libSBML Python API
5.8.0
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SBML converter for replacing initial assignments.
This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. It is a class used in the implementation of extra functionality provided by libSBML.
This is an SBML converter for replacing InitialAssignment objects (when possible) by setting the initial value attributes on the model objects being assigned. In other words, for every object that is the target of an initial assignment in the model, it evaluates the mathematical expression of the assignment to get a numerical value, and then sets the corresponding attribute of the object to the value. The effects for different kinds of SBML components are as follows:
Component | Effect |
---|---|
Compartment | Sets the value of the size attribute. |
Species | Sets the value of either the initialAmount or the initialConcentration attributes, depending on the value of the Species object's hasOnlySubstanceUnits attribute. |
Parameter | Sets the value of the value attribute. |
SpeciesReference | Sets the value of the stoichiometry attribute in the Reaction object where the SpeciesReference object appears. |
Public Member Functions | |
def | clone |
def | convert |
def | getDefaultProperties |
def | getDocument |
def | getProperties |
def | getTargetNamespaces |
def | init |
def | matchesProperties |
def | setDocument |
def | setProperties |
def libsbml.SBMLInitialAssignmentConverter.clone | ( | self | ) |
Python method signature(s):
clone(SBMLInitialAssignmentConverter self)SBMLConverter
Creates and returns a deep copy of this SBMLInitialAssignmentConverter object.
def libsbml.SBMLInitialAssignmentConverter.convert | ( | self | ) |
Python method signature(s):
convert(SBMLInitialAssignmentConverter self)int
Perform the conversion.
This method causes the converter to do the actual conversion work, that is, to convert the SBMLDocument object set by SBMLConverter.setDocument() and with the configuration options set by SBMLConverter.setProperties().
def libsbml.SBMLInitialAssignmentConverter.getDefaultProperties | ( | self | ) |
Python method signature(s):
getDefaultProperties(SBMLInitialAssignmentConverter self)ConversionProperties
Returns the default properties of this converter.
A given converter exposes one or more properties that can be adjusted in order to influence the behavior of the converter. This method returns the default property settings for this converter. It is meant to be called in order to discover all the settings for the converter object.
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inherited |
Python method signature(s):
getDocument(SBMLConverter self)SBMLDocument getDocument(SBMLConverter self)
SBMLDocument
Returns the SBML document that is the subject of the conversions.
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inherited |
Python method signature(s):
getProperties(SBMLConverter self)ConversionProperties
Returns the current properties in effect for this converter.
A given converter exposes one or more properties that can be adjusted in order to influence the behavior of the converter. This method returns the current properties for this converter; in other words, the settings in effect at this moment. To change the property values, you can use SBMLConverter.setProperties().
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inherited |
Python method signature(s):
getTargetNamespaces(SBMLConverter self)SBMLNamespaces
Returns the target SBML namespaces of the currently set properties.
SBML namespaces are used by libSBML to express the Level+Version of the SBML document (and, possibly, any SBML Level 3 packages in use). Some converters' behavior is affected by the SBML namespace configured in the converter. For example, the actions of SBMLLevelVersionConverter, the converter for converting SBML documents from one Level+Version combination to another, are fundamentally dependent on the SBML namespaces being targeted.
def libsbml.SBMLInitialAssignmentConverter.init | ( | ) |
SBML converter for replacing initial assignments.
This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. It is a class used in the implementation of extra functionality provided by libSBML.
This is an SBML converter for replacing InitialAssignment objects (when possible) by setting the initial value attributes on the model objects being assigned. In other words, for every object that is the target of an initial assignment in the model, it evaluates the mathematical expression of the assignment to get a numerical value, and then sets the corresponding attribute of the object to the value. The effects for different kinds of SBML components are as follows:
Component | Effect |
---|---|
Compartment | Sets the value of the size attribute. |
Species | Sets the value of either the initialAmount or the initialConcentration attributes, depending on the value of the Species object's hasOnlySubstanceUnits attribute. |
Parameter | Sets the value of the value attribute. |
SpeciesReference | Sets the value of the stoichiometry attribute in the Reaction object where the SpeciesReference object appears. |
init()
def libsbml.SBMLInitialAssignmentConverter.matchesProperties | ( | self, | |
args | |||
) |
Python method signature(s):
matchesProperties(SBMLInitialAssignmentConverter self, ConversionProperties props)bool
Returns True
if this converter object's properties match the given properties.
A typical use of this method involves creating a ConversionProperties object, setting the options desired, and then calling this method on an SBMLInitialAssignmentConverter object to find out if the object's property values match the given ones. This method is also used by SBMLConverterRegistry.getConverterFor() to search across all registered converters for one matching particular properties.
props | the properties to match. |
True
if this converter's properties match, False
otherwise.
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inherited |
Python method signature(s):
setDocument(SBMLConverter self, SBMLDocument doc)int
Sets the current SBML document to the given SBMLDocument object.
doc | the document to use for this conversion. |
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inherited |
Python method signature(s):
setProperties(SBMLConverter self, ConversionProperties props)int
Sets the configuration properties to be used by this converter.
A given converter exposes one or more properties that can be adjusted in order to influence the behavior of the converter. This method sets the current properties for this converter.
props | the ConversionProperties object defining the properties to set. |