libSBML Python API  5.18.0
libsbml.FbcSBMLDocumentPlugin Class Reference
Inheritance diagram for libsbml.FbcSBMLDocumentPlugin:
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Detailed Description

fbc Extension of SBMLDocument for the “fbc” package.

The FbcSBMLDocumentPlugin class inherits from the SBMLDocumentPlugin class, and codifies the extensions to the SBMLDocument class defined in the SBML Level 3 Flux Balance Constraints (“fbc”) package. This extension defines a required flag named 'required', which indicates whether “fbc” constructs can be used to change the core mathematical interpretation of the Model defined in the SBML input. Since “fbc” constructs cannot, this attribute must be set to the value 'False'.

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 FbcSBMLDocumentPlugin 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 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 getRequired (self)
 Returns the value of the 'required' attribute. 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 isSetRequired (self)
 Returns the value of the 'required' attribute. 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 setRequired (self, value)
 Sets the SBML 'required' attribute value. More...
 
def unsetRequired (self)
 Unsets the value of the 'required' attribute of this SBMLDocumentPlugin. More...
 

Constructor & Destructor Documentation

def libsbml.FbcSBMLDocumentPlugin.__init__ (   self,
  args 
)

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

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

Each variant is described separately below.


Method variant with the following signature:
FbcSBMLDocumentPlugin(string uri, string prefix, FbcPkgNamespaces fbcns)

Creates a new FbcSBMLDocumentPlugin 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
urithe URI of the SBML Level 3 package implemented by this libSBML package extension.
prefixthe XML namespace prefix being used for the package.
fbcnsthe namespaces object for the package.

Method variant with the following signature:
FbcSBMLDocumentPlugin(FbcSBMLDocumentPlugin orig)

Copy constructor for FbcSBMLDocumentPlugin.

Parameters
origthe FbcSBMLDocumentPlugin instance to copy.

Member Function Documentation

def libsbml.FbcSBMLDocumentPlugin.clone (   self)

Creates and returns a deep copy of this FbcSBMLDocumentPlugin object.

clone()   FbcSBMLDocumentPlugin
Returns
a (deep) copy of this FbcSBMLDocumentPlugin 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
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.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.SBMLDocumentPlugin.getRequired (   self)
inherited

Returns the value of the 'required' attribute.

getRequired()   bool
SBML Level 3 requires that every package defines an attribute named 'required' on the root <sbml> element in an SBML file or data stream. The attribute, being in the namespace of the Level 3 package in question, must be prefixed by the XML namespace prefix associated with the package. The value of the 'required' attribute indicates whether constructs in that package may change the mathematical interpretation of constructs defined in SBML Level 3 Core. A 'required' value of True indicates that the package may do so. The value of the attribute is set by the Level 3 package specification, and does not depend on the actual presence or absence of particular package constructs in a given SBML document: in other words, if the package specification defines any construct that can change the model's meaning, the value of the 'required' attribute must always be set to True in any SBML document that uses the package.

The XML namespace declaration for an SBML Level 3 package is an indication that a model makes use of features defined by that package, while the 'required' attribute indicates whether the features may be ignored without compromising the mathematical meaning of the model. Both are necessary for a complete reference to an SBML Level 3 package.

Returns
the bool value of 'required' attribute for the SBML package.
See also
setRequired()
isSetRequired()
unsetRequired()
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.SBMLDocumentPlugin.isSetRequired (   self)
inherited

Returns the value of the 'required' attribute.

isSetRequired()   bool
SBML Level 3 requires that every package defines an attribute named 'required' on the root <sbml> element in an SBML file or data stream. The attribute, being in the namespace of the Level 3 package in question, must be prefixed by the XML namespace prefix associated with the package. The value of the 'required' attribute indicates whether constructs in that package may change the mathematical interpretation of constructs defined in SBML Level 3 Core. A 'required' value of True indicates that the package may do so. The value of the attribute is set by the Level 3 package specification, and does not depend on the actual presence or absence of particular package constructs in a given SBML document: in other words, if the package specification defines any construct that can change the model's meaning, the value of the 'required' attribute must always be set to True in any SBML document that uses the package.

The XML namespace declaration for an SBML Level 3 package is an indication that a model makes use of features defined by that package, while the 'required' attribute indicates whether the features may be ignored without compromising the mathematical meaning of the model. Both are necessary for a complete reference to an SBML Level 3 package.

Returns
True if the 'required' attribute of this SBMLDocument has been set to True, False otherwise.
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
oldidthe old identifier.
newidthe 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
oldidthe old identifier.
newidthe 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
oldidthe old identifier.
newidthe 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
urithe 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:
See also
getElementNamespace()
def libsbml.SBMLDocumentPlugin.setRequired (   self,
  value 
)
inherited

Sets the SBML 'required' attribute value.

setRequired(bool value)   int
SBML Level 3 requires that every package defines an attribute named 'required' on the root <sbml> element in an SBML file or data stream. The attribute, being in the namespace of the Level 3 package in question, must be prefixed by the XML namespace prefix associated with the package. The value of the 'required' attribute indicates whether constructs in that package may change the mathematical interpretation of constructs defined in SBML Level 3 Core. A 'required' value of True indicates that the package may do so. The value of the attribute is set by the Level 3 package specification, and does not depend on the actual presence or absence of particular package constructs in a given SBML document: in other words, if the package specification defines any construct that can change the model's meaning, the value of the 'required' attribute must always be set to True in any SBML document that uses the package.

The XML namespace declaration for an SBML Level 3 package is an indication that a model makes use of features defined by that package, while the 'required' attribute indicates whether the features may be ignored without compromising the mathematical meaning of the model. Both are necessary for a complete reference to an SBML Level 3 package.

Parameters
valuethe value to be assigned to the 'required' attribute. The 'required' attribute takes a Boolean value, either True or False.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getRequired()
isSetRequired()
unsetRequired()
def libsbml.SBMLDocumentPlugin.unsetRequired (   self)
inherited

Unsets the value of the 'required' attribute of this SBMLDocumentPlugin.

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