fbc
Extension of
Reaction by the “fbc” package.
The FbcReactionPlugin class inherits from the SBasePlugin class, and codifies the extentions to the Reaction class defined in the Flux Balance Constraints package (“fbc”). This extention allows the modeler to define (in Version 2 of the “fbc” package) an upper and lower flux bound, with the 'upperFluxBound' and 'lowerFluxBound' attributes, as well as a way to reference any GeneProduct associated with this Reaction, through the GeneProductAssociation child.
- Note
- In Version 1 of “fbc”, the FluxBound element is used instead of the 'upperFluxBound' and 'lowerFluxBound' attributes. There is no equivalent of the GeneProductAssociation, which was added in Version 2.
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| def | __init__ (self, args) |
| | This method has multiple variants; they differ in the arguments they accept. More...
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| def | clone (self) |
| | Creates and returns a deep copy of this FbcReactionPlugin object. More...
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| def | createGeneProductAssociation (self) |
| | Creates a new GeneProductAssociation object and adds it to the FbcReactionPlugin object. More...
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| def | getElementByMetaId (self, metaid) |
| | Return the first child object found with a given meta identifier. More...
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| def | getElementBySId (self, id) |
| | Return the first child object found with a given identifier. More...
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| def | getElementNamespace (self) |
| | Returns the namespace URI of the package to which this plugin object belongs. More...
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| def | getGeneProductAssociation (self, args) |
| | Returns the GeneProductAssociation from this FbcReactionPlugin object. More...
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| def | getLevel (self) |
| | Returns the SBML Level of the package extension of this plugin object. More...
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| def | getListOfAllElements (self, filter=None) |
| | Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth. More...
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| def | getLowerFluxBound (self) |
| | Returns the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin. More...
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| def | getPackageName (self) |
| | Returns the short-form name of the package to which this plugin object belongs. More...
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| def | getPackageVersion (self) |
| | Returns the package version of the package extension of this plugin object. More...
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| def | getParentSBMLObject (self, args) |
| | Returns the parent object to which this plugin object is connected. More...
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| def | getPrefix (self) |
| | Returns the XML namespace prefix of the package to which this plugin object belongs. More...
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| def | getSBMLDocument (self, args) |
| | Returns the SBMLDocument object containing this object instance. More...
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| def | getUpperFluxBound (self) |
| | Returns the value of the 'upperFluxBound' attribute of this FbcReactionPlugin. More...
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| def | getURI (self) |
| | Returns the XML namespace URI for the package to which this object belongs. More...
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| def | getVersion (self) |
| | Returns the Version within the SBML Level of the package extension of this plugin object. More...
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| def | isSetGeneProductAssociation (self) |
| | Predicate returning True if this FbcReactionPlugin's 'GeneProductAssociation' element has been set. More...
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| def | isSetLowerFluxBound (self) |
| | Predicate returning True if this FbcReactionPlugin's 'lowerFluxBound' attribute is set. More...
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| def | isSetUpperFluxBound (self) |
| | Predicate returning True if this FbcReactionPlugin's 'upperFluxBound' attribute is set. More...
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| def | isValidTypeForList (self, item) |
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| def | renameMetaIdRefs (self, oldid, newid) |
| | Replaces all uses of a given meta identifier attribute value with another value. More...
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| def | renameSIdRefs (self, oldid, newid) |
| | Replaces all uses of a given SIdRef type attribute value with another value. More...
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| def | renameUnitSIdRefs (self, oldid, newid) |
| | Replaces all uses of a given UnitSIdRef type attribute value with another value. More...
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| def | setElementNamespace (self, uri) |
| | Sets the XML namespace to which this object belongs. More...
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| def | setGeneProductAssociation (self, geneProductAssociation) |
| | Sets the GeneProductAssociation element in this FbcReactionPlugin object. More...
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| def | setLowerFluxBound (self, lowerFluxBound) |
| | Sets the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin. More...
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| def | setUpperFluxBound (self, upperFluxBound) |
| | Sets the value of the 'upperFluxBound' attribute of this FbcReactionPlugin. More...
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| def | unsetGeneProductAssociation (self) |
| | Unsets the the 'geneProduct' element of this FbcReactionPlugin. More...
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| def | unsetLowerFluxBound (self) |
| | Unsets the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin. More...
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| def | unsetUpperFluxBound (self) |
| | Unsets the value of the 'upperFluxBound' attribute of this FbcReactionPlugin. More...
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| def libsbml.FbcReactionPlugin.__init__ |
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args |
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This method has multiple variants; they differ in the arguments they accept.
__init__(string uri, string prefix, FbcPkgNamespaces fbcns) FbcReactionPlugin
__init__(FbcReactionPlugin orig) FbcReactionPlugin
Each variant is described separately below.
Method variant with the following signature: FbcReactionPlugin(FbcReactionPlugin orig)
Copy constructor for FbcReactionPlugin.
- Parameters
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Method variant with the following signature: FbcReactionPlugin(string uri, string prefix, FbcPkgNamespaces fbcns)
Creates a new FbcReactionPlugin 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
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| 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. |
| fbcns | the namespaces object for the package. |
| def libsbml.SBasePlugin.getElementBySId |
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self, |
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id |
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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.
- Parameters
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| id | string representing the identifier of the object to find. |
- Returns
- pointer to the first object with the given
id.
| def libsbml.SBasePlugin.renameMetaIdRefs |
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self, |
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oldid, |
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newid |
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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
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| oldid | the old identifier. |
| newid | the new identifier. |
| def libsbml.FbcReactionPlugin.renameSIdRefs |
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self, |
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oldid, |
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newid |
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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
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| oldid | the old identifier. |
| newid | the new identifier. |
| def libsbml.SBasePlugin.renameUnitSIdRefs |
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self, |
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oldid, |
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newid |
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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
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| oldid | the old identifier. |
| newid | the new identifier. |
