libsbml.Species Class Reference

Inheritance diagram for libsbml.Species:

Inheritance graph
[legend]

List of all members.

Detailed Description

LibSBML implementation of SBML's Species construct.

A species refers to a pool of reacting entities of a specific species type that take part in reactions and are located in a specific compartment. The Species data structure is intended to represent these pools. A Species definition has several parts: an optional identifier (defined by the attribute 'id'), an optional name (defined by the attribute 'name'), a required attribute 'compartment', and optional attributes 'speciesType', 'initialAmount', 'initialConcentration', 'substanceUnits', 'hasOnlySubstanceUnits', 'boundaryCondition', 'charge' and 'constant'. These various parts are described next.

As with other major structures in SBML, Species has a mandatory attribute, 'id', used to give the species type an identifier in the model. The identifier must be a text string conforming to the identifer syntax permitted in SBML. Species also has an optional 'name' attribute, of type string. The 'id' and 'name' must be used according to the guidelines described in the SBML specification (e.g., Section 3.3 in the Level 2 Version 4 specification).

The required attribute 'compartment' is used to identify the compartment in which the species is located. The attribute's value must be the identifier of an existing Compartment structure. It is important to note that there is no default value for the 'compartment' attribute on Species; every species in an SBML model must be assigned a compartment, and consequently, a model must define at least one compartment if that model contains any species.

Each species in a model may optionally be designated as belonging to a particular species type. The optional attribute 'speciesType' is used to identify the species type of the chemical entities that make up the pool represented by the Species structure. The attribute's value must be the identifier of an existing SpeciesType structure. If the 'speciesType' attribute is not present on a particular species definition, it means the pool contains chemical entities of a type unique to that pool; in effect, a virtual species type is assumed for that species, and no other species can belong to that species type. The value of 'speciesType' attributes on species have no effect on the numerical interpretation of a model; simulators and other numerical analysis software may ignore 'speciesType' attributes.

There can be only one species of a given species type in any given compartment of a model. More specifically, for all Species structures having a value for the 'speciesType' attribute, the pair

('speciesType' attribute value, 'compartment' attribute value)

must be unique across the set of all Species structures in a model.

The initial amount and concentration of a species

The optional attributes 'initialAmount' and 'initialConcentration', both having a data type of float, are used to set the initial quantity of the species in the compartment where the species is located. These attributes are mutually exclusive; i.e., only one can have a value on any given instance of a Species structure. Missing 'initialAmount' and 'initialConcentration' values implies that their values either are unknown, or to be obtained from an external source, or determined by an InitialAssignment or Rule object elsewhere in the model. In the case where a species' compartment has a 'spatialDimensions' value of 0 (zero), the species cannot have a value for 'initialConcentration' because the concepts of concentration and density break down when a container has zero dimensions.

A species' initial quantity is set by the 'initialAmount' or 'initialConcentration' attributes exactly once. If the species' 'constant' attribute is true (the default), then the size is fixed and cannot be changed except by an InitialAssignment. These methods differ in that the 'initialAmount' and 'initialConcentration' attributes can only be used to set the species quantity to a literal scalar value, whereas InitialAssignment allows the value to be set using an arbitrary mathematical expression. If the species' 'constant' attribute is false, the species' quantity value may be overridden by an InitialAssignment or changed by AssignmentRule or AlgebraicRule, and in addition, for t < 0, it may also be changed by a RateRule or Event. (However, some constructs are mutually exclusive; see the SBML specification for more details.) It is not an error to define 'initialAmount' or 'initialConcentration' on a species and also redefine the value using an InitialAssignment, but the 'initialAmount' or 'initialConcentration' setting in that case is ignored.

The units of a species' amount or concentration

The units associated with a species' quantity, referred to as the units of the species, are determined via the optional attributes 'substanceUnits' and 'hasOnlySubstanceUnits', in combination with the units of the size defined for the compartment object in which the species are located. The way this is done is as follows.

The units of the value in the 'initialConcentration' attribute are substance/size units, where the units of substance are those defined by the 'substanceUnits' attribute and the size units are those given in the definition of the size of the Compartment in which the species is located. The units of the value in the 'initialAmount' attribute are determined by the 'substanceUnits' attribute of the species structure. The role of the attribute 'hasOnlySubstanceUnits' is to indicate whether the units of the species, when the species identifier appears in mathematical formulas, are intended to be concentration or amount. The attribute takes on boolean values and defaults to false. Although it may seem as though this intention could be determined based on whether 'initialConcentration' or 'initialAmount' is set, the fact that these two attributes are optional means that a separate flag is needed. (Consider the situation where neither is set, and instead the species' quantity is established by an InitialAssignment or AssignmentRule.)

The possible values of units of the species are summarized in the following table. (The dependence on the number of spatial dimensions of the compartment is due to the fact that a zero-dimensional compartment cannot support concentrations or densities.)

Interpretation of species' units.
Value of
hasOnlySubstanceUnits 		Units of the species when
spatialDimensions is greater than 0 		Units of the species when
spatialDimensions is 0
false (default) substance/size substance
true (default) substance substance

The value assigned to 'substanceUnits' must be chosen from one of the following possibilities: one of the base unit identifiers defined in SBML; the built-in unit identifier 'substance'; or the identifier of a new unit defined in the list of unit definitions in the enclosing Model structure. The chosen units for 'substanceUnits' must be be 'dimensionless', 'mole', 'item', 'kilogram', 'gram', or units derived from these. The 'substanceUnits' attribute defaults to the the built-in unit 'substance'.

The units of the species are used in the following ways:

The 'constant' and 'boundaryCondition' attributes

The Species structure has two optional boolean attributes named 'constant' and 'boundaryCondition', used to indicate whether and how the quantity of that species can vary during a simulation. The following table shows how to interpret the combined values of these attributes.

Interpretation of species' constant and boundaryCondition attributes.
constant
value 		boundaryCondition
value 		Can have
assignment
or rate rule? 		Can be
reactant
or product? 		Species' quantity
can be changed by
true true no yes (never changes)
false true yes yes rules and events
true false no no (never changes)
false false yes yes reactions or rules (but not both at the same time), and events

By default, when a species is a product or reactant of one or more reactions, its quantity is determined by those reactions. In SBML, it is possible to indicate that a given species' quantity is not determined by the set of reactions even when that species occurs as a product or reactant; i.e., the species is on the boundary of the reaction system, and its quantity is not determined by the reactions. The boolean attribute 'boundaryCondition' can be used to indicate this. The value of the attribute defaults to false, indicating the species is part of the reaction system.

The 'constant' attribute indicates whether the species' quantity can be changed at all, regardless of whether by reactions, rules, or constructs other than InitialAssignment. The default value is false, indicating that the species' quantity can be changed, since the purpose of most simulations is precisely to calculate changes in species quantities. Note that the initial quantity of a species can be set by an InitialAssignment irrespective of the value of the 'constant' attribute.

In practice, a 'boundaryCondition' value of true means a differential equation derived from the reaction definitions should not be generated for the species. However, the species' quantity may still be changed by AssignmentRule, RateRule, AlgebraicRule, Event, and InitialAssignment constructs if its 'constant' attribute is false. Conversely, if the species' 'constant' attribute is true, then its value cannot be changed by anything except InitialAssignment.

A species having 'boundaryCondition'=false and 'constant'=false can appear as a product and/or reactant of one or more reactions in the model. If the species is a reactant or product of a reaction, it must not also appear as the target of any AssignmentRule or RateRule structure in the model. If instead the species has 'boundaryCondition'=false and 'constant'=true, then it cannot appear as a reactant or product, or as the target of any AssignmentRule, RateRule or EventAssignment structure in the model.

Warning:
In versions of SBML Level 2 before Version 3, the class Species included an attribute called 'spatialSizeUnits, which allowed explicitly setting the units of size for initial concentration. LibSBML retains this attribute for compatibility with older definitions of Level 2, but its use is strongly discouraged because it is incompatible with Level 2 Version 3 andLevel 2 Version 4.

Definition at line 13089 of file libsbml.py.


Public Member Functions

def __eq__
def __init__
def __init__
def __ne__
def addCVTerm
def appendAnnotation
def appendNotes
def clone
def getAncestorOfType
def getAnnotation
def getAnnotationString
def getBoundaryCondition
def getCharge
def getColumn
def getCompartment
def getConstant
def getCVTerm
def getCVTerms
def getDerivedUnitDefinition
def getElementName
def getHasOnlySubstanceUnits
def getId
def getInitialAmount
def getInitialConcentration
def getLevel
def getLine
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 getSpatialSizeUnits
def getSpeciesType
def getSubstanceUnits
def getTypeCode
def getUnits
def getVersion
def hasRequiredAttributes
def hasRequiredElements
def hasValidLevelVersionNamespaceCombination
def initDefaults
def isSetAnnotation
def isSetCharge
def isSetCompartment
def isSetId
def isSetInitialAmount
def isSetInitialConcentration
def isSetMetaId
def isSetName
def isSetNotes
def isSetSBOTerm
def isSetSpatialSizeUnits
def isSetSpeciesType
def isSetSubstanceUnits
def isSetUnits
def setAnnotation
def setBoundaryCondition
def setCharge
def setCompartment
def setConstant
def setHasOnlySubstanceUnits
def setId
def setInitialAmount
def setInitialConcentration
def setMetaId
def setName
def setNamespaces
def setNotes
def setSBOTerm
def setSpatialSizeUnits
def setSpeciesType
def setSubstanceUnits
def setUnits
def toSBML
def unsetAnnotation
def unsetCharge
def unsetCVTerms
def unsetInitialAmount
def unsetInitialConcentration
def unsetMetaId
def unsetName
def unsetNotes
def unsetSBOTerm
def unsetSpatialSizeUnits
def unsetSpeciesType
def unsetSubstanceUnits
def unsetUnits

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.Species.__init__ (   self,
  args 
)

Python method signature(s): 

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

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

Note:
The required attributes for a Species object are: id (name L1); compartment; initialAmount (L1 only)
Returns:
a boolean value indicating whether all the required attributes for this object have been defined.
Deprecated:
libSBML internal

Definition at line 13292 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.Species.clone (   self  ) 

Python method signature(s): 

clone(self)    Species

Creates and returns a deep copy of this Species.

Returns:
a (deep) copy of this Species.

Reimplemented from libsbml.SBase.

Definition at line 13317 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.Species.getBoundaryCondition (   self  ) 

Python method signature(s): 

getBoundaryCondition(self)    bool

Get the value of the 'boundaryCondition' attribute.

Returns:
true if this Species' 'boundaryCondition' attribute value is nonzero, false otherwise.

Definition at line 13514 of file libsbml.py.

def libsbml.Species.getCharge (   self  ) 

Python method signature(s): 

getCharge(self)    int

Get the value of the 'charge' attribute.

Returns:
the charge of this Species.
Note:
Beginning in SBML Level 2 Version 2, the 'charge' attribute on Species is deprecated and its use strongly discouraged. Its presence is considered a misfeature in earlier definitions of SBML because its implications for the mathematics of a model were never defined, and in any case, no known modeling system ever used it. Instead, models take account of charge values directly in their definitions of species by (for example) having separate species identities for the charged and uncharged versions of the same species. This allows the condition to affect model mathematics directly. LibSBML retains this method for easier compatibility with SBML Level 1.

Definition at line 13530 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.Species.getCompartment (   self  ) 

Python method signature(s): 

getCompartment(self)    string

Get the compartment in which this species is located.

Returns:
the value of the 'compartment' attribute of this Species, as a string.

Definition at line 13398 of file libsbml.py.

def libsbml.Species.getConstant (   self  ) 

Python method signature(s): 

getConstant(self)    bool

Get the value of the 'constant' attribute.

Returns:
true if this Species's 'constant' attribute value is nonzero, false otherwise.

Definition at line 13557 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.Species.getDerivedUnitDefinition (   self,
  args 
)

Python method signature(s): 

getDerivedUnitDefinition(self)    UnitDefinition
getDerivedUnitDefinition(self)    UnitDefinition

Constructs and returns a UnitDefinition that corresponds to the units of this Species' amount or concentration.

Species in SBML have an attribute ('substanceUnits') for declaring the units of measurement intended for the species' amount or concentration (depending on which one applies). In the absence of a value given for 'substanceUnits', the units are taken from the enclosing Model's definition of 'substance' or 'substance'/(size of the compartment) in which the species is located, or finally, if these are not redefined by the Model, the relevant SBML default units for those quantities. Following that procedure, the method getDerivedUnitDefinition() returns a UnitDefinition based on the interpreted units of this species's amount or concentration.

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.

Note also that unit declarations for Species are in terms of the identifier of a unit, but this method returns a UnitDefinition object, not a unit identifier. It does this by constructing an appropriate UnitDefinition. Callers may find this particularly useful when used in conjunction with the helper methods on UnitDefinition for comparing different UnitDefinition objects.

In SBML Level 2 specifications prior to Version 3, Species includes an additional attribute named 'spatialSizeUnits', which allows explicitly setting the units of size for initial concentration. The getDerivedUnitDefinition() takes this into account for models expressed in SBML Level 2 Versions 1 and 2.

Returns:
a UnitDefinition that expresses the units of this Species.
See also:
getSubstanceUnits()

Definition at line 14343 of file libsbml.py.

def libsbml.Species.getElementName (   self  ) 

Python method signature(s): 

getElementName(self)    string

Returns the XML element name of this object, which for Species, is always 'species'.

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

Reimplemented from libsbml.SBase.

Definition at line 14421 of file libsbml.py.

def libsbml.Species.getHasOnlySubstanceUnits (   self  ) 

Python method signature(s): 

getHasOnlySubstanceUnits(self)    bool

Get the value of the 'hasOnlySubstanceUnits' attribute.

Returns:
true if this Species' 'hasOnlySubstanceUnits' attribute value is nonzero, false otherwise.

Definition at line 13498 of file libsbml.py.

def libsbml.Species.getId (   self  ) 

Python method signature(s): 

getId(self)    string

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

Returns:
the id of this Species.

Reimplemented from libsbml.SBase.

Definition at line 13351 of file libsbml.py.

def libsbml.Species.getInitialAmount (   self  ) 

Python method signature(s): 

getInitialAmount(self)    float

Get the value of the 'initialAmount' attribute.

Returns:
the initialAmount of this Species, as a float-point number.

Definition at line 13414 of file libsbml.py.

def libsbml.Species.getInitialConcentration (   self  ) 

Python method signature(s): 

getInitialConcentration(self)    float

Get the value of the 'initialConcentration' attribute.

Returns:
the initialConcentration of this Species,, as a float-point number.

Definition at line 13429 of file libsbml.py.

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

Python method signature(s): 

getLevel(self)    unsigned int

Returns the SBML Level of the overall SBML document.

Returns:
the SBML level of this SBML object.
See also:
getVersion()

Definition at line 3134 of file libsbml.py.

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

Python method signature(s): 

getLine(self)    unsigned int

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

Returns:
the line number of this SBML object.
See also:
getColumn()

Definition at line 2199 of file libsbml.py.

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

Python method signature(s): 

getMetaId(self)    string

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

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

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

setMetaId(const std.string& metaid)

Definition at line 1790 of file libsbml.py.

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

Python method signature(s): 

getModel(self)    Model

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

Returns:
the parent Model of this SBML object.

Definition at line 3119 of file libsbml.py.

def libsbml.Species.getName (   self  ) 

Python method signature(s): 

getName(self)    string

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

Returns:
the name of this Species.

Reimplemented from libsbml.SBase.

Definition at line 13366 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.Species.getSpatialSizeUnits (   self  ) 

Python method signature(s): 

getSpatialSizeUnits(self)    string

Get the value of the 'spatialSizeUnits' attribute.

Returns:
the spatialSizeUnits of this Species.
Warning:
In versions of SBML Level~2 before Version 3, the class Species included an attribute called 'spatialSizeUnits', which allowed explicitly setting the units of size for initial concentration. This attribute was removed in SBML Level 2 Version 3. LibSBML retains this attribute for compatibility with older definitions of Level 2, but its use is strongly discouraged because it is incompatible with Level 2 Version 3 and Level 2 Version 4.

Definition at line 13460 of file libsbml.py.

def libsbml.Species.getSpeciesType (   self  ) 

Python method signature(s): 

getSpeciesType(self)    string

Get the species type of this Species, as indicated by the Species object's 'speciesType' attribute value.

Returns:
the value of the 'speciesType' attribute of this Species as a string.

Definition at line 13381 of file libsbml.py.

def libsbml.Species.getSubstanceUnits (   self  ) 

Python method signature(s): 

getSubstanceUnits(self)    string

Get the value of the 'substanceUnit' attribute.

Returns:
the substanceUnits of this Species, as a string.

Definition at line 13445 of file libsbml.py.

def libsbml.Species.getTypeCode (   self  ) 

Python method signature(s): 

getTypeCode(self)    SBMLTypeCode_t

Returns the libSBML type code for this SBML object.

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

Reimplemented from libsbml.SBase.

Definition at line 14392 of file libsbml.py.

def libsbml.Species.getUnits (   self  ) 

Python method signature(s): 

getUnits(self)    string

(SBML Level 1 only) Get the value of the 'units' attribute.

Returns:
the units of this Species (L1 only).

Definition at line 13483 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.Species.hasRequiredAttributes (   self  ) 

Python method signature(s): 

hasRequiredAttributes(self)    bool

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

Note:
The required attributes for a Species object are: id (name L1); compartment; initialAmount (L1 only)
Returns:
a boolean value indicating whether all the required attributes for this object have been defined.

Reimplemented from libsbml.SBase.

Definition at line 14437 of file libsbml.py.

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

Python method signature(s): 

hasRequiredElements(self)    bool

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

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

Deprecated:
libSBML internal

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

Definition at line 3275 of file libsbml.py.

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

Python method signature(s): 

hasValidLevelVersionNamespaceCombination(self)    bool

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

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

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

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

Definition at line 3192 of file libsbml.py.

def libsbml.Species.initDefaults (   self  ) 

Python method signature(s): 

initDefaults(self)

Initializes the fields of this Species to the defaults defined in the specification of the relevant Level/Version of SBML.

  • sets 'boundaryCondition' to 1 (true)
  • (Level 2 only) sets 'constant' to 0 (false)
  • (Level 2 only) sets 'hasOnlySubstanceUnits' to 0 (false)

Definition at line 13332 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.Species.isSetCharge (   self  ) 

Python method signature(s): 

isSetCharge(self)    bool

Predicate returning true or false depending on whether this Species's 'charge' 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 'charge' attribute of this Species has been set, false otherwise.
Note:
Beginning in SBML Level 2 Version 2, the 'charge' attribute on Species in SBML is deprecated and its use strongly discouraged. Its presence is considered a misfeature in earlier definitions of SBML because its implications for the mathematics of a model were never defined, and in any case, no known modeling system ever used it. Instead, models take account of charge values directly in their definitions of species by (for example) having separate species identities for the charged and uncharged versions of the same species. This allows the condition to affect model mathematics directly. LibSBML retains this method for easier compatibility with SBML Level 1.

Definition at line 13758 of file libsbml.py.

def libsbml.Species.isSetCompartment (   self  ) 

Python method signature(s): 

isSetCompartment(self)    bool

Predicate returning true or false depending on whether this Species's 'compartment' 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 'compartment' attribute of this Species has been set, false otherwise.

Definition at line 13630 of file libsbml.py.

def libsbml.Species.isSetId (   self  ) 

Python method signature(s): 

isSetId(self)    bool

Predicate returning true or false depending on whether this Species'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 Species has been set, false otherwise.

Reimplemented from libsbml.SBase.

Definition at line 13573 of file libsbml.py.

def libsbml.Species.isSetInitialAmount (   self  ) 

Python method signature(s): 

isSetInitialAmount(self)    bool

Predicate returning true or false depending on whether this Species's 'initialAmount' 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 'initialAmount' attribute of this Species has been set, false otherwise.
Note:
In SBML Level 1, Species' 'initialAmount' is required and therefore should always be set. (However, in Level 1, the attribute has no default value either, so this method will not return true until a value has been assigned.) In SBML Level 2, 'initialAmount' is optional and as such may or may not be set.

Definition at line 13649 of file libsbml.py.

def libsbml.Species.isSetInitialConcentration (   self  ) 

Python method signature(s): 

isSetInitialConcentration(self)    bool

Predicate returning true or false depending on whether this Species's 'initialConcentration' 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 'initialConcentration' attribute of this Species has been set, false otherwise.

Definition at line 13674 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.Species.isSetName (   self  ) 

Python method signature(s): 

isSetName(self)    bool

Predicate returning true or false depending on whether this Species'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 Species has been set, false otherwise.

Reimplemented from libsbml.SBase.

Definition at line 13592 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.Species.isSetSpatialSizeUnits (   self  ) 

Python method signature(s): 

isSetSpatialSizeUnits(self)    bool

Predicate returning true or false depending on whether this Species's 'spatialSizeUnits' 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 'spatialSizeUnits' attribute of this Species has been set, false otherwise.
Warning:
In versions of SBML Level~2 before Version 3, the class Species included an attribute called 'spatialSizeUnits', which allowed explicitly setting the units of size for initial concentration. This attribute was removed in SBML Level 2 Version 3. LibSBML retains this attribute for compatibility with older definitions of Level 2, but its use is strongly discouraged because it is incompatible with Level 2 Version 3 and Level 2 Version 4.

Definition at line 13712 of file libsbml.py.

def libsbml.Species.isSetSpeciesType (   self  ) 

Python method signature(s): 

isSetSpeciesType(self)    bool

Predicate returning true or false depending on whether this Species's 'speciesType' 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 'speciesType' attribute of this Species has been set, false otherwise.

Definition at line 13611 of file libsbml.py.

def libsbml.Species.isSetSubstanceUnits (   self  ) 

Python method signature(s): 

isSetSubstanceUnits(self)    bool

Predicate returning true or false depending on whether this Species's 'substanceUnits' 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 'substanceUnits' attribute of this Species has been set, false otherwise.

Definition at line 13693 of file libsbml.py.

def libsbml.Species.isSetUnits (   self  ) 

Python method signature(s): 

isSetUnits(self)    bool

(SBML Level 1 only) Predicate returning true or false depending on whether this Species's 'units' 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 'units' attribute of this Species has been set, false otherwise.

Definition at line 13739 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.Species.setBoundaryCondition (   self,
  args 
)

Python method signature(s): 

setBoundaryCondition(self, bool value)    int

Sets the 'boundaryCondition' attribute of this Species.

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 boolean value for the 'boundaryCondition' attribute.
Returns:
integer value indicating success/failure of the function. The possible values returned by this function are:
  • LIBSBML_OPERATION_SUCCESS

Definition at line 14066 of file libsbml.py.

def libsbml.Species.setCharge (   self,
  args 
)

Python method signature(s): 

setCharge(self, int value)    int

Sets the 'charge' attribute of this Species.

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 an integer to which to set the 'charge' to.
Note:
Beginning in SBML Level 2 Version 2, the 'charge' attribute on Species in SBML is deprecated and its use strongly discouraged. Its presence is considered a misfeature in earlier definitions of SBML because its implications for the mathematics of a model were never defined, and in any case, no known modeling system ever used it. Instead, models take account of charge values directly in their definitions of species by (for example) having separate species identities for the charged and uncharged versions of the same species. This allows the condition to affect model mathematics directly. LibSBML retains this method for easier compatibility with SBML Level 1.
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 14089 of file libsbml.py.

def libsbml.Species.setCompartment (   self,
  args 
)

Python method signature(s): 

setCompartment(self, string sid)    int

Sets the 'compartment' attribute of this Species.

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 identifier of a Compartment object defined elsewhere in this Model.
Returns:
integer value indicating success/failure of the function. The possible values returned by this function are:
  • LIBSBML_OPERATION_SUCCESS
  • LIBSBML_INVALID_ATTRIBUTE_VALUE

Definition at line 13881 of file libsbml.py.

def libsbml.Species.setConstant (   self,
  args 
)

Python method signature(s): 

setConstant(self, bool value)    int

Sets the 'constant' attribute of this Species.

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 a boolean value for the 'constant' attribute
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 14125 of file libsbml.py.

def libsbml.Species.setHasOnlySubstanceUnits (   self,
  args 
)

Python method signature(s): 

setHasOnlySubstanceUnits(self, bool value)    int

Sets the 'hasOnlySubstanceUnits' attribute of this Species.

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 boolean value for the 'hasOnlySubstanceUnits' attribute.
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 14042 of file libsbml.py.

def libsbml.Species.setId (   self,
  args 
)

Python method signature(s): 

setId(self, string sid)    int

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

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 Species
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 13789 of file libsbml.py.

def libsbml.Species.setInitialAmount (   self,
  args 
)

Python method signature(s): 

setInitialAmount(self, float value)    int

Sets the 'initialAmount' attribute of this Species and marks the field as set.

This method also unsets the 'initialConcentration' 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 value to which the 'initialAmount' attribute should be set.
Returns:
integer value indicating success/failure of the function. The possible values returned by this function are:
  • LIBSBML_OPERATION_SUCCESS

Definition at line 13906 of file libsbml.py.

def libsbml.Species.setInitialConcentration (   self,
  args 
)

Python method signature(s): 

setInitialConcentration(self, float value)    int

Sets the 'initialConcentration' attribute of this Species and marks the field as set.

This method also unsets the 'initialAmount' 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 value to which the 'initialConcentration' attribute should be set.
Returns:
integer value indicating success/failure of the function. The possible values returned by this function are:
  • LIBSBML_OPERATION_SUCCESS
  • LIBSBML_UNEXPECTED_ATTRIBUTE

Definition at line 13933 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.Species.setName (   self,
  args 
)

Python method signature(s): 

setName(self, string name)    int

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

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 Species
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 13829 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.Species.setSpatialSizeUnits (   self,
  args 
)

Python method signature(s): 

setSpatialSizeUnits(self, string sid)    int

Sets the 'spatialSizeUnits' attribute of this Species.

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 identifier of the unit to use.
Warning:
In versions of SBML Level~2 before Version 3, the class Species included an attribute called 'spatialSizeUnits', which allowed explicitly setting the units of size for initial concentration. This attribute was removed in SBML Level 2 Version 3. LibSBML retains this attribute for compatibility with older definitions of Level 2, but its use is strongly discouraged because it is incompatible with Level 2 Version 3 and Level 2 Version 4.
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 13985 of file libsbml.py.

def libsbml.Species.setSpeciesType (   self,
  args 
)

Python method signature(s): 

setSpeciesType(self, string sid)    int

Sets the 'speciesType' attribute of this Species.

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 identifier of a SpeciesType object defined elsewhere in this Model.
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 13855 of file libsbml.py.

def libsbml.Species.setSubstanceUnits (   self,
  args 
)

Python method signature(s): 

setSubstanceUnits(self, string sid)    int

Sets the 'substanceUnits' attribute of this Species.

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 identifier of the unit to use.
Returns:
integer value indicating success/failure of the function. The possible values returned by this function are:
  • LIBSBML_OPERATION_SUCCESS
  • LIBSBML_INVALID_ATTRIBUTE_VALUE

Definition at line 13961 of file libsbml.py.

def libsbml.Species.setUnits (   self,
  args 
)

Python method signature(s): 

setUnits(self, string sname)    int

(SBML Level 1 only) Sets the units of this Species.

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:
sname the identifier of the unit to use.
Returns:
integer value indicating success/failure of the function. The possible values returned by this function are:
  • LIBSBML_OPERATION_SUCCESS
  • LIBSBML_INVALID_ATTRIBUTE_VALUE

Definition at line 14018 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.Species.unsetCharge (   self  ) 

Python method signature(s): 

unsetCharge(self)    int

Unsets the 'charge' attribute value of this Species.

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
Note:
Beginning in SBML Level 2 Version 2, the 'charge' attribute on Species in SBML is deprecated and its use strongly discouraged. Its presence is considered a misfeature in earlier definitions of SBML because its implications for the mathematics of a model were never defined, and in any case, no known modeling system ever used it. Instead, models take account of charge values directly in their definitions of species by (for example) having separate species identities for the charged and uncharged versions of the same species. This allows the condition to affect model mathematics directly. LibSBML retains this method for easier compatibility with SBML Level 1.

Definition at line 14309 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.Species.unsetInitialAmount (   self  ) 

Python method signature(s): 

unsetInitialAmount(self)    int

Unsets the 'initialAmount' attribute value of this Species.

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

Definition at line 14193 of file libsbml.py.

def libsbml.Species.unsetInitialConcentration (   self  ) 

Python method signature(s): 

unsetInitialConcentration(self)    int

Unsets the 'initialConcentration' attribute value of this Species.

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

Definition at line 14214 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.Species.unsetName (   self  ) 

Python method signature(s): 

unsetName(self)    int

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

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 14149 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.

def libsbml.Species.unsetSpatialSizeUnits (   self  ) 

Python method signature(s): 

unsetSpatialSizeUnits(self)    int

Unsets the 'spatialSizeUnits' attribute value of this Species.

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
Warning:
In versions of SBML Level~2 before Version 3, the class Species included an attribute called 'spatialSizeUnits', which allowed explicitly setting the units of size for initial concentration. This attribute was removed in SBML Level 2 Version 3. LibSBML retains this attribute for compatibility with older definitions of Level 2, but its use is strongly discouraged because it is incompatible with Level 2 Version 3 and Level 2 Version 4.

Definition at line 14257 of file libsbml.py.

def libsbml.Species.unsetSpeciesType (   self  ) 

Python method signature(s): 

unsetSpeciesType(self)    int

Unsets the 'speciesType' attribute value of this Species.

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 14171 of file libsbml.py.

def libsbml.Species.unsetSubstanceUnits (   self  ) 

Python method signature(s): 

unsetSubstanceUnits(self)    int

Unsets the 'substanceUnits' attribute value of this Species.

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 14235 of file libsbml.py.

def libsbml.Species.unsetUnits (   self  ) 

Python method signature(s): 

unsetUnits(self)    int

(SBML Level 1 only) Unsets the 'units' attribute value of this Species.

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 14287 of file libsbml.py.

Member Data Documentation

libsbml.Species.this

Reimplemented from libsbml.SBase.

Definition at line 13316 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.