libSBML Python API
5.11.0
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A reaction represents any transformation, transport or binding process, typically a chemical reaction, that can change the quantity of one or more species. In SBML, a reaction is defined primarily in terms of the participating reactants and products (and their corresponding stoichiometries), along with optional modifier species, an optional rate at which the reaction takes place, and optional parameters.
As with other major objects in SBML, Reaction has a mandatory attribute, 'id', used to give the compartment type an identifier. The identifier must be a text string conforming to the identifer syntax permitted in SBML. In SBML Level 2 and Level 3, the reaction 'id' identifier can be used in mathematical formulas elsewhere in an SBML model to represent the rate of that reaction; this usage is explained below. Reaction also has an optional 'name' attribute, of type string
. The 'id' and 'name' must be used according to the guidelines described in the SBML specification.
The species participating as reactants, products, and/or modifiers in a reaction are declared using lists of SpeciesReference and/or ModifierSpeciesReference instances stored in subelements 'listOfReactants', 'listOfProducts' and 'listOfModifiers'. Certain restrictions are placed on the appearance of species in reaction definitions:
The ability of a species to appear as a reactant or product of any reaction in a model is governed by certain flags in that species' definition; see the definition of Species for more information.
Any species appearing in the mathematical formula of the subelement 'kineticLaw' (described below) of a Reaction must be declared in at least one of that Reaction's lists of reactants, products, and/or modifiers. Put another way, it is an error for a reaction's kinetic law formula to refer to species that have not been declared for that reaction.
A reaction can contain up to one KineticLaw object in a subelement named 'kineticLaw'. It defines the speed at which the process defined by the reaction takes place. The description of KineticLaw provides more details about its use. Note that although the inclusion of a KineticLaw object in an instance of a Reaction component is optional, there is no useful default that can be substituted in place of a missing rate expression in a reaction. Moreover, a reaction's rate cannot be defined in any other way in SBML—InitialAssignment, AssignmentRule, RateRule, AlgebraicRule, Event, and other constructs in SBML cannot be used to set the reaction rate separately. Nevertheless, for some modeling applications, reactions without any defined rate can be perfectly acceptable.
Reaction also has a boolean attribute named 'reversible' for indicating whether the reaction is reversible. This attribute is optional in SBML Level 2, with a default of True
; it is mandatory in SBML Level 3 (with no default value). To say that a reaction is reversible is to say it can proceed in either the forward or the reverse direction. Although the reversibility of a reaction can sometimes be deduced by inspecting its rate expression, this is not always the case, especially for complicated expressions. Moreover, the need in SBML to allow rate expressions (i.e., KineticLaw) to be optional leads to the need for a separate flag indicating reversibility. Note that labeling a reaction as irreversible is an assertion that the reaction always proceeds in the given forward direction. (Why else would it be flagged as irreversible?) This implies the rate expression in the KineticLaw always has a non-negative value during simulations. Software tools could provide a means of optionally testing that this condition holds. The presence of reversibility information in two places (i.e., the rate expression and the 'reversible' attribute on Reaction) leaves open the possibility that a model could contain contradictory information, but the creation of such a model would be an error on the part of the software generating it.
The Reaction object class has another boolean attribute called 'fast'. This attribute is optional in SBML Level 2, with a default of False
; it is mandatory in SBML Level 3 (with no default value). It is used to indicate that a reaction occurs on a vastly faster time scale than others in a system. Readers are directed to the SBML Level 2 Version 4 specification, which provides more detail about the conditions under which a reaction can be considered to be fast in this sense. The attribute's default value is False
. SBML Level 1 and Level 2 Version 1 incorrectly claimed that software tools could ignore this attribute if they did not implement support for the corresponding concept; however, further research in SBML has revealed that this is not true, and 'fast' cannot be ignored if it is set to True
. SBML Level 2 Versions 2–4 therefore stipulate that if a model has any reactions with 'fast' set to True
, a software tool must be able to respect the attribute or else indicate to the user that it does not have the capacity to do so. Analysis software cannot ignore the value of the 'fast' attribute because doing so may lead to different results as compared to a software system that does make use of 'fast'.
In SBML Level 3 Version 1, the Reaction object has an additional optional attribute named 'compartment', whose value must be the identifier of a compartment defined in the enclosing Model object. The 'compartment' attribute can be used to indicate the compartment in which the reaction is assumed to take place. If the attribute is present, its value must be the identifier of a Compartment object defined in the enclosing Model object. Similar to the 'reversible' attribute, the value of the 'compartment' attribute has no direct impact on the construction of mathematical equations for the SBML model. When a kinetic law is given for a reaction, the compartment location may already be implicit in the kinetic law (although this cannot always be guaranteed). Nevertheless, software tools may find the 'compartment' attribute value useful for such purposes as analyzing the structure of the model, guiding the modeler in constructing correct rate formulas, and visualization purposes.
Readers are urged to read the SBML specification for more details about the proper use of Reaction.
Public Member Functions | |
def | __init__ (self, args) |
An SBML reaction between species in an SBML model. More... | |
def | addCVTerm |
Adds a copy of the given CVTerm object to this SBML object. More... | |
def | addModifier (self, msr) |
Adds a given ModifierSpeciesReference object as a product in this Reaction. More... | |
def | addProduct (self, sr) |
Adds a given SpeciesReference object as a product in this Reaction. More... | |
def | addReactant (self, sr) |
Adds a given SpeciesReference object as a reactant in this Reaction. More... | |
def | appendAnnotation (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | appendNotes (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | clone (self) |
Creates and returns a deep copy of this Reaction object. More... | |
def | connectToChild (self) |
def | createKineticLaw (self) |
Creates a new KineticLaw object, installs it as this Reaction's 'kineticLaw' subelement, and returns it. More... | |
def | createModifier (self) |
Creates a new ModifierSpeciesReference, adds it to this Reaction's list of modifiers and returns it. More... | |
def | createProduct (self) |
Creates a new SpeciesReference, adds it to this Reaction's list of products, and returns it. More... | |
def | createReactant (self) |
Creates a new SpeciesReference, adds it to this Reaction's list of reactants, and returns it. More... | |
def | deleteDisabledPlugins |
Deletes all information stored in disabled plugins. More... | |
def | disablePackage (self, pkgURI, pkgPrefix) |
Disables the given SBML Level 3 package on this object. More... | |
def | enablePackage (self, pkgURI, pkgPrefix, flag) |
Enables or disables the given SBML Level 3 package on this object. More... | |
def | getAncestorOfType (self, args) |
Returns the first ancestor object that has the given SBML type code from the given package. More... | |
def | getAnnotation (self, args) |
Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects. More... | |
def | getAnnotationString (self, args) |
Returns the content of the 'annotation' subelement of this object as a character string. More... | |
def | getColumn (self) |
Returns the column number on which this object first appears in the XML representation of the SBML document. More... | |
def | getCompartment (self) |
def | getCVTerm (self, n) |
Returns the nth CVTerm in the list of CVTerms of this SBML object. More... | |
def | getCVTerms (self, args) |
Returns a list of CVTerm objects in the annotations of this SBML object. More... | |
def | getDisabledPlugin (self, args) |
Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
def | getElementByMetaId (self, metaid) |
Returns the first child element it can find with 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 | getElementName (self) |
Returns the XML element name of this object, which for Reaction, is always 'reaction' . More... | |
def | getFast (self) |
Returns the value of the 'fast' attribute of this Reaction. More... | |
def | getId (self) |
Returns the value of the 'id' attribute of this Reaction. More... | |
def | getKineticLaw (self, args) |
Returns the KineticLaw object contained in this Reaction. More... | |
def | getLevel (self) |
Returns the SBML Level of the SBMLDocument object containing this object. More... | |
def | getLine (self) |
Returns the line number on which this object first appears in the XML representation of the SBML document. More... | |
def | getListOfAllElements |
Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth. More... | |
def | getListOfAllElementsFromPlugins |
Returns a List of all child SBase objects contained in SBML package plug-ins. More... | |
def | getListOfModifiers (self, args) |
Returns the list of modifiers in this Reaction object. More... | |
def | getListOfProducts (self, args) |
Returns the list of products in this Reaction object. More... | |
def | getListOfReactants (self, args) |
Returns the list of reactants in this Reaction object. More... | |
def | getMetaId (self) |
Returns the value of the 'metaid' attribute of this object. More... | |
def | getModel (self) |
Returns the Model object for the SBML Document in which the current object is located. More... | |
def | getModelHistory (self, args) |
Returns the ModelHistory object, if any, attached to this object. More... | |
def | getModifier (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | getName (self) |
Returns the value of the 'name' attribute of this Reaction. More... | |
def | getNamespaces (self) |
Returns a list of the XML Namespaces declared on the SBML document owning this object. More... | |
def | getNotes (self, args) |
Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects. More... | |
def | getNotesString (self, args) |
Returns the content of the 'notes' subelement of this object as a string. More... | |
def | getNumCVTerms (self) |
Returns the number of CVTerm objects in the annotations of this SBML object. More... | |
def | getNumDisabledPlugins (self) |
Returns the number of disabled plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More... | |
def | getNumModifiers (self) |
Returns the number of modifier species in this Reaction. More... | |
def | getNumPlugins (self) |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More... | |
def | getNumProducts (self) |
Returns the number of product species in this Reaction. More... | |
def | getNumReactants (self) |
Returns the number of reactant species in this Reaction. More... | |
def | getPackageName (self) |
Returns the name of the SBML Level 3 package in which this element is defined. More... | |
def | getPackageVersion (self) |
Returns the Version of the SBML Level 3 package to which this element belongs to. More... | |
def | getParentSBMLObject (self, args) |
Returns the parent SBML object containing this object. More... | |
def | getPlugin (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | getPrefix (self) |
Returns the namespace prefix of this element. More... | |
def | getProduct (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | getReactant (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | getResourceBiologicalQualifier (self, resource) |
Returns the MIRIAM biological qualifier associated with the given resource. More... | |
def | getResourceModelQualifier (self, resource) |
Returns the MIRIAM model qualifier associated with the given resource. More... | |
def | getReversible (self) |
Returns the value of the 'reversible' attribute on the Reaction as a boolean value. More... | |
def | getSBMLDocument (self, args) |
Returns the SBMLDocument object containing this object instance. More... | |
def | getSBOTerm (self) |
Returns the integer portion of the value of the 'sboTerm' attribute of this object. More... | |
def | getSBOTermAsURL (self) |
Returns the URL representation of the 'sboTerm' attribute of this object. More... | |
def | getSBOTermID (self) |
Returns the string representation of the 'sboTerm' attribute of this object. More... | |
def | getTypeCode (self) |
Returns the libSBML type code for this SBML object. More... | |
def | getURI (self) |
Gets the namespace URI to which this element belongs to. More... | |
def | getVersion (self) |
Returns the Version within the SBML Level of the SBMLDocument object containing this object. More... | |
def | hasRequiredAttributes (self) |
Predicate returning True if all the required attributes for this Reaction object have been set. More... | |
def | hasValidLevelVersionNamespaceCombination (self) |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More... | |
def | initDefaults (self) |
Initializes the fields of this Reaction object to 'typical' default values. More... | |
def | isPackageEnabled (self, pkgName) |
Predicate returning True if the given SBML Level 3 package is enabled with this object. More... | |
def | isPackageURIEnabled (self, pkgURI) |
Predicate returning True if an SBML Level 3 package with the given URI is enabled with this object. More... | |
def | isPkgEnabled (self, pkgName) |
Predicate returning True if the given SBML Level 3 package is enabled with this object. More... | |
def | isPkgURIEnabled (self, pkgURI) |
Predicate returning True if an SBML Level 3 package with the given URI is enabled with this object. More... | |
def | isSetAnnotation (self) |
Predicate returning True if this object's 'annotation' subelement exists and has content. More... | |
def | isSetCompartment (self) |
Predicate returning True if this Reaction's 'compartment' attribute is set. More... | |
def | isSetFast (self) |
Predicate returning True if the value of the 'fast' attribute on this Reaction. More... | |
def | isSetId (self) |
Predicate returning True if this Reaction's 'id' attribute is set. More... | |
def | isSetKineticLaw (self) |
Predicate returning True if this Reaction contains a kinetic law object. More... | |
def | isSetMetaId (self) |
Predicate returning True if this object's 'metaid' attribute is set. More... | |
def | isSetModelHistory (self) |
Predicate returning True if this object has a ModelHistory object attached to it. More... | |
def | isSetName (self) |
Predicate returning True if this Reaction's 'name' attribute is set. More... | |
def | isSetNotes (self) |
Predicate returning True if this object's 'notes' subelement exists and has content. More... | |
def | isSetReversible (self) |
Predicate returning True if this Reaction's 'reversible' attribute is set. More... | |
def | isSetSBOTerm (self) |
Predicate returning True if this object's 'sboTerm' attribute is set. More... | |
def | matchesRequiredSBMLNamespacesForAddition (self, args) |
Returns True if this object's set of XML namespaces are a subset of the given object's XML namespaces. More... | |
def | matchesSBMLNamespaces (self, args) |
Returns True if this object's set of XML namespaces are the same as the given object's XML namespaces. More... | |
def | removeFromParentAndDelete (self) |
Removes this object from its parent. More... | |
def | removeModifier (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | removeProduct (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | removeReactant (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | removeTopLevelAnnotationElement (self, args) |
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. 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 | replaceTopLevelAnnotationElement (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | setAnnotation (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | setCompartment (self, sid) |
Sets the value of the 'compartment' attribute of this Reaction. More... | |
def | setFast (self, value) |
Sets the value of the 'fast' attribute of this Reaction. More... | |
def | setId (self, sid) |
Sets the value of the 'id' attribute of this Reaction. More... | |
def | setKineticLaw (self, kl) |
Sets the 'kineticLaw' subelement of this Reaction to a copy of the given KineticLaw object. More... | |
def | setMetaId (self, metaid) |
Sets the value of the meta-identifier attribute of this object. More... | |
def | setModelHistory (self, history) |
Sets the ModelHistory of this object. More... | |
def | setName (self, name) |
Sets the value of the 'name' attribute of this Reaction. More... | |
def | setNamespaces (self, xmlns) |
Sets the namespaces relevant of this SBML object. More... | |
def | setNotes (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | setReversible (self, value) |
Sets the value of the 'reversible' attribute of this Reaction. More... | |
def | setSBOTerm (self, args) |
This method has multiple variants; they differ in the arguments they accept. More... | |
def | toSBML (self) |
Returns a string consisting of a partial SBML corresponding to just this object. More... | |
def | toXMLNode (self) |
Returns this element as an XMLNode. More... | |
def | unsetAnnotation (self) |
Unsets the value of the 'annotation' subelement of this SBML object. More... | |
def | unsetCompartment (self) |
Unsets the value of the 'compartment' attribute of this Reaction. More... | |
def | unsetCVTerms (self) |
Clears the list of CVTerm objects attached to this SBML object. More... | |
def | unsetFast (self) |
Unsets the value of the 'fast' attribute of this Reaction. More... | |
def | unsetId (self) |
Unsets the value of the 'id' attribute of this SBML object. More... | |
def | unsetKineticLaw (self) |
Unsets the 'kineticLaw' subelement of this Reaction. More... | |
def | unsetMetaId (self) |
Unsets the value of the 'metaid' attribute of this SBML object. More... | |
def | unsetModelHistory (self) |
Unsets the ModelHistory object attached to this object. More... | |
def | unsetName (self) |
Unsets the value of the 'name' attribute of this Reaction. More... | |
def | unsetNotes (self) |
Unsets the value of the 'notes' subelement of this SBML object. More... | |
def | unsetSBOTerm (self) |
Unsets the value of the 'sboTerm' attribute of this SBML object. More... | |
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inherited |
Adds a copy of the given CVTerm object to this SBML object.
addCVTerm(CVTerm term, bool newBag=False) int addCVTerm(CVTerm term) int
term | the CVTerm to assign. |
newBag | if True , creates a new RDF bag with the same identifier as a previous bag, and if False , adds the term to an existing RDF bag with the same type of qualifier as the term being added. |
create
) for alternatives that do not lead to these issues. def libsbml.Reaction.addModifier | ( | self, | |
msr | |||
) |
Adds a given ModifierSpeciesReference object as a product in this Reaction.
addModifier(ModifierSpeciesReference msr) int
The ModifierSpeciesReference instance in msr
is copied.
msr | a ModifierSpeciesReference object referring to a Species in the enclosing Model |
create
) for alternatives that do not lead to these issues.def libsbml.Reaction.addProduct | ( | self, | |
sr | |||
) |
Adds a given SpeciesReference object as a product in this Reaction.
addProduct(SpeciesReference sr) int
The SpeciesReference instance in sr
is copied.
sr | a SpeciesReference object referring to a Species in the enclosing Model |
create
) for alternatives that do not lead to these issues.def libsbml.Reaction.addReactant | ( | self, | |
sr | |||
) |
Adds a given SpeciesReference object as a reactant in this Reaction.
addReactant(SpeciesReference sr) int
The SpeciesReference instance in sr
is copied.
sr | a SpeciesReference object referring to a Species in the enclosing Model |
create
) for alternatives that do not lead to these issues.
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inherited |
This method has multiple variants; they differ in the arguments they accept.
appendAnnotation(XMLNode annotation) int appendAnnotation(string annotation) int
Each variant is described separately below.
appendAnnotation(string annotation)
Appends the given annotation
to the 'annotation' subelement of this object.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Unlike SBase.setAnnotation() or SBase.setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.
annotation | an XML string that is to be copied and appended to the content of the 'annotation' subelement of this object |
appendAnnotation(XMLNode annotation)
Appends the given annotation
to the 'annotation' subelement of this object.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Unlike SBase.setAnnotation() or SBase.setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.
annotation | an XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object |
|
inherited |
This method has multiple variants; they differ in the arguments they accept.
appendNotes(XMLNode notes) int appendNotes(string notes) int
Each variant is described separately below.
appendNotes(string notes)
Appends the given notes
to the 'notes' subelement of this object.
The content of the parameter notes
is copied.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
notes | an XML string that is to appended to the content of the 'notes' subelement of this object |
appendNotes(XMLNode notes)
Appends the given notes
to the 'notes' subelement of this object.
The content of notes
is copied.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
notes | an XML node structure that is to appended to the content of the 'notes' subelement of this object |
def libsbml.Reaction.clone | ( | self | ) |
def libsbml.Reaction.connectToChild | ( | self | ) |
connectToChild()
def libsbml.Reaction.createKineticLaw | ( | self | ) |
Creates a new KineticLaw object, installs it as this Reaction's 'kineticLaw' subelement, and returns it.
createKineticLaw() KineticLaw
If this Reaction had a previous KineticLaw, it will be destroyed.
def libsbml.Reaction.createModifier | ( | self | ) |
Creates a new ModifierSpeciesReference, adds it to this Reaction's list of modifiers and returns it.
createModifier() ModifierSpeciesReference
def libsbml.Reaction.createProduct | ( | self | ) |
Creates a new SpeciesReference, adds it to this Reaction's list of products, and returns it.
createProduct() SpeciesReference
def libsbml.Reaction.createReactant | ( | self | ) |
Creates a new SpeciesReference, adds it to this Reaction's list of reactants, and returns it.
createReactant() SpeciesReference
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inherited |
Deletes all information stored in disabled plugins.
deleteDisabledPlugins(bool recursive=True) deleteDisabledPlugins()
recursive | if True , the disabled information will be deleted also from all child elements, otherwise only from this SBase element. |
|
inherited |
Disables the given SBML Level 3 package on this object.
disablePackage(string pkgURI, string pkgPrefix) int
This method disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
An example of when this may be useful is during construction of model components when mixing existing and new models. Suppose your application read an SBML document containing a model that used the SBML Hierarchical Model Composition (“comp”) package, and extracted parts of that model in order to construct a new model in memory. The new, in-memory model will not accept a component drawn from an other SBMLDocument with different package namespace declarations. You could reconstruct the same namespaces in the in-memory model first, but as a shortcut, you could also disable the package namespace on the object being added. Here is a code example to help clarify this:
pkgURI | the URI of the package |
pkgPrefix | the XML prefix of the package |
|
inherited |
Enables or disables the given SBML Level 3 package on this object.
enablePackage(string pkgURI, string pkgPrefix, bool flag) int
This method enables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object. This method is the converse of SBase.disablePackage().
pkgURI | the URI of the package. |
pkgPrefix | the XML prefix of the package |
flag | whether to enable (True ) or disable (False ) the package |
|
inherited |
Returns the first ancestor object that has the given SBML type code from the given package.
getAncestorOfType(int type, string pkgName) SBase getAncestorOfType(int type) SBase
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_
.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code from the given pkgName
.
type | the SBML type code of the object sought |
pkgName | (optional) the short name of an SBML Level 3 package to which the sought-after object must belong |
None
if no ancestor exists.pkgName
must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the 'core' namespace alone, not find any corresponding elements, and return None.
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inherited |
Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.
getAnnotation() XMLNode
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.
|
inherited |
Returns the content of the 'annotation' subelement of this object as a character string.
getAnnotationString() string
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in string form. See the method getAnnotation() for a version that returns annotations in XML form.
|
inherited |
Returns the column number on which this object first appears in the XML representation of the SBML document.
getColumn() long
def libsbml.Reaction.getCompartment | ( | self | ) |
|
inherited |
|
inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
getCVTerms() List *
|
inherited |
Returns the nth disabled plug-in object (extension interface) for an SBML Level 3 package extension.
getDisabledPlugin(long n) SBasePlugin
n | the index of the disabled plug-in to return |
def libsbml.Reaction.getElementByMetaId | ( | self, | |
metaid | |||
) |
Returns the first child element it can find with 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.Reaction.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
id | string representing the id of objects to find. |
id
. def libsbml.Reaction.getElementName | ( | self | ) |
Returns the XML element name of this object, which for Reaction, is always 'reaction'
.
getElementName() string
'reaction'
. def libsbml.Reaction.getFast | ( | self | ) |
Returns the value of the 'fast' attribute of this Reaction.
getFast() bool
True
. Beginning with SBML Level 2 Versions 2, the SBML specifications therefore stipulate that if a model has any reactions with 'fast' set to True
, a software tool must be able to respect the attribute or else indicate to the user that it does not have the capacity to do so. Readers are directed to the SBML specifications, which provides more detail about the conditions under which a reaction can be considered to be fast in this sense. def libsbml.Reaction.getId | ( | self | ) |
def libsbml.Reaction.getKineticLaw | ( | self, | |
args | |||
) |
Returns the KineticLaw object contained in this Reaction.
getKineticLaw() KineticLaw
|
inherited |
Returns the SBML Level of the SBMLDocument object containing this object.
getLevel() long
|
inherited |
Returns the line number on which this object first appears in the XML representation of the SBML document.
getLine() long
|
inherited |
Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth.
getListOfAllElements(ElementFilter filter=None) SBaseList getListOfAllElements() SBaseList
|
inherited |
Returns a List of all child SBase objects contained in SBML package plug-ins.
getListOfAllElementsFromPlugins(ElementFilter filter=None) SBaseList getListOfAllElementsFromPlugins() SBaseList
This method walks down the list of all SBML Level 3 packages used by this object and returns all child objects defined by those packages.
def libsbml.Reaction.getListOfModifiers | ( | self, | |
args | |||
) |
Returns the list of modifiers in this Reaction object.
getListOfModifiers() ListOfSpeciesReferences
def libsbml.Reaction.getListOfProducts | ( | self, | |
args | |||
) |
Returns the list of products in this Reaction object.
getListOfProducts() ListOfSpeciesReferences
def libsbml.Reaction.getListOfReactants | ( | self, | |
args | |||
) |
Returns the list of reactants in this Reaction object.
getListOfReactants() ListOfSpeciesReferences
|
inherited |
Returns the value of the 'metaid' attribute of this object.
getMetaId() string
ID
, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID
type. Although SBML itself specifies the use of XML ID
only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID
's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.
|
inherited |
|
inherited |
Returns the ModelHistory object, if any, attached to this object.
getModelHistory() ModelHistory
None
if none exist.def libsbml.Reaction.getModifier | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
getModifier(long n) ModifierSpeciesReference getModifier(string species) ModifierSpeciesReference
Each variant is described separately below.
getModifier(string species)
Returns the modifier species (as a ModifierSpeciesReference object) having a specific identifier in this Reaction.
species | the identifier of the modifier Species ('species' attribute of the ModifierSpeciesReference object) |
None
if no species with the given identifier species
appears as a modifier in this Reaction.getModifier(long n)
Returns the nth modifier species (as a ModifierSpeciesReference object) in the list of modifiers of this Reaction.
Callers should first call getNumModifiers() to find out how many modifiers there are, to avoid using an invalid index number.
n | the index of the modifier species sought |
def libsbml.Reaction.getName | ( | self | ) |
|
inherited |
Returns a list of the XML Namespaces declared on the SBML document owning this object.
getNamespaces() XMLNamespaces
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.
None
in certain very usual circumstances where a namespace is not set.
|
inherited |
Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.
getNotes() XMLNode
The format of 'notes' elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
The 'notes' element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().
|
inherited |
Returns the content of the 'notes' subelement of this object as a string.
getNotesString() string
The format of 'notes' elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); this method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.
|
inherited |
Returns the number of CVTerm objects in the annotations of this SBML object.
getNumCVTerms() long
|
inherited |
Returns the number of disabled plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
getNumDisabledPlugins() long
def libsbml.Reaction.getNumModifiers | ( | self | ) |
|
inherited |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
getNumPlugins() long
def libsbml.Reaction.getNumProducts | ( | self | ) |
def libsbml.Reaction.getNumReactants | ( | self | ) |
|
inherited |
Returns the name of the SBML Level 3 package in which this element is defined.
getPackageName() string
"core"
will be returned if this element is defined in SBML Level 3 Core. The string "unknown"
will be returned if this element is not defined in any SBML package.
|
inherited |
Returns the Version of the SBML Level 3 package to which this element belongs to.
getPackageVersion() long
0
will be returned if this element belongs to the SBML Level 3 Core package.
|
inherited |
Returns the parent SBML object containing this object.
getParentSBMLObject() SBase
This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.
|
inherited |
This method has multiple variants; they differ in the arguments they accept.
getPlugin(string package) SBasePlugin getPlugin(long n) SBasePlugin
Each variant is described separately below.
getPlugin(string package)
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.
package | the name or URI of the package |
getPlugin(long n)
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.
n | the index of the plug-in to return |
|
inherited |
Returns the namespace prefix of this element.
getPrefix() string
def libsbml.Reaction.getProduct | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
getProduct(long n) SpeciesReference getProduct(string species) SpeciesReference
Each variant is described separately below.
getProduct(string species)
Returns the product species (as a SpeciesReference object) having a specific identifier in this Reaction.
species | the identifier of the product Species ('species' attribute of the product SpeciesReference object) |
None
if no species with the given identifier species
appears as a product in this Reaction.getProduct(long n)
Returns the nth product species (as a SpeciesReference object) in the list of products in this Reaction.
Callers should first call getNumProducts() to find out how many products there are, to avoid using an invalid index number.
n | the index of the product sought. |
def libsbml.Reaction.getReactant | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
getReactant(long n) SpeciesReference getReactant(string species) SpeciesReference
Each variant is described separately below.
getReactant(string species)
Returns the reactant species (as a SpeciesReference object) having a specific identifier in this Reaction.
species | the identifier of the reactant Species ('species' attribute of the reactant SpeciesReference object) |
None
if no species with the given identifier species
appears as a reactant in this Reaction.getReactant(long n)
Returns the nth reactant species (as a SpeciesReference object) in the list of reactants in this Reaction.
Callers should first call getNumReactants() to find out how many reactants there are, to avoid using an invalid index number.
n | the index of the reactant sought. |
|
inherited |
Returns the MIRIAM biological qualifier associated with the given resource.
getResourceBiologicalQualifier(string resource) long
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include 'is' and 'has part', but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using valueswhose names begin with BQB_
in the interface class libsbml.
This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource
. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a valuewhose name begins with BQB_
from the interface class libsbml.
resource | string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892' . |
BQB_
constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
|
inherited |
Returns the MIRIAM model qualifier associated with the given resource.
getResourceModelQualifier(string resource) long
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is 'isDerivedFrom', to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using valueswhose names begin with BQM_
in the interface class libsbml.
This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource
. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a valuewhose name begins with BQM_
from the interface class libsbml.
resource | string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892' . |
BQM_
constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time. def libsbml.Reaction.getReversible | ( | self | ) |
|
inherited |
Returns the SBMLDocument object containing this object instance.
getSBMLDocument() SBMLDocument
This method allows the caller to obtain the SBMLDocument for the current object.
|
inherited |
Returns the integer portion of the value of the 'sboTerm' attribute of this object.
getSBOTerm() int
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers. (For convenience, libSBML offers methods for returning both the integer form and a text-string form of the SBO identifier.)
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
-1
if the value is not set.
|
inherited |
Returns the URL representation of the 'sboTerm' attribute of this object.
getSBOTermAsURL() string
This method returns the entire SBO identifier as a text string in the form http
://identifiers.org/biomodels.sbo/SBO:NNNNNNN'
.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
|
inherited |
Returns the string representation of the 'sboTerm' attribute of this object.
getSBOTermID() string
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers. This method returns the entire SBO identifier as a text string in the form 'SBO:NNNNNNN'.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
def libsbml.Reaction.getTypeCode | ( | self | ) |
Returns the libSBML type code for this SBML object.
getTypeCode() int
SBML_
. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the getPackageName()
method on the object.
|
inherited |
Gets the namespace URI to which this element belongs to.
getURI() string
For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'
; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1'
.
This function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found, it willreturn the XML namespace to which this element belongs.
|
inherited |
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
getVersion() long
def libsbml.Reaction.hasRequiredAttributes | ( | self | ) |
Predicate returning True
if all the required attributes for this Reaction object have been set.
hasRequiredAttributes() bool
The required attributes for a Reaction object are:
True
if the required attributes have been set, False
otherwise.
|
inherited |
Predicate returning true
if this object's level/version and namespace values correspond to a valid SBML specification.
hasValidLevelVersionNamespaceCombination() bool
The valid combinations of SBML Level, Version and Namespace as of this release of libSBML are the following:
http
://www.sbml.org/sbml/level1
http
://www.sbml.org/sbml/level2
http
://www.sbml.org/sbml/level2/version2
http
://www.sbml.org/sbml/level2/version3
http
://www.sbml.org/sbml/level2/version4
http
://www.sbml.org/sbml/level3/version1/core
true
if the level, version and namespace values of this SBML object correspond to a valid set of values, false
otherwise. def libsbml.Reaction.initDefaults | ( | self | ) |
Initializes the fields of this Reaction object to 'typical' default values.
initDefaults()
The SBML Reaction component has slightly different aspects and default attribute values in different SBML Levels and Versions. This method sets the values to certain common defaults, based mostly on what they are in SBML Level 2. Specifically:
True
False
True
. Beginning with SBML Level 2 Versions 2, the SBML specifications therefore stipulate that if a model has any reactions with 'fast' set to True
, a software tool must be able to respect the attribute or else indicate to the user that it does not have the capacity to do so. Readers are directed to the SBML specifications, which provides more detail about the conditions under which a reaction can be considered to be fast in this sense.
|
inherited |
Predicate returning True
if the given SBML Level 3 package is enabled with this object.
isPackageEnabled(string pkgName) bool
The search ignores the package version.
pkgName | the name of the package |
True
if the given package is enabled within this object, False
otherwise.
|
inherited |
Predicate returning True
if an SBML Level 3 package with the given URI is enabled with this object.
isPackageURIEnabled(string pkgURI) bool
pkgURI | the URI of the package |
True
if the given package is enabled within this object, False
otherwise.
|
inherited |
Predicate returning True
if the given SBML Level 3 package is enabled with this object.
isPkgEnabled(string pkgName) bool
The search ignores the package version.
pkgName | the name of the package |
True
if the given package is enabled within this object, False
otherwise.
|
inherited |
Predicate returning True
if an SBML Level 3 package with the given URI is enabled with this object.
isPkgURIEnabled(string pkgURI) bool
pkgURI | the URI of the package |
True
if the given package is enabled within this object, False
otherwise.
|
inherited |
Predicate returning True
if this object's 'annotation' subelement exists and has content.
isSetAnnotation() bool
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
True
if a 'annotation' subelement exists, False
otherwise.def libsbml.Reaction.isSetCompartment | ( | self | ) |
Predicate returning True
if this Reaction's 'compartment' attribute is set.
isSetCompartment() bool
True
if the 'compartment' attribute of this Reaction is set, False
otherwise.def libsbml.Reaction.isSetFast | ( | self | ) |
Predicate returning True
if the value of the 'fast' attribute on this Reaction.
isSetFast() bool
True
if the 'fast' attribute is true, False
otherwise.True
. Beginning with SBML Level 2 Versions 2, the SBML specifications therefore stipulate that if a model has any reactions with 'fast' set to True
, a software tool must be able to respect the attribute or else indicate to the user that it does not have the capacity to do so. Readers are directed to the SBML specifications, which provides more detail about the conditions under which a reaction can be considered to be fast in this sense. def libsbml.Reaction.isSetId | ( | self | ) |
def libsbml.Reaction.isSetKineticLaw | ( | self | ) |
Predicate returning True
if this Reaction contains a kinetic law object.
isSetKineticLaw() bool
True
if a KineticLaw is present in this Reaction,, False
otherwise.
|
inherited |
Predicate returning True
if this object's 'metaid' attribute is set.
isSetMetaId() bool
ID
, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID
type. Although SBML itself specifies the use of XML ID
only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID
's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.True
if the 'metaid' attribute of this SBML object is set, False
otherwise.
|
inherited |
Predicate returning True
if this object has a ModelHistory object attached to it.
isSetModelHistory() bool
True
if the ModelHistory of this object is set, False
otherwise.def libsbml.Reaction.isSetName | ( | self | ) |
|
inherited |
Predicate returning True
if this object's 'notes' subelement exists and has content.
isSetNotes() bool
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
True
if a 'notes' subelement exists, False
otherwise.def libsbml.Reaction.isSetReversible | ( | self | ) |
|
inherited |
Predicate returning True
if this object's 'sboTerm' attribute is set.
isSetSBOTerm() bool
True
if the 'sboTerm' attribute of this SBML object is set, False
otherwise.
|
inherited |
Returns True
if this object's set of XML namespaces are a subset of the given object's XML namespaces.
matchesRequiredSBMLNamespacesForAddition(SBase sb) bool
sb | an object to compare with respect to namespaces |
True
if this object's collection of namespaces is a subset of sb's
, False
otherwise.
|
inherited |
Returns True
if this object's set of XML namespaces are the same as the given object's XML namespaces.
matchesSBMLNamespaces(SBase sb) bool
sb | an object to compare with respect to namespaces |
True
if this object's collection of namespaces is the same as sb's
, False
otherwise.
|
inherited |
Removes this object from its parent.
removeFromParentAndDelete() int
If the parent was storing this object as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). This is a pure virtual method, as every SBase element has different parents, and therefore different methods of removing itself. Will fail (and not delete itself) if it has no parent object. This function is designed to be overridden, but for all objects whose parent is of the class ListOf, the default implementation will work.
def libsbml.Reaction.removeModifier | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
removeModifier(long n) ModifierSpeciesReference removeModifier(string species) ModifierSpeciesReference
Each variant is described separately below.
removeModifier(string species)
Removes the modifier species (ModifierSpeciesReference object) having the given 'species' attribute in this Reaction and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
species | the 'species' attribute of the ModifierSpeciesReference object |
None
if no ModifierSpeciesReference object with the given 'species' attribute species
exists in this Reaction.removeModifier(long n)
Removes the nth modifier species (ModifierSpeciesReference object) in the list of modifiers in this Reaction and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. The caller should first call getNumModifiers() to find out how many modifiers there are, to avoid using an invalid index number.
n | the index of the ModifierSpeciesReference object to remove |
None
if the given index is out of range. def libsbml.Reaction.removeProduct | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
removeProduct(long n) SpeciesReference removeProduct(string species) SpeciesReference
Each variant is described separately below.
removeProduct(string species)
Removes the product species (SpeciesReference object) having the given 'species' attribute in this Reaction and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
species | the 'species' attribute of the product SpeciesReference object |
None
if no product SpeciesReference object with the given 'species' attribute species
exists in this Reaction.removeProduct(long n)
Removes the nth product species (SpeciesReference object) in the list of products in this Reaction and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. The caller should first call getNumProducts() to find out how many products there are, to avoid using an invalid index number.
n | the index of the product SpeciesReference object to remove |
None
if the given index is out of range. def libsbml.Reaction.removeReactant | ( | self, | |
args | |||
) |
This method has multiple variants; they differ in the arguments they accept.
removeReactant(long n) SpeciesReference removeReactant(string species) SpeciesReference
Each variant is described separately below.
removeReactant(string species)
Removes the reactant species (SpeciesReference object) having the given 'species' attribute in this Reaction and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
species | the 'species' attribute of the reactant SpeciesReference object |
None
if no reactant SpeciesReference object with the given 'species' attribute species
exists in this Reaction.removeReactant(long n)
Removes the nth reactant species (SpeciesReference object) in the list of reactants in this Reaction and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. The caller should first call getNumReactants() to find out how many reactants there are, to avoid using an invalid index number.
n | the index of the reactant SpeciesReference object to remove |
None
if the given index is out of range.
|
inherited |
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.
removeTopLevelAnnotationElement(string elementName, string elementURI, bool removeEmpty=True) int removeTopLevelAnnotationElement(string elementName, string elementURI) int removeTopLevelAnnotationElement(string elementName) int
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.
elementName | a string representing the name of the top level annotation element that is to be removed |
elementURI | an optional string that is used to check both the name and URI of the top level element to be removed |
removeEmpty | if after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default). |
|
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 |
def libsbml.Reaction.renameSIdRefs | ( | self, | |
oldid, | |||
newid | |||
) |
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 |
|
inherited |
This method has multiple variants; they differ in the arguments they accept.
replaceTopLevelAnnotationElement(XMLNode annotation) int replaceTopLevelAnnotationElement(string annotation) int
Each variant is described separately below.
replaceTopLevelAnnotationElement(string annotation)
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name)
followed by calling appendAnnotation(annotation_with_name)
, with the exception that the placement of the annotation element remains the same.
annotation | string representing the replacement top level annotation |
replaceTopLevelAnnotationElement(XMLNode annotation)
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name)
followed by calling appendAnnotation(annotation_with_name)
, with the exception that the placement of the annotation element remains the same.
annotation | XMLNode representing the replacement top level annotation |
|
inherited |
This method has multiple variants; they differ in the arguments they accept.
setAnnotation(XMLNode annotation) int setAnnotation(string annotation) int
Each variant is described separately below.
setAnnotation(string annotation)
Sets the value of the 'annotation' subelement of this SBML object.
The content of annotation
is copied, and any previous content of this object's 'annotation' subelement is deleted.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation
that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase.appendAnnotation() or SBase.appendAnnotation().
annotation | an XML string that is to be used as the content of the 'annotation' subelement of this object |
setAnnotation(XMLNode annotation)
Sets the value of the 'annotation' subelement of this SBML object.
The content of annotation
is copied, and any previous content of this object's 'annotation' subelement is deleted.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation
that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase.appendAnnotation() or SBase.appendAnnotation().
annotation | an XML structure that is to be used as the new content of the 'annotation' subelement of this object |
def libsbml.Reaction.setCompartment | ( | self, | |
sid | |||
) |
Sets the value of the 'compartment' attribute of this Reaction.
setCompartment(string sid) int
The string sid
is copied.
sid | the string to use as the compartment of this Reaction |
def libsbml.Reaction.setFast | ( | self, | |
value | |||
) |
Sets the value of the 'fast' attribute of this Reaction.
setFast(bool value) int
value | the value of the 'fast' attribute. |
True
. Beginning with SBML Level 2 Versions 2, the SBML specifications therefore stipulate that if a model has any reactions with 'fast' set to True
, a software tool must be able to respect the attribute or else indicate to the user that it does not have the capacity to do so. Readers are directed to the SBML specifications, which provides more detail about the conditions under which a reaction can be considered to be fast in this sense. def libsbml.Reaction.setId | ( | self, | |
sid | |||
) |
Sets the value of the 'id' attribute of this Reaction.
setId(string sid) int
The string sid
is copied.
SId
, which defines the permitted syntax of identifiers. We express the syntax using an extended form of BNF notation: letter ::= 'a'..'z','A'..'Z' digit ::= '0'..'9' idChar ::= letter | digit | '_' SId ::= ( letter | '_' ) idChar*The characters
(
and )
are used for grouping, the character *
'zero or more times', and the character |
indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. In addition, there are a few conditions for the uniqueness of identifiers in an SBML model. Please consult the SBML specifications for the exact details of the uniqueness requirements.sid | the string to use as the identifier of this Reaction |
def libsbml.Reaction.setKineticLaw | ( | self, | |
kl | |||
) |
Sets the 'kineticLaw' subelement of this Reaction to a copy of the given KineticLaw object.
setKineticLaw(KineticLaw kl) int
kl | the KineticLaw object to use. |
|
inherited |
Sets the value of the meta-identifier attribute of this object.
setMetaId(string metaid) int
ID
, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID
type. Although SBML itself specifies the use of XML ID
only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID
's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.The string metaid
is copied.
metaid | the identifier string to use as the value of the 'metaid' attribute |
|
inherited |
Sets the ModelHistory of this object.
setModelHistory(ModelHistory history) int
The content of history
is copied, and this object's existing model history content is deleted.
history | ModelHistory of this object. |
def libsbml.Reaction.setName | ( | self, | |
name | |||
) |
|
inherited |
Sets the namespaces relevant of this SBML object.
setNamespaces(XMLNamespaces xmlns) int
The content of xmlns
is copied, and this object's existing namespace content is deleted.
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.
xmlns | the namespaces to set |
|
inherited |
This method has multiple variants; they differ in the arguments they accept.
setNotes(XMLNode notes) int setNotes(string notes, bool addXHTMLMarkup=False) int setNotes(string notes) int
Each variant is described separately below.
setNotes(XMLNode notes)
Sets the value of the 'notes' subelement of this SBML object.
The content of notes
is copied, and any existing content of this object's 'notes' subelement is deleted.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
notes | an XML structure that is to be used as the content of the 'notes' subelement of this object |
setNotes(string notes, bool addXHTMLMarkup = false)
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes
.
The content of notes
is copied, and any existing content of this object's 'notes' subelement is deleted.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component.
notes | an XML string that is to be used as the content of the 'notes' subelement of this object |
addXHTMLMarkup | a boolean indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p> ) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup. |
def libsbml.Reaction.setReversible | ( | self, | |
value | |||
) |
Sets the value of the 'reversible' attribute of this Reaction.
setReversible(bool value) int
value | the value of the 'reversible' attribute. |
|
inherited |
This method has multiple variants; they differ in the arguments they accept.
setSBOTerm(int value) int setSBOTerm(string sboid) int
Each variant is described separately below.
setSBOTerm(int value)
Sets the value of the 'sboTerm' attribute.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
value | the NNNNNNN integer portion of the SBO identifier |
setSBOTerm(stringsboid)
Sets the value of the 'sboTerm' attribute by string.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers. This method lets you set the value of 'sboTerm' as a complete string of the form 'SBO:NNNNNNN', whereas setSBOTerm(int value) allows you to set it using the integer form.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
|
inherited |
Returns a string consisting of a partial SBML corresponding to just this object.
toSBML() string
|
inherited |
|
inherited |
Unsets the value of the 'annotation' subelement of this SBML object.
unsetAnnotation() int
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
def libsbml.Reaction.unsetCompartment | ( | self | ) |
Unsets the value of the 'compartment' attribute of this Reaction.
unsetCompartment() int
|
inherited |
Clears the list of CVTerm objects attached to this SBML object.
unsetCVTerms() int
def libsbml.Reaction.unsetFast | ( | self | ) |
Unsets the value of the 'fast' attribute of this Reaction.
unsetFast() int
True
. Beginning with SBML Level 2 Versions 2, the SBML specifications therefore stipulate that if a model has any reactions with 'fast' set to True
, a software tool must be able to respect the attribute or else indicate to the user that it does not have the capacity to do so. Readers are directed to the SBML specifications, which provides more detail about the conditions under which a reaction can be considered to be fast in this sense.
|
inherited |
Unsets the value of the 'id' attribute of this SBML object.
unsetId() int
Most (but not all) objects in SBML include two common attributes: 'id' and 'name'. The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier.
def libsbml.Reaction.unsetKineticLaw | ( | self | ) |
Unsets the 'kineticLaw' subelement of this Reaction.
unsetKineticLaw() int
|
inherited |
Unsets the value of the 'metaid' attribute of this SBML object.
unsetMetaId() int
ID
, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID
type. Although SBML itself specifies the use of XML ID
only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID
's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.
|
inherited |
Unsets the ModelHistory object attached to this object.
unsetModelHistory() int
def libsbml.Reaction.unsetName | ( | self | ) |
Unsets the value of the 'name' attribute of this Reaction.
unsetName() int
|
inherited |
Unsets the value of the 'notes' subelement of this SBML object.
unsetNotes() int
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
|
inherited |
Unsets the value of the 'sboTerm' attribute of this SBML object.
unsetSBOTerm() int