libSBML Python API
5.18.0
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The MultiSpeciesReferencePlugin class inherits from the MultiSimpleSpeciesReferencePlugin class, and extends the SpeciesReference class to establish component mappings between the reactant species and the product species when the mappings cannot be inferred from the ids of the SpeciesTypeInstance objects. A MultiSpeciesReferencePlugin object defines an optional ListOfSpeciesTypeComponentMapInProducts child. Only a reaction product can contain the ListOfSpeciesTypeComponentMapInProducts child and it is not necessary to store the mappings again in the reactants.
Public Member Functions | |
def | __init__ (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | addSpeciesTypeComponentMapInProduct (self, speciesTypeComponentMapInProduct) |
Adds a copy of the given SpeciesTypeComponentMapInProduct to the ListOfSpeciesTypeComponentMapInProducts. More... | |
def | clone (self) |
Creates and returns a deep copy of this MultiSpeciesReferencePlugin object. More... | |
def | createSpeciesTypeComponentMapInProduct (self) |
Creates a new SpeciesTypeComponentMapInProduct object and adds it to the ListOfSpeciesTypeComponentMapInProducts. More... | |
def | getCompartmentReference (self) |
Returns the value of the 'compartmentReference' attribute of this SimpleSpeciesReference. 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 | getListOfSpeciesTypeComponentMapInProducts (self, args) |
Returns the ListOfSpeciesTypeComponentMapInProducts object. More... | |
def | getNumSpeciesTypeComponentMapInProducts (self) |
Returns the number of SpeciesTypeComponentMapInProduct objects. 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 | getSpeciesTypeComponentMapInProduct (self, args) |
This method has multiple variants; they differ in the arguments they accept. 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 | hasRequiredElements (self) |
Returns True if this object has all the required elements. More... | |
def | isSetCompartmentReference (self) |
Returns True if this SimpleSpeciesReference's 'compartmentReference' attribute has been set. More... | |
def | isValidTypeForList (self, item) |
def | removeSpeciesTypeComponentMapInProduct (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
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 | setCompartmentReference (self, compartmentReference) |
Sets the value of the 'compartmentReference' attribute of this SimpleSpeciesReference. More... | |
def | setElementNamespace (self, uri) |
Sets the XML namespace to which this object belongs. More... | |
def | unsetCompartmentReference (self) |
Unsets the value of the 'compartmentReference' attribute of this SimpleSpeciesReference. More... | |
def libsbml.MultiSpeciesReferencePlugin.__init__ | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
__init__(string uri, string prefix, MultiPkgNamespaces multins) MultiSpeciesReferencePlugin __init__(MultiSpeciesReferencePlugin orig) MultiSpeciesReferencePlugin
Each variant is described separately below.
MultiSpeciesReferencePlugin(MultiSpeciesReferencePlugin orig)
Copy constructor for MultiSpeciesReferencePlugin.
orig | the MultiSpeciesReferencePlugin instance to copy. |
MultiSpeciesReferencePlugin(string uri, string prefix, MultiPkgNamespaces multins)
Creates a new MultiSpeciesReferencePlugin object.
'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 of the SBML Level 3 package implemented by this libSBML package extension. |
prefix | the XML namespace prefix being used for the package. |
multins | the namespaces object for the package. |
def libsbml.MultiSpeciesReferencePlugin.addSpeciesTypeComponentMapInProduct | ( | self, | |
speciesTypeComponentMapInProduct | |||
) |
Adds a copy of the given SpeciesTypeComponentMapInProduct to the ListOfSpeciesTypeComponentMapInProducts.
addSpeciesTypeComponentMapInProduct(SpeciesTypeComponentMapInProduct speciesTypeComponentMapInProduct) int
speciesTypeComponentMapInProduct | the speciesTypeComponentMapInProduct to be added. |
def libsbml.MultiSpeciesReferencePlugin.clone | ( | self | ) |
Creates and returns a deep copy of this MultiSpeciesReferencePlugin object.
clone() MultiSpeciesReferencePlugin
def libsbml.MultiSpeciesReferencePlugin.createSpeciesTypeComponentMapInProduct | ( | self | ) |
Creates a new SpeciesTypeComponentMapInProduct object and adds it to the ListOfSpeciesTypeComponentMapInProducts.
createSpeciesTypeComponentMapInProduct() SpeciesTypeComponentMapInProduct
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inherited |
Returns the value of the 'compartmentReference' attribute of this SimpleSpeciesReference.
getCompartmentReference() string
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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.
metaid | string, the metaid of the object to find. |
metaid
.
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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.
id | string representing the identifier of the object to find. |
id
.
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inherited |
Returns the namespace URI of the package to which this plugin object belongs.
getElementNamespace() string
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inherited |
Returns the SBML Level of the package extension of this plugin object.
getLevel() long
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inherited |
Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth.
getListOfAllElements(ElementFilter filter) SBaseList getListOfAllElements() SBaseList
def libsbml.MultiSpeciesReferencePlugin.getListOfSpeciesTypeComponentMapInProducts | ( | self, | |
args | |||
) |
Returns the ListOfSpeciesTypeComponentMapInProducts object.
getListOfSpeciesTypeComponentMapInProducts() ListOfSpeciesTypeComponentMapInProducts
def libsbml.MultiSpeciesReferencePlugin.getNumSpeciesTypeComponentMapInProducts | ( | self | ) |
Returns the number of SpeciesTypeComponentMapInProduct objects.
getNumSpeciesTypeComponentMapInProducts() long
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inherited |
Returns the short-form name of the package to which this plugin object belongs.
getPackageName() string
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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.
def libsbml.MultiSpeciesReferencePlugin.getSpeciesTypeComponentMapInProduct | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
getSpeciesTypeComponentMapInProduct(long n) SpeciesTypeComponentMapInProduct getSpeciesTypeComponentMapInProduct(string sid) SpeciesTypeComponentMapInProduct
Each variant is described separately below.
getSpeciesTypeComponentMapInProduct(long n)
Returns the nth SpeciesTypeComponentMapInProduct object.
n | the index number of the SpeciesTypeComponentMapInProduct to get. |
getSpeciesTypeComponentMapInProduct(string sid)
Returns the SpeciesTypeComponentMapInProduct object with the given identifier sid
.
sid | a string representing the id of the SpeciesTypeComponentMapInProduct to get. |
None
if no such SpeciesTypeComponentMapInProduct exists.
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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().
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inherited |
Returns the Version within the SBML Level of the package extension of this plugin object.
getVersion() long
def libsbml.MultiSpeciesReferencePlugin.hasRequiredElements | ( | self | ) |
Returns True
if this object has all the required elements.
hasRequiredElements() bool
True
if this object has all the elements required by the package specification; otherwise, False
will be returned.
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inherited |
Returns True
if this SimpleSpeciesReference's 'compartmentReference' attribute has been set.
isSetCompartmentReference() bool
True
if this SimpleSpeciesReference's 'compartmentReference' attribute has been set; otherwise, False
is returned.
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inherited |
isValidTypeForList(SBase item) bool
def libsbml.MultiSpeciesReferencePlugin.removeSpeciesTypeComponentMapInProduct | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
removeSpeciesTypeComponentMapInProduct(long n) SpeciesTypeComponentMapInProduct removeSpeciesTypeComponentMapInProduct(string sid) SpeciesTypeComponentMapInProduct
Each variant is described separately below.
removeSpeciesTypeComponentMapInProduct(long n)
Removes the nth SpeciesTypeComponentMapInProduct object and returns a pointer to it.
n | the index of the SpeciesTypeComponentMapInProduct to remove. |
None
index was out of range. Note that the caller owns the returned object and is responsible for deleting it.removeSpeciesTypeComponentMapInProduct(string sid)
Removes the SpeciesTypeComponentMapInProduct object with the given id and returns a pointer to it.
sid | a string representing the id of the SpeciesTypeComponentMapInProduct to remove. |
None
if no such SpeciesTypeComponentMapInProduct exists. Note that the caller owns the returned object and is responsible for deleting it.
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inherited |
Replaces all uses of a given meta identifier attribute value with another value.
renameMetaIdRefs(string oldid, string newid)
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.
oldid | the old identifier. |
newid | the new identifier. |
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inherited |
Replaces all uses of a given SIdRef
type attribute value with another value.
renameSIdRefs(string oldid, string newid)
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.
oldid | the old identifier. |
newid | the new identifier. |
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inherited |
Replaces all uses of a given UnitSIdRef
type attribute value with another value.
renameUnitSIdRefs(string oldid, string newid)
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.
oldid | the old identifier. |
newid | the new identifier. |
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inherited |
Sets the value of the 'compartmentReference' attribute of this SimpleSpeciesReference.
setCompartmentReference(string compartmentReference) int
compartmentReference | the new value of the 'compartmentReference' attribute. |
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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. |
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inherited |
Unsets the value of the 'compartmentReference' attribute of this SimpleSpeciesReference.
unsetCompartmentReference() int