libSBML Python API  5.11.0
libsbml.FbcSpeciesPlugin Class Reference
Inheritance diagram for libsbml.FbcSpeciesPlugin:
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Detailed Description

fbc Extension of Species.

The Flux Balance Constraints package extends the SBML Level 3 Version 1 Core Species class with the addition of two attributes: 'charge' and 'chemicalFormula'.

Public Member Functions

def __init__ (self, args)
 fbc Extension of Species. More...
 
def clone (self)
 Creates and returns a deep copy of this FbcSpeciesPlugin object. More...
 
def getCharge (self)
 Returns the value of the 'charge' attribute of this FbcSpeciesPlugin. More...
 
def getChemicalFormula (self)
 Returns the value of the 'chemicalFormula' attribute of this FbcSpeciesPlugin. More...
 
def getElementByMetaId (self, metaid)
 Return the first child object found with a given meta identifier. More...
 
def getElementBySId (self, id)
 Return the first child object found with a given identifier. More...
 
def getElementNamespace (self)
  Base class for extending SBML objects in packages. More...
 
def getLevel (self)
 Returns the SBML Level of the package extension of this plugin object. More...
 
def getListOfAllElements
 Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth. More...
 
def getPackageName (self)
 Returns the short-form name of the package to which this plugin object belongs. More...
 
def getPackageVersion (self)
 Returns the package version of the package extension of this plugin object. More...
 
def getParentSBMLObject (self, args)
 Returns the parent object to which this plugin object is connected. More...
 
def getPrefix (self)
 Returns the XML namespace prefix of the package to which this plugin object belongs. More...
 
def getSBMLDocument (self, args)
 Returns the SBMLDocument object containing this object instance. More...
 
def getURI (self)
 Returns the XML namespace URI for the package to which this object belongs. More...
 
def getVersion (self)
 Returns the Version within the SBML Level of the package extension of this plugin object. More...
 
def isSetCharge (self)
 Predicate returning True or False depending on whether this FbcSpeciesPlugin 'charge' attribute has been set. More...
 
def isSetChemicalFormula (self)
 Predicate returning True or False depending on whether this FbcSpeciesPlugin 'chemicalFormula' attribute has been set. More...
 
def setCharge (self, charge)
 Sets the value of the 'charge' attribute of this FbcSpeciesPlugin. More...
 
def setChemicalFormula (self, chemicalFormula)
 Sets the value of the 'chemicalFormula' attribute of this FbcSpeciesPlugin. More...
 
def setElementNamespace (self, uri)
 Sets the XML namespace to which this object belongs. More...
 
def unsetCharge (self)
 Unsets the value of the 'charge' attribute of this FbcSpeciesPlugin. More...
 
def unsetChemicalFormula (self)
 Unsets the value of the 'chemicalFormula' attribute of this FbcSpeciesPlugin. More...
 

Member Function Documentation

def libsbml.FbcSpeciesPlugin.clone (   self)

Creates and returns a deep copy of this FbcSpeciesPlugin object.

clone()   FbcSpeciesPlugin
Returns
a (deep) copy of this FbcSpeciesPlugin object
def libsbml.FbcSpeciesPlugin.getCharge (   self)

Returns the value of the 'charge' attribute of this FbcSpeciesPlugin.

getCharge()   int
Returns
the value of the 'charge' attribute of this FbcSpeciesPlugin.
def libsbml.FbcSpeciesPlugin.getChemicalFormula (   self)

Returns the value of the 'chemicalFormula' attribute of this FbcSpeciesPlugin.

getChemicalFormula()   string
Returns
the value of the 'chemicalFormula' attribute of this FbcSpeciesPlugin.
def libsbml.SBasePlugin.getElementByMetaId (   self,
  metaid 
)
inherited

Return the first child object found with a given meta identifier.

getElementByMetaId(string metaid)   SBase

This method searches all the subobjects under this one, compares their meta identifiers to metaid, and returns the first one that machines.

Parameters
metaidstring, the metaid of the object to find.
Returns
pointer to the first object found with the given metaid.
def libsbml.SBasePlugin.getElementBySId (   self,
  id 
)
inherited

Return the first child object found with a given identifier.

getElementBySId(string id)   SBase

This method searches all the subobjects under this one, compares their identifiers to id, and returns the first one that machines.

Normally, SId type identifier values are unique across a model in SBML. However, in some circumstances they may not be, such as if a model is invalid because of multiple objects having the same identifier.

Parameters
idstring representing the identifier of the object to find
Returns
pointer to the first object with the given id.
def libsbml.SBasePlugin.getLevel (   self)
inherited

Returns the SBML Level of the package extension of this plugin object.

getLevel()   long
Returns
the SBML Level.
See also
getVersion()
def libsbml.SBasePlugin.getListOfAllElements (   self,
  filter = None 
)
inherited

Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth.

getListOfAllElements(ElementFilter filter=None)   SBaseList
getListOfAllElements()   SBaseList
Returns
a list of all objects that are children of this object.
def libsbml.SBasePlugin.getPackageName (   self)
inherited

Returns the short-form name of the package to which this plugin object belongs.

getPackageName()   string
Returns
the short-form package name (or nickname) of the SBML package implemented by this package extension.
def libsbml.SBasePlugin.getPackageVersion (   self)
inherited

Returns the package version of the package extension of this plugin object.

getPackageVersion()   long
Returns
the package version of the package extension of this plugin object.
See also
getLevel()
getVersion()
def libsbml.SBasePlugin.getParentSBMLObject (   self,
  args 
)
inherited

Returns the parent object to which this plugin object is connected.

getParentSBMLObject()   SBase
Returns
the parent object of this object.
def libsbml.SBasePlugin.getPrefix (   self)
inherited

Returns the XML namespace prefix of the package to which this plugin object belongs.

getPrefix()   string
Returns
the XML namespace prefix of the SBML Level 3 package implemented by this libSBML package extension.
def libsbml.SBasePlugin.getSBMLDocument (   self,
  args 
)
inherited

Returns the SBMLDocument object containing this object instance.

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

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

Returns
the parent SBMLDocument object of this plugin object.
See also
getParentSBMLObject()
def libsbml.SBasePlugin.getURI (   self)
inherited

Returns the XML namespace URI for the package to which this object belongs.

getURI()   string
In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI 'http://www.sbml.org/sbml/level3/version1/core'. Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace 'http://www.sbml.org/sbml/level3/version1/layout/version1/'.

This method first looks into the SBMLNamespaces object possessed by the parent SBMLDocument object of the current object. If this cannot be found, this method returns the result of getElementNamespace().

Returns
a string, the URI of the XML namespace to which this object belongs.
See also
getPackageName()
getElementNamespace()
SBMLDocument.getSBMLNamespaces()
getSBMLDocument()
def libsbml.SBasePlugin.getVersion (   self)
inherited

Returns the Version within the SBML Level of the package extension of this plugin object.

getVersion()   long
Returns
the SBML Version.
See also
getLevel()
def libsbml.FbcSpeciesPlugin.isSetCharge (   self)

Predicate returning True or False depending on whether this FbcSpeciesPlugin 'charge' attribute has been set.

isSetCharge()   bool
Returns
True if this FbcSpeciesPlugin 'charge' attribute has been set, otherwise False is returned.
def libsbml.FbcSpeciesPlugin.isSetChemicalFormula (   self)

Predicate returning True or False depending on whether this FbcSpeciesPlugin 'chemicalFormula' attribute has been set.

isSetChemicalFormula()   bool
Returns
True if this FbcSpeciesPlugin 'chemicalFormula' attribute has been set, otherwise False is returned.
def libsbml.FbcSpeciesPlugin.setCharge (   self,
  charge 
)

Sets the value of the 'charge' attribute of this FbcSpeciesPlugin.

setCharge(int charge)   int
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.FbcSpeciesPlugin.setChemicalFormula (   self,
  chemicalFormula 
)

Sets the value of the 'chemicalFormula' attribute of this FbcSpeciesPlugin.

setChemicalFormula(string chemicalFormula)   int

The format of chemicalFormula must consist only of atomic names (as in the Periodic Table) or user defined compounds either of which take the form of a single capital letter followed by zero or more lowercase letters. Where there is more than a single atom present, this is indicated with an integer. With regards to order (and enhance inter-operability) it is recommended to use the Hill system order. (However, no error-checking is performed by this routine.)

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

Sets the XML namespace to which this object belongs.

setElementNamespace(string uri)   int
In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI 'http://www.sbml.org/sbml/level3/version1/core'. Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace 'http://www.sbml.org/sbml/level3/version1/layout/version1/'.
Parameters
urithe URI to assign to this object.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getElementNamespace()
def libsbml.FbcSpeciesPlugin.unsetCharge (   self)

Unsets the value of the 'charge' attribute of this FbcSpeciesPlugin.

unsetCharge()   int
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.FbcSpeciesPlugin.unsetChemicalFormula (   self)

Unsets the value of the 'chemicalFormula' attribute of this FbcSpeciesPlugin.

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