libsbml.Unit Class Reference

Inheritance diagram for libsbml.Unit:

[legend]

List of all members.

---

Detailed Description

LibSBML implementation of SBML's Unit construct.

The SBML unit definition facility uses two classes of objects, UnitDefinition and Unit. The approach to defining units in SBML is compositional; for example, meter second ^–2 is constructed by combining a Unit object representing meter with another Unit object representing second ^–2. The combination is wrapped inside a UnitDefinition, which provides for assigning an identifier and optional name to the combination. The identifier can then be referenced from elsewhere in a model. Thus, the UnitDefinition class is the container, and Unit instances are placed inside UnitDefinition instances.

A Unit structure has four attributes named 'kind', 'exponent', 'scale' and 'multiplier'. It represents a (possibly transformed) reference to a base unit. The attribute 'kind' on Unit indicates the chosen base unit. Its value in SBML Level 2 Version 4 must be one of the following predefined strings:

ampere	gram	katal	lux	pascal	tesla
becquerel	gray	kelvin	meter	radian	volt
candela	henry	kilogram	metre	second	watt
coulomb	hertz	liter	mole	siemens	weber
dimensionless	item	litre	newton	sievert
farad	joule	lumen	ohm	steradian

(See also the definition of the UNIT_KIND_ constants in the section below.) For SBML Level 2 Version 1 models, the string Celsius is also permitted. Note also that the table above contains two names not strictly defined in SBML Level 2: liter and meter. For convenience, libSBML defines the American English spellings of these units, although the SBML specification limits the valid unit names to those defined by SI.

The optional attribute named 'exponent' on Unit represents an exponent on the unit. Its default value is 1 (one). A Unit structure also has an optional attribute called 'scale'; its value must be an integer exponent for a power-of-ten multiplier used to set the scale of the unit. For example, a unit having a 'kind' value of gram and a 'scale' value of -3 signifies 10 ^–3 * gram, or milligrams. The default value of 'scale' is 0 (zero), because 10 ⁰ = 1. Lastly, the optional attribute named 'multiplier' can be used to multiply the kind unit by a real-numbered factor; this enables the definition of units that are not power-of-ten multiples of SI units. For instance, a multiplier of 0.3048 could be used to define foot as a measure of length in terms of a metre. The 'multiplier' attribute has a default value of 1 (one).

UnitKind_t

SBML defines a set of base units which serves as the starting point for new unit definitions. This set of base units consists of the SI units and a small number of additional convenience units.

• The alternate spelling 'meter' is included in addition to the official SI spelling 'metre'.

• The alternate spelling 'liter' is included in addition to the official SI spelling 'litre'.

• The unit 'Celsius' is included because of its presence in specifications of SBML prior to SBML Level 2 Version 3.

Enumerator	Meaning
UNIT_KIND_AMPERE	The ampere unit
UNIT_KIND_BECQUEREL	The becquerel unit.
UNIT_KIND_CANDELA	The candela unit.
UNIT_KIND_CELSIUS	The Celsius unit.
UNIT_KIND_COULOMB	The coulomb unit.
UNIT_KIND_DIMENSIONLESS	A pseudo-unit indicating a dimensionless quantity. (This is in fact defined in the SBML specification.)
UNIT_KIND_FARAD	The farad unit.
UNIT_KIND_GRAM	The gram unit.
UNIT_KIND_GRAY	The gray unit.
UNIT_KIND_HENRY	The henry unit.
UNIT_KIND_HERTZ	The hertz unit.
UNIT_KIND_ITEM	A pseudo-unit representing a single "thing". (This is in fact defined in the SBML specification.)
UNIT_KIND_JOULE	The joule unit.
UNIT_KIND_KATAL	The katal unit.
UNIT_KIND_KELVIN	The kelvin unit.
UNIT_KIND_KILOGRAM	The kilogram unit.
UNIT_KIND_LITER	Alternate spelling of litre.
UNIT_KIND_LITRE	The litre unit.
UNIT_KIND_LUMEN	The lumen unit.
UNIT_KIND_LUX	The lux unit.
UNIT_KIND_METER	Alternate spelling of metre.
UNIT_KIND_METRE	The metre unit.
UNIT_KIND_MOLE	The mole unit.
UNIT_KIND_NEWTON	The newton unit.
UNIT_KIND_OHM	The ohm unit.
UNIT_KIND_PASCAL	The pascal unit.
UNIT_KIND_RADIAN	The radian unit.
UNIT_KIND_SECOND	The second unit.
UNIT_KIND_SIEMENS	The siemens unit.
UNIT_KIND_SIEVERT	The sievert unit.
UNIT_KIND_STERADIAN	The steradian unit.
UNIT_KIND_TESLA	The tesla unit.
UNIT_KIND_VOLT	The volt unit.
UNIT_KIND_WATT	The watt unit.
UNIT_KIND_WEBER	The weber unit.
UNIT_KIND_INVALID	Marker used by libSBML to indicate an invalid or unset unit.

Definition at line 7879 of file libsbml.py.

Public Member Functions
def	__eq__
def	__init__
def	__init__
def	__ne__
def	addCVTerm
def	appendAnnotation
def	appendNotes
def	areEquivalent
def	areIdentical
def	clone
def	convertToSI
def	getAncestorOfType
def	getAnnotation
def	getAnnotationString
def	getColumn
def	getCVTerm
def	getCVTerms
def	getElementName
def	getExponent
def	getId
def	getKind
def	getLevel
def	getLine
def	getMetaId
def	getModel
def	getMultiplier
def	getName
def	getNamespaces
def	getNotes
def	getNotesString
def	getNumCVTerms
def	getOffset
def	getParentSBMLObject
def	getResourceBiologicalQualifier
def	getResourceModelQualifier
def	getSBMLDocument
def	getSBOTerm
def	getSBOTermID
def	getScale
def	getTypeCode
def	getVersion
def	hasRequiredAttributes
def	hasRequiredElements
def	hasValidLevelVersionNamespaceCombination
def	initDefaults
def	isAmpere
def	isBecquerel
def	isBuiltIn
def	isCandela
def	isCelsius
def	isCoulomb
def	isDimensionless
def	isFarad
def	isGram
def	isGray
def	isHenry
def	isHertz
def	isItem
def	isJoule
def	isKatal
def	isKelvin
def	isKilogram
def	isLitre
def	isLumen
def	isLux
def	isMetre
def	isMole
def	isNewton
def	isOhm
def	isPascal
def	isRadian
def	isSecond
def	isSetAnnotation
def	isSetId
def	isSetKind
def	isSetMetaId
def	isSetName
def	isSetNotes
def	isSetSBOTerm
def	isSiemens
def	isSievert
def	isSteradian
def	isTesla
def	isUnitKind
def	isVolt
def	isWatt
def	isWeber
def	merge
def	removeScale
def	setAnnotation
def	setExponent
def	setId
def	setKind
def	setMetaId
def	setMultiplier
def	setName
def	setNamespaces
def	setNotes
def	setOffset
def	setSBOTerm
def	setScale
def	toSBML
def	unsetAnnotation
def	unsetCVTerms
def	unsetMetaId
def	unsetNotes
def	unsetSBOTerm
Public Attributes
	this

---

Member Function Documentation

def libsbml.SBase.__eq__	(		self,
			rhs
	)			[inherited]

Definition at line 3296 of file libsbml.py.

def libsbml.SBase.__init__	(		self,
			args,
			kwargs
	)			[inherited]

Reimplemented in libsbml.SimpleSpeciesReference.

Definition at line 1771 of file libsbml.py.

def libsbml.Unit.__init__	(		self,
			args
	)

Python method signature(s):

__init__(self, unsigned int level, unsigned int version)    Unit
__init__(self, SBMLNamespaces sbmlns)    Unit
__init__(self, Unit orig)    Unit

Predicate returning true or false depending on whether all the required attributes for this Unit object have been set.

Note:

The required attributes for a Unit object are: kind

Returns:

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

Deprecated:

libSBML internal

Definition at line 7992 of file libsbml.py.

def libsbml.SBase.__ne__	(		self,
			rhs
	)			[inherited]

Definition at line 3303 of file libsbml.py.

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

Python method signature(s):

addCVTerm(self, CVTerm term)    int

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

Parameters:

term

the CVTerm to assign

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
• LIBSBML_INVALID_OBJECT

Note:

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

Warning:

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

Definition at line 2974 of file libsbml.py.

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

Python method signature(s):

appendAnnotation(self, XMLNode annotation)    int
appendAnnotation(self, string annotation)    int

Appends the annotation content given by annotation to any existing content in 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(const XMLNode* annotation) or SBase.setAnnotation(const std.string& annotation), this method allows other annotations to be preserved when an application adds its own data.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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

See also:

getAnnotationString()

isSetAnnotation()

setAnnotation(const XMLNode* annotation)

setAnnotation(const std.string& annotation)

appendAnnotation(const XMLNode* annotation)

unsetAnnotation()

Reimplemented in libsbml.Model, and libsbml.SpeciesReference.

Definition at line 2624 of file libsbml.py.

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

Python method signature(s):

appendNotes(self, XMLNode notes)    int
appendNotes(self, string notes)    int

Appends notes content to the 'notes' element attached to this object.

The content in notes is copied.

The optional 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. The SBML Level 2 specification has considerable detail about how 'notes' element content must be handled; please refer to the specifications.

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(const XMLNode* notes)

setNotes(const std.string& notes)

appendNotes(const XMLNode* notes)

unsetNotes()

Definition at line 2726 of file libsbml.py.

def libsbml.Unit.areEquivalent

(

args

)

Python method signature(s):

areEquivalent(Unit unit1, Unit unit2)    bool

Predicate returning true or false depending on whether Unit objects are equivalent.

Two Unit objects are considered to be equivalent if their 'kind' and 'exponent' attributes are equal. (Contrast this to the method Unit.areIdentical(Unit * unit1, Unit * unit2), which compares Unit objects with respect to all attributes, not just the kind and exponent.)

Parameters:

	unit1	the first Unit object to compare
	unit2	the second Unit object to compare

Returns:

true if the 'kind' and 'exponent' attributes of unit1 are identical to the kind and exponent attributes of unit2, false otherwise.

See also:

areIdentical(Unit * unit1, Unit * unit2)

Definition at line 8958 of file libsbml.py.

def libsbml.Unit.areIdentical

(

args

)

Python method signature(s):

areIdentical(Unit unit1, Unit unit2)    bool

Predicate returning true or false depending on whether two Unit objects are identical.

Two Unit objects are considered to be identical if they match in all attributes. (Contrast this to the method Unit.areEquivalent(Unit * unit1, Unit * unit2), which compares Unit objects only with respect to certain attributes.)

Parameters:

	unit1	the first Unit object to compare
	unit2	the second Unit object to compare

Returns:

true if all the attributes of unit1 are identical to the attributes of unit2, false otherwise.

See also:

areEquivalent(Unit * unit1, Unit * unit2)

Definition at line 8929 of file libsbml.py.

def libsbml.Unit.clone

(

self

)

Python method signature(s):

clone(self)    Unit

Creates and returns a deep copy of this Unit.

Returns:

a (deep) copy of this Unit.

Reimplemented from libsbml.SBase.

Definition at line 8017 of file libsbml.py.

def libsbml.Unit.convertToSI

(

args

)

Python method signature(s):

convertToSI(Unit unit)    UnitDefinition

Returns a UnitDefinition object which contains the argument Unit converted to the appropriate SI unit.

Parameters:

unit

the Unit object to convert to SI

Returns:

a UnitDefinition object containing the SI unit.

Definition at line 9049 of file libsbml.py.

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

Python method signature(s):

getAncestorOfType(self, SBMLTypeCode_t type)    SBase

Returns the ancestor SBML object that corresponds to the given SBMLTypeCode_t.

This function allows any object to determine its exact location/function within a model. For example a StoichiometryMath object has ancestors of type SpeciesReference, ListOfProducts/ListOfReactants/ListOfModifiers, Reaction, ListOfReactions and Model; any of which can be accessed via this function.

Parameters:

type

the SBMLTypeCode_t of the ancestor to be returned.

Returns:

the ancestor SBML object of this SBML object, that corresponds to the given SBMLTypeCode_t, NULL if none exists.

Definition at line 2115 of file libsbml.py.

def libsbml.SBase.getAnnotation

(

self

)

[inherited]

Python method signature(s):

getAnnotation(self)    XMLNode

Returns the content of the 'annotation' subelement of this object as an XML node tree.

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.

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 an XMLNode

See also:

getAnnotationString()

isSetAnnotation()

setAnnotation(const XMLNode* annotation)

setAnnotation(const std.string& annotation)

appendAnnotation(const XMLNode* annotation)

appendAnnotation(const std.string& annotation)

unsetAnnotation()

Definition at line 1971 of file libsbml.py.

def libsbml.SBase.getAnnotationString

(

self

)

[inherited]

Python method signature(s):

getAnnotationString(self)    string

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

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.

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

Returns:

the annotation string of this SBML object.

See also:

getAnnotation()

isSetAnnotation()

setAnnotation(const XMLNode* annotation)

setAnnotation(const std.string& annotation)

appendAnnotation(const XMLNode* annotation)

appendAnnotation(const std.string& annotation)

unsetAnnotation()

Definition at line 2014 of file libsbml.py.

def libsbml.SBase.getColumn

(

self

)

[inherited]

Python method signature(s):

getColumn(self)    unsigned int

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

Returns:

the column number of this SBML object.

See also:

getLine()

Definition at line 2217 of file libsbml.py.

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

Python method signature(s):

getCVTerm(self, unsigned int n)    CVTerm

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

Parameters:

n

unsigned int the index of the CVTerm to retrieve

Returns:

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

Definition at line 3042 of file libsbml.py.

def libsbml.SBase.getCVTerms

(

self

)

[inherited]

Python method signature(s):

getCVTerms(self)    CVTermList

Get the CVTermList of CVTerm objects in this SBase.

Returns:

the CVTermList for this SBase.

Definition at line 3010 of file libsbml.py.

def libsbml.Unit.getElementName

(

self

)

Python method signature(s):

getElementName(self)    string

Returns the XML element name of this object, which for Unit, is always 'unit'.

Returns:

the name of this element, i.e., 'unit'.

Reimplemented from libsbml.SBase.

Definition at line 8845 of file libsbml.py.

def libsbml.Unit.getExponent

(

self

)

Python method signature(s):

getExponent(self)    int

Returns the value of the 'exponent' attribute of this unit.

Returns:

the 'exponent' value of this Unit, as an integer

Definition at line 8070 of file libsbml.py.

def libsbml.SBase.getId

(

self

)

[inherited]

Python method signature(s):

getId(self)    string

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

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

Returns:

the metaid of this SBML object.

See also:

isSetMetaId()

setMetaId(const std.string& metaid)

Deprecated:

libSBML internal

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

Definition at line 1823 of file libsbml.py.

def libsbml.Unit.getKind

(

self

)

Python method signature(s):

getKind(self)    UnitKind_t

Returns the 'kind' of Unit this is.

Returns:

the value of the 'kind' attribute of this Unit as a value from the UnitKind_t enumeration

Definition at line 8054 of file libsbml.py.

def libsbml.SBase.getLevel

(

self

)

[inherited]

Python method signature(s):

getLevel(self)    unsigned int

Returns the SBML Level of the overall SBML document.

Returns:

the SBML level of this SBML object.

See also:

getVersion()

Definition at line 3134 of file libsbml.py.

def libsbml.SBase.getLine

(

self

)

[inherited]

Python method signature(s):

getLine(self)    unsigned int

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

Returns:

the line number of this SBML object.

See also:

getColumn()

Definition at line 2199 of file libsbml.py.

def libsbml.SBase.getMetaId

(

self

)

[inherited]

Python method signature(s):

getMetaId(self)    string

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

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

Returns:

the metaid of this SBML object.

See also:

isSetMetaId()

setMetaId(const std.string& metaid)

Definition at line 1790 of file libsbml.py.

def libsbml.SBase.getModel

(

self

)

[inherited]

Python method signature(s):

getModel(self)    Model

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

Returns:

the parent Model of this SBML object.

Definition at line 3119 of file libsbml.py.

def libsbml.Unit.getMultiplier

(

self

)

Python method signature(s):

getMultiplier(self)    float

Returns the value of the 'multiplier' attribute of this Unit.

Returns:

the 'multiplier' value of this Unit, as a float

Definition at line 8100 of file libsbml.py.

def libsbml.SBase.getName

(

self

)

[inherited]

Python method signature(s):

getName(self)    string

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

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

Returns:

the metaid of this SBML object.

See also:

isSetMetaId()

setMetaId(const std.string& metaid)

Deprecated:

libSBML internal

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

Definition at line 1857 of file libsbml.py.

def libsbml.SBase.getNamespaces

(

self

)

[inherited]

Python method signature(s):

getNamespaces(self)    XMLNamespaces

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

Returns:

the XML Namespaces associated with this SBML object

Reimplemented in libsbml.SBMLDocument.

Definition at line 2053 of file libsbml.py.

def libsbml.SBase.getNotes

(

self

)

[inherited]

Python method signature(s):

getNotes(self)    XMLNode

Returns the content of the 'notes' subelement of this object as a tree of XML nodes.

The optional 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. The SBML Level 2 specification has considerable detail about how 'notes' element content must be handled; please refer to the specifications.

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.

Returns:

the content of the 'notes' subelement of this SBML object.

See also:

getNotesString()

isSetNotes()

setNotes(const XMLNode* notes)

setNotes(const std.string& notes)

appendNotes(const XMLNode* notes)

appendNotes(const std.string& notes)

unsetNotes()

Definition at line 1891 of file libsbml.py.

def libsbml.SBase.getNotesString

(

self

)

[inherited]

Python method signature(s):

getNotesString(self)    string

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

The optional 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. The SBML Level 2 specification has considerable detail about how 'notes' element content must be handled; please refer to the specifications.

Returns:

the content of the 'notes' subelement of this SBML object.

See also:

getNotes()

isSetNotes()

setNotes(const XMLNode* notes)

setNotes(const std.string& notes)

appendNotes(const XMLNode* notes)

appendNotes(const std.string& notes)

unsetNotes()

Definition at line 1934 of file libsbml.py.

def libsbml.SBase.getNumCVTerms

(

self

)

[inherited]

Python method signature(s):

getNumCVTerms(self)    unsigned int

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

Returns:

the number of CVTerms for this SBML object.

Definition at line 3026 of file libsbml.py.

def libsbml.Unit.getOffset

(

self

)

Python method signature(s):

getOffset(self)    float

Returns the value of the 'offset' attribute of this Unit.

Warning:

The 'offset' attribute is only available in SBML Level 2 Version 1. This attribute is not present in SBML Level 2 Version 2 or above. When producing SBML models using these later specifications, modelers and software tools need to account for units with offsets explicitly. The SBML specification document offers a number of suggestions for how to achieve this. LibSBML methods such as this one related to 'offset' are retained for compatibility with earlier versions of SBML Level 2, but their use is strongly discouraged.

Returns:

the 'offset' value of this Unit, as a float

Definition at line 8115 of file libsbml.py.

def libsbml.SBase.getParentSBMLObject

(

self

)

[inherited]

Python method signature(s):

getParentSBMLObject(self)    SBase

Returns the parent SBML object.

This method is convenient when holding an object nested inside other objects in an SBML model. It allows direct access to the <model> element containing it.

Returns:

the parent SBML object of this SBML object.

Definition at line 2096 of file libsbml.py.

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

Python method signature(s):

getResourceBiologicalQualifier(self, string resource)    BiolQualifierType_t

Returns the BiologicalQualifier associated with this resource, or BQB_UNKNOWN if the resource does not exist.

Parameters:

resource

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

Returns:

the BiolQualifierType_t value associated with the resource

Definition at line 3081 of file libsbml.py.

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

Python method signature(s):

getResourceModelQualifier(self, string resource)    ModelQualifierType_t

Returns the ModelQualifier associated with this resource, or BQM_UNKNOWN if the resource does not exist.

Parameters:

resource

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

Returns:

the ModelQualifierType_t value associated with the resource

Definition at line 3100 of file libsbml.py.

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

Python method signature(s):

getSBMLDocument(self)    SBMLDocument
getSBMLDocument(self)    SBMLDocument

Returns the parent SBMLDocument object.

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 2 specification, 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 or Level 2.)

This method allows the SBMLDocument for the current object to be retrieved.

Returns:

the parent SBMLDocument object of this SBML object.

Definition at line 2068 of file libsbml.py.

def libsbml.SBase.getSBOTerm

(

self

)

[inherited]

Python method signature(s):

getSBOTerm(self)    int

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

In SBML Level 2 Versions 2, 3 and 4, the data type of the attribute is a string of the form SBO:NNNNNNN, where NNNNNNN is a seven digit integer number; libSBML simplifies the representation by only storing the NNNNNNN integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns:

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

Definition at line 2141 of file libsbml.py.

def libsbml.SBase.getSBOTermID

(

self

)

[inherited]

Python method signature(s):

getSBOTermID(self)    string

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

In SBML Level 2 Versions 2, 3 and 4, the data type of the attribute is a string of the form SBO:NNNNNNN, where NNNNNNN is a seven digit integer number; libSBML simplifies the representation by only storing the NNNNNNN integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This function recreates the string representation from the stored value. SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns:

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

Definition at line 2169 of file libsbml.py.

def libsbml.Unit.getScale

(

self

)

Python method signature(s):

getScale(self)    int

Returns the value of the 'scale' attribute of this unit.

Returns:

the 'scale' value of this Unit, as an integer.

Definition at line 8085 of file libsbml.py.

def libsbml.Unit.getTypeCode

(

self

)

Python method signature(s):

getTypeCode(self)    SBMLTypeCode_t

Returns the libSBML type code of this object instance.

Returns:

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

See also:

getElementName()

Reimplemented from libsbml.SBase.

Definition at line 8816 of file libsbml.py.

def libsbml.SBase.getVersion

(

self

)

[inherited]

Python method signature(s):

getVersion(self)    unsigned int

Returns the Version within the SBML Level of the overall SBML document.

Returns:

the SBML version of this SBML object.

See also:

getLevel()

Definition at line 3151 of file libsbml.py.

def libsbml.Unit.hasRequiredAttributes

(

self

)

Python method signature(s):

hasRequiredAttributes(self)    bool

Predicate returning true or false depending on whether all the required attributes for this Unit object have been set.

Note:

The required attributes for a Unit object are: kind

Returns:

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

Reimplemented from libsbml.SBase.

Definition at line 9069 of file libsbml.py.

def libsbml.SBase.hasRequiredElements

(

self

)

[inherited]

Python method signature(s):

hasRequiredElements(self)    bool

Subclasses should override this method to write out their contained SBML objects as XML elements. Be sure to call your parents implementation of this method as well. For example:

SBase.writeElements(stream); mReactans.write(stream); mProducts.write(stream); ...

Deprecated:

libSBML internal

Reimplemented in libsbml.Model, libsbml.FunctionDefinition, libsbml.UnitDefinition, libsbml.InitialAssignment, libsbml.Rule, libsbml.Constraint, libsbml.KineticLaw, libsbml.Event, libsbml.EventAssignment, libsbml.Trigger, libsbml.Delay, and libsbml.StoichiometryMath.

Definition at line 3275 of file libsbml.py.

def libsbml.SBase.hasValidLevelVersionNamespaceCombination

(

self

)

[inherited]

Python method signature(s):

hasValidLevelVersionNamespaceCombination(self)    bool

Predicate returning true or false depending on whether this object's level/version and namespace values correspond to a valid SBML specification.

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'

Returns:

true if the level, version and namespace values of this SBML object correspond to a valid set of values, false otherwise.

Definition at line 3192 of file libsbml.py.

def libsbml.Unit.initDefaults

(

self

)

Python method signature(s):

initDefaults(self)

Initializes the attributes of this Unit (except for 'kind') to their defaults values.

The default values are as follows:

• exponent = 1
• scale = 0
• multiplier = 1.0

The 'kind' attribute is left unchanged.

Definition at line 8032 of file libsbml.py.

def libsbml.Unit.isAmpere

(

self

)

Python method signature(s):

isAmpere(self)    bool

Predicate for testing whether this Unit is of the kind ampere.

Returns:

true if the kind of this Unit is ampere, false otherwise.

Definition at line 8140 of file libsbml.py.

def libsbml.Unit.isBecquerel

(

self

)

Python method signature(s):

isBecquerel(self)    bool

Predicate for testing whether this Unit is of the kind becquerel

Returns:

true if the kind of this Unit is becquerel, false otherwise.

Definition at line 8156 of file libsbml.py.

def libsbml.Unit.isBuiltIn

(

args

)

Python method signature(s):

isBuiltIn(string name, unsigned int level)    bool

Predicate to test whether a given string is the name of a predefined SBML unit.

Parameters:

	name	a string to be tested against the predefined unit names
	level	the Level of SBML for which the determination should be made. This is necessary because there are a few small differences in allowed units between SBML Level 1 and Level 2.

Returns:

true if name is one of the five SBML predefined unit identifiers ('substance', 'volume', 'area', 'length' or 'time'), false otherwise.

Note:

The predefined unit identifiers 'length' and 'area' were added in Level 2 Version 1

Definition at line 8861 of file libsbml.py.

def libsbml.Unit.isCandela

(

self

)

Python method signature(s):

isCandela(self)    bool

Predicate for testing whether this Unit is of the kind candela

Returns:

true if the kind of this Unit is candela, false otherwise.

Definition at line 8172 of file libsbml.py.

def libsbml.Unit.isCelsius

(

self

)

Python method signature(s):

isCelsius(self)    bool

Predicate for testing whether this Unit is of the kind Celsius

Returns:

true if the kind of this Unit is Celsius, false otherwise.

Warning:

The predefined unit Celsius was removed from the list of predefined units in SBML Level 2 Version 2 at the same time that the 'offset' attribute was removed from Unit definitions. LibSBML methods such as this one related to Celsius are retained in order to support SBML Level 2 Version 1, but their use is strongly discouraged.

Definition at line 8188 of file libsbml.py.

def libsbml.Unit.isCoulomb

(

self

)

Python method signature(s):

isCoulomb(self)    bool

Predicate for testing whether this Unit is of the kind coulomb

Returns:

true if the kind of this Unit is coulomb, false otherwise.

Definition at line 8211 of file libsbml.py.

def libsbml.Unit.isDimensionless

(

self

)

Python method signature(s):

isDimensionless(self)    bool

Predicate for testing whether this Unit is of the kind dimensionless

Returns:

true if the kind of this Unit is dimensionless, false

otherwise.

Definition at line 8227 of file libsbml.py.

def libsbml.Unit.isFarad

(

self

)

Python method signature(s):

isFarad(self)    bool

Predicate for testing whether this Unit is of the kind farad

Returns:

true if the kind of this Unit is farad, false otherwise.

Definition at line 8245 of file libsbml.py.

def libsbml.Unit.isGram

(

self

)

Python method signature(s):

isGram(self)    bool

Predicate for testing whether this Unit is of the kind gram

Returns:

true if the kind of this Unit is gram, false otherwise.

Definition at line 8261 of file libsbml.py.

def libsbml.Unit.isGray

(

self

)

Python method signature(s):

isGray(self)    bool

Predicate for testing whether this Unit is of the kind gray

Returns:

true if the kind of this Unit is gray, false otherwise.

Definition at line 8277 of file libsbml.py.

def libsbml.Unit.isHenry

(

self

)

Python method signature(s):

isHenry(self)    bool

Predicate for testing whether this Unit is of the kind henry

Returns:

true if the kind of this Unit is henry, false otherwise.

Definition at line 8293 of file libsbml.py.

def libsbml.Unit.isHertz

(

self

)

Python method signature(s):

isHertz(self)    bool

Predicate for testing whether this Unit is of the kind hertz

Returns:

true if the kind of this Unit is hertz, false otherwise.

Definition at line 8309 of file libsbml.py.

def libsbml.Unit.isItem

(

self

)

Python method signature(s):

isItem(self)    bool

Predicate for testing whether this Unit is of the kind item

Returns:

true if the kind of this Unit is item, false otherwise.

Definition at line 8325 of file libsbml.py.

def libsbml.Unit.isJoule

(

self

)

Python method signature(s):

isJoule(self)    bool

Predicate for testing whether this Unit is of the kind joule

Returns:

true if the kind of this Unit is joule, false otherwise.

Definition at line 8341 of file libsbml.py.

def libsbml.Unit.isKatal

(

self

)

Python method signature(s):

isKatal(self)    bool

Predicate for testing whether this Unit is of the kind katal

Returns:

true if the kind of this Unit is katal, false otherwise.

Definition at line 8357 of file libsbml.py.

def libsbml.Unit.isKelvin

(

self

)

Python method signature(s):

isKelvin(self)    bool

Predicate for testing whether this Unit is of the kind kelvin

Returns:

true if the kind of this Unit is kelvin, false otherwise.

Definition at line 8373 of file libsbml.py.

def libsbml.Unit.isKilogram

(

self

)

Python method signature(s):

isKilogram(self)    bool

Predicate for testing whether this Unit is of the kind kilogram

Returns:

true if the kind of this Unit is kilogram, false otherwise.

Definition at line 8389 of file libsbml.py.

def libsbml.Unit.isLitre

(

self

)

Python method signature(s):

isLitre(self)    bool

Predicate for testing whether this Unit is of the kind litre

Returns:

true if the kind of this Unit is litre or 'liter', false otherwise.

Definition at line 8405 of file libsbml.py.

def libsbml.Unit.isLumen

(

self

)

Python method signature(s):

isLumen(self)    bool

Predicate for testing whether this Unit is of the kind lumen

Returns:

true if the kind of this Unit is lumen, false otherwise.

Definition at line 8422 of file libsbml.py.

def libsbml.Unit.isLux

(

self

)

Python method signature(s):

isLux(self)    bool

Predicate for testing whether this Unit is of the kind lux

Returns:

true if the kind of this Unit is lux, false otherwise.

Definition at line 8438 of file libsbml.py.

def libsbml.Unit.isMetre

(

self

)

Python method signature(s):

isMetre(self)    bool

Predicate for testing whether this Unit is of the kind metre

Returns:

true if the kind of this Unit is metre or 'meter', false otherwise.

Definition at line 8454 of file libsbml.py.

def libsbml.Unit.isMole

(

self

)

Python method signature(s):

isMole(self)    bool

Predicate for testing whether this Unit is of the kind mole

Returns:

true if the kind of this Unit is mole, false otherwise.

Definition at line 8471 of file libsbml.py.

def libsbml.Unit.isNewton

(

self

)

Python method signature(s):

isNewton(self)    bool

Predicate for testing whether this Unit is of the kind newton

Returns:

true if the kind of this Unit is newton, false otherwise.

Definition at line 8487 of file libsbml.py.

def libsbml.Unit.isOhm

(

self

)

Python method signature(s):

isOhm(self)    bool

Predicate for testing whether this Unit is of the kind ohm

Returns:

true if the kind of this Unit is ohm, false otherwise.

Definition at line 8503 of file libsbml.py.

def libsbml.Unit.isPascal

(

self

)

Python method signature(s):

isPascal(self)    bool

Predicate for testing whether this Unit is of the kind pascal

Returns:

true if the kind of this Unit is pascal, false otherwise.

Definition at line 8519 of file libsbml.py.

def libsbml.Unit.isRadian

(

self

)

Python method signature(s):

isRadian(self)    bool

Predicate for testing whether this Unit is of the kind radian

Returns:

true if the kind of this Unit is radian, false otherwise.

Definition at line 8535 of file libsbml.py.

def libsbml.Unit.isSecond

(

self

)

Python method signature(s):

isSecond(self)    bool

Predicate for testing whether this Unit is of the kind second

Returns:

true if the kind of this Unit is second, false otherwise.

Definition at line 8551 of file libsbml.py.

def libsbml.SBase.isSetAnnotation

(

self

)

[inherited]

Python method signature(s):

isSetAnnotation(self)    bool

Predicate returning true or false depending on whether this object's 'annotation' subelement exists and has content.

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

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

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

Returns:

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

See also:

getAnnotation()

getAnnotationString()

setAnnotation(const XMLNode* annotation)

setAnnotation(const std.string& annotation)

appendAnnotation(const XMLNode* annotation)

appendAnnotation(const std.string& annotation)

unsetAnnotation()

Definition at line 2387 of file libsbml.py.

def libsbml.SBase.isSetId

(

self

)

[inherited]

Python method signature(s):

isSetId(self)    bool

Predicate returning true or false depending on whether this object's 'metaid' attribute has been set.

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

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

Returns:

true if the 'metaid' attribute of this SBML object has been set, false otherwise.

See also:

getMetaId()

setMetaId(const std.string& metaid)

Deprecated:

libSBML internal

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

Definition at line 2272 of file libsbml.py.

def libsbml.Unit.isSetKind

(

self

)

Python method signature(s):

isSetKind(self)    bool

Predicate to test whether the 'kind' attribute of this Unit has been set.

Returns:

true if the 'kind' attribute of this Unit has been set, false otherwise.

Definition at line 8679 of file libsbml.py.

def libsbml.SBase.isSetMetaId

(

self

)

[inherited]

Python method signature(s):

isSetMetaId(self)    bool

Predicate returning true or false depending on whether this object's 'metaid' attribute has been set.

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

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

Returns:

true if the 'metaid' attribute of this SBML object has been set, false otherwise.

See also:

getMetaId()

setMetaId(const std.string& metaid)

Definition at line 2235 of file libsbml.py.

def libsbml.SBase.isSetName

(

self

)

[inherited]

Python method signature(s):

isSetName(self)    bool

Predicate returning true or false depending on whether this object's 'metaid' attribute has been set.

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

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

Returns:

true if the 'metaid' attribute of this SBML object has been set, false otherwise.

See also:

getMetaId()

setMetaId(const std.string& metaid)

Deprecated:

libSBML internal

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

Definition at line 2310 of file libsbml.py.

def libsbml.SBase.isSetNotes

(

self

)

[inherited]

Python method signature(s):

isSetNotes(self)    bool

Predicate returning true or false depending on whether this object's 'notes' subelement exists and has content.

The optional 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. The SBML Level 2 specification has considerable detail about how 'notes' element content must be handled; please refer to the specifications.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

Returns:

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

See also:

getNotes()

getNotesString()

setNotes(const XMLNode* notes)

setNotes(const std.string& notes)

appendNotes(const XMLNode* notes)

appendNotes(const std.string& notes)

unsetNotes()

Definition at line 2348 of file libsbml.py.

def libsbml.SBase.isSetSBOTerm

(

self

)

[inherited]

Python method signature(s):

isSetSBOTerm(self)    bool

Predicate returning true or false depending on whether this object's 'sboTerm' attribute has been set.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

Returns:

true if the 'sboTerm' attribute of this SBML object has been set, false otherwise.

Definition at line 2427 of file libsbml.py.

def libsbml.Unit.isSiemens

(

self

)

Python method signature(s):

isSiemens(self)    bool

Predicate for testing whether this Unit is of the kind siemens

Returns:

true if the kind of this Unit is siemens, false otherwise.

Definition at line 8567 of file libsbml.py.

def libsbml.Unit.isSievert

(

self

)

Python method signature(s):

isSievert(self)    bool

Predicate for testing whether this Unit is of the kind sievert

Returns:

true if the kind of this Unit is sievert, false otherwise.

Definition at line 8583 of file libsbml.py.

def libsbml.Unit.isSteradian

(

self

)

Python method signature(s):

isSteradian(self)    bool

Predicate for testing whether this Unit is of the kind steradian

Returns:

true if the kind of this Unit is steradian, false otherwise.

Definition at line 8599 of file libsbml.py.

def libsbml.Unit.isTesla

(

self

)

Python method signature(s):

isTesla(self)    bool

Predicate for testing whether this Unit is of the kind tesla

Returns:

true if the kind of this Unit is tesla, false otherwise.

Definition at line 8615 of file libsbml.py.

def libsbml.Unit.isUnitKind

(

args

)

Python method signature(s):

isUnitKind(string name, unsigned int level, unsigned int version)    bool

Predicate to test whether a given string is the name of a valid base unit in SBML (such as 'gram' or 'mole').

This method exists because prior to SBML Level 2 Version 3, an enumeration called UnitKind was defined by SBML. This enumeration was removed in SBML Level 2 Version 3 and its values were folded into the space of values of a type called UnitSId. This method therefore has less significance in SBML Level 2 Version 3 and Level 2 Version 4, but remains for backward compatibility and support for reading models in older Versions of Level 2.

Parameters:

	name	a string to be tested
	level	an unsigned int representing the SBML specification Level
	version	an unsigned int representing the SBML specification Version

Returns:

true if name is a valid UnitKind, false otherwise

Note:

The allowed unit names differ between SBML Levels 1 and 2 and again slightly between Level 2 Versions 1 and 2.

Definition at line 8890 of file libsbml.py.

def libsbml.Unit.isVolt

(

self

)

Python method signature(s):

isVolt(self)    bool

Predicate for testing whether this Unit is of the kind volt

Returns:

true if the kind of this Unit is volt, false otherwise.

Definition at line 8631 of file libsbml.py.

def libsbml.Unit.isWatt

(

self

)

Python method signature(s):

isWatt(self)    bool

Predicate for testing whether this Unit is of the kind watt

Returns:

true if the kind of this Unit is watt, false otherwise.

Definition at line 8647 of file libsbml.py.

def libsbml.Unit.isWeber

(

self

)

Python method signature(s):

isWeber(self)    bool

Predicate for testing whether this Unit is of the kind weber

Returns:

true if the kind of this Unit is weber, false otherwise.

Definition at line 8663 of file libsbml.py.

def libsbml.Unit.merge

(

args

)

Python method signature(s):

merge(Unit unit1, Unit unit2)

Merges two Unit objects with the same 'kind' attribute value into a single Unit.

For example, the following,

<unit kind='metre' exponent='2'/>
<unit kind='metre' exponent='1'/>

would be merged to become

<unit kind='metre' exponent='3'/>

Parameters:

	unit1	the first Unit object; the result of the operation is left as a new version of this unit, modified in-place.
	unit2	the second Unit object to merge with the first

Definition at line 9018 of file libsbml.py.

def libsbml.Unit.removeScale

(

args

)

Python method signature(s):

removeScale(Unit unit)    int

Manipulates the attributes of the Unit to express the unit with the value of the scale attribute reduced to zero.

For example, 1 millimetre can be expressed as a Unit with kind='metre' multiplier='1' scale='-3' exponent='1'. It can also be expressed as a Unit with kind='metre' multiplier='0.001' scale='0' exponent='1'.

Parameters:

unit

the Unit object to manipulate.

Returns:

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

• LIBSBML_OPERATION_SUCCESS

Definition at line 8989 of file libsbml.py.

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

Python method signature(s):

setAnnotation(self, XMLNode annotation)    int
setAnnotation(self, string annotation)    int

Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation given as a character string.

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(const XMLNode* annotation) or SBase.appendAnnotation(const std.string& annotation).

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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(const XMLNode* annotation)

appendAnnotation(const XMLNode* annotation)

appendAnnotation(const std.string& annotation)

unsetAnnotation()

Reimplemented in libsbml.Model, and libsbml.SpeciesReference.

Definition at line 2568 of file libsbml.py.

def libsbml.Unit.setExponent	(		self,
			args
	)

Python method signature(s):

setExponent(self, int value)    int

Sets the 'exponent' attribute value of this Unit.

Parameters:

value

the integer to which the attribute 'exponent' should be set

Returns:

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

• LIBSBML_OPERATION_SUCCESS

Definition at line 8718 of file libsbml.py.

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

Python method signature(s):

setId(self, string sid)    int

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

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

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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()

Deprecated:

libSBML internal

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

Definition at line 2486 of file libsbml.py.

def libsbml.Unit.setKind	(		self,
			args
	)

Python method signature(s):

setKind(self, UnitKind_t kind)    int

Sets the 'kind' attribute value of this Unit.

Parameters:

kind

a value from the UnitKind_t enumeration

Returns:

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE

Definition at line 8695 of file libsbml.py.

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

Python method signature(s):

setMetaId(self, string metaid)    int

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

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

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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()

Definition at line 2446 of file libsbml.py.

def libsbml.Unit.setMultiplier	(		self,
			args
	)

Python method signature(s):

setMultiplier(self, float value)    int

Sets the 'multipler' attribute value of this Unit.

Parameters:

value

the floating-point value to which the attribute 'multiplier' should be set

Returns:

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_UNEXPECTED_ATTRIBUTE

Definition at line 8760 of file libsbml.py.

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

Python method signature(s):

setName(self, string name)    int

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

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

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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()

Deprecated:

libSBML internal

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

Definition at line 2527 of file libsbml.py.

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

Python method signature(s):

setNamespaces(self, XMLNamespaces xmlns)    int

Sets the namespaces relevant of this SBML object.

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

Definition at line 2811 of file libsbml.py.

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

Python method signature(s):

setNotes(self, XMLNode notes)    int
setNotes(self, string notes)    int

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

Any existing content of the 'notes' subelement is discarded.

The optional 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. The SBML Level 2 specification has considerable detail about how 'notes' element content must be handled; please refer to the specifications.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

Parameters:

notes

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

Returns:

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_OBJECT
• LIBSBML_OPERATION_FAILED

See also:

getNotesString()

isSetNotes()

setNotes(const XMLNode* notes)

appendNotes(const XMLNode* notes)

appendNotes(const std.string& notes)

unsetNotes()

Definition at line 2676 of file libsbml.py.

def libsbml.Unit.setOffset	(		self,
			args
	)

Python method signature(s):

setOffset(self, float value)    int

Sets the 'offset' attribute value of this Unit.

Parameters:

value

the float-point value to which the attribute 'offset' should set

Returns:

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_UNEXPECTED_ATTRIBUTE

Warning:

The 'offset' attribute is only available in SBML Level 2 Version 1. This attribute is not present in SBML Level 2 Version 2 or above. When producing SBML models using these later specifications, modelers and software tools need to account for units with offsets explicitly. The SBML specification document offers a number of suggestions for how to achieve this. LibSBML methods such as this one related to 'offset' are retained for compatibility with earlier versions of SBML Level 2, but their use is strongly discouraged.

Definition at line 8783 of file libsbml.py.

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

Python method signature(s):

setSBOTerm(self, int value)    int
setSBOTerm(self, string sboid)    int

Sets the value of the 'sboTerm' attribute.

In SBML Level 2 Versions 2, 3 and 4, the data type of the SBML 'sboTerm' attribute is a string of the form SBO:NNNNNNN, where NNNNNNN is a seven digit integer number; libSBML simplifies the representation by only storing the NNNNNNN integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

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

Definition at line 2774 of file libsbml.py.

def libsbml.Unit.setScale	(		self,
			args
	)

Python method signature(s):

setScale(self, int value)    int

Sets the 'scale' attribute value of this Unit.

Parameters:

value

the integer to which the attribute 'scale' should be set

Returns:

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

• LIBSBML_OPERATION_SUCCESS

Definition at line 8739 of file libsbml.py.

def libsbml.SBase.toSBML

(

self

)

[inherited]

Python method signature(s):

toSBML(self)    char

Returns a string that consists of the partial SBML describing this object. This is primarily provided for testing and debugging purposes. It may be removed in a future version of libSBML.

Returns:

the partial SBML that describes this SBML object.

Definition at line 3237 of file libsbml.py.

def libsbml.SBase.unsetAnnotation

(

self

)

[inherited]

Python method signature(s):

unsetAnnotation(self)    int

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

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

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

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

Returns:

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

• LIBSBML_OPERATION_SUCCESS

See also:

getAnnotation()

getAnnotationString()

isSetAnnotation()

setAnnotation(const XMLNode* annotation)

setAnnotation(const std.string& annotation)

appendAnnotation(const XMLNode* annotation)

appendAnnotation(const std.string& annotation)

Definition at line 2910 of file libsbml.py.

def libsbml.SBase.unsetCVTerms

(

self

)

[inherited]

Python method signature(s):

unsetCVTerms(self)    int

Clears the list of CVTerms of this SBML object.

Returns:

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

Definition at line 3060 of file libsbml.py.

def libsbml.SBase.unsetMetaId

(

self

)

[inherited]

Python method signature(s):

unsetMetaId(self)    int

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

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

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

Returns:

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

Definition at line 2832 of file libsbml.py.

def libsbml.SBase.unsetNotes

(

self

)

[inherited]

Python method signature(s):

unsetNotes(self)    int

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

The optional 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. The SBML Level 2 specification has considerable detail about how 'notes' element content must be handled; please refer to the specifications.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

Returns:

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

• LIBSBML_OPERATION_SUCCESS

See also:

getNotesString()

isSetNotes()

setNotes(const XMLNode* notes)

setNotes(const std.string& notes)

appendNotes(const XMLNode* notes)

appendNotes(const std.string& notes)

Definition at line 2869 of file libsbml.py.

def libsbml.SBase.unsetSBOTerm

(

self

)

[inherited]

Python method signature(s):

unsetSBOTerm(self)    int

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

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

Returns:

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_UNEXPECTED_ATTRIBUTE

Definition at line 2952 of file libsbml.py.

---

Member Data Documentation

libsbml.Unit.this

Reimplemented from libsbml.SBase.

Definition at line 8016 of file libsbml.py.