libSBML Python API
5.8.0
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SBML converter for reordering rules and assignments in a model.
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 converter reorders assignments in a model. Specifically, it sorts the list of assignment rules (i.e., the AssignmentRule objects contained in the ListOfAssignmentRules within the Model object) and the initial assignments (i.e., the InitialAssignment objects contained in the ListOfInitialAssignments) such that, within each set, assignments that depend on prior values are placed after the values are set. For example, if there is an assignment rule stating a = b + 1, and another rule stating b = 3, the list of rules is sorted and the rules are arranged so that the rule for b = 3 appears before the rule for a = b + 1. Similarly, if dependencies of this sort exist in the list of initial assignments in the model, the initial assignments are sorted as well.
Beginning with SBML Level 2, assignment rules have no ordering required—the order in which the rules appear in an SBML file has no significance. Software tools, however, may need to reorder assignments for purposes of evaluating them. For example, for simulators that use time integration methods, it would be a good idea to reorder assignment rules such as the following,
b = a + 10 seconds
a = time
so that the evaluation of the rules is independent of integrator step sizes. (This is due to the fact that, in this case, the order in which the rules are evaluated changes the result.) This converter can be used to reorder the SBML objects regardless of whether the input file contained them in the desired order. Here is a code fragment to illustrate how to do that:
ConversionProperties props; props.addOption('sortRules', true, 'sort rules'); SBMLConverter converter; converter.setProperties(&props); converter.setDocument(&doc); converter.convert();
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.SBMLRuleConverter.clone | ( | self | ) |
Python method signature(s):
clone(SBMLRuleConverter self)SBMLConverter
Creates and returns a deep copy of this SBMLLevelVersionConverter object.
def libsbml.SBMLRuleConverter.convert | ( | self | ) |
Python method signature(s):
convert(SBMLRuleConverter 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.SBMLRuleConverter.getDefaultProperties | ( | self | ) |
Python method signature(s):
getDefaultProperties(SBMLRuleConverter 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.SBMLRuleConverter.init | ( | ) |
SBML converter for reordering rules and assignments in a model.
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 converter reorders assignments in a model. Specifically, it sorts the list of assignment rules (i.e., the AssignmentRule objects contained in the ListOfAssignmentRules within the Model object) and the initial assignments (i.e., the InitialAssignment objects contained in the ListOfInitialAssignments) such that, within each set, assignments that depend on prior values are placed after the values are set. For example, if there is an assignment rule stating a = b + 1, and another rule stating b = 3, the list of rules is sorted and the rules are arranged so that the rule for b = 3 appears before the rule for a = b + 1. Similarly, if dependencies of this sort exist in the list of initial assignments in the model, the initial assignments are sorted as well.
Beginning with SBML Level 2, assignment rules have no ordering required—the order in which the rules appear in an SBML file has no significance. Software tools, however, may need to reorder assignments for purposes of evaluating them. For example, for simulators that use time integration methods, it would be a good idea to reorder assignment rules such as the following,
b = a + 10 seconds
a = time
so that the evaluation of the rules is independent of integrator step sizes. (This is due to the fact that, in this case, the order in which the rules are evaluated changes the result.) This converter can be used to reorder the SBML objects regardless of whether the input file contained them in the desired order. Here is a code fragment to illustrate how to do that:
ConversionProperties props; props.addOption('sortRules', true, 'sort rules'); SBMLConverter converter; converter.setProperties(&props); converter.setDocument(&doc); converter.convert();
init()
def libsbml.SBMLRuleConverter.matchesProperties | ( | self, | |
args | |||
) |
Python method signature(s):
matchesProperties(SBMLRuleConverter 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 SBMLLevelVersionConverter 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. |