. More...
def	deleteDisabledPlugins (self, recursive=True)
	Deletes all information stored in disabled plugins. More...
def	disablePackage (self, pkgURI, pkgPrefix)
	Disables the given SBML Level 3 package on this object. More...
def	enablePackage (self, pkgURI, pkgPrefix, flag)
	Enables or disables the given SBML Level 3 package on this object. More...
def	getAdditionalGraphicalObject (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...
def	getAncestorOfType (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...
def	getAnnotation (self, args)
	Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects. More...
def	getAnnotationString (self, args)
	Returns the content of the 'annotation' subelement of this object as a character string. More...
def	getColumn (self)
	Returns the column number where this object first appears in the XML representation of the SBML document. More...
def	getCompartmentGlyph (self, args)
	This method has multiple variants; they differ in the arguments they accept. 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	getDimensions (self)
	Returns the dimensions of the layout. More...
def	getDimensionsExplicitlySet (self)
def	getDisabledPlugin (self, args)
	Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More...
def	getElementByMetaId (self, args)
	Returns the first child element it can find with a specific 'metaid' attribute value, or None if no such object is found. More...
def	getElementBySId (self, args)
	Returns the first child element found that has the given id in the model-wide SId namespace, or None if no such object is found. More...
def	getElementName (self)
	Returns the XML element name of this SBML object. More...
def	getGeneralGlyph (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 Layout. More...
def	getIdAttribute (self)
	Returns the value of the 'id' attribute of this SBML object. More...
def	getLevel (self)
	Returns the SBML Level of the SBMLDocument object containing this object. More...
def	getLine (self)
	Returns the line number where this object first appears in the XML representation of the SBML document. More...
def	getListOfAdditionalGraphicalObjects (self)
	Returns the ListOf object that holds all additonal graphical objects. More...
def	getListOfAllElements (self, filter=None)
	Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth. More...
def	getListOfAllElementsFromPlugins (self, filter=None)
	Returns a List of all child SBase objects contained in SBML package plug-ins. More...
def	getListOfCompartmentGlyphs (self)
	Returns the ListOf object that holds all compartment glyphs. More...
def	getListOfReactionGlyphs (self)
	Returns the ListOf object that holds all reaction glyphs. More...
def	getListOfSpeciesGlyphs (self)
	Returns the ListOf object that holds all species glyphs. More...
def	getListOfTextGlyphs (self)
	Returns the ListOf object that holds all text glyphs. More...
def	getMetaId (self)
	Returns the value of the 'metaid' attribute of this SBML object. More...
def	getModel (self)
	Returns the Model object for the SBML Document in which the current object is located. More...
def	getModelHistory (self, args)
	Returns the ModelHistory object, if any, attached to this object. More...
def	getName (self)
	Returns the value of the 'name' attribute of this Layout object. More...
def	getNamespaces (self)
	Returns a list of the XML Namespaces declared on the SBML document owning this object. More...
def	getNotes (self, args)
	Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects. More...
def	getNotesString (self, args)
	Returns the content of the 'notes' subelement of this object as a string. More...
def	getNumAdditionalGraphicalObjects (self)
	Returns the number of additional graphical objects for the layout. More...
def	getNumCompartmentGlyphs (self)
	Returns the number of compartment glyphs for the layout. More...
def	getNumCVTerms (self)
	Returns the number of CVTerm objects in the annotations of this SBML object. More...
def	getNumDisabledPlugins (self)
	Returns the number of disabled plug-in objects (extension interfaces) for SBML Level 3 package extensions known. More...
def	getNumGeneralGlyphs (self)
	Returns the number of general glyphs for the layout. More...
def	getNumPlugins (self)
	Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More...
def	getNumReactionGlyphs (self)
	Returns the number of reaction glyphs for the layout. More...
def	getNumSpeciesGlyphs (self)
	Returns the number of species glyphs for the layout. More...
def	getNumTextGlyphs (self)
	Returns the number of text glyphs for the layout. More...
def	getPackageCoreVersion (self)
	Returns the SBML Core Version within the SBML Level of the actual object. More...
def	getPackageName (self)
	Returns the name of the SBML Level 3 package in which this element is defined. More...
def	getPackageVersion (self)
	Returns the Version of the SBML Level 3 package to which this element belongs to. More...
def	getParentSBMLObject (self, args)
	Returns the parent SBML object containing this object. More...
def	getPlugin (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...
def	getPrefix (self)
	Returns the XML namespace prefix of this element. More...
def	getReactionGlyph (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...
def	getResourceBiologicalQualifier (self, resource)
	Returns the MIRIAM biological qualifier associated with the given resource. More...
def	getResourceModelQualifier (self, resource)
	Returns the MIRIAM model qualifier associated with the given resource. More...
def	getSBMLDocument (self, args)
	Returns the SBMLDocument object containing this object instance. More...
def	getSBOTerm (self)
	Returns the integer portion of the value of the 'sboTerm' attribute of this object. More...
def	getSBOTermAsURL (self)
	Returns the URL representation of the 'sboTerm' attribute of this object. More...
def	getSBOTermID (self)
	Returns the string representation of the 'sboTerm' attribute of this object. More...
def	getSpeciesGlyph (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...
def	getTextGlyph (self, args)
	This method has multiple variants; they differ in the arguments they accept. 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	getVersion (self)
	Returns the Version within the SBML Level of the SBMLDocument object containing this object. More...
def	hasValidLevelVersionNamespaceCombination (self)
	Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More...
def	initDefaults (self)
	Does nothing since no defaults are defined for Layout. 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	isSetId (self)
	Predicate returning True or False depending on whether this Layout's 'id' attribute has been set. More...
def	isSetIdAttribute (self)
	Predicate returning True if this object'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 or False depending on whether this Layout's 'name' attribute has been set. More...
def	isSetNotes (self)
	Predicate returning True if this object's 'notes' subelement exists and has content. More...
def	isSetSBOTerm (self)
	Predicate returning True if this object's 'sboTerm' attribute is set. More...
def	isSetUserData (self)
	Predicate returning true or false depending on whether the user data of this element has been 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	removeAdditionalGraphicalObject (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...
def	removeCompartmentGlyph (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	removeReactionGlyph (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...
def	removeSpeciesGlyph (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...
def	removeSpeciesReferenceGlyph (self, id)
	Remove the species reference glyph with the given id. More...
def	removeTextGlyph (self, args)
	This method has multiple variants; they differ in the arguments they accept. 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	setDimensions (self, dimensions)
	Sets the dimensions of the layout. More...
def	setId (self, sid)
	Sets the value of the 'id' attribute of this Layout. More...
def	setIdAttribute (self, sid)
	Sets the value of the 'id' attribute of this SBML object. More...
def	setMetaId (self, metaid)
	Sets the value of the meta-identifier attribute of this SBML object. More...
def	setModelHistory (self, history)
	Sets the ModelHistory of this object. More...
def	setName (self, name)
	Sets the value of the 'name' attribute of this Layout. More...
def	setNamespaces (self, xmlns)
	Sets the namespaces relevant of this SBML object. More...
def	setNotes (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...
def	setSBOTerm (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...
def	toSBML (self)
	Returns a string consisting of a partial SBML corresponding to just this object. More...
def	toXML (self)
	Creates an XMLNode object from this. More...
def	toXMLNode (self)
	Returns this element as an XMLNode. More...
def	unsetAnnotation (self)
	Unsets the value of the 'annotation' subelement of this SBML object. More...
def	unsetCVTerms (self)
	Clears the list of CVTerm objects attached to this SBML object. More...
def	unsetId (self)
	Unsets the value of the 'id' attribute of this Layout. More...
def	unsetIdAttribute (self)
	Unsets the value of the 'id' attribute of this SBML object. More...
def	unsetMetaId (self)
	Unsets the value of the 'metaid' attribute of this SBML object. More...
def	unsetModelHistory (self)
	Unsets the ModelHistory object attached to this object. More...
def	unsetName (self)
	Unsets the value of the 'name' attribute of this Layout. More...
def	unsetNotes (self)
	Unsets the value of the 'notes' subelement of this SBML object. More...
def	unsetSBOTerm (self)
	Unsets the value of the 'sboTerm' attribute of this SBML object. More...
def	unsetUserData (self)
	Unsets the user data of this element. More...

Constructor & Destructor Documentation

def libsbml.Layout.__init__	(		self,
			args
	)

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

__init__(long  level, long  version, long  pkgVersion)   Layout
__init__(long  level, long  version)   Layout
__init__(long  level)   Layout
__init__()   Layout
__init__(LayoutPkgNamespaces layoutns)   Layout
__init__(LayoutPkgNamespaces layoutns, string id, Dimensions dimensions)   Layout
__init__(XMLNode node, long  l2version=4)   Layout
__init__(XMLNode node)   Layout
__init__(Layout source)   Layout

Each variant is described separately below.

---

Method variant with the following signature:

Layout(Layout source)

Copy constructor.

Parameters

source

the instance to copy.

---

Method variant with the following signature:

Layout(LayoutPkgNamespaces layoutns)

Creates a new Layout with the given LayoutPkgNamespaces object.

The package namespaces object used in this constructor is derived from a SBMLNamespaces object, which encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and package version and name information used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an package namespace object somewhere in a program once, then hand that object as needed to object constructors of that package that accept it as and argument, such as this one.

Parameters

layoutns

the LayoutPkgNamespaces object.

Note

Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.

---

Method variant with the following signature:

Layout(LayoutPkgNamespaces layoutns, string id, Dimensions dimensions)

Creates a new Layout with the given id and dimensions.

(FOR BACKWARD COMPATIBILITY)

---

Method variant with the following signature:

Layout(long level = LayoutExtension.getDefaultLevel(), long version = LayoutExtension.getDefaultVersion(), long pkgVersion = LayoutExtension.getDefaultPackageVersion())

Creates a new Layout with the given level, version, and package version.

Parameters

level	the SBML Level.
version	the Version within the SBML Level.
pkgVersion	the version of the package.

Note

Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.

Owing to the way that language interfaces are created in libSBML, this documentation may show methods that define default values for parameters with text that has the form parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.

---

Method variant with the following signature:

Layout(XMLNode node, long l2version = 4)

Creates a new Layout from the given XMLNode (only for SBML Level2)

(FOR BACKWARD COMPATIBILITY)

Note

Owing to the way that language interfaces are created in libSBML, this documentation may show methods that define default values for parameters with text that has the form parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.

Member Function Documentation

def libsbml.Layout.addAdditionalGraphicalObject	(		self,
			glyph
	)

Adds a new additional graphical object glyph.

addAdditionalGraphicalObject(GraphicalObject glyph)   int

def libsbml.Layout.addCompartmentGlyph	(		self,
			glyph
	)

Adds a new compartment glyph.

addCompartmentGlyph(CompartmentGlyph glyph)   int

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

inherited

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

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

Parameters

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

Returns

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

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

Note

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

This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.

Owing to the way that language interfaces are created in libSBML, this documentation may show methods that define default values for parameters with text that has the form parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.

def libsbml.Layout.addGeneralGlyph	(		self,
			glyph
	)

Adds a new general glyph.

addGeneralGlyph(GeneralGlyph glyph)   int

def libsbml.Layout.addReactionGlyph	(		self,
			glyph
	)

Adds a new reaction glyph.

addReactionGlyph(ReactionGlyph glyph)   int

def libsbml.Layout.addSpeciesGlyph	(		self,
			glyph
	)

Adds a new species glyph.

addSpeciesGlyph(SpeciesGlyph glyph)   int

def libsbml.Layout.addTextGlyph	(		self,
			glyph
	)

Adds a new text glyph.

addTextGlyph(TextGlyph glyph)   int

def libsbml.SBase.appendAnnotation (   self,   args  )

inherited

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

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

Each variant is described separately below.

---

Method variant with the following signature:

appendAnnotation(XMLNode annotation)

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

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

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

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

Parameters

annotation

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

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED
• LIBSBML_UNEXPECTED_ATTRIBUTE (if the parent element does not have the 'metaid' attribute set)
• LIBSBML_DUPLICATE_ANNOTATION_NS (if the parent was already annotated with the annotation in question)

See also

getAnnotationString()

isSetAnnotation()

setAnnotation()

setAnnotation()

appendAnnotation()

unsetAnnotation()

---

Method variant with the following signature:

appendAnnotation(string annotation)

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

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

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

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

Parameters

annotation

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

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED
• LIBSBML_UNEXPECTED_ATTRIBUTE (if the parent element does not have the 'metaid' attribute set)
• LIBSBML_DUPLICATE_ANNOTATION_NS (if the parent was already annotated with the annotation in question)

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(string notes)

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

The content of the parameter notes is copied.

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

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

Parameters

notes

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

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_OBJECT
• LIBSBML_OPERATION_FAILED

See also

getNotesString()

isSetNotes()

setNotes()

setNotes()

appendNotes()

unsetNotes()

SyntaxChecker.hasExpectedXHTMLSyntax()

---

Method variant with the following signature:

appendNotes(XMLNode notes)

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

The content of notes is copied.

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

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

Parameters

notes

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

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_OBJECT
• LIBSBML_OPERATION_FAILED

See also

getNotesString()

isSetNotes()

setNotes()

setNotes()

appendNotes()

unsetNotes()

SyntaxChecker.hasExpectedXHTMLSyntax()

def libsbml.Layout.clone

(

self

)

Creates and returns a deep copy of this Layout.

clone()   Layout

Returns

a (deep) copy of this Layout.

def libsbml.Layout.connectToChild

(

self

)

connectToChild()

def libsbml.Layout.createAdditionalGraphicalObject

(

self

)

Creates a GraphicalObject object, adds it to the end of the additional graphical objects list and returns a pointer to the newly created object.

createAdditionalGraphicalObject()   GraphicalObject

def libsbml.Layout.createCompartmentGlyph

(

self

)

Creates a CompartmentGlyph object, adds it to the end of the compartment glyph objects list and returns a pointer to the newly created object.

createCompartmentGlyph()   CompartmentGlyph

def libsbml.Layout.createCubicBezier

(

self

)

Creates a new CubicBezier for the Curve object of the last ReactionGlyph or the last SpeciesReferenceGlyph in the last ReactionGlyph and adds it to its list of SpeciesReferenceGlyph objects.

createCubicBezier()   CubicBezier

A pointer to the newly created object is returned.

def libsbml.Layout.createGeneralGlyph

(

self

)

Creates a GeneralGlyph object, adds it to the end of the additional objects list and returns a reference to the newly created object.

createGeneralGlyph()   GeneralGlyph

def libsbml.Layout.createLineSegment

(

self

)

Creates a new LineSegment for the Curve object of the last ReactionGlyph or the last SpeciesReferenceGlyph in the last ReactionGlyph and adds it to its list of SpeciesReferenceGlyph objects.

createLineSegment()   LineSegment

A pointer to the newly created object is returned.

def libsbml.Layout.createReactionGlyph

(

self

)

Creates a ReactionGlyph object, adds it to the end of the reaction glyph objects list and returns a pointer to the newly created object.

createReactionGlyph()   ReactionGlyph

def libsbml.Layout.createSpeciesGlyph

(

self

)

Creates a SpeciesGlyph object, adds it to the end of the species glyph objects list and returns a pointer to the newly created object.

createSpeciesGlyph()   SpeciesGlyph

def libsbml.Layout.createSpeciesReferenceGlyph

(

self

)

Creates a new SpeciesReferenceGlyph for the last ReactionGlyph and adds it to its list of SpeciesReferenceGlyph objects.

createSpeciesReferenceGlyph()   SpeciesReferenceGlyph

A pointer to the newly created object is returned.

def libsbml.Layout.createTextGlyph

(

self

)

Creates a TextGlyph object, adds it to the end of the text glyph objects list and returns a pointer to the newly created object.

createTextGlyph()   TextGlyph

def libsbml.SBase.deleteDisabledPlugins (   self,   recursive = True  )

inherited

Deletes all information stored in disabled plugins.

deleteDisabledPlugins(bool recursive)
deleteDisabledPlugins()

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

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

If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.

Parameters

recursive

if True, the disabled information will be deleted also from all child elements, otherwise only from this SBase element.

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:

import sys
import os.path
from libsbml import *

# We read an SBML L3V1 model that uses the 'comp' package.

doc = readSBML('sbml-file-with-comp-elements.xml');
if doc.getNumErrors() > 0:
  print('readSBML encountered errors while reading the file.')
  doc.printErrors()
  sys.exit(1)

# We extract one of the species from the model.

model = doc.getModel()
if model == None:
  print('Unable to retrieve Model object')
  sys.exit(1)

s1 = model.getSpecies(0)
if s1 == None:
  print('Unable to retrieve Species object')
  sys.exit(1)

# We construct a new model.
# This model does not use the 'comp' package.

try:
  newDoc = SBMLDocument(3, 1)
except ValueError:
  print('Could not create SBMLDocument object')
  sys.exit(1)

newModel = newDoc.createModel()
if newModel == None:
  print('Unable to create new Model object')
  sys.exit(1)

# The following would normally fail with an error, because
# addSpecies() would first check that the parent of the given
# object has namespaces declared, and will discover that s1
# does but newModel does not.

#   newModel.addSpecies(s1)

# However, if we disable the 'comp' package on s1, then the
# call to addSpecies will work.

compNS = 'http://www.sbml.org/sbml/level3/version1/comp/version1'
status = s1.disablePackage(compNS, 'comp')
if status != LIBSBML_OPERATION_SUCCESS:
  print('Unable to disable package.')
  sys.exit(1)

newSpecies = newModel.addSpecies(s1)   # This will work now.
if newSpecies == None:
  print('Could not add Species')       # (This will not happen,
  sys.exit(1)                          # but always check errors.)

Parameters

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

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_PKG_UNKNOWN
• LIBSBML_PKG_VERSION_MISMATCH
• LIBSBML_PKG_CONFLICTED_VERSION

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

pkgURI	the URI of the package.
pkgPrefix	the XML prefix of the package.
flag	whether to enable (True) or disable (False) the package.

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_PKG_UNKNOWN
• LIBSBML_PKG_VERSION_MISMATCH
• LIBSBML_PKG_CONFLICTED_VERSION

See also

disablePackage()

def libsbml.Layout.getAdditionalGraphicalObject	(		self,
			args
	)

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

getAdditionalGraphicalObject(long  index)   GraphicalObject
getAdditionalGraphicalObject(string id)   GraphicalObject

Each variant is described separately below.

---

Method variant with the following signature:

getAdditionalGraphicalObject(long index)

Returns the additional graphical object with the given index. If the index is invalid, None is returned.

---

Method variant with the following signature:

getAdditionalGraphicalObject(string id)

Returns the additional graphical object that has the given id, or None if no graphical object has the id.

def libsbml.SBase.getAncestorOfType (   self,   args  )

inherited

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

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

Each variant is described separately below.

---

Method variant with the following signature:

getAncestorOfType(int type, string pkgName = 'core')

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

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

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

Parameters

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

Returns

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

Warning

The optional argument pkgName must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the 'core' namespace alone, not find any corresponding elements, and return None.

Note

Owing to the way that language interfaces are created in libSBML, this documentation may show methods that define default values for parameters with text that has the form parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.

---

Method variant with the following signature:

getAncestorOfType(int type, string pkgName = 'core')

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

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

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

Parameters

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

Returns

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

Warning

The optional argument pkgName must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the 'core' namespace alone, not find any corresponding elements, and return None.

Note

Owing to the way that language interfaces are created in libSBML, this documentation may show methods that define default values for parameters with text that has the form parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.

def libsbml.SBase.getAnnotation (   self,   args  )

inherited

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

getAnnotation()   XMLNode

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

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

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

Returns

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

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

getColumn()   long

Returns

the column number of this SBML object. If this object was created programmatically and not read from a file, this method will return the value 0.

Note

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

See also

getLine()

def libsbml.Layout.getCompartmentGlyph	(		self,
			args
	)

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

getCompartmentGlyph(long  index)   CompartmentGlyph
getCompartmentGlyph(string id)   CompartmentGlyph

Each variant is described separately below.

---

Method variant with the following signature:

getCompartmentGlyph(long index)

Returns the compartment glyph with the given index. If the index is invalid, None is returned.

---

Method variant with the following signature:

getCompartmentGlyph(string id)

Returns the compartment glyph that has the given id, or None if no compartment glyph has the id.

def libsbml.SBase.getCVTerm (   self,   n  )

inherited

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

getCVTerm(long  n)   CVTerm

Parameters

n	long the index of the CVTerm to retrieve.

Returns

the nth CVTerm in the list of CVTerms for this SBML object. If the index n is invalid, None is returned.

def libsbml.SBase.getCVTerms (   self,   args  )

inherited

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

getCVTerms()   List *

Returns

the list of CVTerms for this SBML object.

def libsbml.Layout.getDimensions

(

self

)

Returns the dimensions of the layout.

getDimensions()   Dimensions

def libsbml.Layout.getDimensionsExplicitlySet

(

self

)

getDimensionsExplicitlySet()   bool

Predicate returning true if the dimensions has been set

def libsbml.SBase.getDisabledPlugin (   self,   args  )

inherited

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

getDisabledPlugin(long  n)   SBasePlugin

If no such plugin exists, None is returned.

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

If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.

Parameters

n	the index of the disabled plug-in to return.

Returns

the nth disabled plug-in object (the libSBML extension interface) of a package extension. If the index n is invalid, None is returned.

See also

getNumDisabledPlugins()

getPlugin()

def libsbml.SBase.getElementByMetaId (   self,   args  )

inherited

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

getElementByMetaId(string metaid)   SBase

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

Parameters

metaid

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

Returns

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

def libsbml.SBase.getElementBySId (   self,   args  )

inherited

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

getElementBySId(string id)   SBase

Parameters

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

Returns

pointer to the first element found with the given identifier.

def libsbml.Layout.getElementName

(

self

)

Returns the XML element name of this SBML object.

getElementName()   string

Returns

the string of the name of this element.

def libsbml.Layout.getGeneralGlyph	(		self,
			args
	)

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

getGeneralGlyph(long  index)   GeneralGlyph
getGeneralGlyph(string id)   GeneralGlyph

Each variant is described separately below.

---

Method variant with the following signature:

getGeneralGlyph(long index)

Returns the general glyph with the given index. If the index is invalid, None is returned.

---

Method variant with the following signature:

getGeneralGlyph(string id)

Returns the general glyph that has the given id, or None if no graphical object has the id.

def libsbml.Layout.getId

(

self

)

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

getId()   string

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

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

The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

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

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

Returns

the id of this Layout.

Note

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

See also

getIdAttribute()

setIdAttribute()

isSetIdAttribute()

unsetIdAttribute()

def libsbml.SBase.getIdAttribute (   self )

inherited

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

getIdAttribute()   string

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

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

The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

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

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

Returns

the id of this SBML object, if set and valid for this level and version of SBML; an empty string otherwise.

Note

Because of the inconsistent behavior of this function with respect to assignments and rules, callers should use getIdAttribute() instead.

See also

setIdAttribute()

isSetIdAttribute()

unsetIdAttribute()

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

getLine()   long

Returns

the line number of this SBML object. If this object was created programmatically and not read from a file, this method will return the value 0.

Note

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

See also

getColumn()

def libsbml.Layout.getListOfAdditionalGraphicalObjects

(

self

)

Returns the ListOf object that holds all additonal graphical objects.

getListOfAdditionalGraphicalObjects()   ListOfGraphicalObjects

def libsbml.SBase.getListOfAllElements (   self,   filter = None  )

inherited

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

getListOfAllElements(ElementFilter filter)   SBaseList
getListOfAllElements()   SBaseList

Returns

a list of all objects that are children of this object.

def libsbml.SBase.getListOfAllElementsFromPlugins (   self,   filter = None  )

inherited

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

getListOfAllElementsFromPlugins(ElementFilter filter)   SBaseList
getListOfAllElementsFromPlugins()   SBaseList

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

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

Returns

a pointer to a List of pointers to all children objects from plug-ins.

def libsbml.Layout.getListOfCompartmentGlyphs

(

self

)

Returns the ListOf object that holds all compartment glyphs.

getListOfCompartmentGlyphs()   ListOfCompartmentGlyphs

def libsbml.Layout.getListOfReactionGlyphs

(

self

)

Returns the ListOf object that holds all reaction glyphs.

getListOfReactionGlyphs()   ListOfReactionGlyphs

def libsbml.Layout.getListOfSpeciesGlyphs

(

self

)

Returns the ListOf object that holds all species glyphs.

getListOfSpeciesGlyphs()   ListOfSpeciesGlyphs

def libsbml.Layout.getListOfTextGlyphs

(

self

)

Returns the ListOf object that holds all text glyphs.

getListOfTextGlyphs()   ListOfTextGlyphs

def libsbml.SBase.getMetaId (   self )

inherited

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

getMetaId()   string

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

Returns

the meta-identifier of this SBML object.

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.Layout.getName

(

self

)

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

getName()   string

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

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

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

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

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

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

Returns

the name of this SBML object, or the empty string if not set or unsettable.

See also

getIdAttribute()

isSetName()

setName()

unsetName()

def libsbml.SBase.getNamespaces (   self )

inherited

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

getNamespaces()   XMLNamespaces

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

Returns

the XML Namespaces associated with this SBML object, or None in certain very usual circumstances where a namespace is not set.

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.Layout.getNumAdditionalGraphicalObjects

(

self

)

Returns the number of additional graphical objects for the layout.

getNumAdditionalGraphicalObjects()   long

def libsbml.Layout.getNumCompartmentGlyphs

(

self

)

Returns the number of compartment glyphs for the layout.

getNumCompartmentGlyphs()   long

def libsbml.SBase.getNumCVTerms (   self )

inherited

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

getNumCVTerms()   long

Returns

the number of CVTerms for this SBML object.

def libsbml.SBase.getNumDisabledPlugins (   self )

inherited

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

getNumDisabledPlugins()   long

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

If a plugin is disabled, the package information it contains is no longer considered to be part of the SBML document for the purposes of searching the document or writing out the document. However, the information is still retained, so if the plugin is enabled again, the same information will once again be available, and will be written out to the final model.

Returns

the number of disabled plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.

def libsbml.Layout.getNumGeneralGlyphs

(

self

)

Returns the number of general glyphs for the layout.

getNumGeneralGlyphs()   long

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.Layout.getNumReactionGlyphs

(

self

)

Returns the number of reaction glyphs for the layout.

getNumReactionGlyphs()   long

def libsbml.Layout.getNumSpeciesGlyphs

(

self

)

Returns the number of species glyphs for the layout.

getNumSpeciesGlyphs()   long

def libsbml.Layout.getNumTextGlyphs

(

self

)

Returns the number of text glyphs for the layout.

getNumTextGlyphs()   long

def libsbml.SBase.getPackageCoreVersion (   self )

inherited

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

getPackageCoreVersion()   long

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

Returns

the SBML core version of this SBML object.

def libsbml.SBase.getPackageName (   self )

inherited

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

getPackageName()   string

Returns

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

def libsbml.SBase.getPackageVersion (   self )

inherited

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

getPackageVersion()   long

Returns

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

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. The returned plug-in will be the appropriate type of plugin requested: calling Model.getPlugin() will return an FbcModelPlugin; calling Parameter.getPlugin() will return CompSBasePlugin, etc.

If no such plugin exists, None is returned.

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

Parameters

n	the index of the plug-in to return.

Returns

the nth plug-in object (the libSBML extension interface) of a package extension. If the index n is invalid, None is returned.

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. The returned plug-in will be the appropriate type of plugin requested: calling Model.getPlugin() will return an FbcModelPlugin; calling Parameter.getPlugin() will return CompSBasePlugin, etc.

If no such plugin exists, None is returned.

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

Parameters

package

the name or URI of the package.

Returns

the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.

See also

getPlugin()

def libsbml.SBase.getPrefix (   self )

inherited

Returns the XML namespace prefix of this element.

getPrefix()   string

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

Returns

a text string representing the XML namespace prefix.

def libsbml.Layout.getReactionGlyph	(		self,
			args
	)

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

getReactionGlyph(long  index)   ReactionGlyph
getReactionGlyph(string id)   ReactionGlyph

Each variant is described separately below.

---

Method variant with the following signature:

getReactionGlyph(long index)

Returns the reaction glyph with the given index. If the index is invalid, None is returned.

---

Method variant with the following signature:

getReactionGlyph(string id)

Returns the reaction glyph that has the given id, or None if no reaction glyph has the id.

def libsbml.SBase.getResourceBiologicalQualifier (   self,   resource  )

inherited

Returns the MIRIAM biological qualifier associated with the given resource.

getResourceBiologicalQualifier(string resource)   long

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

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

Parameters

resource

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

Returns

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

Note

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

def libsbml.SBase.getResourceModelQualifier (   self,   resource  )

inherited

Returns the MIRIAM model qualifier associated with the given resource.

getResourceModelQualifier(string resource)   long

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

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

Parameters

resource

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

Returns

the model qualifier type associated with the resource, or BQM_UNKNOWN if the resource does not exist.

Note

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

def libsbml.SBase.getSBMLDocument (   self,   args  )

inherited

Returns the SBMLDocument object containing this object instance.

getSBMLDocument()   SBMLDocument

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

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

Returns

the parent SBMLDocument object of this SBML object.

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

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. More details can be found in SBML specifications for Level 2 Version 2 and above.

Returns

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

def libsbml.SBase.getSBOTermAsURL (   self )

inherited

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

getSBOTermAsURL()   string

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

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. More details can be found in SBML specifications for Level 2 Version 2 and above.

Returns

the value of the 'sboTerm' attribute as an identifiers.org URL, or an empty string if the value is not set.

def libsbml.SBase.getSBOTermID (   self )

inherited

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

getSBOTermID()   string

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

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. More details can be found in SBML specifications for Level 2 Version 2 and above.

Returns

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

def libsbml.Layout.getSpeciesGlyph	(		self,
			args
	)

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

getSpeciesGlyph(long  index)   SpeciesGlyph
getSpeciesGlyph(string id)   SpeciesGlyph

Each variant is described separately below.

---

Method variant with the following signature:

getSpeciesGlyph(long index)

Returns the species glyph with the given index. If the index is invalid, None is returned.

---

Method variant with the following signature:

getSpeciesGlyph(string id)

Returns the species glyph that has the given id, or None if no species glyph has the id.

def libsbml.Layout.getTextGlyph	(		self,
			args
	)

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

getTextGlyph(long  index)   TextGlyph
getTextGlyph(string id)   TextGlyph

Each variant is described separately below.

---

Method variant with the following signature:

getTextGlyph(long index)

Returns the text glyph with the given index. If the index is invalid, None is returned.

---

Method variant with the following signature:

getTextGlyph(string id)

Returns the text glyph that has the given id, or None if no text glyph has the id.

def libsbml.Layout.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 SBase.getPackageName() method on the object.

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

Returns

the SBML type code for this object: SBML_LAYOUT_LAYOUT.

Warning

The specific integer values of the possible type codes may be reused by different libSBML plug-ins for SBML Level 3. packages, To fully identify the correct code, it is necessary to invoke both getPackageName() and getTypeCode() (or ListOf.getItemTypeCode()).

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 will then look for the namespace associated with the element itself.

Returns

the URI of this element, as a text string.

See also

getSBMLDocument()

getPackageName()

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.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.Layout.initDefaults

(

self

)

Does nothing since no defaults are defined for Layout.

initDefaults()

def libsbml.SBase.isPackageEnabled (   self,   pkgName  )

inherited

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

isPackageEnabled(string pkgName)   bool

The search ignores the package version.

Parameters

pkgName

the name of the package.

Returns

True if the given package is enabled within this object, False otherwise.

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

pkgURI

the URI of the package.

Returns

True if the given package is enabled within this object, False otherwise.

See also

isPackageEnabled()

def libsbml.SBase.isPkgEnabled (   self,   pkgName  )

inherited

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

isPkgEnabled(string pkgName)   bool

The search ignores the package version.

Parameters

pkgName

the name of the package.

Returns

True if the given package is enabled within this object, False otherwise.

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

pkgURI

the 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.Layout.isSetId

(

self

)

Predicate returning True or False depending on whether this Layout's 'id' attribute has been set.

isSetId()   bool

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

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

The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

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

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

Returns

True if the 'id' attribute of this SBML object is set, False otherwise.

Note

Because of the inconsistent behavior of this function with respect to assignments and rules, it is recommended that callers use isSetIdAttribute() instead.

See also

getIdAttribute()

setIdAttribute()

unsetIdAttribute()

isSetIdAttribute()

def libsbml.SBase.isSetIdAttribute (   self )

inherited

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

isSetIdAttribute()   bool

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

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

The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

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

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

Returns

True if the 'id' attribute of this SBML object is set, False otherwise.

See also

getIdAttribute()

setIdAttribute()

unsetIdAttribute()

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.Layout.isSetName

(

self

)

Predicate returning True or False depending on whether this Layout's 'name' attribute has been set.

isSetName()   bool

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

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

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

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

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

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

Returns

True if the 'name' attribute of this SBML object is set, False otherwise.

See also

getName()

setName()

unsetName()

def libsbml.SBase.isSetNotes (   self )

inherited

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

isSetNotes()   bool

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

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

Returns

True if a 'notes' subelement exists, False otherwise.

See also

getNotes()

getNotesString()

setNotes()

setNotes()

appendNotes()

appendNotes()

unsetNotes()

SyntaxChecker.hasExpectedXHTMLSyntax()

def libsbml.SBase.isSetSBOTerm (   self )

inherited

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

isSetSBOTerm()   bool

Returns

True if the 'sboTerm' attribute of this SBML object is set, False otherwise.

def libsbml.SBase.isSetUserData (   self )

inherited

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

isSetUserData()   bool

The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.

Returns

boolean, True if this object's user data has been set, False otherwise.

def libsbml.SBase.matchesRequiredSBMLNamespacesForAddition (   self,   args  )

inherited

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

matchesRequiredSBMLNamespacesForAddition(SBase sb)   bool

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

Parameters

sb	an object to compare with respect to namespaces.

Returns

boolean, True if this object's collection of namespaces is a subset of sb's, False otherwise.

def libsbml.SBase.matchesSBMLNamespaces (   self,   args  )

inherited

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

matchesSBMLNamespaces(SBase sb)   bool

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

Parameters

sb	an object to compare with respect to namespaces.

Returns

boolean, True if this object's collection of namespaces is the same as sb's, False otherwise.

def libsbml.Layout.removeAdditionalGraphicalObject	(		self,
			args
	)

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

removeAdditionalGraphicalObject(long  index)   GraphicalObject
removeAdditionalGraphicalObject(string id)   GraphicalObject

Each variant is described separately below.

---

Method variant with the following signature:

removeAdditionalGraphicalObject(long index)

Removes the graphical object with the given index from the layout. A pointer to the graphical object that was removed is returned. If no graphical object has been removed, None is returned.

---

Method variant with the following signature:

removeAdditionalGraphicalObject(string id)

Remove the graphical object with the given id. A pointer to the removed graphical object is returned. If no graphical object has been removed, None is returned.

def libsbml.Layout.removeCompartmentGlyph	(		self,
			args
	)

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

removeCompartmentGlyph(long  index)   CompartmentGlyph
removeCompartmentGlyph(string id)   CompartmentGlyph

Each variant is described separately below.

---

Method variant with the following signature:

removeCompartmentGlyph(long index)

Removes the compartment glyph with the given index from the layout. A pointer to the compartment glyph that was removed is returned. If no compartment glyph has been removed, None is returned.

---

Method variant with the following signature:

removeCompartmentGlyph(string id)

Remove the compartment glyph with the given id. A pointer to the removed compartment glyph is returned. If no compartment glyph has been removed, None is returned.

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:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

def libsbml.Layout.removeReactionGlyph	(		self,
			args
	)

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

removeReactionGlyph(long  index)   ReactionGlyph
removeReactionGlyph(string id)   ReactionGlyph

Each variant is described separately below.

---

Method variant with the following signature:

removeReactionGlyph(long index)

Removes the reaction glyph with the given index from the layout. A pointer to the reaction glyph that was removed is returned. If no reaction glyph has been removed, None is returned.

---

Method variant with the following signature:

removeReactionGlyph(string id)

Remove the reaction glyph with the given id. A pointer to the removed reaction glyph is returned. If no reaction glyph has been removed, None is returned.

def libsbml.Layout.removeSpeciesGlyph	(		self,
			args
	)

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

removeSpeciesGlyph(long  index)   SpeciesGlyph
removeSpeciesGlyph(string id)   SpeciesGlyph

Each variant is described separately below.

---

Method variant with the following signature:

removeSpeciesGlyph(long index)

Removes the species glyph with the given index from the layout. A pointer to the species glyph that was removed is returned. If no species glyph has been removed, None is returned.

---

Method variant with the following signature:

removeSpeciesGlyph(string id)

Remove the species glyph with the given id. A pointer to the removed species glyph is returned. If no species glyph has been removed, None is returned.

def libsbml.Layout.removeSpeciesReferenceGlyph	(		self,
			id
	)

Remove the species reference glyph with the given id.

removeSpeciesReferenceGlyph(string id)   SpeciesReferenceGlyph

A pointer to the removed species reference glyph is returned. If no species reference glyph has been removed, None is returned.

def libsbml.Layout.removeTextGlyph	(		self,
			args
	)

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

removeTextGlyph(long  index)   TextGlyph
removeTextGlyph(string id)   TextGlyph

Each variant is described separately below.

---

Method variant with the following signature:

removeTextGlyph(long index)

Removes the text glyph with the given index from the layout. A pointer to the text glyph that was removed is returned. If no text glyph has been removed, None is returned.

---

Method variant with the following signature:

removeTextGlyph(string id)

Remove the text glyph with the given id. A pointer to the removed text glyph is returned. If no text glyph has been removed, None is returned.

def libsbml.SBase.removeTopLevelAnnotationElement (   self,   args  )

inherited

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

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

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

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

Parameters

elementName	a string representing the name of the top level annotation element that is to be removed.
elementURI	an optional string that is used to check both the name and URI of the top level element to be removed.
removeEmpty	if after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default).

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED
• LIBSBML_ANNOTATION_NAME_NOT_FOUND
• LIBSBML_ANNOTATION_NS_NOT_FOUND

See also

replaceTopLevelAnnotationElement()

replaceTopLevelAnnotationElement()

Note

Owing to the way that language interfaces are created in libSBML, this documentation may show methods that define default values for parameters with text that has the form parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.

def libsbml.SBase.renameMetaIdRefs (   self,   oldid,   newid  )

inherited

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

renameMetaIdRefs(string oldid, string newid)

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

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

Parameters

oldid	the old identifier.
newid	the new identifier.

def libsbml.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 SIdRef in Level 3. These and other methods of libSBML refer to the type SIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

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

Parameters

oldid	the old identifier.
newid	the new identifier.

def libsbml.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

oldid	the old identifier.
newid	the new identifier.

def libsbml.SBase.replaceTopLevelAnnotationElement (   self,   args  )

inherited

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

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

Each variant is described separately below.

---

Method variant with the following signature:

replaceTopLevelAnnotationElement(XMLNode annotation)

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

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

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

Parameters

annotation

XMLNode representing the replacement top level annotation.

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED
• LIBSBML_INVALID_OBJECT

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

annotation

string representing the replacement top level annotation.

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED
• LIBSBML_INVALID_OBJECT

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

annotation

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

Returns

integer value indicating success/failure of the function. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:

• LIBSBML_OPERATION_SUCCESS

See also

getAnnotationString()

isSetAnnotation()

setAnnotation()

appendAnnotation()

appendAnnotation()

unsetAnnotation()

---

Method variant with the following signature:

setAnnotation(string annotation)

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

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

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

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

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

Parameters

annotation

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

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

See also

getAnnotationString()

isSetAnnotation()

setAnnotation()

appendAnnotation()

appendAnnotation()

unsetAnnotation()

def libsbml.Layout.setDimensions	(		self,
			dimensions
	)

Sets the dimensions of the layout.

setDimensions(Dimensions dimensions)

def libsbml.Layout.setId	(		self,
			sid
	)

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

setId(string sid)   int

The string sid is copied.

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

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

The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

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

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

Parameters

sid	the string to use as the identifier of this object.

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE
• LIBSBML_UNEXPECTED_ATTRIBUTE

See also

getIdAttribute()

setIdAttribute()

isSetIdAttribute()

unsetIdAttribute()

def libsbml.SBase.setIdAttribute (   self,   sid  )

inherited

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

setIdAttribute(string sid)   int

The string sid is copied.

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

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

The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

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

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

Parameters

sid	the string to use as the identifier of this object.

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE
• LIBSBML_UNEXPECTED_ATTRIBUTE

See also

getIdAttribute()

setIdAttribute()

isSetIdAttribute()

unsetIdAttribute()

def libsbml.SBase.setMetaId (   self,   metaid  )

inherited

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

setMetaId(string metaid)   int

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

The string metaid is copied.

Parameters

metaid

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

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE
• LIBSBML_UNEXPECTED_ATTRIBUTE

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

history

ModelHistory of this object.

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_UNEXPECTED_ATTRIBUTE
• LIBSBML_INVALID_OBJECT

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.Layout.setName	(		self,
			name
	)

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

setName(string name)   int

The string in name is copied.

Parameters

name	the new name for the SBML object.

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE

def libsbml.SBase.setNamespaces (   self,   xmlns  )

inherited

Sets the namespaces relevant of this SBML object.

setNamespaces(XMLNamespaces xmlns)   int

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

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

Parameters

xmlns

the namespaces to set.

Returns

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

• LIBSBML_OPERATION_SUCCESS

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)   int
setNotes(string notes)   int

Each variant is described separately below.

---

Method variant with the following signature:

setNotes(string notes, bool addXHTMLMarkup = false)

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

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

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

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

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

try:
  sbmlDoc = SBMLDocument(3, 1)
except ValueError:
  print('Could not create SBMLDocument object')
  sys.exit(1)

note = '<body xmlns='http://www.w3.org/1999/xhtml'><p>here is my note</p></body>'

status = sbmlDoc.setNotes(note)
if status != LIBSBML_OPERATION_SUCCESS:
  # Do something to handle the error here.
  print('Unable to set notes on the SBML document object')
  sys.exit(1)

Parameters

notes	an XML string that is to be used as the content of the 'notes' subelement of this object.
addXHTMLMarkup	a boolean indicating whether to wrap the contents of the notes argument with XHTML paragraph (<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:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_OBJECT
• LIBSBML_OPERATION_FAILED

See also

getNotesString()

isSetNotes()

setNotes()

appendNotes()

appendNotes()

unsetNotes()

SyntaxChecker.hasExpectedXHTMLSyntax()

Note

Owing to the way that language interfaces are created in libSBML, this documentation may show methods that define default values for parameters with text that has the form parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.

---

Method variant with the following signature:

setNotes(XMLNode notes)

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

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

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

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

Parameters

notes

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

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_OBJECT

See also

getNotesString()

isSetNotes()

setNotes()

appendNotes()

appendNotes()

unsetNotes()

SyntaxChecker.hasExpectedXHTMLSyntax()

def libsbml.SBase.setSBOTerm (   self,   args  )

inherited

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

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

Each variant is described separately below.

---

Method variant with the following signature:

setSBOTerm(int value)

Sets the value of the 'sboTerm' attribute.

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

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. More details can be found in SBML specifications for Level 2 Version 2 and above.

Parameters

value

the NNNNNNN integer portion of the SBO identifier.

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE
• LIBSBML_UNEXPECTED_ATTRIBUTE

See also

setSBOTerm()

---

Method variant with the following signature:

setSBOTerm(string sboid)

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

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

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. More details can be found in SBML specifications for Level 2 Version 2 and above.

Parameters

sboid

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

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE
• LIBSBML_UNEXPECTED_ATTRIBUTE

See also

setSBOTerm()

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.Layout.toXML

(

self

)

Creates an XMLNode object from this.

toXML()   XMLNode

def libsbml.SBase.toXMLNode (   self )

inherited

Returns this element as an XMLNode.

toXMLNode()   XMLNode

Returns

this element as an XMLNode.

Warning

This operation is computationally expensive, because the element has to be fully serialized to a string and then parsed into the XMLNode structure. Attempting to convert a large tree structure (e.g., a large Model) may consume significant computer memory and time.

def libsbml.SBase.unsetAnnotation (   self )

inherited

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

unsetAnnotation()   int

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

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

Returns

integer value indicating success/failure of the function. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:

• LIBSBML_OPERATION_SUCCESS

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:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

def libsbml.Layout.unsetId

(

self

)

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

unsetId()   int

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

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

The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.

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

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

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

See also

getIdAttribute()

setIdAttribute()

isSetIdAttribute()

unsetIdAttribute()

def libsbml.SBase.unsetIdAttribute (   self )

inherited

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

unsetIdAttribute()   int

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

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

See also

getIdAttribute()

setIdAttribute()

isSetIdAttribute()

def libsbml.SBase.unsetMetaId (   self )

inherited

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

unsetMetaId()   int

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

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_UNEXPECTED_ATTRIBUTE
• LIBSBML_OPERATION_FAILED

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:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_UNEXPECTED_ATTRIBUTE
• LIBSBML_OPERATION_FAILED

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.Layout.unsetName

(

self

)

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

unsetName()   int

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

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

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

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

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

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

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

See also

getName()

setName()

isSetName()

def libsbml.SBase.unsetNotes (   self )

inherited

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

unsetNotes()   int

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

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

Returns

integer value indicating success/failure of the function. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:

• LIBSBML_OPERATION_SUCCESS

See also

getNotesString()

isSetNotes()

setNotes()

setNotes()

appendNotes()

appendNotes()

SyntaxChecker.hasExpectedXHTMLSyntax()

def libsbml.SBase.unsetSBOTerm (   self )

inherited

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

unsetSBOTerm()   int

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_UNEXPECTED_ATTRIBUTE

def libsbml.SBase.unsetUserData (   self )

inherited

Unsets the user data of this element.

unsetUserData()   int

The user data associated with an SBML object can be used by an application developer to attach custom information to that object in the model. In case of a deep copy, this data will passed as-is. The data attribute will never be interpreted by libSBML.

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED