Inheritance diagram for libsbml.FbcReactionPlugin:

Detailed Description

fbc Extension of Reaction by the “fbc” package.

The FbcReactionPlugin class inherits from the SBasePlugin class, and codifies the extentions to the Reaction class defined in the Flux Balance Constraints package (“fbc”). This extention allows the modeler to define (in Version 2 of the “fbc” package) an upper and lower flux bound, with the 'upperFluxBound' and 'lowerFluxBound' attributes, as well as a way to reference any GeneProduct associated with this Reaction, through the GeneProductAssociation child.

Note: In Version 1 of “fbc”, the FluxBound element is used instead of the 'upperFluxBound' and 'lowerFluxBound' attributes. There is no equivalent of the GeneProductAssociation, which was added in Version 2.

Public Member Functions
def	__init__ (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...

def	clone (self)
	Creates and returns a deep copy of this FbcReactionPlugin object. More...

def	createGeneProductAssociation (self)
	Creates a new GeneProductAssociation object and adds it to the FbcReactionPlugin object. 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)
	Returns the namespace URI of the package to which this plugin object belongs. More...

def	getGeneProductAssociation (self, args)
	Returns the GeneProductAssociation from this FbcReactionPlugin object. More...

def	getLevel (self)
	Returns the SBML Level of the package extension of this plugin object. More...

def	getListOfAllElements (self, filter=None)
	Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth. More...

def	getLowerFluxBound (self)
	Returns the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin. 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	getUpperFluxBound (self)
	Returns the value of the 'upperFluxBound' attribute of this FbcReactionPlugin. 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	isSetGeneProductAssociation (self)
	Predicate returning `True` if this FbcReactionPlugin's 'GeneProductAssociation' element has been set. More...

def	isSetLowerFluxBound (self)
	Predicate returning `True` if this FbcReactionPlugin's 'lowerFluxBound' attribute is set. More...

def	isSetUpperFluxBound (self)
	Predicate returning `True` if this FbcReactionPlugin's 'upperFluxBound' attribute is set. More...

def	isValidTypeForList (self, item)

def	renameMetaIdRefs (self, oldid, newid)
	Replaces all uses of a given meta identifier attribute value with another value. More...

def	renameSIdRefs (self, oldid, newid)
	Replaces all uses of a given `SIdRef` type attribute value with another value. More...

def	renameUnitSIdRefs (self, oldid, newid)
	Replaces all uses of a given `UnitSIdRef` type attribute value with another value. More...

def	setElementNamespace (self, uri)
	Sets the XML namespace to which this object belongs. More...

def	setGeneProductAssociation (self, geneProductAssociation)
	Sets the GeneProductAssociation element in this FbcReactionPlugin object. More...

def	setLowerFluxBound (self, lowerFluxBound)
	Sets the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin. More...

def	setUpperFluxBound (self, upperFluxBound)
	Sets the value of the 'upperFluxBound' attribute of this FbcReactionPlugin. More...

def	unsetGeneProductAssociation (self)
	Unsets the the 'geneProduct' element of this FbcReactionPlugin. More...

def	unsetLowerFluxBound (self)
	Unsets the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin. More...

def	unsetUpperFluxBound (self)
	Unsets the value of the 'upperFluxBound' attribute of this FbcReactionPlugin. More...

Constructor & Destructor Documentation

def libsbml.FbcReactionPlugin.__init__	(	self,
		args
	)

This method has multiple variants; they differ in the arguments they accept.

__init__(string uri, string prefix, FbcPkgNamespaces fbcns)   FbcReactionPlugin
__init__(FbcReactionPlugin orig)   FbcReactionPlugin

Each variant is described separately below.

Method variant with the following signature:

FbcReactionPlugin(FbcReactionPlugin orig)

Copy constructor for FbcReactionPlugin.

Parameters

orig	the FbcReactionPlugin instance to copy.

Method variant with the following signature:

FbcReactionPlugin(string uri, string prefix, FbcPkgNamespaces fbcns)

Creates a new FbcReactionPlugin object using the given parameters.

: 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/'.

: The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.

Parameters

uri	the URI of the SBML Level 3 package implemented by this libSBML package extension.
prefix	the XML namespace prefix being used for the package.
fbcns	the namespaces object for the package.

Member Function Documentation

def libsbml.FbcReactionPlugin.clone ( self )

Creates and returns a deep copy of this FbcReactionPlugin object.

clone()   FbcReactionPlugin

Returns: a (deep) copy of this FbcReactionPlugin object.

def libsbml.FbcReactionPlugin.createGeneProductAssociation ( self )

Creates a new GeneProductAssociation object and adds it to the FbcReactionPlugin object.

createGeneProductAssociation()   GeneProductAssociation

Note: GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.

Returns: the newly created GeneProductAssociation object.

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

metaid string, 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

id	string representing the identifier of the object to find.

Returns: pointer to the first object with the given id.

def libsbml.SBasePlugin.getElementNamespace ( self )

inherited

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

getElementNamespace()   string

Returns: the XML namespace URI of the SBML Level 3 package implemented by this libSBML package extension.

def libsbml.FbcReactionPlugin.getGeneProductAssociation	(	self,
		args
	)

Returns the GeneProductAssociation from this FbcReactionPlugin object.

getGeneProductAssociation()   GeneProductAssociation

Note: GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.

Returns: the GeneProductAssociation from object in this FbcReactionPlugin object.

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)   SBaseList
getListOfAllElements()   SBaseList

Returns: a list of all objects that are children of this object.

def libsbml.FbcReactionPlugin.getLowerFluxBound ( self )

Returns the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin.

getLowerFluxBound()   string

Note: The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.

Returns: the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin as a string.

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.FbcReactionPlugin.getUpperFluxBound ( self )

Returns the value of the 'upperFluxBound' attribute of this FbcReactionPlugin.

getUpperFluxBound()   string

Note: The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.

Returns: the value of the 'upperFluxBound' attribute of this FbcReactionPlugin as a string.

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(); 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.FbcReactionPlugin.isSetGeneProductAssociation ( self )

Predicate returning True if this FbcReactionPlugin's 'GeneProductAssociation' element has been set.

isSetGeneProductAssociation()   bool

Note: GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.

Returns: True if the 'GeneProductAssociation' element has been set, otherwise False is returned.

def libsbml.FbcReactionPlugin.isSetLowerFluxBound ( self )

Predicate returning True if this FbcReactionPlugin's 'lowerFluxBound' attribute is set.

isSetLowerFluxBound()   bool

Note: The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.

Returns: True if this FbcReactionPlugin's 'lowerFluxBound' attribute has been set, otherwise False is returned.

def libsbml.FbcReactionPlugin.isSetUpperFluxBound ( self )

Predicate returning True if this FbcReactionPlugin's 'upperFluxBound' attribute is set.

isSetUpperFluxBound()   bool

Note: The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.

Returns: True if this FbcReactionPlugin's 'upperFluxBound' attribute has been set, otherwise False is returned.

def libsbml.SBasePlugin.isValidTypeForList	(	self,
		item
	)

inherited

isValidTypeForList(SBase item)   bool

def libsbml.SBasePlugin.renameMetaIdRefs	(	self,
		oldid,
		newid
	)

inherited

Replaces all uses of a given meta identifier attribute value with another value.

renameMetaIdRefs(string oldid, string newid)

: In SBML, object 'meta' identifiers are of the XML data type ID; the SBML object attribute itself is typically named metaid. All attributes that hold values referring to values of type ID are of the XML data type IDREF. They are also sometimes informally referred to as 'metaid refs', in analogy to the SBML-defined type SIdRef.

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

Parameters

oldid	the old identifier.
newid	the new identifier.

def libsbml.FbcReactionPlugin.renameSIdRefs	(	self,
		oldid,
		newid
	)

Replaces all uses of a given SIdRef type attribute value with another value.

renameSIdRefs(string oldid, string newid)

: In SBML, object identifiers are of a data type called SId. In SBML Level 3, an explicit data type called SIdRef was introduced for attribute values that refer to SId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to an identifier', but the effective data type was the same as SIdRef in Level 3. These and other methods of libSBML refer to the type SIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

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

Parameters

oldid	the old identifier.
newid	the new identifier.

def libsbml.SBasePlugin.renameUnitSIdRefs	(	self,
		oldid,
		newid
	)

inherited

Replaces all uses of a given UnitSIdRef type attribute value with another value.

renameUnitSIdRefs(string oldid, string newid)

: In SBML, unit definitions have identifiers of type UnitSId. In SBML Level 3, an explicit data type called UnitSIdRef was introduced for attribute values that refer to UnitSId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to a unit identifier', but the effective data type was the same as UnitSIdRef in Level 3. These and other methods of libSBML refer to the type UnitSIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

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

Parameters

oldid	the old identifier.
newid	the new identifier.

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

uri	the URI to assign to this object.

Returns

integer value indicating success/failure of the function. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:

LIBSBML_OPERATION_SUCCESS

See also: getElementNamespace()

def libsbml.FbcReactionPlugin.setGeneProductAssociation	(	self,
		geneProductAssociation
	)

Sets the GeneProductAssociation element in this FbcReactionPlugin object.

setGeneProductAssociation(GeneProductAssociation geneProductAssociation)   int

Note: GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.

Parameters

geneProductAssociation the geneProductAssociation to be set.

Returns

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

LIBSBML_OPERATION_SUCCESS

def libsbml.FbcReactionPlugin.setLowerFluxBound	(	self,
		lowerFluxBound
	)

Sets the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin.

setLowerFluxBound(string lowerFluxBound)   int

Note: The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.

Parameters

lowerFluxBound the value of the 'lowerFluxBound' attribute to be set.

Returns

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

def libsbml.FbcReactionPlugin.setUpperFluxBound	(	self,
		upperFluxBound
	)

Sets the value of the 'upperFluxBound' attribute of this FbcReactionPlugin.

setUpperFluxBound(string upperFluxBound)   int

Note: The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.

Parameters

upperFluxBound the value of the 'upperFluxBound' attribute to be set.

Returns

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

def libsbml.FbcReactionPlugin.unsetGeneProductAssociation ( self )

Unsets the the 'geneProduct' element of this FbcReactionPlugin.

unsetGeneProductAssociation()   int

Note: The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.

Returns

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

def libsbml.FbcReactionPlugin.unsetLowerFluxBound ( self )

Unsets the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin.

unsetLowerFluxBound()   int

Note: The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.

Returns

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

def libsbml.FbcReactionPlugin.unsetUpperFluxBound ( self )

Unsets the value of the 'upperFluxBound' attribute of this FbcReactionPlugin.

unsetUpperFluxBound()   int

Note: The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.

Returns

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

Detailed Description

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation