libSBML Python API
5.8.0
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Implementation of SBML's InitialAssignment construct.
SBML Level 2 Versions 2–4 and SBML Level 3 provide two ways of assigning initial values to entities in a model. The simplest and most basic is to set the values of the appropriate attributes in the relevant components; for example, the initial value of a model parameter (whether it is a constant or a variable) can be assigned by setting its 'value' attribute directly in the model definition. However, this approach is not suitable when the value must be calculated, because the initial value attributes on different components such as species, compartments, and parameters are single values and not mathematical expressions. In those situations, the InitialAssignment construct can be used; it permits the calculation of the value of a constant or the initial value of a variable from the values of other quantities in a model.
As explained below, the provision of InitialAssignment does not mean that models necessarily must use this construct when defining initial values of quantities in a model. If a value can be set directly using the relevant attribute of a component in a model, then that approach may be more efficient and more portable to other software tools. InitialAssignment should be used when the other mechanism is insufficient for the needs of a particular model.
The InitialAssignment construct has some similarities to AssignmentRule. The main differences are: (a) an InitialAssignment can set the value of a constant whereas an AssignmentRule cannot, and (b) unlike AssignmentRule, an InitialAssignment definition only applies up to and including the beginning of simulation time, i.e., t <= 0, while an AssignmentRule applies at all times.
InitialAssignment has a required attribute, 'symbol', whose value must follow the guidelines for identifiers described in the SBML specification (e.g., Section 3.3 in the Level 2 Version 4 specification). The value of this attribute in an InitialAssignment object can be the identifier of a Compartment, Species or global Parameter elsewhere in the model. The InitialAssignment defines the initial value of the constant or variable referred to by the 'symbol' attribute. (The attribute's name is 'symbol' rather than 'variable' because it may assign values to constants as well as variables in a model.) Note that an initial assignment cannot be made to reaction identifiers, that is, the 'symbol' attribute value of an InitialAssignment cannot be an identifier that is the 'id' attribute value of a Reaction object in the model. This is identical to a restriction placed on rules.
InitialAssignment also has a required 'math' subelement that contains a MathML expression used to calculate the value of the constant or the initial value of the variable. The units of the value computed by the formula in the 'math' subelement should (in SBML Level 2 Version 4 and in SBML Level 3) or must (in previous Versions) be identical to be the units associated with the identifier given in the 'symbol' attribute. (That is, the units are the units of the species, compartment, or parameter, as appropriate for the kind of object identified by the value of 'symbol'.)
InitialAssignment was introduced in SBML Level 2 Version 2. It is not available in SBML Level 2 Version 1 nor in any version of Level 1.
The value calculated by an InitialAssignment object overrides the value assigned to the given symbol by the object defining that symbol. For example, if a compartment's 'size' attribute is set in its definition, and the model also contains an InitialAssignment having that compartment's identifier as its 'symbol' attribute value, then the interpretation is that the 'size' assigned in the Compartment object should be ignored and the value assigned based on the computation defined in the InitialAssignment. Initial assignments can take place for Compartment, Species and global Parameter objects regardless of the value of their 'constant' attribute.
The actions of all InitialAssignment objects are in general terms the same, but differ in the precise details depending on the type of variable being set:
In the case of a species, an InitialAssignment sets the referenced species' initial quantity (concentration or amount of substance) to the value determined by the formula in the 'math' subelement. The overall units of the formula should (in SBML Level 2 Version 4 and in SBML Level 3) or must (in previous Versions) be the same as the units specified for the species.
In the case of a compartment, an InitialAssignment sets the referenced compartment's initial size to the size determined by the formula in 'math'. The overall units of the formula should (in SBML Level 2 Version 4 and in SBML Level 3) or must (in previous Versions) be the same as the units specified for the size of the compartment.
In the context of a simulation, initial assignments establish values that are in effect prior to and including the start of simulation time, i.e., t <= 0. Section 3.4.8 in the SBML Level 2 Version 4 and SBML Level 3 Version 1 Core specifications provides information about the interpretation of assignments, rules, and entity values for simulation time up to and including the start time t = 0; this is important for establishing the initial conditions of a simulation if the model involves expressions containing the delay 'csymbol'.
There cannot be two initial assignments for the same symbol in a model; that is, a model must not contain two or more InitialAssignment objects that both have the same identifier as their 'symbol' attribute value. A model must also not define initial assignments and assignment rules for the same entity. That is, there cannot be both an InitialAssignment and an AssignmentRule for the same symbol in a model, because both kinds of constructs apply prior to and at the start of simulated time—allowing both to exist for a given symbol would result in indeterminism).
The ordering of InitialAssignment objects is not significant. The combined set of InitialAssignment, AssignmentRule and KineticLaw objects form a set of assignment statements that must be considered as a whole. The combined set of assignment statements should not contain algebraic loops: a chain of dependency between these statements should terminate. (More formally, consider the directed graph of assignment statements where nodes are a model's assignment statements and directed arcs exist for each occurrence of a symbol in an assignment statement 'math' attribute. The directed arcs in this graph start from the statement assigning the symbol and end at the statement that contains the symbol in their math elements. Such a graph must be acyclic.)
Finally, it is worth being explicit about the expected behavior in the following situation. Suppose (1) a given symbol has a value x assigned to it in its definition, and (2) there is an initial assignment having the identifier as its 'symbol' value and reassigning the value to y, and (3) the identifier is also used in the mathematical formula of a second initial assignment. What value should the second initial assignment use? It is y, the value assigned to the symbol by the first initial assignment, not whatever value was given in the symbol's definition. This follows directly from the behavior described above: if an InitialAssignment object exists for a given symbol, then the symbol's value is overridden by that initial assignment.
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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):
appendAnnotation(SBase self, XMLNode annotation)int appendAnnotation(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:
appendAnnotation(XMLNode annotation)
Appends the given annotation
to the 'annotation' subelement of this object.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Unlike SBase.setAnnotation() or SBase.setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.
annotation | an XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object |
Method variant with the following signature:
appendAnnotation(string annotation)
Appends the given annotation
to the 'annotation' subelement of this object.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Unlike SBase.setAnnotation() or SBase.setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.
annotation | an XML string that is to be copied and appended to the content of the 'annotation' subelement of this object |
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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.InitialAssignment.clone | ( | self | ) |
Implementation of SBML's InitialAssignment construct.
SBML Level 2 Versions 2–4 and SBML Level 3 provide two ways of assigning initial values to entities in a model. The simplest and most basic is to set the values of the appropriate attributes in the relevant components; for example, the initial value of a model parameter (whether it is a constant or a variable) can be assigned by setting its 'value' attribute directly in the model definition. However, this approach is not suitable when the value must be calculated, because the initial value attributes on different components such as species, compartments, and parameters are single values and not mathematical expressions. In those situations, the InitialAssignment construct can be used; it permits the calculation of the value of a constant or the initial value of a variable from the values of other quantities in a model.
As explained below, the provision of InitialAssignment does not mean that models necessarily must use this construct when defining initial values of quantities in a model. If a value can be set directly using the relevant attribute of a component in a model, then that approach may be more efficient and more portable to other software tools. InitialAssignment should be used when the other mechanism is insufficient for the needs of a particular model.
The InitialAssignment construct has some similarities to AssignmentRule. The main differences are: (a) an InitialAssignment can set the value of a constant whereas an AssignmentRule cannot, and (b) unlike AssignmentRule, an InitialAssignment definition only applies up to and including the beginning of simulation time, i.e., t <= 0, while an AssignmentRule applies at all times.
InitialAssignment has a required attribute, 'symbol', whose value must follow the guidelines for identifiers described in the SBML specification (e.g., Section 3.3 in the Level 2 Version 4 specification). The value of this attribute in an InitialAssignment object can be the identifier of a Compartment, Species or global Parameter elsewhere in the model. The InitialAssignment defines the initial value of the constant or variable referred to by the 'symbol' attribute. (The attribute's name is 'symbol' rather than 'variable' because it may assign values to constants as well as variables in a model.) Note that an initial assignment cannot be made to reaction identifiers, that is, the 'symbol' attribute value of an InitialAssignment cannot be an identifier that is the 'id' attribute value of a Reaction object in the model. This is identical to a restriction placed on rules.
InitialAssignment also has a required 'math' subelement that contains a MathML expression used to calculate the value of the constant or the initial value of the variable. The units of the value computed by the formula in the 'math' subelement should (in SBML Level 2 Version 4 and in SBML Level 3) or must (in previous Versions) be identical to be the units associated with the identifier given in the 'symbol' attribute. (That is, the units are the units of the species, compartment, or parameter, as appropriate for the kind of object identified by the value of 'symbol'.)
InitialAssignment was introduced in SBML Level 2 Version 2. It is not available in SBML Level 2 Version 1 nor in any version of Level 1.
The value calculated by an InitialAssignment object overrides the value assigned to the given symbol by the object defining that symbol. For example, if a compartment's 'size' attribute is set in its definition, and the model also contains an InitialAssignment having that compartment's identifier as its 'symbol' attribute value, then the interpretation is that the 'size' assigned in the Compartment object should be ignored and the value assigned based on the computation defined in the InitialAssignment. Initial assignments can take place for Compartment, Species and global Parameter objects regardless of the value of their 'constant' attribute.
The actions of all InitialAssignment objects are in general terms the same, but differ in the precise details depending on the type of variable being set:
In the case of a species, an InitialAssignment sets the referenced species' initial quantity (concentration or amount of substance) to the value determined by the formula in the 'math' subelement. The overall units of the formula should (in SBML Level 2 Version 4 and in SBML Level 3) or must (in previous Versions) be the same as the units specified for the species.
In the case of a compartment, an InitialAssignment sets the referenced compartment's initial size to the size determined by the formula in 'math'. The overall units of the formula should (in SBML Level 2 Version 4 and in SBML Level 3) or must (in previous Versions) be the same as the units specified for the size of the compartment.
In the context of a simulation, initial assignments establish values that are in effect prior to and including the start of simulation time, i.e., t <= 0. Section 3.4.8 in the SBML Level 2 Version 4 and SBML Level 3 Version 1 Core specifications provides information about the interpretation of assignments, rules, and entity values for simulation time up to and including the start time t = 0; this is important for establishing the initial conditions of a simulation if the model involves expressions containing the delay 'csymbol'.
There cannot be two initial assignments for the same symbol in a model; that is, a model must not contain two or more InitialAssignment objects that both have the same identifier as their 'symbol' attribute value. A model must also not define initial assignments and assignment rules for the same entity. That is, there cannot be both an InitialAssignment and an AssignmentRule for the same symbol in a model, because both kinds of constructs apply prior to and at the start of simulated time—allowing both to exist for a given symbol would result in indeterminism).
The ordering of InitialAssignment objects is not significant. The combined set of InitialAssignment, AssignmentRule and KineticLaw objects form a set of assignment statements that must be considered as a whole. The combined set of assignment statements should not contain algebraic loops: a chain of dependency between these statements should terminate. (More formally, consider the directed graph of assignment statements where nodes are a model's assignment statements and directed arcs exist for each occurrence of a symbol in an assignment statement 'math' attribute. The directed arcs in this graph start from the statement assigning the symbol and end at the statement that contains the symbol in their math elements. Such a graph must be acyclic.)
Finally, it is worth being explicit about the expected behavior in the following situation. Suppose (1) a given symbol has a value x assigned to it in its definition, and (2) there is an initial assignment having the identifier as its 'symbol' value and reassigning the value to y, and (3) the identifier is also used in the mathematical formula of a second initial assignment. What value should the second initial assignment use? It is y, the value assigned to the symbol by the first initial assignment, not whatever value was given in the symbol's definition. This follows directly from the behavior described above: if an InitialAssignment object exists for a given symbol, then the symbol's value is overridden by that initial assignment. Python method signature(s):
clone(InitialAssignment self)InitialAssignment
Creates and returns a deep copy of this InitialAssignment.
def libsbml.InitialAssignment.containsUndeclaredUnits | ( | self, | |
args | |||
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Python method signature(s):
containsUndeclaredUnits(InitialAssignment self)bool containsUndeclaredUnits(InitialAssignment self)
bool
Predicate returning True
if the math expression of this InitialAssignment contains parameters/numbers with undeclared units.
True
if the math expression of this InitialAssignment includes parameters/numbers with undeclared units, False
otherwise.True
indicates that the UnitDefinition returned by getDerivedUnitDefinition() may not accurately represent the units of the expression.
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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):
getCVTerms()CVTermList
Get the CVTermList of CVTerm objects in this SBase.
Returns the CVTermList for this SBase.
def libsbml.InitialAssignment.getDerivedUnitDefinition | ( | self, | |
args | |||
) |
Python method signature(s):
getDerivedUnitDefinition(InitialAssignment self)UnitDefinition getDerivedUnitDefinition(InitialAssignment self)
UnitDefinition
Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the 'math' expression of this InitialAssignment.
The units are calculated based on the mathematical expression in the InitialAssignment and the model quantities referenced by <ci>
elements used within that expression. The getDerivedUnitDefinition() method returns the calculated units.
Note that the functionality that facilitates unit analysis depends on the model as a whole. Thus, in cases where the object has not been added to a model or the model itself is incomplete, unit analysis is not possible and this method will return None
.
None
if one cannot be constructed.
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Python method signature(s):
getElementByMetaId(SBase self, string metaid)SBase
Returns the first child element it can find with a specific 'metaid' attribute value, or None
if no such object is found.
metaid | string representing the 'metaid' attribute value of the object to find. |
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Python method signature(s):
getElementBySId(SBase 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' attribute value of the object to find. |
def libsbml.InitialAssignment.getElementName | ( | self | ) |
Python method signature(s):
getElementName(InitialAssignment self)string
Returns the XML element name of this object, which for InitialAssignment, is always 'initialAssignment'
.
'initialAssignment'
. def libsbml.InitialAssignment.getId | ( | self | ) |
Python method signature(s):
getId(InitialAssignment self)string
Predicate returning True
if all the required elements for this InitialAssignment object have been set.
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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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def libsbml.InitialAssignment.getMath | ( | self | ) |
Python method signature(s):
getMath(InitialAssignment self)ASTNode
Get the mathematical formula of this InitialAssignment.
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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):
getNumPlugins(SBase self)long
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
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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):
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):
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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inherited |
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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inherited |
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.
def libsbml.InitialAssignment.getSymbol | ( | self | ) |
Python method signature(s):
getSymbol(InitialAssignment self)string
Get the value of the 'symbol' attribute of this InitialAssignment.
def libsbml.InitialAssignment.getTypeCode | ( | self | ) |
Python method signature(s):
getTypeCode(InitialAssignment 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):
getVersion(SBase self)long
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
def libsbml.InitialAssignment.hasRequiredAttributes | ( | self | ) |
Python method signature(s):
hasRequiredAttributes(InitialAssignment self)bool
Predicate returning True
if all the required attributes for this InitialAssignment object have been set.
def libsbml.InitialAssignment.hasRequiredElements | ( | self | ) |
Python method signature(s):
hasRequiredElements(InitialAssignment self)bool
Predicate returning True
if all the required elements for this InitialAssignment 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):
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.def libsbml.InitialAssignment.isSetMath | ( | self | ) |
Python method signature(s):
isSetMath(InitialAssignment self)bool
Predicate returning True
if this InitialAssignment's 'math' subelement contains a value.
True
if the 'math' for this InitialAssignment is set, False
otherwise.
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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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inherited |
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 |
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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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. def libsbml.InitialAssignment.isSetSymbol | ( | self | ) |
Python method signature(s):
isSetSymbol(InitialAssignment self)bool
Predicate returning True
if this InitialAssignment's 'symbol' attribute is set.
True
if the 'symbol' attribute of this InitialAssignment 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):
removeFromParentAndDelete(SBase self)int
Removes itself from its parent. If the parent was storing it as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). Pure virutal, as every SBase element has different parents, and therefore different methods of removing itself. Will fail (and not delete itself) if it has no parent object. This function is designed to be overridden, but for all objects whose parent is of the class ListOf, the default implementation will work.
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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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inherited |
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 |
def libsbml.InitialAssignment.renameSIdRefs | ( | self, | |
args | |||
) |
Python method signature(s):
renameSIdRefs(InitialAssignment self, string oldid, string newid)
Renames all the SIdRef attributes on this element, including any found in MathML
def libsbml.InitialAssignment.renameUnitSIdRefs | ( | self, | |
args | |||
) |
Python method signature(s):
renameUnitSIdRefs(InitialAssignment 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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inherited |
Python method signature(s):
setAnnotation(SBase self, XMLNode annotation)int setAnnotation(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:
setAnnotation(XMLNode annotation)
Sets the value of the 'annotation' subelement of this SBML object.
The content of annotation
is copied, and any previous content of this object's 'annotation' subelement is deleted.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation
that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase.appendAnnotation() or SBase.appendAnnotation().
annotation | an XML structure that is to be used as the new content of the 'annotation' subelement of this object |
Method variant with the following signature:
setAnnotation(string annotation)
Sets the value of the 'annotation' subelement of this SBML object.
The content of annotation
is copied, and any previous content of this object's 'annotation' subelement is deleted.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation
that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase.appendAnnotation() or SBase.appendAnnotation().
annotation | an XML string that is to be used as the content of the 'annotation' subelement of this object |
def libsbml.InitialAssignment.setMath | ( | self, | |
args | |||
) |
Python method signature(s):
setMath(InitialAssignment self, ASTNode math)int
Sets the 'math' subelement of this InitialAssignment.
The AST passed in math
is copied.
math | an AST containing the mathematical expression to be used as the formula for this InitialAssignment. |
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inherited |
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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inherited |
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):
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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inherited |
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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inherited |
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.
def libsbml.InitialAssignment.setSymbol | ( | self, | |
args | |||
) |
Python method signature(s):
setSymbol(InitialAssignment self, string sid)int
Sets the 'symbol' attribute value of this InitialAssignment.
sid | the identifier of a Species, Compartment or Parameter object defined elsewhere in this 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 |
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inherited |
Python method signature(s):
unsetId(SBase self)int
Unsets the value of the 'id' attribute of this SBML object.
Most (but not all) objects in SBML include two common attributes: 'id' and 'name'. The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always either Sid
or UnitSId
, depending on the object in question. Both data types are defined as follows:
letter ::= 'a'..'z','A'..'Z' digit ::= '0'..'9' idChar ::= letter | digit | '_' SId ::= ( letter | '_' ) idChar*
The equality of SId
and UnitSId
type values in SBML is determined by an exact character sequence match; i.e., comparisons of these identifiers must be performed in a case-sensitive manner. This applies to all uses of SId
and UnitSId
.
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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 |
Python method signature(s):
unsetName(SBase self)int
Unsets the value of the 'name' attribute of this SBML object.
Most (but not all) objects in SBML include two common attributes: 'id' and 'name'. In contrast to the 'id' attribute, the 'name' attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of 'name' is the type string
defined in XML Schema. SBML imposes no restrictions as to the content of 'name' attributes beyond those restrictions defined by the string
type in XML Schema.
The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)
As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.
An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.
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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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Python method signature(s):
unsetSBOTerm(SBase self)int
Unsets the value of the 'sboTerm' attribute of this SBML object.