libsbml.StoichiometryMath Class Reference

Inheritance diagram for libsbml.StoichiometryMath:

Inheritance graph
[legend]

List of all members.

Detailed Description

LibSBML implementation of SBML's StoichiometryMath construct.

In SBML Level 2, product and reactant stoichiometries can be specified using either the 'stoichiometry' attribute or a 'stoichiometryMath' element in a SpeciesReference object. The 'stoichiometry' attribute is of type float and should contain values greater than zero (0). The 'stoichiometryMath' element is implemented as an element containing a MathML expression. These two are mutually exclusive; only one of 'stoichiometry' or 'stoichiometryMath' should be defined in a given SpeciesReference instance. When neither the attribute nor the element is present, the value of 'stoichiometry' in the enclosing SpeciesReference instance defaults to 1.

For maximum interoperability, SpeciesReference's 'stoichiometry' attribute should be used in preference to 'stoichiometryMath' when a species' stoichiometry is a simple scalar number (integer or decimal). When the stoichiometry is a rational number, or when it is a more complicated formula, 'stoichiometryMath' must be used. The MathML expression in 'stoichiometryMath' may also refer to identifiers of entities in a model (except reaction identifiers). However, the only species identifiers that can be used in 'stoichiometryMath' are those referenced in the enclosing Reaction's list of reactants, products and modifiers.

The 'stoichiometry' attribute and the 'stoichiometryMath' element, when either is used, is each interpreted as a factor applied to the reaction rate to produce the rate of change of the species identified by the 'species' attribute in the enclosing SpeciesReference. This is the normal interpretation of a stoichiometry, but in SBML, one additional consideration has to be taken into account. The reaction rate, which is the result of the KineticLaw's 'math' element, is always in the model's substance per time units. However, the rate of change of the species will involve the species' substance units (i.e., the units identified by the Species object's 'substanceUnits' attribute), and these units may be different from the model's default substance units. If the units are different, the stoichiometry must incorporate a conversion factor for converting the model's substance units to the species' substance units. The conversion factor is assumed to be included in the scalar value of the 'stoichiometry' attribute if 'stoichiometry' is used. If instead 'stoichiometryMath' is used, then the product of the model's 'substance' units times the 'stoichiometryMath' units must match the substance units of the species. Note that in either case, if the species' units and the model's default substance units are the same, the stoichiometry ends up being a dimensionless number and equivalent to the standard chemical stoichiometry found in textbooks. Examples and more explanations of this are given in the SBML specification.

The following is a simple example of a species reference for species 'X0', with stoichiometry 2, in a list of reactants within a reaction having the identifier 'J1': 

<model>
    ...
    <listOfReactions>
        <reaction id='J1'>
            <listOfReactants>
                <speciesReference species='X0' stoichiometry='2'>
            </listOfReactants>
            ...
        </reaction>
        ...
    </listOfReactions>
    ...
</model>

The following is a more complex example of a species reference for species 'X0', with a stoichiometry formula consisting of a rational number: 

<model>
    ...
    <listOfReactions>
        <reaction id='J1'>
            <listOfReactants>
                <speciesReference species='X0'>
                    <stoichiometryMath>
                        <math xmlns='http://www.w3.org/1998/Math/MathML'> 
                            <cn type='rational'> 3 <sep/> 2 </cn>
                        </math>
                    </stoichiometryMath>
                </speciesReference>
            </listOfReactants>
            ...
        </reaction>
        ...
    </listOfReactions>
    ...
</model>

Additional discussions of stoichiometries and implications for species and reactions are included in the documentation of SpeciesReference class.

See also:
SpeciesReference

Reaction

Definition at line 24810 of file libsbml.py.


Public Member Functions

def __eq__
def __init__
def __init__
def __ne__
def addCVTerm
def appendAnnotation
def appendNotes
def clone
def containsUndeclaredUnits
def getAncestorOfType
def getAnnotation
def getAnnotationString
def getColumn
def getCVTerm
def getCVTerms
def getDerivedUnitDefinition
def getElementName
def getId
def getLevel
def getLine
def getMath
def getMetaId
def getModel
def getName
def getNamespaces
def getNotes
def getNotesString
def getNumCVTerms
def getParentSBMLObject
def getResourceBiologicalQualifier
def getResourceModelQualifier
def getSBMLDocument
def getSBOTerm
def getSBOTermID
def getTypeCode
def getVersion
def hasRequiredAttributes
def hasRequiredElements
def hasValidLevelVersionNamespaceCombination
def isSetAnnotation
def isSetId
def isSetMath
def isSetMetaId
def isSetName
def isSetNotes
def isSetSBOTerm
def setAnnotation
def setId
def setMath
def setMetaId
def setName
def setNamespaces
def setNotes
def setSBOTerm
def toSBML
def unsetAnnotation
def unsetCVTerms
def unsetMetaId
def unsetNotes
def unsetSBOTerm

Public Attributes

 this

Member Function Documentation

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

Definition at line 3296 of file libsbml.py.

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

Reimplemented in libsbml.SimpleSpeciesReference.

Definition at line 1771 of file libsbml.py.

def libsbml.StoichiometryMath.__init__ (   self,
  args 
)

Python method signature(s): 

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

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

Note:
The required elements for a StoichiometryMath object are: math
Returns:
a boolean value indicating whether all the required elements for this object have been defined.
Deprecated:
libSBML internal

Definition at line 24921 of file libsbml.py.

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

Definition at line 3303 of file libsbml.py.

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

Python method signature(s): 

addCVTerm(self, CVTerm term)    int

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

Parameters:
term the CVTerm to assign
Returns:
integer value indicating success/failure of the function. The possible values returned by this function are:
  • LIBSBML_OPERATION_SUCCESS
  • LIBSBML_OPERATION_FAILED
  • LIBSBML_UNEXPECTED_ATTRIBUTE
  • LIBSBML_INVALID_OBJECT
Note:
Since the CV Term uses the metaid of the object as a reference, if the object has no metaid set the CVTerm will not be added.
Warning:
The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance added here. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result.

Definition at line 2974 of file libsbml.py.

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

Python method signature(s): 

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

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

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

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

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

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

Parameters:
annotation an XML string that is to be copied and appended to the content of the 'annotation' subelement of this object
Returns:
integer value indicating success/failure of the function. The possible values returned by this function are:
  • LIBSBML_OPERATION_SUCCESS
  • LIBSBML_OPERATION_FAILED
See also:
getAnnotationString()

isSetAnnotation()

setAnnotation(const XMLNode* annotation)

setAnnotation(const std.string& annotation)

appendAnnotation(const XMLNode* annotation)

unsetAnnotation()

Reimplemented in libsbml.Model, and libsbml.SpeciesReference.

Definition at line 2624 of file libsbml.py.

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

Python method signature(s): 

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

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

The content in notes is copied.

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

Parameters:
notes an XML string that is to appended to the content of the 'notes' subelement of this object
Returns:
integer value indicating success/failure of the function. The possible values returned by this function are:
  • LIBSBML_OPERATION_SUCCESS
  • LIBSBML_INVALID_OBJECT
  • LIBSBML_OPERATION_FAILED
See also:
getNotesString()

isSetNotes()

setNotes(const XMLNode* notes)

setNotes(const std.string& notes)

appendNotes(const XMLNode* notes)

unsetNotes()

Definition at line 2726 of file libsbml.py.

def libsbml.StoichiometryMath.clone (   self  ) 

Python method signature(s): 

clone(self)    StoichiometryMath

Creates and returns a deep copy of this StoichiometryMath object.

Returns:
a (deep) copy of this StoichiometryMath.

Reimplemented from libsbml.SBase.

Definition at line 24946 of file libsbml.py.

def libsbml.StoichiometryMath.containsUndeclaredUnits (   self,
  args 
)

Python method signature(s): 

containsUndeclaredUnits(self)    bool
containsUndeclaredUnits(self)    bool

Predicate returning true or false depending on whether the math expression of this StoichiometryMath object contains literal numbers or parameters with undeclared units.

The StoichiometryMath.getDerivedUnitDefinition() method returns what libSBML computes the units of the Stoichiometry to be, to the extent that libSBML can compute them. However, if the expression contains literal numbers or parameters with undeclared units, libSBML may not be able to compute the full units of the expression and will only return what it can compute. Callers should always use StoichiometryMath.containsUndeclaredUnits() when using StoichiometryMath.getDerivedUnitDefinition() to decide whether the returned units may be incomplete.

Returns:
true if the math expression of this StoichiometryMath includes numbers/parameters with undeclared units, false otherwise.
Note:
A return value of true indicates that the UnitDefinition returned by StoichiometryMath.getDerivedUnitDefinition() may not accurately represent the units of the expression.
See also:
getDerivedUnitDefinition()

Definition at line 25062 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.StoichiometryMath.getDerivedUnitDefinition (   self,
  args 
)

Python method signature(s): 

getDerivedUnitDefinition(self)    UnitDefinition
getDerivedUnitDefinition(self)    UnitDefinition

Calculates and returns a UnitDefinition object that expresses the units returned by the math expression in this StoichiometryMath object.

The units are calculated based on the mathematical expression in the StoichiometryMath and the model quantities referenced by <ci> elements used within that expression. The StoichiometryMath.getDerivedUnitDefinition() method returns the calculated units.

Note that the functionality that facilitates unit analysis depends on the model as a whole. Thus, in cases where the object has not been added to a model or the model itself is incomplete, unit analysis is not possible and this method will return NULL.

Warning:
Note that it is possible the 'math' expression in the StoichiometryMath instance contains literal numbers or parameters with undeclared units. In those cases, it is not possible to calculate the units of the overall expression without making assumptions. LibSBML does not make assumptions about the units, and StoichiometryMath.getDerivedUnitDefinition() only returns the units as far as it is able to determine them. For example, in an expression X + Y, if X has unambiguously-defined units and Y does not, it will return the units of X. When using this method, it is critical that callers also invoke the method StoichiometryMath.containsUndeclaredUnits() to determine whether this situation holds. Callers should take suitable action in those situations.
Returns:
a UnitDefinition that expresses the units of the math
See also:
containsUndeclaredUnits()

Definition at line 25017 of file libsbml.py.

def libsbml.StoichiometryMath.getElementName (   self  ) 

Python method signature(s): 

getElementName(self)    string

Returns the XML element name of this object, which for StoichiometryMath, is always 'stoichiometryMath'.

Returns:
the name of this element, i.e., 'stoichiometryMath'.

Reimplemented from libsbml.SBase.

Definition at line 25126 of file libsbml.py.

def libsbml.SBase.getId (   self  )  [inherited]

Python method signature(s): 

getId(self)    string

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

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

Returns:
the metaid of this SBML object.
See also:
isSetMetaId()

setMetaId(const std.string& metaid)

Deprecated:
libSBML internal

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

Definition at line 1823 of file libsbml.py.

def libsbml.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.StoichiometryMath.getMath (   self  ) 

Python method signature(s): 

getMath(self)    ASTNode

Retrieves the mathematical formula within this StoichiometryMath and return it as an AST.

Returns:
the math of this StoichiometryMath.

Definition at line 24961 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.SBase.getName (   self  )  [inherited]

Python method signature(s): 

getName(self)    string

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

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

Returns:
the metaid of this SBML object.
See also:
isSetMetaId()

setMetaId(const std.string& metaid)

Deprecated:
libSBML internal

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

Definition at line 1857 of file libsbml.py.

def libsbml.SBase.getNamespaces (   self  )  [inherited]

Python method signature(s): 

getNamespaces(self)    XMLNamespaces

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

Returns:
the XML Namespaces associated with this SBML object

Reimplemented in libsbml.SBMLDocument.

Definition at line 2053 of file libsbml.py.

def libsbml.SBase.getNotes (   self  )  [inherited]

Python method signature(s): 

getNotes(self)    XMLNode

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

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

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

Returns:
the content of the 'notes' subelement of this SBML object.
See also:
getNotesString()

isSetNotes()

setNotes(const XMLNode* notes)

setNotes(const std.string& notes)

appendNotes(const XMLNode* notes)

appendNotes(const std.string& notes)

unsetNotes()

Definition at line 1891 of file libsbml.py.

def libsbml.SBase.getNotesString (   self  )  [inherited]

Python method signature(s): 

getNotesString(self)    string

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

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

Returns:
the content of the 'notes' subelement of this SBML object.
See also:
getNotes()

isSetNotes()

setNotes(const XMLNode* notes)

setNotes(const std.string& notes)

appendNotes(const XMLNode* notes)

appendNotes(const std.string& notes)

unsetNotes()

Definition at line 1934 of file libsbml.py.

def libsbml.SBase.getNumCVTerms (   self  )  [inherited]

Python method signature(s): 

getNumCVTerms(self)    unsigned int

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

Returns:
the number of CVTerms for this SBML object.

Definition at line 3026 of file libsbml.py.

def libsbml.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.StoichiometryMath.getTypeCode (   self  ) 

Python method signature(s): 

getTypeCode(self)    SBMLTypeCode_t

Returns the libSBML type code of this object instance.

Returns:
the SBML type code for this object, or SBML_UNKNOWN (default).
See also:
getElementName()

Reimplemented from libsbml.SBase.

Definition at line 25097 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.SBase.hasRequiredAttributes (   self  )  [inherited]

Python method signature(s): 

hasRequiredAttributes(self)    bool

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

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

Deprecated:
libSBML internal

Reimplemented in libsbml.FunctionDefinition, libsbml.Unit, libsbml.UnitDefinition, libsbml.CompartmentType, libsbml.SpeciesType, libsbml.Compartment, libsbml.Species, libsbml.Parameter, libsbml.InitialAssignment, libsbml.Rule, libsbml.AlgebraicRule, libsbml.AssignmentRule, libsbml.RateRule, libsbml.Reaction, libsbml.KineticLaw, libsbml.SpeciesReference, libsbml.ModifierSpeciesReference, and libsbml.EventAssignment.

Definition at line 3254 of file libsbml.py.

def libsbml.StoichiometryMath.hasRequiredElements (   self  ) 

Python method signature(s): 

hasRequiredElements(self)    bool

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

Note:
The required elements for a StoichiometryMath object are: math
Returns:
a boolean value indicating whether all the required elements for this object have been defined.

Reimplemented from libsbml.SBase.

Definition at line 25142 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.SBase.isSetId (   self  )  [inherited]

Python method signature(s): 

isSetId(self)    bool

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

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

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

Returns:
true if the 'metaid' attribute of this SBML object has been set, false otherwise.
See also:
getMetaId()

setMetaId(const std.string& metaid)

Deprecated:
libSBML internal

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

Definition at line 2272 of file libsbml.py.

def libsbml.StoichiometryMath.isSetMath (   self  ) 

Python method signature(s): 

isSetMath(self)    bool

Predicate to test whether the math for this StoichiometryMath object has been set.

Returns:
true if the formula (meaning the math subelement) of this StoichiometryMath has been set, false otherwise.

Definition at line 24977 of file libsbml.py.

def libsbml.SBase.isSetMetaId (   self  )  [inherited]

Python method signature(s): 

isSetMetaId(self)    bool

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

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

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

Returns:
true if the 'metaid' attribute of this SBML object has been set, false otherwise.
See also:
getMetaId()

setMetaId(const std.string& metaid)

Definition at line 2235 of file libsbml.py.

def libsbml.SBase.isSetName (   self  )  [inherited]

Python method signature(s): 

isSetName(self)    bool

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

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

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

Returns:
true if the 'metaid' attribute of this SBML object has been set, false otherwise.
See also:
getMetaId()

setMetaId(const std.string& metaid)

Deprecated:
libSBML internal

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

Definition at line 2310 of file libsbml.py.

def libsbml.SBase.isSetNotes (   self  )  [inherited]

Python method signature(s): 

isSetNotes(self)    bool

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

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

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

Returns:
true if a 'notes' subelement exists, false otherwise.
See also:
getNotes()

getNotesString()

setNotes(const XMLNode* notes)

setNotes(const std.string& notes)

appendNotes(const XMLNode* notes)

appendNotes(const std.string& notes)

unsetNotes()

Definition at line 2348 of file libsbml.py.

def libsbml.SBase.isSetSBOTerm (   self  )  [inherited]

Python method signature(s): 

isSetSBOTerm(self)    bool

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

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

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

Definition at line 2427 of file libsbml.py.

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

Python method signature(s): 

setId(self, string sid)    int

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

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

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

Parameters:
metaid the identifier string to use as the value of the 'metaid' attribute
Returns:
integer value indicating success/failure of the function. The possible values returned by this function are:
  • LIBSBML_OPERATION_SUCCESS
  • LIBSBML_INVALID_ATTRIBUTE_VALUE
  • LIBSBML_UNEXPECTED_ATTRIBUTE
See also:
getMetaId()

isSetMetaId()

Deprecated:
libSBML internal

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

Definition at line 2486 of file libsbml.py.

def libsbml.StoichiometryMath.setMath (   self,
  args 
)

Python method signature(s): 

setMath(self, ASTNode math)    int

Sets the 'math' expression of this StoichiometryMath instance to a copy of the given ASTNode.

Parameters:
math an ASTNode representing a formula tree.
Returns:
integer value indicating success/failure of the function. The possible values returned by this function are:
  • LIBSBML_OPERATION_SUCCESS
  • LIBSBML_INVALID_OBJECT

Definition at line 24994 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.SBase.setName (   self,
  args 
) [inherited]

Python method signature(s): 

setName(self, string name)    int

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

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

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

Parameters:
metaid the identifier string to use as the value of the 'metaid' attribute
Returns:
integer value indicating success/failure of the function. The possible values returned by this function are:
  • LIBSBML_OPERATION_SUCCESS
  • LIBSBML_INVALID_ATTRIBUTE_VALUE
  • LIBSBML_UNEXPECTED_ATTRIBUTE
See also:
getMetaId()

isSetMetaId()

Deprecated:
libSBML internal

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

Definition at line 2527 of file libsbml.py.

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

Python method signature(s): 

setNamespaces(self, XMLNamespaces xmlns)    int

Sets the namespaces relevant of this SBML object.

Parameters:
xmlns the namespaces to set
Returns:
integer value indicating success/failure of the function. The possible values returned by this function are:
  • LIBSBML_OPERATION_SUCCESS

Definition at line 2811 of file libsbml.py.

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

Python method signature(s): 

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

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

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

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

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

Parameters:
notes an XML string that is to be used as the content of the 'notes' subelement of this object
Returns:
integer value indicating success/failure of the function. The possible values returned by this function are:
  • LIBSBML_OPERATION_SUCCESS
  • LIBSBML_INVALID_OBJECT
  • LIBSBML_OPERATION_FAILED
See also:
getNotesString()

isSetNotes()

setNotes(const XMLNode* notes)

appendNotes(const XMLNode* notes)

appendNotes(const std.string& notes)

unsetNotes()

Definition at line 2676 of file libsbml.py.

def libsbml.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.SBase.toSBML (   self  )  [inherited]

Python method signature(s): 

toSBML(self)    char

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

Returns:
the partial SBML that describes this SBML object.

Definition at line 3237 of file libsbml.py.

def libsbml.SBase.unsetAnnotation (   self  )  [inherited]

Python method signature(s): 

unsetAnnotation(self)    int

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

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

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

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

Returns:
integer value indicating success/failure of the function. The possible values returned by this function are:
  • LIBSBML_OPERATION_SUCCESS
See also:
getAnnotation()

getAnnotationString()

isSetAnnotation()

setAnnotation(const XMLNode* annotation)

setAnnotation(const std.string& annotation)

appendAnnotation(const XMLNode* annotation)

appendAnnotation(const std.string& annotation)

Definition at line 2910 of file libsbml.py.

def libsbml.SBase.unsetCVTerms (   self  )  [inherited]

Python method signature(s): 

unsetCVTerms(self)    int

Clears the list of CVTerms of this SBML object.

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

Definition at line 3060 of file libsbml.py.

def libsbml.SBase.unsetMetaId (   self  )  [inherited]

Python method signature(s): 

unsetMetaId(self)    int

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

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

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

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

Definition at line 2832 of file libsbml.py.

def libsbml.SBase.unsetNotes (   self  )  [inherited]

Python method signature(s): 

unsetNotes(self)    int

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

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

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

Returns:
integer value indicating success/failure of the function. The possible values returned by this function are:
  • LIBSBML_OPERATION_SUCCESS
See also:
getNotesString()

isSetNotes()

setNotes(const XMLNode* notes)

setNotes(const std.string& notes)

appendNotes(const XMLNode* notes)

appendNotes(const std.string& notes)

Definition at line 2869 of file libsbml.py.

def libsbml.SBase.unsetSBOTerm (   self  )  [inherited]

Python method signature(s): 

unsetSBOTerm(self)    int

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

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

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

Definition at line 2952 of file libsbml.py.

Member Data Documentation

libsbml.StoichiometryMath.this

Reimplemented from libsbml.SBase.

Definition at line 24945 of file libsbml.py.


SBML Team
http://www.sbml.org/
sbml-team@caltech.edu

HTML documentation generated on Thu Jan 21 16:56:19 2010 using Doxygen 1.5.8.