libSBML Python API
5.18.0
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The MultiSpeciesPlugin class extends the Species class to have a new attribute 'speciesType', and two extra optional ListOfOutwardBindingSites and ListOfSpeciesFeatures children. A species may have a ListOfOutwardBindingSites child and/or a ListOfSpeciesFeatures child only when its speciesType attribute has been defined. The relationship among the elements of a ListOfOutwardBindingSites or a ListOfSpeciesFeatures is 'and'.
Public Member Functions | |
def | __init__ (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | addOutwardBindingSite (self, outwardBindingSite) |
Adds a copy of the given OutwardBindingSite to the ListOfOutwardBindingSites. More... | |
def | addSpeciesFeature (self, speciesFeature) |
Adds a copy of the given SpeciesFeature to the ListOfSpeciesFeatures of this 'multi' Species. More... | |
def | addSubListOfSpeciesFeatures (self, subListOfSpeciesFeatures) |
Adds a copy of the given SubListOfSpeciesFeatures to the ListOfSpeciesFeatures. More... | |
def | clone (self) |
Creates and returns a deep copy of this MultiSpeciesPlugin object. More... | |
def | createOutwardBindingSite (self) |
Creates a new OutwardBindingSite object and adds it to the ListOfOutwardBindingSites. More... | |
def | createSpeciesFeature (self) |
Creates a new SpeciesFeature object and adds it to the ListOfSpeciesFeatures of this 'multi' Species. More... | |
def | createSubListOfSpeciesFeatures (self) |
Creates a new SubListOfSpeciesFeatures object and adds it to the SubListOfSpeciesFeatures. 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 | getListOfOutwardBindingSites (self, args) |
Returns the ListOfOutwardBindingSites of this 'multi' Species. More... | |
def | getListOfSpeciesFeatures (self, args) |
Returns the ListOfSpeciesFeatures of this 'multi' Species. More... | |
def | getNumOutwardBindingSites (self) |
Returns the number of OutwardBindingSite objects of this 'multi' Species. More... | |
def | getNumSpeciesFeatures (self) |
Returns the number of SpeciesFeature objects of this 'multi' Species. More... | |
def | getNumSubListOfSpeciesFeatures (self) |
Returns the number of SubListOfSpeciesFeatures objects of this 'multi' Species. More... | |
def | getOutwardBindingSite (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 | getSpeciesFeature (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | getSpeciesType (self) |
Returns the value of the 'speciesType' attribute of this 'multi' Species. More... | |
def | getSubListOfSpeciesFeatures (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 | isSetSpeciesType (self) |
Returns True if the 'speciesType' attribute of this 'multi' Species has been set. More... | |
def | isValidTypeForList (self, item) |
def | removeOutwardBindingSite (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | removeSpeciesFeature (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 | setElementNamespace (self, uri) |
Sets the XML namespace to which this object belongs. More... | |
def | setSpeciesType (self, speciesType) |
Sets the value of the 'speciesType' attribute on this 'multi' Species. More... | |
def | unsetSpeciesType (self) |
Unsets the value of the 'speciesType' attribute on this 'multi' Species. More... | |
def libsbml.MultiSpeciesPlugin.__init__ | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
__init__(string uri, string prefix, MultiPkgNamespaces multins) MultiSpeciesPlugin __init__(MultiSpeciesPlugin orig) MultiSpeciesPlugin
Each variant is described separately below.
MultiSpeciesPlugin(string uri, string prefix, MultiPkgNamespaces multins)
Creates a new MultiSpeciesPlugin 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. |
MultiSpeciesPlugin(MultiSpeciesPlugin orig)
Copy constructor for MultiSpeciesPlugin.
orig | the MultiSpeciesPlugin instance to copy. |
def libsbml.MultiSpeciesPlugin.addOutwardBindingSite | ( | self, | |
outwardBindingSite | |||
) |
Adds a copy of the given OutwardBindingSite to the ListOfOutwardBindingSites.
addOutwardBindingSite(OutwardBindingSite outwardBindingSite) int
outwardBindingSite | the outwardBindingSite to be added. |
def libsbml.MultiSpeciesPlugin.addSpeciesFeature | ( | self, | |
speciesFeature | |||
) |
Adds a copy of the given SpeciesFeature to the ListOfSpeciesFeatures of this 'multi' Species.
addSpeciesFeature(SpeciesFeature speciesFeature) int
speciesFeature | the SpeciesFeature to be added. |
def libsbml.MultiSpeciesPlugin.addSubListOfSpeciesFeatures | ( | self, | |
subListOfSpeciesFeatures | |||
) |
Adds a copy of the given SubListOfSpeciesFeatures to the ListOfSpeciesFeatures.
addSubListOfSpeciesFeatures(SubListOfSpeciesFeatures subListOfSpeciesFeatures) int
subListOfSpeciesFeatures | the SubListOfSpeciesFeatures to be added. |
def libsbml.MultiSpeciesPlugin.clone | ( | self | ) |
Creates and returns a deep copy of this MultiSpeciesPlugin object.
clone() MultiSpeciesPlugin
def libsbml.MultiSpeciesPlugin.createOutwardBindingSite | ( | self | ) |
Creates a new OutwardBindingSite object and adds it to the ListOfOutwardBindingSites.
createOutwardBindingSite() OutwardBindingSite
def libsbml.MultiSpeciesPlugin.createSpeciesFeature | ( | self | ) |
Creates a new SpeciesFeature object and adds it to the ListOfSpeciesFeatures of this 'multi' Species.
createSpeciesFeature() SpeciesFeature
def libsbml.MultiSpeciesPlugin.createSubListOfSpeciesFeatures | ( | self | ) |
Creates a new SubListOfSpeciesFeatures object and adds it to the SubListOfSpeciesFeatures.
createSubListOfSpeciesFeatures() SubListOfSpeciesFeatures
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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
.
|
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.MultiSpeciesPlugin.getListOfOutwardBindingSites | ( | self, | |
args | |||
) |
Returns the ListOfOutwardBindingSites of this 'multi' Species.
getListOfOutwardBindingSites() ListOfOutwardBindingSites
def libsbml.MultiSpeciesPlugin.getListOfSpeciesFeatures | ( | self, | |
args | |||
) |
Returns the ListOfSpeciesFeatures of this 'multi' Species.
getListOfSpeciesFeatures() ListOfSpeciesFeatures
def libsbml.MultiSpeciesPlugin.getNumOutwardBindingSites | ( | self | ) |
Returns the number of OutwardBindingSite objects of this 'multi' Species.
getNumOutwardBindingSites() long
def libsbml.MultiSpeciesPlugin.getNumSpeciesFeatures | ( | self | ) |
Returns the number of SpeciesFeature objects of this 'multi' Species.
getNumSpeciesFeatures() long
def libsbml.MultiSpeciesPlugin.getNumSubListOfSpeciesFeatures | ( | self | ) |
Returns the number of SubListOfSpeciesFeatures objects of this 'multi' Species.
getNumSubListOfSpeciesFeatures() long
def libsbml.MultiSpeciesPlugin.getOutwardBindingSite | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
getOutwardBindingSite(long n) OutwardBindingSite getOutwardBindingSite(string sid) OutwardBindingSite
Each variant is described separately below.
getOutwardBindingSite(long n)
Returns the nth OutwardBindingSite object.
n | the index number of the OutwardBindingSite to get |
getOutwardBindingSite(string sid)
Returns the OutwardBindingSite object with the given identifier sid
.
sid | a string representing the id of the OutwardBindingSite to get. |
None
if no such OutwardBindingSite exists.
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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.MultiSpeciesPlugin.getSpeciesFeature | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
getSpeciesFeature(long n) SpeciesFeature getSpeciesFeature(string sid) SpeciesFeature
Each variant is described separately below.
getSpeciesFeature(long n)
Returns the nth SpeciesFeature object.
n | the index number of the SpeciesFeature to get. |
getSpeciesFeature(string sid)
Returns the SpeciesFeature object with the given identifier sid
.
sid | a string representing the id of the SpeciesFeature to get |
sid
, or None
if no such SpeciesFeature exists. def libsbml.MultiSpeciesPlugin.getSpeciesType | ( | self | ) |
Returns the value of the 'speciesType' attribute of this 'multi' Species.
getSpeciesType() string
def libsbml.MultiSpeciesPlugin.getSubListOfSpeciesFeatures | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
getSubListOfSpeciesFeatures(long n) SubListOfSpeciesFeatures getSubListOfSpeciesFeatures(string sid) SubListOfSpeciesFeatures
Each variant is described separately below.
getSubListOfSpeciesFeatures(long n)
Returns the nth SubListOfSpeciesFeatures object.
n | the index number of the SubListOfSpeciesFeatures to get |
getSubListOfSpeciesFeatures(string sid)
Returns the SubListOfSpeciesFeatures object with the given identifier sid
.
sid | the id of the SubListOfSpeciesFeatures to get. |
sid
, or None
if no such SubListOfSpeciesFeatures 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.MultiSpeciesPlugin.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. def libsbml.MultiSpeciesPlugin.isSetSpeciesType | ( | self | ) |
Returns True
if the 'speciesType' attribute of this 'multi' Species has been set.
isSetSpeciesType() bool
True
if this SpeciesPlugin's 'speciesType' attribute has been set, otherwise False
is returned.
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inherited |
isValidTypeForList(SBase item) bool
def libsbml.MultiSpeciesPlugin.removeOutwardBindingSite | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
removeOutwardBindingSite(long n) OutwardBindingSite removeOutwardBindingSite(string sid) OutwardBindingSite
Each variant is described separately below.
removeOutwardBindingSite(long n)
Removes the nth OutwardBindingSite object and returns a pointer to it.
n | the index of the OutwardBindingSite to remove. |
None
index was out of range. Note that the caller owns the returned object and is responsible for deleting it.removeOutwardBindingSite(string sid)
Removes the OutwardBindingSite object with the given id sid
and returns a pointer to it.
sid | a string representing the id of the OutwardBindingSite to remove. |
None
index was out of range. Note that the caller owns the returned object and is responsible for deleting it. def libsbml.MultiSpeciesPlugin.removeSpeciesFeature | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
removeSpeciesFeature(long n) SpeciesFeature removeSpeciesFeature(string sid) SpeciesFeature
Each variant is described separately below.
removeSpeciesFeature(long n)
Removes the nth SpeciesFeature object and returns a pointer to it.
n | the index of the SpeciesFeature to remove. |
None
index was out of range. Note that the caller owns the returned object and is responsible for deleting it.removeSpeciesFeature(string sid)
Removes the SpeciesFeature object with the given identifier sid
.
sid | a string representing the id of the SpeciesFeature to get. |
None
index was out of range. Note that the caller owns the returned object and is responsible for deleting it.
|
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. |
|
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. |
|
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 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.MultiSpeciesPlugin.setSpeciesType | ( | self, | |
speciesType | |||
) |
Sets the value of the 'speciesType' attribute on this 'multi' Species.
setSpeciesType(string speciesType) int
speciesType | the new value for the attribute. |
def libsbml.MultiSpeciesPlugin.unsetSpeciesType | ( | self | ) |
Unsets the value of the 'speciesType' attribute on this 'multi' Species.
unsetSpeciesType() int