libSBML Python API
5.8.0
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Proxy of C++ ModelDefinition class.
def libsbml.ModelDefinition.acceptComp | ( | self, | |
args | |||
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acceptComp(ModelDefinition self, CompVisitor & v) bool
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Python method signature(s):
addCompartment(Model self, Compartment c)int
Adds a copy of the given Compartment object to this Model.
c | the Compartment object to add |
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Python method signature(s):
addCompartmentType(Model self, CompartmentType ct)int
Adds a copy of the given CompartmentType object to this Model.
ct | the CompartmentType object to add |
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Python method signature(s):
addConstraint(Model self, Constraint c)int
Adds a copy of the given Constraint object to this Model.
c | the Constraint object to add |
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Python method signature(s):
addCVTerm(SBase self, CVTerm term, bool newBag=False)int addCVTerm(SBase self, CVTerm term)
int
Adds a copy of the given CVTerm object to this SBML object.
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. |
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Python method signature(s):
addEvent(Model self, Event e)int
Adds a copy of the given Event object to this Model.
e | the Event object to add |
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Python method signature(s):
addFunctionDefinition(Model self, FunctionDefinition fd)int
Adds a copy of the given FunctionDefinition object to this Model.
fd | the FunctionDefinition to add |
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Python method signature(s):
addInitialAssignment(Model self, InitialAssignment ia)int
Adds a copy of the given InitialAssignment object to this Model.
ia | the InitialAssignment object to add |
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Python method signature(s):
addParameter(Model self, Parameter p)int
Adds a copy of the given Parameter object to this Model.
p | the Parameter object to add |
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Python method signature(s):
addReaction(Model self, Reaction r)int
Adds a copy of the given Reaction object to this Model.
r | the Reaction object to add |
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Python method signature(s):
addRule(Model self, Rule r)int
Adds a copy of the given Rule object to this Model.
r | the Rule object to add |
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Python method signature(s):
addSpecies(Model self, Species s)int
Adds a copy of the given Species object to this Model.
s | the Species object to add |
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Python method signature(s):
addSpeciesType(Model self, SpeciesType st)int
Adds a copy of the given SpeciesType object to this Model.
st | the SpeciesType object to add |
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Python method signature(s):
addUnitDefinition(Model self, UnitDefinition ud)int
Adds a copy of the given UnitDefinition object to this Model.
ud | the UnitDefinition object to add |
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Python method signature(s):
appendAnnotation(Model self, XMLNode annotation)int appendAnnotation(Model self, string annotation)
int
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
appendAnnotation(XMLNode annotation)
Appends annotation content to any existing content in the 'annotation' subelement of this object.
The content in annotation
is copied. Unlike 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 |
Method variant with the following signature:
appendAnnotation(string annotation)
Appends annotation content to any existing content in the 'annotation' subelement of this object.
The content in annotation
is copied. Unlike 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 |
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Python method signature(s):
appendFrom(Model self, Model model)int
Takes the contents of the passed-in Model, makes copies of everything, and appends those copies to the appropriate places in this Model. Also calls 'appendFrom' on all plugin objects.
model | the Model to merge with this one. |
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Python method signature(s):
appendNotes(SBase self, XMLNode notes)int appendNotes(SBase self, string notes)
int
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
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 |
Method variant with the following signature:
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.ModelDefinition.clone | ( | self | ) |
Proxy of C++ ModelDefinition class.
Python method signature(s):
clone(ModelDefinition self)ModelDefinition
Creates and returns a deep copy of this Model object.
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Python method signature(s):
createAlgebraicRule(Model self)AlgebraicRule
Creates a new AlgebraicRule inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
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Python method signature(s):
createAssignmentRule(Model self)AssignmentRule
Creates a new AssignmentRule inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
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Python method signature(s):
createCompartment(Model self)Compartment
Creates a new Compartment inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
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Python method signature(s):
createCompartmentType(Model self)CompartmentType
Creates a new CompartmentType inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
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Python method signature(s):
createConstraint(Model self)Constraint
Creates a new Constraint inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
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Python method signature(s):
createDelay(Model self)Delay
Creates a new Delay inside the last Event object created in this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The mechanism by which the last Event object in this model was created is not significant. It could have been created in a variety of ways, for example by using createEvent(). If no Event object exists in this Model object, a new Delay is not created and None
is returned instead.
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Python method signature(s):
createEvent(Model self)Event
Creates a new Event inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
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Python method signature(s):
createEventAssignment(Model self)EventAssignment
Creates a new EventAssignment inside the last Event object created in this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The mechanism by which the last Event object in this model was created is not significant. It could have been created in a variety of ways, for example by using createEvent(). If no Event object exists in this Model object, a new EventAssignment is not created and None
is returned instead.
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Python method signature(s):
createFunctionDefinition(Model self)FunctionDefinition
Creates a new FunctionDefinition inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
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Python method signature(s):
createInitialAssignment(Model self)InitialAssignment
Creates a new InitialAssignment inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
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Python method signature(s):
createKineticLaw(Model self)KineticLaw
Creates a new KineticLaw inside the last Reaction object created in this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, or a Reaction exists but already has a KineticLaw, a new KineticLaw is not created and None
is returned instead.
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Python method signature(s):
createKineticLawLocalParameter(Model self)LocalParameter
Creates a new LocalParameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The last KineticLaw object in this Model could have been created in a variety of ways. For example, it could have been added using createKineticLaw(), or it could be the result of using Reaction.createKineticLaw() on the Reaction object created by a createReaction(). If a Reaction does not exist for this model, or the last Reaction does not contain a KineticLaw object, a new Parameter is not created and None
is returned instead.
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Python method signature(s):
createKineticLawParameter(Model self)Parameter
Creates a new local Parameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The last KineticLaw object in this Model could have been created in a variety of ways. For example, it could have been added using createKineticLaw(), or it could be the result of using Reaction.createKineticLaw() on the Reaction object created by a createReaction(). If a Reaction does not exist for this model, or the last Reaction does not contain a KineticLaw object, a new Parameter is not created and None
is returned instead.
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Python method signature(s):
createModifier(Model self)ModifierSpeciesReference
Creates a new ModifierSpeciesReference object for a modifier species inside the last Reaction object in this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, a new ModifierSpeciesReference is not created and None
is returned instead.
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Python method signature(s):
createParameter(Model self)Parameter
Creates a new Parameter inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
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Python method signature(s):
createProduct(Model self)SpeciesReference
Creates a new SpeciesReference object for a product inside the last Reaction object in this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, a new SpeciesReference is not created and None
is returned instead.
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Python method signature(s):
createRateRule(Model self)RateRule
Creates a new RateRule inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
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Python method signature(s):
createReactant(Model self)SpeciesReference
Creates a new SpeciesReference object for a reactant inside the last Reaction object in this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, a new SpeciesReference is not created and None
is returned instead.
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Python method signature(s):
createReaction(Model self)Reaction
Creates a new Reaction inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
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Python method signature(s):
createSpecies(Model self)Species
Creates a new Species inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
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Python method signature(s):
createSpeciesType(Model self)SpeciesType
Creates a new SpeciesType inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
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Python method signature(s):
createTrigger(Model self)Trigger
Creates a new Trigger inside the last Event object created in this Model, and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The mechanism by which the last Event object in this model was created is not significant. It could have been created in a variety of ways, for example by using createEvent(). If no Event object exists in this Model object, a new Trigger is not created and None
is returned instead.
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Python method signature(s):
createUnit(Model self)Unit
Creates a new Unit object within the last UnitDefinition object created in this model and returns a pointer to it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
The mechanism by which the UnitDefinition was created is not significant. If a UnitDefinition object does not exist in this model, a new Unit is not created and None
is returned instead.
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Python method signature(s):
createUnitDefinition(Model self)UnitDefinition
Creates a new UnitDefinition inside this Model and returns it.
The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.
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Python method signature(s):
disablePackage(SBase self, string pkgURI, string pkgPrefix)int
Disables the given SBML Level 3 package
This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
pkgURI | the URI of the package |
pkgPrefix | the XML prefix of the package |
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Python method signature(s):
enablePackage(SBase self, string pkgURI, string pkgPrefix, bool flag)int
Enables or disables the given SBML Level 3 package
This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
pkgURI | the URI of the package |
pkgPrefix | the XML prefix of the package |
flag | whether to enable (True ) or disable (False ) the package |
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Python method signature(s):
getAncestorOfType(SBase self, int type, string pkgName="core")SBase getAncestorOfType(SBase self, int type)
SBase getAncestorOfType(SBase self, int type, string pkgName="core")
SBase getAncestorOfType(SBase self, int type)
SBase
Returns the first ancestor object that has the given SBML type code.
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. If the optional argument pkgName
is given, it will cause the search to be limited to the SBML Level 3 package given.
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.
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Python method signature(s):
getAnnotation(SBase self)XMLNode getAnnotation(SBase self)
XMLNode
Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.
Whereas the SBML '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.
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.
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Python method signature(s):
getAnnotationString(SBase self)string getAnnotationString(SBase self)
string
Returns the content of the 'annotation' subelement of this object as a character string.
Whereas the SBML '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.
The annotations returned by this method will be in string form.
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Python method signature(s):
getColumn(SBase self)long
Returns the column number on which this object first appears in the XML representation of the SBML document.
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Python method signature(s):
getCompartment(Model self, long n)Compartment getCompartment(Model self, long n)
Compartment getCompartment(Model self, string sid)
Compartment getCompartment(Model self, string sid)
Compartment
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
getCompartment(long n)
Get the nth Compartment object in this Model.
Method variant with the following signature:
getCompartment(string sid)
Get a Compartment object based on its identifier.
sid
or None
if no such Compartment exists.
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Python method signature(s):
getCompartmentType(Model self, long n)CompartmentType getCompartmentType(Model self, long n)
CompartmentType getCompartmentType(Model self, string sid)
CompartmentType getCompartmentType(Model self, string sid)
CompartmentType
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
getCompartmentType(long n)
Get the nth CompartmentType object in this Model.
Method variant with the following signature:
getCompartmentType(string sid)
Get a CompartmentType object based on its identifier.
sid
or None
if no such CompartmentType exists.
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Python method signature(s):
getConstraint(Model self, long n)Constraint getConstraint(Model self, long n)
Constraint
Get the nth Constraint object in this Model.
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Python method signature(s):
getCVTerms()CVTermList
Get the CVTermList of CVTerm objects in this SBase.
Returns the CVTermList for this SBase.
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Python method signature(s):
getElementByMetaId(Model self, string metaid)SBase
Returns the first child element it can find with the given metaid
, or None if no such object is found.
metaid | string representing the metaid of objects to find |
metaid
.
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Python method signature(s):
getElementBySId(Model self, string id)SBase
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.
id | string representing the id of objects to find. |
id
. def libsbml.ModelDefinition.getElementName | ( | self | ) |
Python method signature(s):
getElementName(ModelDefinition self)string
Returns the XML element name of this object, which for Model, is always 'model'
.
'model'
.
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Python method signature(s):
getEvent(Model self, long n)Event getEvent(Model self, long n)
Event getEvent(Model self, string sid)
Event getEvent(Model self, string sid)
Event
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
getEvent(long n)
Get the nth Event object in this Model.
Method variant with the following signature:
getEvent(string sid)
Get an Event object based on its identifier.
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Python method signature(s):
getFunctionDefinition(Model self, long n)FunctionDefinition getFunctionDefinition(Model self, long n)
FunctionDefinition getFunctionDefinition(Model self, string sid)
FunctionDefinition getFunctionDefinition(Model self, string sid)
FunctionDefinition
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
getFunctionDefinition(long n)
Get the nth FunctionDefinitions object in this Model.
Method variant with the following signature:
getFunctionDefinition(string sid)
Get a FunctionDefinition object based on its identifier.
sid
or None
if no such FunctionDefinition exists.
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Python method signature(s):
getInitialAssignment(Model self, long n)InitialAssignment getInitialAssignment(Model self, long n)
InitialAssignment getInitialAssignment(Model self, string symbol)
InitialAssignment getInitialAssignment(Model self, string symbol)
InitialAssignment
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
getInitialAssignment(string symbol)
Get an InitialAssignment object based on the symbol to which it assigns a value.
None
if no such InitialAssignment exists.Method variant with the following signature:
getInitialAssignment(long n)
Get the nth InitialAssignment object in this Model.
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Python method signature(s):
getLevel(SBase self)long
Returns the SBML Level of the SBMLDocument object containing this object.
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Python method signature(s):
getLine(SBase self)long
Returns the line number on which this object first appears in the XML representation of the SBML document.
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Python method signature(s):
getListOfCompartments(Model self)ListOfCompartments getListOfCompartments(Model self)
ListOfCompartments
Get the ListOfCompartments object in this Model.
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Python method signature(s):
getListOfCompartmentTypes(Model self)ListOfCompartmentTypes getListOfCompartmentTypes(Model self)
ListOfCompartmentTypes
Get the ListOfCompartmentTypes object in this Model.
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Python method signature(s):
getListOfConstraints(Model self)ListOfConstraints getListOfConstraints(Model self)
ListOfConstraints
Get the ListOfConstraints object in this Model.
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Python method signature(s):
getListOfEvents(Model self)ListOfEvents getListOfEvents(Model self)
ListOfEvents
Get the ListOfEvents object in this Model.
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Python method signature(s):
getListOfFunctionDefinitions(Model self)ListOfFunctionDefinitions getListOfFunctionDefinitions(Model self)
ListOfFunctionDefinitions
Get the ListOfFunctionDefinitions object in this Model.
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Python method signature(s):
getListOfInitialAssignments(Model self)ListOfInitialAssignments getListOfInitialAssignments(Model self)
ListOfInitialAssignments
Get the ListOfInitialAssignments object in this Model.
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Python method signature(s):
getListOfParameters(Model self)ListOfParameters getListOfParameters(Model self)
ListOfParameters
Get the ListOfParameters object in this Model.
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Python method signature(s):
getListOfReactions(Model self)ListOfReactions getListOfReactions(Model self)
ListOfReactions
Get the ListOfReactions object in this Model.
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Python method signature(s):
getListOfRules(Model self)ListOfRules getListOfRules(Model self)
ListOfRules
Get the ListOfRules object in this Model.
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Python method signature(s):
getListOfSpecies(Model self)ListOfSpecies getListOfSpecies(Model self)
ListOfSpecies
Get the ListOfSpecies object in this Model.
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Python method signature(s):
getListOfSpeciesTypes(Model self)ListOfSpeciesTypes getListOfSpeciesTypes(Model self)
ListOfSpeciesTypes
Get the ListOfSpeciesTypes object in this Model.
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Python method signature(s):
getListOfUnitDefinitions(Model self)ListOfUnitDefinitions getListOfUnitDefinitions(Model self)
ListOfUnitDefinitions
Get the ListOfUnitDefinitions object in this Model.
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Python method signature(s):
getMetaId(SBase self)string
Returns the value of the 'metaid' attribute of this object.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, 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 XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.
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Python method signature(s):
getModelHistory(SBase self)ModelHistory getModelHistory(SBase self)
ModelHistory
Returns the ModelHistory object, if any, attached to this object.
None
if none exist.
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Python method signature(s):
getNamespaces(SBase self)XMLNamespaces
Returns a list of the XML Namespaces declared on this SBML document.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in SBML Level 3) packages used in addition to SBML Level 3 Core.
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Python method signature(s):
getNotes(SBase self)XMLNode getNotes(SBase self)
XMLNode
Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.
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 '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().
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Python method signature(s):
getNotesString(SBase self)string getNotesString(SBase self)
string
Returns the content of the 'notes' subelement of this object as a string.
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.
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.
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Python method signature(s):
getNumCompartments(Model self)long
Get the number of Compartment objects in this Model.
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inherited |
Python method signature(s):
getNumCompartmentTypes(Model self)long
Get the number of CompartmentType objects in this Model.
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inherited |
Python method signature(s):
getNumConstraints(Model self)long
Get the number of Constraint objects in this Model.
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inherited |
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inherited |
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Python method signature(s):
getNumFunctionDefinitions(Model self)long
Get the number of FunctionDefinition objects in this Model.
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inherited |
Python method signature(s):
getNumInitialAssignments(Model self)long
Get the number of InitialAssignment objects in this Model.
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inherited |
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Python method signature(s):
getNumPlugins(SBase self)long
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
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inherited |
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inherited |
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inherited |
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Python method signature(s):
getNumSpeciesTypes(Model self)long
Get the number of SpeciesType objects in this Model.
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inherited |
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Python method signature(s):
getNumUnitDefinitions(Model self)long
Get the number of UnitDefinition objects in this Model.
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inherited |
Python method signature(s):
getPackageName(SBase self)string
Returns the name of the SBML Level 3 package in which this element is defined.
"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.
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Python method signature(s):
getPackageVersion(SBase self)long
Returns the Version of the SBML Level 3 package to which this element belongs to.
0
will be returned if this element belongs to the SBML Level 3 Core package.
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Python method signature(s):
getParameter(Model self, long n)Parameter getParameter(Model self, long n)
Parameter getParameter(Model self, string sid)
Parameter getParameter(Model self, string sid)
Parameter
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
getParameter(long n)
Get the nth Parameter object in this Model.
Method variant with the following signature:
getParameter(string sid)
Get a Parameter object based on its identifier.
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Python method signature(s):
getParentSBMLObject(SBase self)SBase getParentSBMLObject(SBase self)
SBase
Returns the parent SBML object containing this object.
This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.
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Python method signature(s):
getPlugin(SBase self, string package)SBasePlugin getPlugin(SBase self, string package)
SBasePlugin getPlugin(SBase self, long n)
SBasePlugin getPlugin(SBase self, long n)
SBasePlugin
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
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 |
Method variant with the following signature:
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 |
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Python method signature(s):
getReaction(Model self, long n)Reaction getReaction(Model self, long n)
Reaction getReaction(Model self, string sid)
Reaction getReaction(Model self, string sid)
Reaction
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
getReaction(long n)
Get the nth Reaction object in this Model.
Method variant with the following signature:
getReaction(string sid)
Get a Reaction object based on its identifier.
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Python method signature(s):
getResourceBiologicalQualifier(SBase self, string resource)long
Returns the MIRIAM biological qualifier associated with the given resource.
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.
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Python method signature(s):
getResourceModelQualifier(SBase self, string resource)long
Returns the MIRIAM model qualifier associated with the given resource.
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.
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Python method signature(s):
getRule(Model self, long n)Rule getRule(Model self, long n)
Rule getRule(Model self, string variable)
Rule getRule(Model self, string variable)
Rule
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
getRule(string variable)
Get a Rule object based on the variable to which it assigns a value.
None
if no such Rule exists.Method variant with the following signature:
getRule(long n)
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Python method signature(s):
getSBMLDocument(SBase self)SBMLDocument getSBMLDocument(SBase self)
SBMLDocument
Returns the SBMLDocument object containing this object instance.
LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
This method allows the caller to obtain the SBMLDocument for the current object.
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Python method signature(s):
getSBOTerm(SBase self)int
Returns the integer portion of the value of the 'sboTerm' attribute of this object.
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.
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Python method signature(s):
getSBOTermAsURL(SBase self)string
Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object.
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.
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Python method signature(s):
getSBOTermID(SBase self)string
Returns the string representation of the 'sboTerm' attribute of this object.
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.
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Python method signature(s):
getSpecies(Model self, long n)Species getSpecies(Model self, long n)
Species getSpecies(Model self, string sid)
Species getSpecies(Model self, string sid)
Species
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
getSpecies(long n)
Get the nth Species object in this Model.
Method variant with the following signature:
getSpecies(string sid)
Get a Species object based on its identifier.
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Python method signature(s):
getSpeciesReference(Model self, string sid)SpeciesReference getSpeciesReference(Model self, string sid)
SpeciesReference
Get a SpeciesReference object based on its identifier.
sid
or None
if no such SpeciesReference exists.
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Python method signature(s):
getSpeciesType(Model self, long n)SpeciesType getSpeciesType(Model self, long n)
SpeciesType getSpeciesType(Model self, string sid)
SpeciesType getSpeciesType(Model self, string sid)
SpeciesType
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
getSpeciesType(long n)
Get the nth SpeciesType object in this Model.
Method variant with the following signature:
getSpeciesType(string sid)
Get a SpeciesType object based on its identifier.
sid
or None
if no such SpeciesType exists.
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def libsbml.ModelDefinition.getTypeCode | ( | self | ) |
Python method signature(s):
getTypeCode(ModelDefinition self)int
Returns the libSBML type code for this SBML object.
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_
.
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Python method signature(s):
getUnitDefinition(Model self, long n)UnitDefinition getUnitDefinition(Model self, long n)
UnitDefinition getUnitDefinition(Model self, string sid)
UnitDefinition getUnitDefinition(Model self, string sid)
UnitDefinition
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
getUnitDefinition(long n)
Get the nth UnitDefinition object in this Model.
Method variant with the following signature:
getUnitDefinition(string sid)
Get a UnitDefinition based on its identifier.
sid
or None
if no such UnitDefinition exists.
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Python method signature(s):
getVersion(SBase self)long
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
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Python method signature(s):
hasRequiredElements(Model self)bool
Predicate returning True
if all the required elements for this Model object have been set.
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inherited |
Python method signature(s):
hasValidLevelVersionNamespaceCombination(SBase self)bool
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Python method signature(s):
isPackageEnabled(SBase self, string pkgName)bool
Predicate returning True
if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
pkgName | the name of the package |
True
if the given package is enabled within this object, false
otherwise.
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Python method signature(s):
isPackageURIEnabled(SBase self, string pkgURI)bool
Predicate returning True
if an SBML Level 3 package with the given URI is enabled with this object.
pkgURI | the URI of the package |
True
if the given package is enabled within this object, false
otherwise.
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inherited |
Python method signature(s):
isPkgEnabled(SBase self, string pkgName)bool
Predicate returning True
if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
pkgName | the name of the package |
True
if the given package is enabled within this object, false
otherwise.
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inherited |
Python method signature(s):
isPkgURIEnabled(SBase self, string pkgURI)bool
Predicate returning True
if an SBML Level 3 package with the given URI is enabled with this object.
pkgURI | the URI of the package |
True
if the given package is enabled within this object, false
otherwise.
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inherited |
Python method signature(s):
isPopulatedListFormulaUnitsData(Model self)bool
Predicate returning True
if the list of FormulaUnitsData is populated.
True
if the list of FormulaUnitsData is populated, False
otherwise.
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inherited |
Python method signature(s):
isSetAnnotation(SBase self)bool
Predicate returning True
if this object's 'annotation' subelement exists and has content.
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.
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Python method signature(s):
isSetAreaUnits(Model self)bool
Predicate returning True
if this Model's 'areaUnits' attribute is set.
True
if the 'areaUnits' attribute of this Model is set, False
otherwise.
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inherited |
Python method signature(s):
isSetConversionFactor(Model self)bool
Predicate returning True
if this Model's 'conversionFactor' attribute is set.
True
if the 'conversionFactor' attribute of this Model is set, False
otherwise.
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inherited |
Python method signature(s):
isSetExtentUnits(Model self)bool
Predicate returning True
if this Model's 'extentUnits' attribute is set.
True
if the 'extentUnits' attribute of this Model is set, False
otherwise.
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inherited |
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inherited |
Python method signature(s):
isSetLengthUnits(Model self)bool
Predicate returning True
if this Model's 'lengthUnits' attribute is set.
True
if the 'lengthUnits' attribute of this Model is set, False
otherwise.
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inherited |
Python method signature(s):
isSetMetaId(SBase self)bool
Predicate returning True
if this object's 'metaid' attribute is set.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, 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 XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.
True
if the 'metaid' attribute of this SBML object is set, False
otherwise.
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Python method signature(s):
isSetModelHistory(SBase self)bool
Predicate returning True
if this object has a ModelHistory object attached to it.
True
if the ModelHistory of this object is set, false
otherwise.
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inherited |
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inherited |
Python method signature(s):
isSetNotes(SBase self)bool
Predicate returning True
if this object's 'notes' subelement exists and has content.
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.
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inherited |
Python method signature(s):
isSetSBOTerm(SBase self)bool
Predicate returning True
if this object's 'sboTerm' attribute is set.
True
if the 'sboTerm' attribute of this SBML object is set, False
otherwise.
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inherited |
Python method signature(s):
isSetSubstanceUnits(Model self)bool
Predicate returning True
if this Model's 'substanceUnits' attribute is set.
True
if the 'substanceUnits' attribute of this Model is set, False
otherwise.
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inherited |
Python method signature(s):
isSetTimeUnits(Model self)bool
Predicate returning True
if this Model's 'timeUnits' attribute is set.
True
if the 'timeUnits' attribute of this Model is set, False
otherwise.
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inherited |
Python method signature(s):
isSetVolumeUnits(Model self)bool
Predicate returning True
if this Model's 'volumeUnits' attribute is set.
True
if the 'volumeUnits' attribute of this Model is set, False
otherwise.
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inherited |
Python method signature(s):
matchesRequiredSBMLNamespacesForAddition(SBase self, SBase sb)bool matchesRequiredSBMLNamespacesForAddition(SBase self, SBase sb)
bool
Returns True
if this object's set of XML namespaces are a subset of the given object's XML namespaces.
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.
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inherited |
Python method signature(s):
matchesSBMLNamespaces(SBase self, SBase sb)bool matchesSBMLNamespaces(SBase self, SBase sb)
bool
Returns True
if this object's set of XML namespaces are the same as the given object's XML namespaces.
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.
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inherited |
Python method signature(s):
populateListFormulaUnitsData(Model self)
Populates the list of FormulaDataUnits with the units derived for the model. The list contains elements of class FormulaUnitsData.
The first element of the list refers to the default units of 'substance per time' derived from the model and has the unitReferenceId 'subs_per_time'. This facilitates the comparison of units derived from mathematical formula with the expected units.
The next elements of the list record the units of the compartments and species established from either explicitly declared or default units.
The next elements record the units of any parameters.
Subsequent elements of the list record the units derived for each mathematical expression encountered within the model.
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inherited |
Python method signature(s):
removeCompartment(Model self, long n)Compartment removeCompartment(Model self, string sid)
Compartment
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
removeCompartment(long n)
Removes the nth Compartment object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the Compartment object to remove |
None
is returned if the given index is out of range.Method variant with the following signature:
removeCompartment(string sid)
Removes the Compartment object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the Compartment objects in this Model object have the identifier sid
, then None
is returned.
sid | the identifier of the Compartment object to remove |
None
is returned if no Compartment object with the identifier exists in this Model object.
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inherited |
Python method signature(s):
removeCompartmentType(Model self, long n)CompartmentType removeCompartmentType(Model self, string sid)
CompartmentType
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
removeCompartmentType(long n)
Removes the nth CompartmentType object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the CompartmentType object to remove |
None
is returned if the given index is out of range.Method variant with the following signature:
removeCompartmentType(string sid)
Removes the CompartmentType object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the CompartmentType objects in this Model object have the identifier sid
, then None
is returned.
sid | the identifier of the object to remove |
None
is returned if no CompartmentType object with the identifier exists in this Model object.
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inherited |
Python method signature(s):
removeConstraint(Model self, long n)Constraint
Removes the nth Constraint object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the Constraint object to remove |
None
is returned if the given index is out of range.
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inherited |
Python method signature(s):
removeEvent(Model self, long n)Event removeEvent(Model self, string sid)
Event
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
removeEvent(long n)
Removes the nth Event object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the Event object to remove |
None
is returned if the given index is out of range.Method variant with the following signature:
removeEvent(string sid)
Removes the Event object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the Event objects in this Model object have the identifier sid
, then None
is returned.
sid | the identifier of the Event object to remove |
def libsbml.ModelDefinition.removeFromParentAndDelete | ( | self | ) |
Python method signature(s):
removeFromParentAndDelete(ModelDefinition self)int
Finds this Model's parent SBMLDocument and calls setModel(None) on it, indirectly deleting itself. Overridden from the SBase function since the parent is not a ListOf.
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inherited |
Python method signature(s):
removeFunctionDefinition(Model self, long n)FunctionDefinition removeFunctionDefinition(Model self, string sid)
FunctionDefinition
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
removeFunctionDefinition(long n)
Removes the nth FunctionDefinition object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the FunctionDefinition object to remove |
None
is returned if the given index is out of range.Method variant with the following signature:
removeFunctionDefinition(string sid)
Removes the FunctionDefinition object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the FunctionDefinition objects in this Model object have the identifier sid
, then None
is returned.
sid | the identifier of the FunctionDefinition object to remove |
None
is returned if no FunctionDefinition object with the identifier exists in this Model object.
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inherited |
Python method signature(s):
removeInitialAssignment(Model self, long n)InitialAssignment removeInitialAssignment(Model self, string symbol)
InitialAssignment
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
removeInitialAssignment(string symbol)
Removes the InitialAssignment object with the given 'symbol' attribute from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the InitialAssignment objects in this Model object have the 'symbol' attribute symbol
, then None
is returned.
symbol | the 'symbol' attribute of the InitialAssignment object to remove |
None
is returned if no InitialAssignment object with the 'symbol' attribute exists in this Model object.Method variant with the following signature:
removeInitialAssignment(long n)
Removes the nth InitialAssignment object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the InitialAssignment object to remove |
None
is returned if the given index is out of range.
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inherited |
Python method signature(s):
removeParameter(Model self, long n)Parameter removeParameter(Model self, string sid)
Parameter
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
removeParameter(long n)
Removes the nth Parameter object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the Parameter object to remove |
None
is returned if the given index is out of range.Method variant with the following signature:
removeParameter(string sid)
Removes the Parameter object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the Parameter objects in this Model object have the identifier sid
, then None
is returned.
sid | the identifier of the Parameter object to remove |
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Python method signature(s):
removeReaction(Model self, long n)Reaction removeReaction(Model self, string sid)
Reaction
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
removeReaction(long n)
Removes the nth Reaction object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the Reaction object to remove |
None
is returned if the given index is out of range.Method variant with the following signature:
removeReaction(string sid)
Removes the Reaction object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the Reaction objects in this Model object have the identifier sid
, then None
is returned.
sid | the identifier of the Reaction object to remove |
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Python method signature(s):
removeRule(Model self, long n)Rule removeRule(Model self, string variable)
Rule
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
removeRule(string variable)
Removes the Rule object with the given 'variable' attribute from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the Rule objects in this Model object have the 'variable' attribute variable
, then None
is returned.
variable | the 'variable' attribute of the Rule object to remove |
None
is returned if no Rule object with the 'variable' attribute exists in this Model object.Method variant with the following signature:
removeRule(long n)
Removes the nth Rule object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the Rule object to remove |
None
is returned if the given index is out of range.
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inherited |
Python method signature(s):
removeSpecies(Model self, long n)Species removeSpecies(Model self, string sid)
Species
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
removeSpecies(long n)
Removes the nth Species object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the Species object to remove |
None
is returned if the given index is out of range.Method variant with the following signature:
removeSpecies(string sid)
Removes the Species object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the Species objects in this Model object have the identifier sid
, then None
is returned.
sid | the identifier of the Species object to remove |
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Python method signature(s):
removeSpeciesType(Model self, long n)SpeciesType removeSpeciesType(Model self, string sid)
SpeciesType
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
removeSpeciesType(long n)
Removes the nth SpeciesType object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the SpeciesType object to remove |
None
is returned if the given index is out of range.Method variant with the following signature:
removeSpeciesType(string sid)
Removes the SpeciesType object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the SpeciesType objects in this Model object have the identifier sid
, then None
is returned.
sid | the identifier of the SpeciesType object to remove |
None
is returned if no SpeciesType object with the identifier exists in this Model object.
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Python method signature(s):
removeTopLevelAnnotationElement(SBase self, string elementName, string elementURI="")int removeTopLevelAnnotationElement(SBase self, string elementName)
int
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.
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 |
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Python method signature(s):
removeUnitDefinition(Model self, long n)UnitDefinition removeUnitDefinition(Model self, string sid)
UnitDefinition
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
removeUnitDefinition(long n)
Removes the nth UnitDefinition object from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the UnitDefinition object to remove |
None
is returned if the given index is out of range.Method variant with the following signature:
removeUnitDefinition(string sid)
Removes the UnitDefinition object with the given identifier from this Model object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it. If none of the UnitDefinition objects in this Model object have the identifier sid
, then None
is returned.
sid | the identifier of the UnitDefinition object to remove |
None
is returned if no UnitDefinition object with the identifier exists in this Model object.
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Python method signature(s):
renameMetaIdRefs(SBase self, string oldid, string newid)
Renames all the MetaIdRef
attributes on this element.
This method works by looking at all meta-attribute values, comparing the identifiers to the value of oldid
. If any matches are found, the matching identifiers are replaced with newid
. The method does not descend into child elements.
oldid | the old identifier |
newid | the new identifier |
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inherited |
Python method signature(s):
renameSIdRefs(Model self, string oldid, string newid)
Renames all the SIdRef attributes on this element, including any found in MathML
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inherited |
Python method signature(s):
renameUnitSIdRefs(Model self, string oldid, string newid)
Renames all the UnitSIdRef attributes on this element
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inherited |
Python method signature(s):
replaceTopLevelAnnotationElement(SBase self, XMLNode annotation)int replaceTopLevelAnnotationElement(SBase self, string annotation)
int
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
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); 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 |
Method variant with the following signature:
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); 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 |
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Python method signature(s):
setAnnotation(Model self, XMLNode annotation)int setAnnotation(Model self, string annotation)
int
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
setAnnotation(XMLNode annotation)
Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation
.
Any existing content of the 'annotation' subelement is 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 appendAnnotation().
annotation | an XML structure that is to be used as the content of the 'annotation' subelement of this object |
Method variant with the following signature:
setAnnotation(string annotation)
Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation
.
Any existing content of the 'annotation' subelement is 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 appendAnnotation().
annotation | an XML string that is to be used as the content of the 'annotation' subelement of this object |
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Python method signature(s):
setAreaUnits(Model self, string units)int
Sets the value of the 'areaUnits' attribute of this Model.
The string in units
is copied.
units | the new areaUnits for the Model |
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inherited |
Python method signature(s):
setConversionFactor(Model self, string units)int
Sets the value of the 'conversionFactor' attribute of this Model.
The string in units
is copied.
units | the new conversionFactor for the Model |
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inherited |
Python method signature(s):
setExtentUnits(Model self, string units)int
Sets the value of the 'extentUnits' attribute of this Model.
The string in units
is copied.
units | the new extentUnits for the Model |
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inherited |
Python method signature(s):
setId(Model self, string sid)int
Sets the value of the 'id' attribute of this Model.
The string sid
is copied. Note that SBML has strict requirements for the syntax of identifiers. The following is a summary of the definition of the SBML identifier type
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
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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 formulations.
sid | the string to use as the identifier of this Model |
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Python method signature(s):
setLengthUnits(Model self, string units)int
Sets the value of the 'lengthUnits' attribute of this Model.
The string in units
is copied.
units | the new lengthUnits for the Model |
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Python method signature(s):
setMetaId(SBase self, string metaid)int
Sets the value of the 'metaid' attribute of this object.
The string metaid
is copied. The value of metaid
must be an identifier conforming to the syntax defined by the XML 1.0 data type ID. Among other things, this type requires that a value is unique among all the values of type XML ID in an SBMLDocument. Although SBML only uses XML ID for the 'metaid' attribute, callers 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.
metaid | the identifier string to use as the value of the 'metaid' attribute |
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Python method signature(s):
setModelHistory(SBase self, ModelHistory history)int
Sets the ModelHistory of this object.
The content of history
is copied, and this object's existing model history content is deleted.
history | ModelHistory of this object. |
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inherited |
Python method signature(s):
setName(Model self, string name)int
Sets the value of the 'name' attribute of this Model.
The string in name
is copied.
name | the new name for the Model |
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inherited |
Python method signature(s):
setNamespaces(SBase self, XMLNamespaces xmlns)int
Sets the namespaces relevant of this SBML object.
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 |
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Python method signature(s):
setNotes(SBase self, XMLNode notes)int setNotes(SBase self, string notes, bool addXHTMLMarkup=False)
int setNotes(SBase self, string notes)
int
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
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. |
Method variant with the following signature:
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 |
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Python method signature(s):
setSBOTerm(SBase self, int value)int setSBOTerm(SBase self, string sboid)
int
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
Method variant with the following signature:
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 |
Method variant with the following signature:
setSBOTerm(string &sboid)
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.
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Python method signature(s):
setSubstanceUnits(Model self, string units)int
Sets the value of the 'substanceUnits' attribute of this Model.
The string in units
is copied.
units | the new substanceUnits for the Model |
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inherited |
Python method signature(s):
setTimeUnits(Model self, string units)int
Sets the value of the 'timeUnits' attribute of this Model.
The string in units
is copied.
units | the new timeUnits for the Model |
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inherited |
Python method signature(s):
setVolumeUnits(Model self, string units)int
Sets the value of the 'volumeUnits' attribute of this Model.
The string in units
is copied.
units | the new volumeUnits for the Model |
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inherited |
toSBML(SBase self) string *
Returns a string consisting of a partial SBML corresponding to just this object.
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inherited |
Python method signature(s):
unsetAnnotation(SBase self)int
Unsets the value of the 'annotation' subelement of this SBML 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.
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inherited |
Python method signature(s):
unsetAreaUnits(Model self)int
Unsets the value of the 'areaUnits' attribute of this Model.
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inherited |
Python method signature(s):
unsetConversionFactor(Model self)int
Unsets the value of the 'conversionFactor' attribute of this Model.
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inherited |
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inherited |
Python method signature(s):
unsetExtentUnits(Model self)int
Unsets the value of the 'extentUnits' attribute of this Model.
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inherited |
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inherited |
Python method signature(s):
unsetLengthUnits(Model self)int
Unsets the value of the 'lengthUnits' attribute of this Model.
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inherited |
Python method signature(s):
unsetMetaId(SBase self)int
Unsets the value of the 'metaid' attribute of this SBML object.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, 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 XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.
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inherited |
Python method signature(s):
unsetModelHistory(SBase self)int
Unsets the ModelHistory object attached to this object.
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inherited |
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inherited |
Python method signature(s):
unsetNotes(SBase self)int
Unsets the value of the 'notes' subelement of this SBML object.
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.
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inherited |
Python method signature(s):
unsetSBOTerm(SBase self)int
Unsets the value of the 'sboTerm' attribute of this SBML object.
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inherited |
Python method signature(s):
unsetSubstanceUnits(Model self)int
Unsets the value of the 'substanceUnits' attribute of this Model.
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inherited |
Python method signature(s):
unsetTimeUnits(Model self)int
Unsets the value of the 'timeUnits' attribute of this Model.
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inherited |
Python method signature(s):
unsetVolumeUnits(Model self)int
Unsets the value of the 'volumeUnits' attribute of this Model.