libSBML Python API  5.11.0
libsbml.FbcModelPlugin Class Reference
Inheritance diagram for libsbml.FbcModelPlugin:
[legend]

Detailed Description

fbc Extension of Model.

Public Member Functions

def __init__ (self, args)
 fbc Extension of Model. More...
 
def addFluxBound (self, bound)
 Adds a copy of the given FluxBound object to the list of FluxBounds. More...
 
def addGeneAssociation (self, association)
 Adds a copy of the given GeneAssociation object to the list of GeneAssociations. More...
 
def addObjective (self, bound)
 Adds a copy of the given Objective object to the list of Objectives. More...
 
def clone (self)
 Creates and returns a deep copy of this FbcModelPlugin object. More...
 
def createFluxBound (self)
 Creates a new FluxBound object and adds it to the list of FluxBound objects and returns it. More...
 
def createGeneAssociation (self)
 Creates a new GeneAssociation object and adds it to the list of GeneAssociation objects and returns it. More...
 
def createObjective (self)
 Creates a new Objective object and adds it to the list of Objective objects and returns it. More...
 
def getActiveObjective (self, args)
 Returns the current active objective. More...
 
def getActiveObjectiveId (self)
 returns the id of the current active objective. More...
 
def getElementByMetaId (self, metaid)
 Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or None if no such object is found. More...
 
def getElementBySId (self, id)
 Returns the first child element found that has the given id in the model-wide SId namespace, or None if no such object is found. More...
 
def getElementNamespace (self)
  Base class for extending SBML objects in packages. More...
 
def getFluxBound (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def getFluxBoundsForReaction (self, reaction)
 
def getGeneAssociation (self, args)
 This method has multiple variants; they differ in the arguments they accept. 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 getListOfFluxBounds (self, args)
 Returns the ListOfFluxBounds in this plugin object. More...
 
def getListOfGeneAssociations (self, args)
 Returns the ListOfObjectives in this plugin object. More...
 
def getListOfObjectives (self, args)
 Returns the ListOfObjectives in this plugin object. More...
 
def getNumFluxBounds (self)
 Returns the number of FluxBound object in this plugin object. More...
 
def getNumGeneAssociations (self)
 Returns the number of GeneAssociation object in this plugin object. More...
 
def getNumObjectives (self)
 Returns the number of Objective object in this plugin object. More...
 
def getObjective (self, args)
 This method has multiple variants; they differ in the arguments they accept. 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 removeFluxBound (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def removeGeneAssociation (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def removeObjective (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def setActiveObjectiveId (self, objectiveId)
 Sets the id of the active objective. More...
 
def setElementNamespace (self, uri)
 Sets the XML namespace to which this object belongs. More...
 
def unsetActiveObjectiveId (self)
 Unsets the active objective. More...
 

Member Function Documentation

def libsbml.FbcModelPlugin.addFluxBound (   self,
  bound 
)

Adds a copy of the given FluxBound object to the list of FluxBounds.

addFluxBound(FluxBound bound)   int
Parameters
boundthe FluxBound object to be added to the list of FluxBounds.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.FbcModelPlugin.addGeneAssociation (   self,
  association 
)

Adds a copy of the given GeneAssociation object to the list of GeneAssociations.

addGeneAssociation(GeneAssociation association)   int
Parameters
associationthe GeneAssociation object to be added to the list of GeneAssociations.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.FbcModelPlugin.addObjective (   self,
  bound 
)

Adds a copy of the given Objective object to the list of Objectives.

addObjective(Objective bound)   int
Parameters
boundthe Objective object to be added to the list of Objectives.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.FbcModelPlugin.clone (   self)

Creates and returns a deep copy of this FbcModelPlugin object.

clone()   FbcModelPlugin
Returns
a (deep) copy of this FbcModelPlugin object
def libsbml.FbcModelPlugin.createFluxBound (   self)

Creates a new FluxBound object and adds it to the list of FluxBound objects and returns it.

createFluxBound()   FluxBound
Returns
a newly created FluxBound object
def libsbml.FbcModelPlugin.createGeneAssociation (   self)

Creates a new GeneAssociation object and adds it to the list of GeneAssociation objects and returns it.

createGeneAssociation()   GeneAssociation
Returns
a newly created GeneAssociation object
def libsbml.FbcModelPlugin.createObjective (   self)

Creates a new Objective object and adds it to the list of Objective objects and returns it.

createObjective()   Objective
Returns
a newly created Objective object
def libsbml.FbcModelPlugin.getActiveObjective (   self,
  args 
)

Returns the current active objective.

getActiveObjective()   Objective
def libsbml.FbcModelPlugin.getActiveObjectiveId (   self)

returns the id of the current active objective.

getActiveObjectiveId()   string
def libsbml.FbcModelPlugin.getElementByMetaId (   self,
  metaid 
)

Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or None if no such object is found.

getElementByMetaId(string metaid)   SBase
Parameters
metaidstring representing the metaid of objects to find
Returns
a pointer to the SBase element with the given metaid.
def libsbml.FbcModelPlugin.getElementBySId (   self,
  id 
)

Returns the first child element found that has the given id in the model-wide SId namespace, or None if no such object is found.

getElementBySId(string id)   SBase
Parameters
idstring representing the id of objects to find
Returns
a pointer to the SBase element with the given id.
def libsbml.FbcModelPlugin.getFluxBound (   self,
  args 
)

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

getFluxBound(long n)   FluxBound
getFluxBound(string sid)   FluxBound

Each variant is described separately below.


Method variant with the following signature:
getFluxBound(long n)

Returns the FluxBound object that belongs to the given index. If the index is invalid, None is returned.

Parameters
nthe index number of the FluxBound to get.
Returns
the nth FluxBound in the ListOfFluxBounds.

Method variant with the following signature:
getFluxBound(string sid)

Returns the FluxBound object based on its identifier.

Parameters
sida string representing the identifier of the FluxBound to get.
Returns
FluxBound in the ListOfFluxBounds with the given sid or None if no such FluxBound exists.
See also
getFluxBound()
getListOfFluxBounds()
def libsbml.FbcModelPlugin.getFluxBoundsForReaction (   self,
  reaction 
)
getFluxBoundsForReaction(string reaction)   ListOfFluxBounds
 
def libsbml.FbcModelPlugin.getGeneAssociation (   self,
  args 
)

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

getGeneAssociation(long n)   GeneAssociation
getGeneAssociation(string sid)   GeneAssociation

Each variant is described separately below.


Method variant with the following signature:
getGeneAssociation(long n)

Returns the GeneAssociation object that belongs to the given index. If the index is invalid, None is returned.

Parameters
nthe index number of the GeneAssociation to get.
Returns
the nth GeneAssociation in the ListOfGeneAssociations.

Method variant with the following signature:
getGeneAssociation(string sid)

Returns the GeneAssociation object based on its identifier.

Parameters
sida string representing the identifier of the GeneAssociation to get.
Returns
GeneAssociation in the ListOfGeneAssociations with the given sid or None if no such GeneAssociation exists.
See also
getGeneAssociation()
getListOfGeneAssociations()
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.FbcModelPlugin.getListOfFluxBounds (   self,
  args 
)

Returns the ListOfFluxBounds in this plugin object.

getListOfFluxBounds()   ListOfFluxBounds
Returns
ListOfFluxBounds object in this plugin object.
def libsbml.FbcModelPlugin.getListOfGeneAssociations (   self,
  args 
)

Returns the ListOfObjectives in this plugin object.

getListOfGeneAssociations()   ListOfGeneAssociations
Returns
ListOfObjectives object in this plugin object.
def libsbml.FbcModelPlugin.getListOfObjectives (   self,
  args 
)

Returns the ListOfObjectives in this plugin object.

getListOfObjectives()   ListOfObjectives
Returns
ListOfObjectives object in this plugin object.
def libsbml.FbcModelPlugin.getNumFluxBounds (   self)

Returns the number of FluxBound object in this plugin object.

getNumFluxBounds()   long
Returns
the number of FluxBound object in this plugin object.
def libsbml.FbcModelPlugin.getNumGeneAssociations (   self)

Returns the number of GeneAssociation object in this plugin object.

getNumGeneAssociations()   int
Returns
the number of GeneAssociation object in this plugin object.
def libsbml.FbcModelPlugin.getNumObjectives (   self)

Returns the number of Objective object in this plugin object.

getNumObjectives()   long
Returns
the number of Objective object in this plugin object.
def libsbml.FbcModelPlugin.getObjective (   self,
  args 
)

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

getObjective(long n)   Objective
getObjective(string sid)   Objective

Each variant is described separately below.


Method variant with the following signature:
getObjective(long n)

Returns the Objective object that belongs to the given index. If the index is invalid, None is returned.

Parameters
nthe index number of the Objective to get.
Returns
the nth Objective in the ListOfObjectives.

Method variant with the following signature:
getObjective(string sid)

Returns the Objective object based on its identifier.

Parameters
sida string representing the identifier of the Objective to get.
Returns
Objective in the ListOfObjectives with the given sid or None if no such Objective exists.
See also
getObjective()
getListOfObjectives()
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.FbcModelPlugin.removeFluxBound (   self,
  args 
)

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

removeFluxBound(long n)   FluxBound
removeFluxBound(string sid)   FluxBound

Each variant is described separately below.


Method variant with the following signature:
removeFluxBound(long n)

Removes the nth FluxBound object from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the FluxBound object to remove
Returns
the FluxBound object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range.

Method variant with the following signature:
removeFluxBound(string sid)

Removes the FluxBound object with the given sid attribute from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
sidthe id attribute of the FluxBound object to remove
Returns
the FluxBound object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range.
def libsbml.FbcModelPlugin.removeGeneAssociation (   self,
  args 
)

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

removeGeneAssociation(long n)   GeneAssociation
removeGeneAssociation(string sid)   GeneAssociation

Each variant is described separately below.


Method variant with the following signature:
removeGeneAssociation(long n)

Removes the nth GeneAssociation object from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the GeneAssociation object to remove
Returns
the GeneAssociation object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range.

Method variant with the following signature:
removeGeneAssociation(string sid)

Removes the GeneAssociation object with the given sid attribute from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
sidthe id attribute of the GeneAssociation object to remove
Returns
the GeneAssociation object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range.
def libsbml.FbcModelPlugin.removeObjective (   self,
  args 
)

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

removeObjective(long n)   Objective
removeObjective(string sid)   Objective

Each variant is described separately below.


Method variant with the following signature:
removeObjective(long n)

Removes the nth Objective object from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the Objective object to remove
Returns
the Objective object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range.

Method variant with the following signature:
removeObjective(string sid)

Removes the Objective object with the given sid attribute from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
sidthe id attribute of the Objective object to remove
Returns
the Objective object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range.
def libsbml.FbcModelPlugin.setActiveObjectiveId (   self,
  objectiveId 
)

Sets the id of the active objective.

setActiveObjectiveId(string objectiveId)   int
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.FbcModelPlugin.unsetActiveObjectiveId (   self)

Unsets the active objective.

unsetActiveObjectiveId()