libSBML Python API  5.8.0
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libsbml.Unit Class Reference
Inheritance diagram for libsbml.Unit:
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Detailed Description

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 must be one of the text strings listed below; this list corresponds to SBML Level 3 Version 1 Core:

amperefaradjouleluxradianvolt
avogadrogramkatalmetresecondwatt
becquerelgraykelvinmolesiemensweber
candelahenrykilogramnewtonsievert
coulombhertzlitreohmsteradian
dimensionlessitemlumenpascaltesla

A few small differences exist between the Level 3 list of base units and the list defined in other Level/Version combinations of SBML. Specifically, Levels of SBML before Level 3 do not define avogadro; conversely, Level 2 Version 1 defines Celsius, and Level 1 defines celsius, meter, and liter, none of which are available in Level 3. In libSBML, each of the predefined base unit names is represented by an enumeration value whose name begins with the characters UNIT_KIND_, discussed in a separate section below.

The attribute named 'exponent' on Unit represents an exponent on the unit. In SBML Level 2, the attribute is optional and has a default value of 1 (one); in SBML Level 3, the attribute is mandatory and there is no default value. A Unit structure also has an 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. In SBML Level 2, the attribute is optional and has a default value of 0 (zero), because 10 0 = 1; in SBML Level 3, the attribute is mandatory and has no default value. Lastly, the attribute named 'multiplier' can be used to multiply the 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 is optional in SBML Level 2, where it has a default value of 1 (one); in SBML Level 3, the attribute is mandatory and has not default value.

Unit identification codes

As discussed above, 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.

In SBML Level 2 Versions before Version 3, there existed an enumeration of units called UnitKind. In Version 3, this enumeration was removed and the identifier class UnitSId redefined to include the previous UnitKind values as reserved symbols. This change has no net effect on permissible models, their representation or their syntax. The purpose of the change in the SBML specification was simply to clean up an inconsistency about the contexts in which these values were usable. However, libSBML maintains UnitKind in the form of of a set of static integer constants whose names begin with the characters UNIT_KIND_. These constants are defined in the class libsbml.

As a consequence of the fact that libSBML supports models in all Levels and Versions of SBML, libSBML's set of UNIT_KIND_ values is a union of all the possible base unit names defined in the different SBML specifications. However, not every base unit is allowed in every Level+Version combination of SBML. Note in particular the following exceptions:

  • The alternate spelling 'meter' is included in addition to the official SI spelling 'metre'. This spelling is only permitted in SBML Level 1 models.

  • The alternate spelling 'liter' is included in addition to the official SI spelling 'litre'. This spelling is only permitted in SBML Level 1 models.

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

  • The unit avogadro was introduced in SBML Level 3, and is only permitted for use in SBML Level 3 models.

The table below lists the unit constants defined in libSBML, and their meanings.

Enumerator Meaning
UNIT_KIND_AMPEREThe ampere unit.
UNIT_KIND_AVOGADROThe unit dimensionless multiplied by the numerical value of Avogadro's constant. (Only usable in SBML Level 3 models.)
UNIT_KIND_BECQUERELThe becquerel unit.
UNIT_KIND_CANDELAThe candela unit.
UNIT_KIND_CELSIUSThe Celsius unit. (Only usable in SBML Level 1 and SBML Level 2 Version 1 models.)
UNIT_KIND_COULOMBThe coulomb unit.
UNIT_KIND_DIMENSIONLESSA pseudo-unit indicating a dimensionless quantity.
UNIT_KIND_FARADThe farad unit.
UNIT_KIND_GRAMThe gram unit.
UNIT_KIND_GRAYThe gray unit.
UNIT_KIND_HENRYThe henry unit.
UNIT_KIND_HERTZThe hertz unit.
UNIT_KIND_ITEMA pseudo-unit representing a single "thing".
UNIT_KIND_JOULEThe joule unit.
UNIT_KIND_KATALThe katal unit.
UNIT_KIND_KELVINThe kelvin unit.
UNIT_KIND_KILOGRAMThe kilogram unit.
UNIT_KIND_LITERAlternate spelling of litre.
UNIT_KIND_LITREThe litre unit.
UNIT_KIND_LUMENThe lumen unit.
UNIT_KIND_LUXThe lux unit.
UNIT_KIND_METERAlternate spelling of metre.
UNIT_KIND_METREThe metre unit.
UNIT_KIND_MOLEThe mole unit.
UNIT_KIND_NEWTONThe newton unit.
UNIT_KIND_OHMThe ohm unit.
UNIT_KIND_PASCALThe pascal unit.
UNIT_KIND_RADIANThe radian unit.
UNIT_KIND_SECONDThe second unit.
UNIT_KIND_SIEMENSThe siemens unit.
UNIT_KIND_SIEVERTThe sievert unit.
UNIT_KIND_STERADIANThe steradian unit.
UNIT_KIND_TESLAThe tesla unit.
UNIT_KIND_VOLTThe volt unit.
UNIT_KIND_WATTThe watt unit.
UNIT_KIND_WEBERThe weber unit.
UNIT_KIND_INVALIDMarker used by libSBML to indicate an invalid or unset unit.

Public Member Functions

def addCVTerm
 
def appendAnnotation
 
def appendNotes
 
def areEquivalent
 
def areIdentical
 
def clone
 
def convertToSI
 
def disablePackage
 
def enablePackage
 
def getAncestorOfType
 
def getAnnotation
 
def getAnnotationString
 
def getColumn
 
def getCVTerm
 
def getCVTerms
 
def getElementByMetaId
 
def getElementBySId
 
def getElementName
 
def getExponent
 
def getExponentAsDouble
 
def getKind
 
def getLevel
 
def getLine
 
def getListOfAllElements
 
def getListOfAllElementsFromPlugins
 
def getMetaId
 
def getModel
 
def getModelHistory
 
def getMultiplier
 
def getNamespaces
 
def getNotes
 
def getNotesString
 
def getNumCVTerms
 
def getNumPlugins
 
def getOffset
 
def getPackageName
 
def getPackageVersion
 
def getParentSBMLObject
 
def getPlugin
 
def getResourceBiologicalQualifier
 
def getResourceModelQualifier
 
def getSBMLDocument
 
def getSBOTerm
 
def getSBOTermAsURL
 
def getSBOTermID
 
def getScale
 
def getTypeCode
 
def getVersion
 
def hasRequiredAttributes
 
def hasValidLevelVersionNamespaceCombination
 
def initDefaults
 
def isAmpere
 
def isAvogadro
 
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 isPackageEnabled
 
def isPackageURIEnabled
 
def isPascal
 
def isPkgEnabled
 
def isPkgURIEnabled
 
def isRadian
 
def isSecond
 
def isSetAnnotation
 
def isSetExponent
 
def isSetKind
 
def isSetMetaId
 
def isSetModelHistory
 
def isSetMultiplier
 
def isSetNotes
 
def isSetSBOTerm
 
def isSetScale
 
def isSiemens
 
def isSievert
 
def isSteradian
 
def isTesla
 
def isUnitKind
 
def isVolt
 
def isWatt
 
def isWeber
 
def matchesRequiredSBMLNamespacesForAddition
 
def matchesSBMLNamespaces
 
def merge
 
def removeFromParentAndDelete
 
def removeScale
 
def removeTopLevelAnnotationElement
 
def renameMetaIdRefs
 
def renameSIdRefs
 
def renameUnitSIdRefs
 
def replaceTopLevelAnnotationElement
 
def setAnnotation
 
def setExponent
 
def setKind
 
def setMetaId
 
def setModelHistory
 
def setMultiplier
 
def setNamespaces
 
def setNotes
 
def setOffset
 
def setSBOTerm
 
def setScale
 
def toSBML
 
def unsetAnnotation
 
def unsetCVTerms
 
def unsetId
 
def unsetMetaId
 
def unsetModelHistory
 
def unsetName
 
def unsetNotes
 
def unsetSBOTerm
 

Member Function Documentation

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

Python method signature(s):

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

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

Parameters
termthe CVTerm to assign.
newBagif True, creates a new RDF bag with the same identifier as a previous bag, and if False, adds the term to an existing RDF bag with the same type of qualifier as the term being added.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.
Warning
The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance added here. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result.
Documentation note:
The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.
def libsbml.SBase.appendAnnotation (   self,
  args 
)
inherited

Python method signature(s):

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

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


Method variant with the following signature:

appendAnnotation(XMLNode annotation)

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

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

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

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

Parameters
annotationan XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
unsetAnnotation()

Method variant with the following signature:

appendAnnotation(string annotation)

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

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

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

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

Parameters
annotationan XML string that is to be copied and appended to the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.SBase.appendNotes (   self,
  args 
)
inherited

Python method signature(s):

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

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


Method variant with the following signature:

appendNotes(string notes)

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

The content of the parameter notes is copied.

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

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

Parameters
notesan XML string that is to appended to the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()

Method variant with the following signature:

appendNotes(XMLNode notes)

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

The content of notes is copied.

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

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

Parameters
notesan XML node structure that is to appended to the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.Unit.areEquivalent (   args)

Python method signature(s):

areEquivalent(Unit unit1, Unit unit2)   bool

Predicate returning True if Unit objects are equivalent.

Two Unit objects are considered to be equivalent either if (1) both have a 'kind' attribute value of dimensionless, or (2) their 'kind', 'exponent' and (for SBML Level 2 Version 1) 'offset' attribute values are equal. (Contrast this to the method areIdentical(), which compares Unit objects with respect to all attributes, not just the 'kind' and 'exponent'.)

Parameters
unit1the first Unit object to compare
unit2the 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.
Note
Because this is a static method, the non-C++ language interfaces for libSBML will contain two variants. One will be a static method on the class (i.e., Unit), and the other will be a standalone top-level function with the name Unit_areEquivalent(). They are functionally identical.
See Also
Unit.areIdentical()
def libsbml.Unit.areIdentical (   args)

Python method signature(s):

areIdentical(Unit unit1, Unit unit2)   bool

Predicate returning True if two Unit objects are identical.

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

Parameters
unit1the first Unit object to compare
unit2the second Unit object to compare
Returns
True if all the attributes of unit1 are identical to the attributes of unit2, False otherwise.
Note
Because this is a static method, the non-C++ language interfaces for libSBML will contain two variants. One will be a static method on the class (i.e., Unit), and the other will be a standalone top-level function with the name Unit_areIdentical(). They are functionally identical.
See Also
Unit.areEquivalent()
def libsbml.Unit.clone (   self)

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 must be one of the text strings listed below; this list corresponds to SBML Level 3 Version 1 Core:

amperefaradjouleluxradianvolt
avogadrogramkatalmetresecondwatt
becquerelgraykelvinmolesiemensweber
candelahenrykilogramnewtonsievert
coulombhertzlitreohmsteradian
dimensionlessitemlumenpascaltesla

A few small differences exist between the Level 3 list of base units and the list defined in other Level/Version combinations of SBML. Specifically, Levels of SBML before Level 3 do not define avogadro; conversely, Level 2 Version 1 defines Celsius, and Level 1 defines celsius, meter, and liter, none of which are available in Level 3. In libSBML, each of the predefined base unit names is represented by an enumeration value whose name begins with the characters UNIT_KIND_, discussed in a separate section below.

The attribute named 'exponent' on Unit represents an exponent on the unit. In SBML Level 2, the attribute is optional and has a default value of 1 (one); in SBML Level 3, the attribute is mandatory and there is no default value. A Unit structure also has an 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. In SBML Level 2, the attribute is optional and has a default value of 0 (zero), because 10 0 = 1; in SBML Level 3, the attribute is mandatory and has no default value. Lastly, the attribute named 'multiplier' can be used to multiply the 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 is optional in SBML Level 2, where it has a default value of 1 (one); in SBML Level 3, the attribute is mandatory and has not default value.

Unit identification codes

As discussed above, 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.

In SBML Level 2 Versions before Version 3, there existed an enumeration of units called UnitKind. In Version 3, this enumeration was removed and the identifier class UnitSId redefined to include the previous UnitKind values as reserved symbols. This change has no net effect on permissible models, their representation or their syntax. The purpose of the change in the SBML specification was simply to clean up an inconsistency about the contexts in which these values were usable. However, libSBML maintains UnitKind in the form of of a set of static integer constants whose names begin with the characters UNIT_KIND_. These constants are defined in the class libsbml.

As a consequence of the fact that libSBML supports models in all Levels and Versions of SBML, libSBML's set of UNIT_KIND_ values is a union of all the possible base unit names defined in the different SBML specifications. However, not every base unit is allowed in every Level+Version combination of SBML. Note in particular the following exceptions:

  • The alternate spelling 'meter' is included in addition to the official SI spelling 'metre'. This spelling is only permitted in SBML Level 1 models.

  • The alternate spelling 'liter' is included in addition to the official SI spelling 'litre'. This spelling is only permitted in SBML Level 1 models.

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

  • The unit avogadro was introduced in SBML Level 3, and is only permitted for use in SBML Level 3 models.

The table below lists the unit constants defined in libSBML, and their meanings.

Enumerator Meaning
UNIT_KIND_AMPEREThe ampere unit.
UNIT_KIND_AVOGADROThe unit dimensionless multiplied by the numerical value of Avogadro's constant. (Only usable in SBML Level 3 models.)
UNIT_KIND_BECQUERELThe becquerel unit.
UNIT_KIND_CANDELAThe candela unit.
UNIT_KIND_CELSIUSThe Celsius unit. (Only usable in SBML Level 1 and SBML Level 2 Version 1 models.)
UNIT_KIND_COULOMBThe coulomb unit.
UNIT_KIND_DIMENSIONLESSA pseudo-unit indicating a dimensionless quantity.
UNIT_KIND_FARADThe farad unit.
UNIT_KIND_GRAMThe gram unit.
UNIT_KIND_GRAYThe gray unit.
UNIT_KIND_HENRYThe henry unit.
UNIT_KIND_HERTZThe hertz unit.
UNIT_KIND_ITEMA pseudo-unit representing a single "thing".
UNIT_KIND_JOULEThe joule unit.
UNIT_KIND_KATALThe katal unit.
UNIT_KIND_KELVINThe kelvin unit.
UNIT_KIND_KILOGRAMThe kilogram unit.
UNIT_KIND_LITERAlternate spelling of litre.
UNIT_KIND_LITREThe litre unit.
UNIT_KIND_LUMENThe lumen unit.
UNIT_KIND_LUXThe lux unit.
UNIT_KIND_METERAlternate spelling of metre.
UNIT_KIND_METREThe metre unit.
UNIT_KIND_MOLEThe mole unit.
UNIT_KIND_NEWTONThe newton unit.
UNIT_KIND_OHMThe ohm unit.
UNIT_KIND_PASCALThe pascal unit.
UNIT_KIND_RADIANThe radian unit.
UNIT_KIND_SECONDThe second unit.
UNIT_KIND_SIEMENSThe siemens unit.
UNIT_KIND_SIEVERTThe sievert unit.
UNIT_KIND_STERADIANThe steradian unit.
UNIT_KIND_TESLAThe tesla unit.
UNIT_KIND_VOLTThe volt unit.
UNIT_KIND_WATTThe watt unit.
UNIT_KIND_WEBERThe weber unit.
UNIT_KIND_INVALIDMarker used by libSBML to indicate an invalid or unset unit.
Python method signature(s):

clone(Unit self)   Unit

Creates and returns a deep copy of this Unit.

Returns
a (deep) copy of this Unit.
def libsbml.Unit.convertToSI (   args)

Python method signature(s):

convertToSI(Unit unit)   UnitDefinition

Returns a UnitDefinition object containing the given unit converted to the appropriate SI unit.

This method exists because some units can be expressed in terms of others when the same physical dimension is involved. For example, one hertz is identical to 1 sec-1, one litre is equivalent to 1 cubic decametre, and so on.

Parameters
unitthe Unit object to convert to SI
Returns
a UnitDefinition object containing the SI unit.
Note
Because this is a static method, the non-C++ language interfaces for libSBML will contain two variants. One will be a static method on the class (i.e., Unit), and the other will be a standalone top-level function with the name Unit_convertToSI(). They are functionally identical.
See Also
Unit.merge()
def libsbml.SBase.disablePackage (   self,
  args 
)
inherited

Python method signature(s):

disablePackage(SBase self, string pkgURI, string pkgPrefix)   int

Disables the given SBML Level 3 package

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

Parameters
pkgURIthe URI of the package
pkgPrefixthe XML prefix of the package
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.enablePackage (   self,
  args 
)
inherited

Python method signature(s):

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

Enables or disables the given SBML Level 3 package

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

Parameters
pkgURIthe URI of the package
pkgPrefixthe XML prefix of the package
flagwhether to enable (True) or disable (False) the package
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.getAncestorOfType (   self,
  args 
)
inherited

Python method signature(s):

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

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

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

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

Parameters
typethe SBML type code of the object sought
pkgName(optional) the short name of an SBML Level 3 package to which the sought-after object must belong
Returns
the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or None if no ancestor exists.
Documentation note:
The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.
def libsbml.SBase.getAnnotation (   self,
  args 
)
inherited

Python method signature(s):

getAnnotation(SBase self)   XMLNode
getAnnotation(SBase self)   XMLNode

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

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

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

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

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

Python method signature(s):

getAnnotationString(SBase self)   string
getAnnotationString(SBase self)   string

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

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

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

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

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

Python method signature(s):

getColumn(SBase self)   long

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

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

Python method signature(s):

getCVTerm(SBase self, long n)   CVTerm

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

Parameters
nlong the index of the CVTerm to retrieve
Returns
the nth CVTerm in the list of CVTerms for this SBML object.
def libsbml.SBase.getCVTerms (   self)
inherited

Python method signature(s):

getCVTerms()   CVTermList

Get the CVTermList of CVTerm objects in this SBase.

Returns the CVTermList for this SBase.

def libsbml.SBase.getElementByMetaId (   self,
  args 
)
inherited

Python method signature(s):

getElementByMetaId(SBase self, string metaid)   SBase

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

Parameters
metaidstring 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

Python method signature(s):

getElementBySId(SBase self, string id)   SBase

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

Parameters
idstring representing the 'id' attribute value of the object to find.
Returns
pointer to the first element found with the given identifier.
def libsbml.Unit.getElementName (   self)

Python method signature(s):

getElementName(Unit 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'.
def libsbml.Unit.getExponent (   self)

Python method signature(s):

getExponent(Unit self)   int

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

Returns
the 'exponent' value of this Unit, as an integer.
def libsbml.Unit.getExponentAsDouble (   self)

Python method signature(s):

getExponentAsDouble(Unit self)   float

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

Returns
the 'exponent' value of this Unit, as a float.
def libsbml.Unit.getKind (   self)

Python method signature(s):

getKind(Unit self)   long

Returns the 'kind' of Unit this is.

Returns
the value of the 'kind' attribute of this Unit as a value from the set of constants whose names begin with UNIT_KIND_ defined in the class libsbml.
def libsbml.SBase.getLevel (   self)
inherited

Python method signature(s):

getLevel(SBase self)   long

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

Returns
the SBML level of this SBML object.
See Also
getVersion()
getNamespaces()
getPackageVersion()
def libsbml.SBase.getLine (   self)
inherited

Python method signature(s):

getLine(SBase self)   long

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

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

Python method signature(s):

getListOfAllElements(SBase self)   SBaseList
def libsbml.SBase.getListOfAllElementsFromPlugins (   self)
inherited

Python method signature(s):

getListOfAllElementsFromPlugins(SBase self)   SBaseList
def libsbml.SBase.getMetaId (   self)
inherited

Python method signature(s):

getMetaId(SBase 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 meta-identifier of this SBML object.
See Also
isSetMetaId()
setMetaId()
def libsbml.SBase.getModel (   self)
inherited

Python method signature(s):

getModel(SBase self)   Model

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

Returns
the parent Model of this SBML object.
See Also
getParentSBMLObject()
getSBMLDocument()
def libsbml.SBase.getModelHistory (   self,
  args 
)
inherited

Python method signature(s):

getModelHistory(SBase self)   ModelHistory
getModelHistory(SBase self)   ModelHistory

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

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

Python method signature(s):

getMultiplier(Unit self)   float

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

Returns
the 'multiplier' value of this Unit, as a float.
def libsbml.SBase.getNamespaces (   self)
inherited

Python method signature(s):

getNamespaces(SBase self)   XMLNamespaces

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

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

Returns
the XML Namespaces associated with this SBML object
See Also
getLevel()
getVersion()
def libsbml.SBase.getNotes (   self,
  args 
)
inherited

Python method signature(s):

getNotes(SBase self)   XMLNode
getNotes(SBase self)   XMLNode

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

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

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

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

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

Python method signature(s):

getNotesString(SBase self)   string
getNotesString(SBase self)   string

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

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

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

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

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

Python method signature(s):

getNumCVTerms(SBase self)   long

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

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

Python method signature(s):

getNumPlugins(SBase self)   long

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

Returns
the number of plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.
def libsbml.Unit.getOffset (   self)

Python method signature(s):

getOffset(Unit 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.
def libsbml.SBase.getPackageName (   self)
inherited

Python method signature(s):

getPackageName(SBase self)   string

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

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

Python method signature(s):

getPackageVersion(SBase self)   long

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

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

Python method signature(s):

getParentSBMLObject(SBase self)   SBase
getParentSBMLObject(SBase self)   SBase

Returns the parent SBML object containing this object.

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

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

Python method signature(s):

getPlugin(SBase self, string package)   SBasePlugin
getPlugin(SBase self, string package)   SBasePlugin
getPlugin(SBase self, long n)   SBasePlugin
getPlugin(SBase self, long n)   SBasePlugin

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


Method variant with the following signature:

getPlugin(long n)

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

Parameters
nthe index of the plug-in to return
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.

Method variant with the following signature:

getPlugin(string package)

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

Parameters
packagethe name or URI of the package
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
def libsbml.SBase.getResourceBiologicalQualifier (   self,
  args 
)
inherited

Python method signature(s):

getResourceBiologicalQualifier(SBase self, string resource)   long

Returns the MIRIAM biological qualifier associated with the given resource.

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

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

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

Python method signature(s):

getResourceModelQualifier(SBase self, string resource)   long

Returns the MIRIAM model qualifier associated with the given resource.

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

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

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

Python method signature(s):

getSBMLDocument(SBase self)   SBMLDocument
getSBMLDocument(SBase self)   SBMLDocument

Returns the SBMLDocument object containing this object instance.

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

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

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

Python method signature(s):

getSBOTerm(SBase self)   int

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

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

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

Returns
the value of the 'sboTerm' attribute as an integer, or -1 if the value is not set.
def libsbml.SBase.getSBOTermAsURL (   self)
inherited

Python method signature(s):

getSBOTermAsURL(SBase self)   string

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

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

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

Returns
the value of the 'sboTerm' attribute as an identifiers.org URL (its value will be of the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'), or an empty string if the value is not set.
def libsbml.SBase.getSBOTermID (   self)
inherited

Python method signature(s):

getSBOTermID(SBase self)   string

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

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

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

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

Python method signature(s):

getScale(Unit self)   int

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

Returns
the 'scale' value of this Unit, as an integer.
def libsbml.Unit.getTypeCode (   self)

Python method signature(s):

getTypeCode(Unit self)   int

Returns the libSBML type code of this object instance.

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

Returns
the SBML type code for this object, or SBML_UNKNOWN (default).
See Also
getElementName()
def libsbml.SBase.getVersion (   self)
inherited

Python method signature(s):

getVersion(SBase self)   long

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

Returns
the SBML version of this SBML object.
See Also
getLevel()
getNamespaces()
def libsbml.Unit.hasRequiredAttributes (   self)

Python method signature(s):

hasRequiredAttributes(Unit self)   bool

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

Note
The required attributes for a Unit object are:
  • 'kind'
  • 'exponent' (required in SBML Level 3; optional in Level 2)
  • 'multiplier' (required in SBML Level 3; optional in Level 2)
  • 'scale' (required in SBML Level 3; optional in Level 2)
Returns
a boolean value indicating whether all the required elements for this object have been defined.
def libsbml.SBase.hasValidLevelVersionNamespaceCombination (   self)
inherited

Python method signature(s):

hasValidLevelVersionNamespaceCombination(SBase self)   bool
def libsbml.Unit.initDefaults (   self)

Python method signature(s):

initDefaults(Unit self)

Initializes the fields of this Unit object to 'typical' default values.

The SBML Unit component has slightly different aspects and default attribute values in different SBML Levels and Versions. This method sets the values to certain common defaults, based mostly on what they are in SBML Level 2. Specifically:

  • Sets attribute 'exponent' to 1
  • Sets attribute 'scale' to 0
  • Sets attribute 'multiplier' to 1.0

The 'kind' attribute is left unchanged.

def libsbml.Unit.isAmpere (   self)

Python method signature(s):

isAmpere(Unit 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.
def libsbml.Unit.isAvogadro (   self)

Python method signature(s):

isAvogadro(Unit self)   bool

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

Returns
True if the kind of this Unit is avogadro, False otherwise.
Note
The unit avogadro was introduced in SBML Level 3, and is only permitted for use in SBML Level 3 models.
def libsbml.Unit.isBecquerel (   self)

Python method signature(s):

isBecquerel(Unit 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.
def libsbml.Unit.isBuiltIn (   args)

Python method signature(s):

isBuiltIn(string name, long level)   bool

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

Parameters
namea string to be tested against the predefined unit names
levelthe 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.
Because this is a static method, the non-C++ language interfaces for libSBML will contain two variants. One will be a static method on the class (i.e., Unit), and the other will be a standalone top-level function with the name Unit_isBuiltIn(). They are functionally identical.
def libsbml.Unit.isCandela (   self)

Python method signature(s):

isCandela(Unit 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.
def libsbml.Unit.isCelsius (   self)

Python method signature(s):

isCelsius(Unit 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.
def libsbml.Unit.isCoulomb (   self)

Python method signature(s):

isCoulomb(Unit 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.
def libsbml.Unit.isDimensionless (   self)

Python method signature(s):

isDimensionless(Unit 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.

def libsbml.Unit.isFarad (   self)

Python method signature(s):

isFarad(Unit 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.
def libsbml.Unit.isGram (   self)

Python method signature(s):

isGram(Unit 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.
def libsbml.Unit.isGray (   self)

Python method signature(s):

isGray(Unit 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.
def libsbml.Unit.isHenry (   self)

Python method signature(s):

isHenry(Unit 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.
def libsbml.Unit.isHertz (   self)

Python method signature(s):

isHertz(Unit 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.
def libsbml.Unit.isItem (   self)

Python method signature(s):

isItem(Unit 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.
def libsbml.Unit.isJoule (   self)

Python method signature(s):

isJoule(Unit 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.
def libsbml.Unit.isKatal (   self)

Python method signature(s):

isKatal(Unit 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.
def libsbml.Unit.isKelvin (   self)

Python method signature(s):

isKelvin(Unit 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.
def libsbml.Unit.isKilogram (   self)

Python method signature(s):

isKilogram(Unit 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.
def libsbml.Unit.isLitre (   self)

Python method signature(s):

isLitre(Unit 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.
def libsbml.Unit.isLumen (   self)

Python method signature(s):

isLumen(Unit 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.
def libsbml.Unit.isLux (   self)

Python method signature(s):

isLux(Unit 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.
def libsbml.Unit.isMetre (   self)

Python method signature(s):

isMetre(Unit 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.
def libsbml.Unit.isMole (   self)

Python method signature(s):

isMole(Unit 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.
def libsbml.Unit.isNewton (   self)

Python method signature(s):

isNewton(Unit 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.
def libsbml.Unit.isOhm (   self)

Python method signature(s):

isOhm(Unit 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.
def libsbml.SBase.isPackageEnabled (   self,
  args 
)
inherited

Python method signature(s):

isPackageEnabled(SBase self, string pkgName)   bool

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

The search ignores the package version.

Parameters
pkgNamethe name of the package
Returns
True if the given package is enabled within this object, false otherwise.
See Also
isPackageURIEnabled()
def libsbml.SBase.isPackageURIEnabled (   self,
  args 
)
inherited

Python method signature(s):

isPackageURIEnabled(SBase self, string pkgURI)   bool

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

Parameters
pkgURIthe URI of the package
Returns
True if the given package is enabled within this object, false otherwise.
See Also
isPackageEnabled()
def libsbml.Unit.isPascal (   self)

Python method signature(s):

isPascal(Unit 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.
def libsbml.SBase.isPkgEnabled (   self,
  args 
)
inherited

Python method signature(s):

isPkgEnabled(SBase self, string pkgName)   bool

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

The search ignores the package version.

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

Python method signature(s):

isPkgURIEnabled(SBase self, string pkgURI)   bool

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

Parameters
pkgURIthe URI of the package
Returns
True if the given package is enabled within this object, false otherwise.
See Also
isPkgEnabled()
def libsbml.Unit.isRadian (   self)

Python method signature(s):

isRadian(Unit 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.
def libsbml.Unit.isSecond (   self)

Python method signature(s):

isSecond(Unit 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.
def libsbml.SBase.isSetAnnotation (   self)
inherited

Python method signature(s):

isSetAnnotation(SBase self)   bool

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

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

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

Returns
True if a 'annotation' subelement exists, False otherwise.
See Also
getAnnotation()
getAnnotationString()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.Unit.isSetExponent (   self)

Python method signature(s):

isSetExponent(Unit self)   bool

Predicate to test whether the 'exponent' attribute of this Unit is set.

Returns
True if the 'exponent' attribute of this Unit is set, False otherwise.
def libsbml.Unit.isSetKind (   self)

Python method signature(s):

isSetKind(Unit self)   bool

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

Returns
True if the 'kind' attribute of this Unit is set, false otherwise.
def libsbml.SBase.isSetMetaId (   self)
inherited

Python method signature(s):

isSetMetaId(SBase self)   bool

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

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

Returns
True if the 'metaid' attribute of this SBML object is set, False otherwise.
See Also
getMetaId()
setMetaId()
def libsbml.SBase.isSetModelHistory (   self)
inherited

Python method signature(s):

isSetModelHistory(SBase self)   bool

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

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

Python method signature(s):

isSetMultiplier(Unit self)   bool

Predicate to test whether the 'multiplier' attribute of this Unit is set.

Returns
True if the 'multiplier' attribute of this Unit is set, False otherwise.
def libsbml.SBase.isSetNotes (   self)
inherited

Python method signature(s):

isSetNotes(SBase self)   bool

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

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

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

Returns
True if a 'notes' subelement exists, False otherwise.
See Also
getNotes()
getNotesString()
setNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBase.isSetSBOTerm (   self)
inherited

Python method signature(s):

isSetSBOTerm(SBase self)   bool

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

Returns
True if the 'sboTerm' attribute of this SBML object is set, False otherwise.
def libsbml.Unit.isSetScale (   self)

Python method signature(s):

isSetScale(Unit self)   bool

Predicate to test whether the 'scale' attribute of this Unit is set.

Returns
True if the 'scale' attribute of this Unit is set, False otherwise.
def libsbml.Unit.isSiemens (   self)

Python method signature(s):

isSiemens(Unit 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.
def libsbml.Unit.isSievert (   self)

Python method signature(s):

isSievert(Unit 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.
def libsbml.Unit.isSteradian (   self)

Python method signature(s):

isSteradian(Unit 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.
def libsbml.Unit.isTesla (   self)

Python method signature(s):

isTesla(Unit 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.
def libsbml.Unit.isUnitKind (   args)

Python method signature(s):

isUnitKind(string name, long level, long 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
namea string to be tested
levela long integer representing the SBML specification Level
versiona long integer representing the SBML specification Version
Returns
True if name is a valid SBML 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.
Because this is a static method, the non-C++ language interfaces for libSBML will contain two variants. One will be a static method on the class (i.e., Unit), and the other will be a standalone top-level function with the name Unit_isUnitKind(). They are functionally identical.
def libsbml.Unit.isVolt (   self)

Python method signature(s):

isVolt(Unit 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.
def libsbml.Unit.isWatt (   self)

Python method signature(s):

isWatt(Unit 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.
def libsbml.Unit.isWeber (   self)

Python method signature(s):

isWeber(Unit 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.
def libsbml.SBase.matchesRequiredSBMLNamespacesForAddition (   self,
  args 
)
inherited

Python method signature(s):

matchesRequiredSBMLNamespacesForAddition(SBase self, SBase sb)   bool
matchesRequiredSBMLNamespacesForAddition(SBase self, SBase sb)   bool

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

Parameters
sban object to compare with respect to namespaces
Returns
boolean, True if this object's collection of namespaces is a subset of sb's, False otherwise.
def libsbml.SBase.matchesSBMLNamespaces (   self,
  args 
)
inherited

Python method signature(s):

matchesSBMLNamespaces(SBase self, SBase sb)   bool
matchesSBMLNamespaces(SBase self, SBase sb)   bool

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

Parameters
sban object to compare with respect to namespaces
Returns
boolean, True if this object's collection of namespaces is the same as sb's, False otherwise.
def libsbml.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
unit1the first Unit object; the result of the operation is left as a new version of this unit, modified in-place.
unit2the second Unit object to merge with the first
Note
Because this is a static method, the non-C++ language interfaces for libSBML will contain two variants. One will be a static method on the class (i.e., Unit), and the other will be a standalone top-level function with the name Unit_merge(). They are functionally identical.
See Also
Unit.convertToSI()
Unit.removeScale()
def libsbml.SBase.removeFromParentAndDelete (   self)
inherited

Python method signature(s):

removeFromParentAndDelete(SBase self)   int

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

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
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
unitthe Unit object to manipulate.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
Because this is a static method, the non-C++ language interfaces for libSBML will contain two variants. One will be a static method on the class (i.e., Unit), and the other will be a standalone top-level function with the name Unit_removeScale(). They are functionally identical.
See Also
Unit.convertToSI()
Unit.merge()
def libsbml.SBase.removeTopLevelAnnotationElement (   self,
  args 
)
inherited

Python method signature(s):

removeTopLevelAnnotationElement(SBase self, string elementName, string elementURI="")   int
removeTopLevelAnnotationElement(SBase self, string elementName)   int

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

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

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

Parameters
elementNamea string representing the name of the top level annotation element that is to be removed
elementURIan optional string that is used to check both the name and URI of the top level element to be removed
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
replaceTopLevelAnnotationElement()
replaceTopLevelAnnotationElement()
def libsbml.SBase.renameMetaIdRefs (   self,
  args 
)
inherited

Python method signature(s):

renameMetaIdRefs(SBase self, string oldid, string newid)

Renames all the MetaIdRef attributes on this element.

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

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

Python method signature(s):

renameSIdRefs(SBase self, string oldid, string newid)

Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists).

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

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

Python method signature(s):

renameUnitSIdRefs(SBase self, string oldid, string newid)

Renames all the UnitSIdRef attributes on this element.

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

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

Python method signature(s):

replaceTopLevelAnnotationElement(SBase self, XMLNode annotation)   int
replaceTopLevelAnnotationElement(SBase self, string annotation)   int

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


Method variant with the following signature:

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); appendAnnotation(annotation_with_name); with the exception that the placement of the annotation element remains the same.

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

Method variant with the following signature:

replaceTopLevelAnnotationElement(string annotation)

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

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

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

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

Python method signature(s):

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

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


Method variant with the following signature:

setAnnotation(XMLNode annotation)

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

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

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

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

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

Parameters
annotationan XML structure that is to be used as the new content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()

Method variant with the following signature:

setAnnotation(string annotation)

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

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

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

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

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

Parameters
annotationan XML string that is to be used as the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getAnnotationString()
isSetAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.Unit.setExponent (   self,
  args 
)

Python method signature(s):

setExponent(Unit self, int value)   int
setExponent(Unit self, float value)   int

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


Method variant with the following signature:

setExponent(int value)

Sets the 'exponent' attribute value of this Unit.

Parameters
valuethe 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:
Method variant with the following signature:
setExponent (float value)

Sets the 'exponent' attribute value of this Unit.

Parameters
valuethe float 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:
def libsbml.Unit.setKind (   self,
  args 
)

Python method signature(s):

setKind(Unit self, long kind)   int

Sets the 'kind' attribute value of this Unit.

Parameters
kinda unit identifier chosen from the set of constants whose names begin with UNIT_KIND_ in libsbml.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.setMetaId (   self,
  args 
)
inherited

Python method signature(s):

setMetaId(SBase 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.

Parameters
metaidthe identifier string to use as the value of the 'metaid' attribute
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getMetaId()
isSetMetaId()
def libsbml.SBase.setModelHistory (   self,
  args 
)
inherited

Python method signature(s):

setModelHistory(SBase self, ModelHistory history)   int

Sets the ModelHistory of this object.

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

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

Python method signature(s):

setMultiplier(Unit self, float value)   int

Sets the 'multipler' attribute value of this Unit.

Parameters
valuethe 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:
def libsbml.SBase.setNamespaces (   self,
  args 
)
inherited

Python method signature(s):

setNamespaces(SBase self, XMLNamespaces xmlns)   int

Sets the namespaces relevant of this SBML object.

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

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

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

Python method signature(s):

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

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


Method variant with the following signature:

setNotes(string notes, 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.

Parameters
notesan XML string that is to be used as the content of the 'notes' subelement of this object
addXHTMLMarkupa boolean indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p>) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()

Method variant with the following signature:

setNotes(XMLNode notes)

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

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

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

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

Parameters
notesan XML structure that is to be used as the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.Unit.setOffset (   self,
  args 
)

Python method signature(s):

setOffset(Unit self, float value)   int

Sets the 'offset' attribute value of this Unit.

Parameters
valuethe 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:
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.
def libsbml.SBase.setSBOTerm (   self,
  args 
)
inherited

Python method signature(s):

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

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


Method variant with the following signature:

setSBOTerm(int value)

Sets the value of the 'sboTerm' attribute.

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

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

Parameters
valuethe NNNNNNN integer portion of the SBO identifier
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
setSBOTerm()

Method variant with the following signature:

setSBOTerm(string &sboid)

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

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

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

Parameters
sboidthe SBO identifier string of the form 'SBO:NNNNNNN'
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
setSBOTerm()
def libsbml.Unit.setScale (   self,
  args 
)

Python method signature(s):

setScale(Unit self, int value)   int

Sets the 'scale' attribute value of this Unit.

Parameters
valuethe 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:
def libsbml.SBase.toSBML (   self)
inherited

toSBML(SBase self) string *

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

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

Python method signature(s):

unsetAnnotation(SBase 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.

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

Python method signature(s):

unsetCVTerms(SBase self)   int

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

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

Python method signature(s):

unsetId(SBase self)   int

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

Most (but not all) objects in SBML include two common attributes: 'id' and 'name'. The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always either Sid or UnitSId, depending on the object in question. Both data types are defined as follows:

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

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

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

Python method signature(s):

unsetMetaId(SBase 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.

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

Python method signature(s):

unsetModelHistory(SBase self)   int

Unsets the ModelHistory object attached to this object.

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

Python method signature(s):

unsetName(SBase self)   int

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

Most (but not all) objects in SBML include two common attributes: 'id' and 'name'. In contrast to the 'id' attribute, the 'name' attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of 'name' is the type string defined in XML Schema. SBML imposes no restrictions as to the content of 'name' attributes beyond those restrictions defined by the string type in XML Schema.

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

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

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

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

Python method signature(s):

unsetNotes(SBase self)   int

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

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

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

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See Also
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
appendNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBase.unsetSBOTerm (   self)
inherited

Python method signature(s):

unsetSBOTerm(SBase self)   int

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

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