libsbml.UnitDefinition Class Reference

Inheritance diagram for libsbml.UnitDefinition:

[legend]

List of all members.

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Detailed Description

LibSBML implementation of SBML's UnitDefinition construct.

Units of measurement may be supplied in a number of contexts in an SBML model. The units of the following mathematical entities can be specified explicitly: the size of a compartment, the initial amount of a species, and the units of constant and variable parameter values. The overall units of any mathematical formula appearing in SBML are those that arise naturally from the components and mathematical expressions comprising the formula, or in other words, the units obtained by doing dimensional analysis on the formula.

Rather than requiring a complete unit definition on every construct, SBML provides a facility for defining units that can be referenced throughout a model. In addition, every kind of SBML mathematical entity has units assigned to it from a set of predefined defaults (listed below); by redefining these predefined default units, it is possible to change the units used throughout a model in a simple and consistent manner.

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.

Summary of the UnitDefinition construct

UnitDefinition in SBML Level 2 has two attributes and one subelement. The two attributes are 'id' and 'name', and the subelement is ListOfUnits.

The required attribute 'id' and optional attribute 'name' are both strings. The 'id' attribute is used to give the defined unit a unique identifier by which other parts of an SBML model definition can refer to it. The 'name' attribute is intended to be used for giving the unit definition an optional human-readable name.

There are two important restrictions about the use of unit definition 'id' values in SBML Level 2 Versions 3–4:

• The 'id' of a UnitDefinition must not contain a value from the list of reserved base unit names (i.e., the strings gram, liter, etc.; see the definition of Unit for the complete list). This constraint simply prevents the redefinition of the base units.

• There is a set of reserved identifiers for the predefined units in SBML; these identifiers are substance, volume, area, length, and time. Using one of these values for the attribute 'id' of a UnitDefinition has the effect of redefining the model-wide default units for the corresponding quantities. The list of predefined units is given in the table below:

  Identifier	Possible scalable units	Default units
  substance	mole, item, gram, kilogram, dimensionless	mole
  volume	litre, cubic metre, dimensionless	litre
  area	square metre, dimensionless	square metre
  length	metre, dimensionless	metre
  time	second, dimensionless	second

  Also, two limitations are imposed on redefining the predefined unit substance, volume, area, length, and time: (1) The UnitDefinition of a predefined SBML unit can only contain a single Unit object within it. (2) The value of the 'kind' attribute in a Unit instance must be drawn from one of the values in the second column of the table above.

A UnitDefinition must contain exactly one ListOfUnits, and this list must contain one or more Unit definitions; see the definitions of these other object classes for more information about them. The following example illustrates a complete unit definition (when written in XML) when they all the pieces are combined together. This defines 'mmls' to be millimoles per litre per second.

<listOfUnitDefinitions>
    <unitDefinition id='mmls'>
        <listOfUnits>
            <unit kind='mole'   scale='-3'/>
            <unit kind='litre'  exponent='-1'/>
            <unit kind='second' exponent='-1'/>
        </listOfUnits>
    </unitDefinition>
</listOfUnitDefinitions>

Further comments about SBML's unit definition system

The vast majority of modeling situations requiring new SBML unit definitions involve simple multiplicative combinations of base units and factors. An example of this might be moles per litre per second. What distinguishes these sorts of simpler unit definitions from more complex ones is that they may be expressed without the use of an additive offset from a zero point. The use of offsets complicates all unit definition systems, yet in the domain of SBML the real-life cases requiring offsets are few (and in fact, to the best of our knowledge, only involve temperature). Consequently, the SBML unit system has been consciously designed in a way that attempts to simplify implementation of unit support for the most common cases in systems biology.

As of SBML Level 2 Version 2, Unit no longer has the attribute called 'offset' introduced in SBML Level 2 Version 1. It turned out that the general case involving units with offsets was incorrectly defined, and few (if any) developers even attempted to support offset-based units in their software. In the development of Level 2 Version 2, a consensus among SBML developers emerged that a fully generalized unit scheme is so confusing and complicated that it actually impedes interoperability. SBML Level 2 Version 2, Version 3 and Version 4 acknowledge this reality by reducing and simplifying the unit system, specifically by removing the 'offset' attribute on Unit and Celsius as a pre-defined unit.

The following guidelines suggest methods for handling units that do require the use of zero offsets for their definitions:

• Handling Celsius. A model in which certain quantities are temperatures measured in degrees Celsius can be converted straightforwardly to a model in which those temperatures are in kelvin. A software tool could do this by performing a straightforward substitution using the following relationship: T _kelvin = T _Celsius + 273.15. In every mathematical formula of the model where a quantity (call it x) in degrees Celsius appears, replace x with x _k+ 273.15, where x _k is now in kelvin. An alternative approach would be to use a FunctionDefinition to define a function encapsulating this relationship above and then using that in the rest of the model as needed. Since Celsius is a commonly-used unit, software tools could help users by providing users with the ability to express temperatures in Celsius in the tools' interfaces, and making substitutions automatically when writing out the SBML.

• Other units requiring offsets. One approach to handling other kinds of units is to use a FunctionDefinition to define a function encapsulating the necessary mathematical relationship, then substituting a call to this function wherever the original quantity appeared in the model. For example, here is a possible definition for converting Fahrenheit to Celsius degrees:

  <functionDefinition id='Fahrenheit_to_kelvin'>
      <math xmlns='http://www.w3.org/1998/Math/MathML'>
          <lambda>
              <bvar><ci> temp_in_fahrenheit </ci></bvar>
              <apply>
                  <divide/>
                  <apply>
                      <plus/>
                      <ci> temp_in_fahrenheit </ci>
                      <cn> 459.67 </cn>
                  </apply>
                  <cn> 1.8 </cn>
              </apply>
          </lambda>
      </math>
  </functionDefinition>
  

• An alternative approach not requiring the use of function definitions is to use an AssignmentRule for each variable in Fahrenheit units. The AssignmentRule could compute the conversion from Fahrenheit to (say) kelvin, assign its value to a variable (in Kelvin units), and then that variable could be used elsewhere in the model.

• Still another approach is to rewrite the mathematical formulas of a model to directly incorporate the conversion formula wherever the original quantity appeared.

Please consult the SBML specifications for more information about this and other issues involving units.

Definition at line 9450 of file libsbml.py.

Public Member Functions
def	__eq__
def	__init__
def	__init__
def	__ne__
def	addCVTerm
def	addUnit
def	appendAnnotation
def	appendNotes
def	areEquivalent
def	areIdentical
def	clone
def	combine
def	convertToSI
def	createUnit
def	getAncestorOfType
def	getAnnotation
def	getAnnotationString
def	getColumn
def	getCVTerm
def	getCVTerms
def	getElementName
def	getId
def	getLevel
def	getLine
def	getListOfUnits
def	getMetaId
def	getModel
def	getName
def	getNamespaces
def	getNotes
def	getNotesString
def	getNumCVTerms
def	getNumUnits
def	getParentSBMLObject
def	getResourceBiologicalQualifier
def	getResourceModelQualifier
def	getSBMLDocument
def	getSBOTerm
def	getSBOTermID
def	getTypeCode
def	getUnit
def	getVersion
def	hasRequiredAttributes
def	hasRequiredElements
def	hasValidLevelVersionNamespaceCombination
def	isSetAnnotation
def	isSetId
def	isSetMetaId
def	isSetName
def	isSetNotes
def	isSetSBOTerm
def	isVariantOfArea
def	isVariantOfDimensionless
def	isVariantOfLength
def	isVariantOfMass
def	isVariantOfSubstance
def	isVariantOfSubstancePerTime
def	isVariantOfTime
def	isVariantOfVolume
def	printUnits
def	removeUnit
def	reorder
def	setAnnotation
def	setId
def	setMetaId
def	setName
def	setNamespaces
def	setNotes
def	setSBOTerm
def	simplify
def	toSBML
def	unsetAnnotation
def	unsetCVTerms
def	unsetMetaId
def	unsetName
def	unsetNotes
def	unsetSBOTerm
Public Attributes
	this

---

Member Function Documentation

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

Definition at line 3296 of file libsbml.py.

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

Reimplemented in libsbml.SimpleSpeciesReference.

Definition at line 1771 of file libsbml.py.

def libsbml.UnitDefinition.__init__	(		self,
			args
	)

Python method signature(s):

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

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

Note:

The required elements for a Constraint object are: listOfUnits (L2 only)

Returns:

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

Deprecated:

libSBML internal

Definition at line 9637 of file libsbml.py.

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

Definition at line 3303 of file libsbml.py.

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

Python method signature(s):

addCVTerm(self, CVTerm term)    int

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

Parameters:

term

the CVTerm to assign

Returns:

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED
• LIBSBML_UNEXPECTED_ATTRIBUTE
• LIBSBML_INVALID_OBJECT

Note:

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

Warning:

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

Definition at line 2974 of file libsbml.py.

def libsbml.UnitDefinition.addUnit	(		self,
			args
	)

Python method signature(s):

addUnit(self, Unit u)    int

Adds a copy of the given Unit to this UnitDefinition.

Parameters:

u

the Unit instance to add to this UnitDefinition.

Returns:

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_LEVEL_MISMATCH
• LIBSBML_VERSION_MISMATCH
• LIBSBML_DUPLICATE_OBJECT_ID
• LIBSBML_OPERATION_FAILED

Note:

This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this UnitDefinition. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in the UnitDefinition. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see UnitDefinition.createUnit() for a method that does not lead to these issues.

See also:

createUnit()

Definition at line 9980 of file libsbml.py.

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

Python method signature(s):

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

Appends the annotation content given by annotation to any existing content in the 'annotation' subelement of this object.

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

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

Unlike SBase.setAnnotation(const XMLNode* annotation) or SBase.setAnnotation(const std.string& annotation), this method allows other annotations to be preserved when an application adds its own data.

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

Parameters:

annotation

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

Returns:

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

See also:

getAnnotationString()

isSetAnnotation()

setAnnotation(const XMLNode* annotation)

setAnnotation(const std.string& annotation)

appendAnnotation(const XMLNode* annotation)

unsetAnnotation()

Reimplemented in libsbml.Model, and libsbml.SpeciesReference.

Definition at line 2624 of file libsbml.py.

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

Python method signature(s):

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

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

The content in notes is copied.

The optional element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models. The format of 'notes' elements must be XHTML 1.0. The SBML Level 2 specification has considerable detail about how 'notes' element content must be handled; please refer to the specifications.

Parameters:

notes

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

Returns:

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_OBJECT
• LIBSBML_OPERATION_FAILED

See also:

getNotesString()

isSetNotes()

setNotes(const XMLNode* notes)

setNotes(const std.string& notes)

appendNotes(const XMLNode* notes)

unsetNotes()

Definition at line 2726 of file libsbml.py.

def libsbml.UnitDefinition.areEquivalent

(

args

)

Python method signature(s):

areEquivalent(UnitDefinition ud1, UnitDefinition ud2)    bool

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

For the purposes of performing this comparison, two UnitDefinition objects are considered equivalent when they contain equivalent list of Unit objects. Unit objects are in turn considered equivalent if they satisfy the predicate Unit.areEquivalent(). The predicate tests a subset of the objects's attributes.

Parameters:

	ud1	the first UnitDefinition object to compare
	ud2	the second UnitDefinition object to compare

Returns:

true if all the Unit objects in ud1 are equivalent to the Unit objects in ud2, false otherwise.

See also:

areIdentical(const UnitDefinition * ud1, const UnitDefinition * ud2)

Unit.areEquivalent(Unit * unit1, Unit * unit2)

Definition at line 10268 of file libsbml.py.

def libsbml.UnitDefinition.areIdentical

(

args

)

Python method signature(s):

areIdentical(UnitDefinition ud1, UnitDefinition ud2)    bool

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

For the purposes of performing this comparison, two UnitDefinition objects are considered identical when they contain identical lists of Unit objects. Pairs of Unit objects in the lists are in turn considered identical if they satisfy the predicate Unit.areIdentical(). The predicate compares every attribute of the Unit objects.

Parameters:

	ud1	the first UnitDefinition object to compare
	ud2	the second UnitDefinition object to compare

Returns:

true if all the Unit objects in ud1 are identical to the Unit objects of ud2, false otherwise.

See also:

areEquivalent(const UnitDefinition * ud1, const UnitDefinition * ud2)

Unit.areIdentical(Unit * unit1, Unit * unit2)

Definition at line 10236 of file libsbml.py.

def libsbml.UnitDefinition.clone

(

self

)

Python method signature(s):

clone(self)    UnitDefinition

Creates and returns a deep copy of this UnitDefinition.

Returns:

a (deep) copy of this UnitDefinition.

Reimplemented from libsbml.SBase.

Definition at line 9662 of file libsbml.py.

def libsbml.UnitDefinition.combine

(

args

)

Python method signature(s):

combine(UnitDefinition ud1, UnitDefinition ud2)    UnitDefinition

Combines two UnitDefinition objects into a single UnitDefinition object which expresses the product of the units of the two UnitDefinition's.

Parameters:

	ud1	the first UnitDefinition object
	ud2	the second UnitDefinition object

Returns:

a UnitDefinition which represents the product of the units of the two argument UnitDefinitions.

Definition at line 10300 of file libsbml.py.

def libsbml.UnitDefinition.convertToSI

(

args

)

Python method signature(s):

convertToSI(UnitDefinition arg0)    UnitDefinition

Convert a given UnitDefinition into a new UnitDefinition object that uses SI units.

Parameters:

ud

the UnitDefinition object to convert to SI

Returns:

a new UnitDefinition object representing the results of the conversion.

Definition at line 10215 of file libsbml.py.

def libsbml.UnitDefinition.createUnit

(

self

)

Python method signature(s):

createUnit(self)    Unit

Creates a new and empty Unit, adds it to this UnitDefinition's list of units, and returns it.

Returns:

a newly constructed (and empty) Unit instance.

Note:

It is worth emphasizing that the attribute 'kind' value of a Unit is a required attribute for a valid Unit definition. The createUnit() method does not assign a valid kind to the constructed unit (instead, it sets the 'kind' to UNIT_KIND_INVALID). Callers are cautioned to set the newly-constructed Unit's kind using Unit.setKind() soon after calling this method.

See also:

addUnit(const Unit* u)

Definition at line 10018 of file libsbml.py.

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

Python method signature(s):

getAncestorOfType(self, SBMLTypeCode_t type)    SBase

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

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

Parameters:

type

the SBMLTypeCode_t of the ancestor to be returned.

Returns:

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

Definition at line 2115 of file libsbml.py.

def libsbml.SBase.getAnnotation

(

self

)

[inherited]

Python method signature(s):

getAnnotation(self)    XMLNode

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

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

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

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

Returns:

the annotation of this SBML object as an XMLNode

See also:

getAnnotationString()

isSetAnnotation()

setAnnotation(const XMLNode* annotation)

setAnnotation(const std.string& annotation)

appendAnnotation(const XMLNode* annotation)

appendAnnotation(const std.string& annotation)

unsetAnnotation()

Definition at line 1971 of file libsbml.py.

def libsbml.SBase.getAnnotationString

(

self

)

[inherited]

Python method signature(s):

getAnnotationString(self)    string

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

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

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

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

Returns:

the annotation string of this SBML object.

See also:

getAnnotation()

isSetAnnotation()

setAnnotation(const XMLNode* annotation)

setAnnotation(const std.string& annotation)

appendAnnotation(const XMLNode* annotation)

appendAnnotation(const std.string& annotation)

unsetAnnotation()

Definition at line 2014 of file libsbml.py.

def libsbml.SBase.getColumn

(

self

)

[inherited]

Python method signature(s):

getColumn(self)    unsigned int

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

Returns:

the column number of this SBML object.

See also:

getLine()

Definition at line 2217 of file libsbml.py.

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

Python method signature(s):

getCVTerm(self, unsigned int n)    CVTerm

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

Parameters:

n

unsigned int the index of the CVTerm to retrieve

Returns:

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

Definition at line 3042 of file libsbml.py.

def libsbml.SBase.getCVTerms

(

self

)

[inherited]

Python method signature(s):

getCVTerms(self)    CVTermList

Get the CVTermList of CVTerm objects in this SBase.

Returns:

the CVTermList for this SBase.

Definition at line 3010 of file libsbml.py.

def libsbml.UnitDefinition.getElementName

(

self

)

Python method signature(s):

getElementName(self)    string

Returns the XML element name of this object, which for UnitDefinition, is always 'unitDefinition'.

Returns:

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

Reimplemented from libsbml.SBase.

Definition at line 10145 of file libsbml.py.

def libsbml.UnitDefinition.getId

(

self

)

Python method signature(s):

getId(self)    string

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

Returns:

the id of this UnitDefinition.

Reimplemented from libsbml.SBase.

Definition at line 9677 of file libsbml.py.

def libsbml.SBase.getLevel

(

self

)

[inherited]

Python method signature(s):

getLevel(self)    unsigned int

Returns the SBML Level of the overall SBML document.

Returns:

the SBML level of this SBML object.

See also:

getVersion()

Definition at line 3134 of file libsbml.py.

def libsbml.SBase.getLine

(

self

)

[inherited]

Python method signature(s):

getLine(self)    unsigned int

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

Returns:

the line number of this SBML object.

See also:

getColumn()

Definition at line 2199 of file libsbml.py.

def libsbml.UnitDefinition.getListOfUnits	(		self,
			args
	)

Python method signature(s):

getListOfUnits(self)    ListOfUnits
getListOfUnits(self)    ListOfUnits

Returns the list of Units for this UnitDefinition instance.

Returns:

the ListOfUnits value for this UnitDefinition.

Definition at line 10043 of file libsbml.py.

def libsbml.SBase.getMetaId

(

self

)

[inherited]

Python method signature(s):

getMetaId(self)    string

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

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

Returns:

the metaid of this SBML object.

See also:

isSetMetaId()

setMetaId(const std.string& metaid)

Definition at line 1790 of file libsbml.py.

def libsbml.SBase.getModel

(

self

)

[inherited]

Python method signature(s):

getModel(self)    Model

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

Returns:

the parent Model of this SBML object.

Definition at line 3119 of file libsbml.py.

def libsbml.UnitDefinition.getName

(

self

)

Python method signature(s):

getName(self)    string

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

Returns:

the name of this UnitDefinition.

Reimplemented from libsbml.SBase.

Definition at line 9692 of file libsbml.py.

def libsbml.SBase.getNamespaces

(

self

)

[inherited]

Python method signature(s):

getNamespaces(self)    XMLNamespaces

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

Returns:

the XML Namespaces associated with this SBML object

Reimplemented in libsbml.SBMLDocument.

Definition at line 2053 of file libsbml.py.

def libsbml.SBase.getNotes

(

self

)

[inherited]

Python method signature(s):

getNotes(self)    XMLNode

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

The optional element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models. The format of 'notes' elements must be XHTML 1.0. The SBML Level 2 specification has considerable detail about how 'notes' element content must be handled; please refer to the specifications.

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

Returns:

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

See also:

getNotesString()

isSetNotes()

setNotes(const XMLNode* notes)

setNotes(const std.string& notes)

appendNotes(const XMLNode* notes)

appendNotes(const std.string& notes)

unsetNotes()

Definition at line 1891 of file libsbml.py.

def libsbml.SBase.getNotesString

(

self

)

[inherited]

Python method signature(s):

getNotesString(self)    string

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

The optional element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models. The format of 'notes' elements must be XHTML 1.0. The SBML Level 2 specification has considerable detail about how 'notes' element content must be handled; please refer to the specifications.

Returns:

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

See also:

getNotes()

isSetNotes()

setNotes(const XMLNode* notes)

setNotes(const std.string& notes)

appendNotes(const XMLNode* notes)

appendNotes(const std.string& notes)

unsetNotes()

Definition at line 1934 of file libsbml.py.

def libsbml.SBase.getNumCVTerms

(

self

)

[inherited]

Python method signature(s):

getNumCVTerms(self)    unsigned int

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

Returns:

the number of CVTerms for this SBML object.

Definition at line 3026 of file libsbml.py.

def libsbml.UnitDefinition.getNumUnits

(

self

)

Python method signature(s):

getNumUnits(self)    unsigned int

Returns the number of Unit objects contained within this UnitDefinition.

Returns:

an integer representing the number of Units in this UnitDefinition.

Definition at line 10076 of file libsbml.py.

def libsbml.SBase.getParentSBMLObject

(

self

)

[inherited]

Python method signature(s):

getParentSBMLObject(self)    SBase

Returns the parent SBML object.

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

Returns:

the parent SBML object of this SBML object.

Definition at line 2096 of file libsbml.py.

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

Python method signature(s):

getResourceBiologicalQualifier(self, string resource)    BiolQualifierType_t

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

Parameters:

resource

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

Returns:

the BiolQualifierType_t value associated with the resource

Definition at line 3081 of file libsbml.py.

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

Python method signature(s):

getResourceModelQualifier(self, string resource)    ModelQualifierType_t

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

Parameters:

resource

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

Returns:

the ModelQualifierType_t value associated with the resource

Definition at line 3100 of file libsbml.py.

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

Python method signature(s):

getSBMLDocument(self)    SBMLDocument
getSBMLDocument(self)    SBMLDocument

Returns the parent SBMLDocument object.

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

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

Returns:

the parent SBMLDocument object of this SBML object.

Definition at line 2068 of file libsbml.py.

def libsbml.SBase.getSBOTerm

(

self

)

[inherited]

Python method signature(s):

getSBOTerm(self)    int

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

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

Returns:

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

Definition at line 2141 of file libsbml.py.

def libsbml.SBase.getSBOTermID

(

self

)

[inherited]

Python method signature(s):

getSBOTermID(self)    string

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

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

Returns:

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

Definition at line 2169 of file libsbml.py.

def libsbml.UnitDefinition.getTypeCode

(

self

)

Python method signature(s):

getTypeCode(self)    SBMLTypeCode_t

Returns the libSBML type code for this object instance.

Returns:

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

See also:

getElementName()

Reimplemented from libsbml.SBase.

Definition at line 10116 of file libsbml.py.

def libsbml.UnitDefinition.getUnit	(		self,
			args
	)

Python method signature(s):

getUnit(self, unsigned int n)    Unit
getUnit(self, unsigned int n)    Unit

Returns a specific Unit instance belonging to this UnitDefinition.

Parameters:

n

an integer, the index of the Unit to be returned.

Returns:

the nth Unit of this UnitDefinition

Definition at line 10058 of file libsbml.py.

def libsbml.SBase.getVersion

(

self

)

[inherited]

Python method signature(s):

getVersion(self)    unsigned int

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

Returns:

the SBML version of this SBML object.

See also:

getLevel()

Definition at line 3151 of file libsbml.py.

def libsbml.UnitDefinition.hasRequiredAttributes

(

self

)

Python method signature(s):

hasRequiredAttributes(self)    bool

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

Note:

The required attributes for a UnitDefinition object are: id (name in L1)

Returns:

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

Reimplemented from libsbml.SBase.

Definition at line 10361 of file libsbml.py.

def libsbml.UnitDefinition.hasRequiredElements

(

self

)

Python method signature(s):

hasRequiredElements(self)    bool

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

Note:

The required elements for a Constraint object are: listOfUnits (L2 only)

Returns:

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

Reimplemented from libsbml.SBase.

Definition at line 10382 of file libsbml.py.

def libsbml.SBase.hasValidLevelVersionNamespaceCombination

(

self

)

[inherited]

Python method signature(s):

hasValidLevelVersionNamespaceCombination(self)    bool

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

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

• Level 1 Version 2 'http://www.sbml.org/sbml/level1'
• Level 2 Version 1 'http://www.sbml.org/sbml/level2'
• Level 2 Version 2 'http://www.sbml.org/sbml/level2/version2'
• Level 2 Version 3 'http://www.sbml.org/sbml/level2/version3'
• Level 2 Version 4 'http://www.sbml.org/sbml/level2/version4'

Returns:

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

Definition at line 3192 of file libsbml.py.

def libsbml.SBase.isSetAnnotation

(

self

)

[inherited]

Python method signature(s):

isSetAnnotation(self)    bool

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

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

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

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

Returns:

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

See also:

getAnnotation()

getAnnotationString()

setAnnotation(const XMLNode* annotation)

setAnnotation(const std.string& annotation)

appendAnnotation(const XMLNode* annotation)

appendAnnotation(const std.string& annotation)

unsetAnnotation()

Definition at line 2387 of file libsbml.py.

def libsbml.UnitDefinition.isSetId

(

self

)

Python method signature(s):

isSetId(self)    bool

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

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

Returns:

true if the 'id' attribute of this UnitDefinition has been set, false otherwise.

Reimplemented from libsbml.SBase.

Definition at line 9707 of file libsbml.py.

def libsbml.SBase.isSetMetaId

(

self

)

[inherited]

Python method signature(s):

isSetMetaId(self)    bool

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

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

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

Returns:

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

See also:

getMetaId()

setMetaId(const std.string& metaid)

Definition at line 2235 of file libsbml.py.

def libsbml.UnitDefinition.isSetName

(

self

)

Python method signature(s):

isSetName(self)    bool

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

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

Returns:

true if the 'name' attribute of this UnitDefinition has been set, false otherwise.

Reimplemented from libsbml.SBase.

Definition at line 9726 of file libsbml.py.

def libsbml.SBase.isSetNotes

(

self

)

[inherited]

Python method signature(s):

isSetNotes(self)    bool

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

The optional element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models. The format of 'notes' elements must be XHTML 1.0. The SBML Level 2 specification has considerable detail about how 'notes' element content must be handled; please refer to the specifications.

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

Returns:

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

See also:

getNotes()

getNotesString()

setNotes(const XMLNode* notes)

setNotes(const std.string& notes)

appendNotes(const XMLNode* notes)

appendNotes(const std.string& notes)

unsetNotes()

Definition at line 2348 of file libsbml.py.

def libsbml.SBase.isSetSBOTerm

(

self

)

[inherited]

Python method signature(s):

isSetSBOTerm(self)    bool

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

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

Returns:

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

Definition at line 2427 of file libsbml.py.

def libsbml.UnitDefinition.isVariantOfArea

(

self

)

Python method signature(s):

isVariantOfArea(self)    bool

Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'area'.

Returns:

true if this UnitDefinition is a variant of the predefined unit area, meaning square metres with only abritrary variations in scale or multiplier values; false otherwise.

Definition at line 9833 of file libsbml.py.

def libsbml.UnitDefinition.isVariantOfDimensionless

(

self

)

Python method signature(s):

isVariantOfDimensionless(self)    bool

Convenience function for testing if a given unit definition is a variant of the unit 'dimensionless'.

Returns:

true if this UnitDefinition is a variant of dimensionless, meaning dimensionless with only abritrary variations in scale or multiplier values; false otherwise.

Definition at line 9924 of file libsbml.py.

def libsbml.UnitDefinition.isVariantOfLength

(

self

)

Python method signature(s):

isVariantOfLength(self)    bool

Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'length'.

Returns:

true if this UnitDefinition is a variant of the predefined unit length, meaning metres with only abritrary variations in scale or multiplier values; false otherwise.

Definition at line 9851 of file libsbml.py.

def libsbml.UnitDefinition.isVariantOfMass

(

self

)

Python method signature(s):

isVariantOfMass(self)    bool

Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'mass'.

Returns:

true if this UnitDefinition is a variant of mass units, meaning gram or kilogram with only abritrary variations in scale or multiplier values; false otherwise.

Definition at line 9942 of file libsbml.py.

def libsbml.UnitDefinition.isVariantOfSubstance

(

self

)

Python method signature(s):

isVariantOfSubstance(self)    bool

Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'substance'.

Returns:

true if this UnitDefinition is a variant of the predefined unit substance, meaning moles or items (and grams or kilograms from SBML Level 2 Version 2 onwards) with only abritrary variations in scale or multiplier values; false otherwise.

Definition at line 9869 of file libsbml.py.

def libsbml.UnitDefinition.isVariantOfSubstancePerTime

(

self

)

Python method signature(s):

isVariantOfSubstancePerTime(self)    bool

Convenience function for testing if a given unit definition is a variant of the predefined unit 'substance' divided by the predefined unit 'time'.

Returns:

true if this UnitDefinition is a variant of the predefined unit substance per predefined unit time, meaning it contains two units one of which is a variant of substance and the other is a variant of time which an exponent of -1; false otherwise.

Definition at line 9960 of file libsbml.py.

def libsbml.UnitDefinition.isVariantOfTime

(

self

)

Python method signature(s):

isVariantOfTime(self)    bool

Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'time'.

Returns:

true if this UnitDefinition is a variant of the predefined unit time, meaning seconds with only abritrary variations in scale or multiplier values; false otherwise.

Definition at line 9888 of file libsbml.py.

def libsbml.UnitDefinition.isVariantOfVolume

(

self

)

Python method signature(s):

isVariantOfVolume(self)    bool

Convenience function for testing if a given unit definition is a variant of the predefined unit identifier 'volume'.

Returns:

true if this UnitDefinition is a variant of the predefined unit volume, meaning litre or cubic metre with only abritrary variations in scale or multiplier values; false otherwise.

Definition at line 9906 of file libsbml.py.

def libsbml.UnitDefinition.printUnits

(

args

)

Python method signature(s):

printUnits(UnitDefinition ud, bool compact = False)    string
printUnits(UnitDefinition ud)    string

Returns a string that expresses the unit definition represented by this UnitDefinition object.

For example printUnits applied to

<unitDefinition>
 <listOfUnits>
   <unit kind='metre' exponent='1'/>
   <unit kind='second' exponent='-2'/>
 </listOfUnits>
<unitDefinition>

will return the string 'metre (exponent = 1, multiplier = 1, scale = 0) second (exponent = -2, multiplier = 1, scale = 0)' or, if compact = true, the string '(1 metre)^1 (1 second)^-2' This may be useful for printing unit information to human users, or in debugging, or other situations.

Parameters:

	ud	the UnitDefinition object
	compact	boolean indicating whether the compact form should be used (defaults to false)

Returns:

a string expressing the unit definition

Definition at line 10323 of file libsbml.py.

def libsbml.UnitDefinition.removeUnit	(		self,
			args
	)

Python method signature(s):

removeUnit(self, unsigned int n)    Unit

Removes the nth Unit object from this UnitDefinition object and returns a pointer to it.

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

Parameters:

n

the index of the Unit object to remove

Returns:

the Unit object removed. As mentioned above, the caller owns the returned item. NULL is returned if the given index is out of range.

Definition at line 10093 of file libsbml.py.

def libsbml.UnitDefinition.reorder

(

args

)

Python method signature(s):

reorder(UnitDefinition ud)

Orders alphabetically the Unit objects within the ListOfUnits of a UnitDefinition.

Parameters:

ud

the UnitDefinition object whose units are to be reordered.

Definition at line 10197 of file libsbml.py.

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

Python method signature(s):

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

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

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

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

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

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

Parameters:

annotation

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

Returns:

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

See also:

getAnnotationString()

isSetAnnotation()

setAnnotation(const XMLNode* annotation)

appendAnnotation(const XMLNode* annotation)

appendAnnotation(const std.string& annotation)

unsetAnnotation()

Reimplemented in libsbml.Model, and libsbml.SpeciesReference.

Definition at line 2568 of file libsbml.py.

def libsbml.UnitDefinition.setId	(		self,
			args
	)

Python method signature(s):

setId(self, string sid)    int

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

The string sid is copied. Note that SBML has strict requirements for the syntax of identifiers. The following is summary of the definition of the SBML identifier type SId (here expressed in an extended form of BNF notation):

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

The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. In addition, there are a few conditions for the uniqueness of identifiers in an SBML model. Please consult the SBML specifications for the exact formulations.

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

Parameters:

sid

the string to use as the identifier of this UnitDefinition

Returns:

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE

Reimplemented from libsbml.SBase.

Definition at line 9745 of file libsbml.py.

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

Python method signature(s):

setMetaId(self, string metaid)    int

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

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

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

Parameters:

metaid

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

Returns:

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE
• LIBSBML_UNEXPECTED_ATTRIBUTE

See also:

getMetaId()

isSetMetaId()

Definition at line 2446 of file libsbml.py.

def libsbml.UnitDefinition.setName	(		self,
			args
	)

Python method signature(s):

setName(self, string name)    int

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

The string in name is copied.

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

Parameters:

name

the new name for the UnitDefinition

Returns:

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE

Reimplemented from libsbml.SBase.

Definition at line 9785 of file libsbml.py.

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

Python method signature(s):

setNamespaces(self, XMLNamespaces xmlns)    int

Sets the namespaces relevant of this SBML object.

Parameters:

xmlns

the namespaces to set

Returns:

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

• LIBSBML_OPERATION_SUCCESS

Definition at line 2811 of file libsbml.py.

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

Python method signature(s):

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

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

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

The optional element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models. The format of 'notes' elements must be XHTML 1.0. The SBML Level 2 specification has considerable detail about how 'notes' element content must be handled; please refer to the specifications.

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

Parameters:

notes

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

Returns:

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_OBJECT
• LIBSBML_OPERATION_FAILED

See also:

getNotesString()

isSetNotes()

setNotes(const XMLNode* notes)

appendNotes(const XMLNode* notes)

appendNotes(const std.string& notes)

unsetNotes()

Definition at line 2676 of file libsbml.py.

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

Python method signature(s):

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

Sets the value of the 'sboTerm' attribute.

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

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

Parameters:

value

the NNNNNNN integer portion of the SBO identifier

Returns:

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE
• LIBSBML_UNEXPECTED_ATTRIBUTE

Definition at line 2774 of file libsbml.py.

def libsbml.UnitDefinition.simplify

(

args

)

Python method signature(s):

simplify(UnitDefinition ud)

Simplifies the UnitDefinition so that any Unit objects occurring within the ListOfUnits occurs only once.

For example, the following definition,

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

will be simplified to

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

Parameters:

ud

the UnitDefinition object to be simplified.

Definition at line 10161 of file libsbml.py.

def libsbml.SBase.toSBML

(

self

)

[inherited]

Python method signature(s):

toSBML(self)    char

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

Returns:

the partial SBML that describes this SBML object.

Definition at line 3237 of file libsbml.py.

def libsbml.SBase.unsetAnnotation

(

self

)

[inherited]

Python method signature(s):

unsetAnnotation(self)    int

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

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

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

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

Returns:

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

• LIBSBML_OPERATION_SUCCESS

See also:

getAnnotation()

getAnnotationString()

isSetAnnotation()

setAnnotation(const XMLNode* annotation)

setAnnotation(const std.string& annotation)

appendAnnotation(const XMLNode* annotation)

appendAnnotation(const std.string& annotation)

Definition at line 2910 of file libsbml.py.

def libsbml.SBase.unsetCVTerms

(

self

)

[inherited]

Python method signature(s):

unsetCVTerms(self)    int

Clears the list of CVTerms of this SBML object.

Returns:

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

Definition at line 3060 of file libsbml.py.

def libsbml.SBase.unsetMetaId

(

self

)

[inherited]

Python method signature(s):

unsetMetaId(self)    int

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

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

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

Returns:

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

Definition at line 2832 of file libsbml.py.

def libsbml.UnitDefinition.unsetName

(

self

)

Python method signature(s):

unsetName(self)    int

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

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

Returns:

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

Definition at line 9811 of file libsbml.py.

def libsbml.SBase.unsetNotes

(

self

)

[inherited]

Python method signature(s):

unsetNotes(self)    int

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

The optional element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models. The format of 'notes' elements must be XHTML 1.0. The SBML Level 2 specification has considerable detail about how 'notes' element content must be handled; please refer to the specifications.

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

Returns:

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

• LIBSBML_OPERATION_SUCCESS

See also:

getNotesString()

isSetNotes()

setNotes(const XMLNode* notes)

setNotes(const std.string& notes)

appendNotes(const XMLNode* notes)

appendNotes(const std.string& notes)

Definition at line 2869 of file libsbml.py.

def libsbml.SBase.unsetSBOTerm

(

self

)

[inherited]

Python method signature(s):

unsetSBOTerm(self)    int

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

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

Returns:

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_UNEXPECTED_ATTRIBUTE

Definition at line 2952 of file libsbml.py.

---

Member Data Documentation

libsbml.UnitDefinition.this

Reimplemented from libsbml.SBase.

Definition at line 9661 of file libsbml.py.