Inheritance diagram for libsbml.FbcSpeciesPlugin:

Detailed Description

fbc Extension of Species.

The FbcSpeciesPlugin class codifies an extension of the core SBML Species class defined in the SBML Level 3 Flux Balance Constraints (“fbc”) package. The “fbc” package adds two attributes named 'charge' and 'chemicalFormula' to Species.

The optional attribute 'charge' can contain a signed integer that refers to the Species object's electrical charge (in terms of electrons, not the SI unit of coulombs). Note that this attribute is therefore defined as it is in the SBML Level 2 Version 1 specification. (The charge attribute was removed in higher Versions and Levels of SBML, and is not an attribute of SBML Species in core SBML Level 3. However, it is useful for flux balance constraints models, and thus, the Level 3 “fbc” package adds it.)

The optional attribute 'chemicalFormula' can contain a text string that represents the elemental composition of the substance represented by the Species object. The purpose of the 'chemicalFormula' attribute is to allow balancing and validating reactions. This is particularly important in constraint-based models. The format of 'chemicalFormula' must consist only of atomic names (as given in the Periodic Table of elements) 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 to enhance interoperability of models), users are advised to employ the Hill system order. Using this notation, the number of carbon atoms in a molecule is indicated first, followed by the number of hydrogen atoms, and then the number of all other chemical elements in alphabetical order. When the formula contains no carbon, all elements including hydrogen are listed alphabetically.

Here is an example of the XML form of an extended Species definition with these attributes:

<species metaid='meta_M_atp_c' id='M_atp_c' name='ATP' compartment='Cytosol'
boundaryCondition='false' initialConcentration='0' hasOnlySubstanceUnits='false'
fbc:charge='-4' fbc:chemicalFormula='C10H12N5O13P3'/>

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 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)
	Returns the namespace URI of the package to which this plugin object belongs. 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	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's 'charge' attribute has been set. More...

def	isSetChemicalFormula (self)
	Predicate returning `True` or `False` depending on whether this FbcSpeciesPlugin's 'chemicalFormula' attribute has been 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	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...

Constructor & Destructor Documentation

def libsbml.FbcSpeciesPlugin.__init__	(	self,
		args
	)

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

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

Each variant is described separately below.

Method variant with the following signature:

FbcSpeciesPlugin(string uri, string prefix, FbcPkgNamespaces fbcns)

Creates a new FbcSpeciesPlugin

Method variant with the following signature:

FbcSpeciesPlugin(FbcSpeciesPlugin orig)

Copy constructor for FbcSpeciesPlugin.

Parameters

orig; the FbcSpeciesPlugin instance to copy.

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 as a integer.

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 as a string.

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.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.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(); 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's 'charge' attribute has been set.

isSetCharge()   bool

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

def libsbml.FbcSpeciesPlugin.isSetChemicalFormula ( self )

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

isSetChemicalFormula()   bool

Returns: True if this FbcSpeciesPlugin's 'chemicalFormula' 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.SBasePlugin.renameSIdRefs	(	self,
		oldid,
		newid
	)

inherited

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.FbcSpeciesPlugin.setCharge	(	self,
		charge
	)

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

setCharge(int charge)   int

Parameters

charge; int value of the 'charge' attribute to be set

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

Parameters

chemicalFormula; string value of the 'chemicalFormula' attribute to be set

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

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.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:

Detailed Description

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation