libSBML Python API
5.11.0
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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... | |
def libsbml.FbcModelPlugin.addFluxBound | ( | self, | |
bound | |||
) |
def libsbml.FbcModelPlugin.addGeneAssociation | ( | self, | |
association | |||
) |
Adds a copy of the given GeneAssociation object to the list of GeneAssociations.
addGeneAssociation(GeneAssociation association) int
association | the GeneAssociation object to be added to the list of GeneAssociations. |
def libsbml.FbcModelPlugin.addObjective | ( | self, | |
bound | |||
) |
def libsbml.FbcModelPlugin.clone | ( | self | ) |
Creates and returns a deep copy of this FbcModelPlugin object.
clone() FbcModelPlugin
def libsbml.FbcModelPlugin.createFluxBound | ( | self | ) |
def libsbml.FbcModelPlugin.createGeneAssociation | ( | self | ) |
Creates a new GeneAssociation object and adds it to the list of GeneAssociation objects and returns it.
createGeneAssociation() GeneAssociation
def libsbml.FbcModelPlugin.createObjective | ( | self | ) |
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
metaid | string representing the metaid of objects to find |
metaid
. def libsbml.FbcModelPlugin.getElementBySId | ( | self, | |
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.
getFluxBound(string sid)
Returns the FluxBound object based on its identifier.
sid | a string representing the identifier of the FluxBound to get. |
sid
or None if no such FluxBound exists.getFluxBound(long n)
Returns the FluxBound object that belongs to the given index. If the index is invalid, None
is returned.
n | the index number of the FluxBound to get. |
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.
getGeneAssociation(string sid)
Returns the GeneAssociation object based on its identifier.
sid | a string representing the identifier of the GeneAssociation to get. |
sid
or None if no such GeneAssociation exists.getGeneAssociation(long n)
Returns the GeneAssociation object that belongs to the given index. If the index is invalid, None
is returned.
n | the index number of the GeneAssociation to get. |
|
inherited |
Returns the SBML Level of the package extension of this plugin object.
getLevel() long
|
inherited |
Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth.
getListOfAllElements(ElementFilter filter=None) SBaseList getListOfAllElements() SBaseList
def libsbml.FbcModelPlugin.getListOfFluxBounds | ( | self, | |
args | |||
) |
Returns the ListOfFluxBounds in this plugin object.
getListOfFluxBounds() ListOfFluxBounds
def libsbml.FbcModelPlugin.getListOfGeneAssociations | ( | self, | |
args | |||
) |
Returns the ListOfObjectives in this plugin object.
getListOfGeneAssociations() ListOfGeneAssociations
def libsbml.FbcModelPlugin.getListOfObjectives | ( | self, | |
args | |||
) |
Returns the ListOfObjectives in this plugin object.
getListOfObjectives() ListOfObjectives
def libsbml.FbcModelPlugin.getNumFluxBounds | ( | self | ) |
def libsbml.FbcModelPlugin.getNumGeneAssociations | ( | self | ) |
Returns the number of GeneAssociation object in this plugin object.
getNumGeneAssociations() int
def libsbml.FbcModelPlugin.getNumObjectives | ( | self | ) |
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.
getObjective(string sid)
Returns the Objective object based on its identifier.
sid | a string representing the identifier of the Objective to get. |
sid
or None if no such Objective exists.getObjective(long n)
Returns the Objective object that belongs to the given index. If the index is invalid, None
is returned.
n | the index number of the Objective to get. |
|
inherited |
Returns the short-form name of the package to which this plugin object belongs.
getPackageName() string
|
inherited |
Returns the package version of the package extension of this plugin object.
getPackageVersion() long
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inherited |
Returns the parent object to which this plugin object is connected.
getParentSBMLObject() SBase
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inherited |
Returns the XML namespace prefix of the package to which this plugin object belongs.
getPrefix() string
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inherited |
Returns the SBMLDocument object containing this object instance.
getSBMLDocument() SBMLDocument
This method allows the caller to obtain the SBMLDocument for the current object.
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inherited |
Returns the XML namespace URI for the package to which this object belongs.
getURI() string
'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().
|
inherited |
Returns the Version within the SBML Level of the package extension of this plugin object.
getVersion() long
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.
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.
sid | the id attribute of the FluxBound object to remove |
None
is returned if the given index is out of range.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.
n | the index of the FluxBound object to remove |
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.
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.
sid | the id attribute of the GeneAssociation object to remove |
None
is returned if the given index is out of range.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.
n | the index of the GeneAssociation object to remove |
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.
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.
sid | the id attribute of the Objective object to remove |
None
is returned if the given index is out of range.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.
n | the index of the Objective object to remove |
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
|
inherited |
Sets the XML namespace to which this object belongs.
setElementNamespace(string uri) int
'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/'
.uri | the URI to assign to this object. |
def libsbml.FbcModelPlugin.unsetActiveObjectiveId | ( | self | ) |
Unsets the active objective.
unsetActiveObjectiveId()