libSBML Python API  5.11.0
Qualitative Models

The libSBML “qual” extension implements support for the SBML Level 3 Qualitative Models package.

Introduction

Quantitative methods for modeling biological networks require an in-depth knowledge of the biochemical reactions and their stoichiometric and kinetic parameters. In many practical cases, this knowledge is missing. This has led to the development of several qualitative modeling methods using information such as gene expression data coming from functional genomic experiments.

The qualitative models contemplated in this SBML Level 3 package for Qualitative Models are essentially based on the definition of regulatory or influence graphs. The components of these models differ from the species and reactions used in current SBML models. For example, qualitative models typically associate discrete levels of activities with entity pools; the processes involving them cannot be described as reactions per se but rather as transitions between states. These systems can be viewed as reactive systems, whose dynamics are represented by means of state transition graphs (or other Kripke structures representing, in the form of a graph, which nodes are the reachable states and in which the edges are the state transitions). In this context, logical regulatory networks (Boolean or multi-valued) and standard Petri nets are the two formalisms mostly used in biology that give rise to such behaviors. Published models using these approaches cover, far from exhaustively, gene regulatory networks, signalling pathways and metabolic pathways.

Despite differences from traditional SBML models, it is desirable to bring these classes of models under a common format scheme. The purpose of this Qualitative Models package for SBML Level 3 is to support encoding qualitative models in SBML.

The specification for this SBML package

This API documentation for libSBML does not provide a complete explanation of the SBML Level 3 Qualitative Models (“qual”) package. If you are developing software that uses “qual”, you are strongly urged to read the actual specification for the package. A link to the specification document current is provided below, along with a link to the page of known issues (if any).

Specification for SBML Level 3 Qualitative Models, current at the time of this libSBML release (5.11.0). Note: an Internet connection is required to access these documents.
Specification (in PDF format) Known issues
Qualitative Models package, Version 1 Release 1 Errata page
More...

Classes

class  libsbml.DefaultTerm
 qual The default result of a Transition. More...
 
class  libsbml.FunctionTerm
 qual A function term. More...
 
class  libsbml.Input
 qual The input to a QualitativeSpecies. More...
 
class  libsbml.ListOfFunctionTerms
 qual A list of FunctionTerm objects. More...
 
class  libsbml.ListOfInputs
 qual A list of Input objects. More...
 
class  libsbml.ListOfOutputs
 qual A list of Output objects. More...
 
class  libsbml.ListOfQualitativeSpecies
 qual A list of QualitativeSpecies objects. More...
 
class  libsbml.ListOfTransitions
 qual A list of Transition objects. More...
 
class  libsbml.Output
 qual The output from a QualitativeSpecies. More...
 
class  libsbml.QualExtension
 qual Base extension class for the package. More...
 
class  libsbml.QualitativeSpecies
 qual Extension of Species. More...
 
class  libsbml.QualModelPlugin
 qual Extension of Model. More...
 
class  libsbml.QualPkgNamespaces
 qual SBMLNamespaces extension for the package. More...
 
class  libsbml.Transition
 qual A transition of a QualitativeSpecies. More...
 

Functions

def libsbml.QualModelPlugin.__init__ (self, args)
 qual Extension of Model. More...
 
def libsbml.FunctionTerm.__init__ (self, args)
 qual A function term. More...
 
def libsbml.ListOfFunctionTerms.__init__ (self, args)
 qual A list of FunctionTerm objects. More...
 
def libsbml.DefaultTerm.__init__ (self, args)
 qual The default result of a Transition. More...
 
def libsbml.Input.__init__ (self, args)
 qual The input to a QualitativeSpecies. More...
 
def libsbml.ListOfInputs.__init__ (self, args)
 qual A list of Input objects. More...
 
def libsbml.Output.__init__ (self, args)
 qual The output from a QualitativeSpecies. More...
 
def libsbml.ListOfOutputs.__init__ (self, args)
 qual A list of Output objects. More...
 
def libsbml.QualitativeSpecies.__init__ (self, args)
 qual Extension of Species. More...
 
def libsbml.ListOfQualitativeSpecies.__init__ (self, args)
 qual A list of QualitativeSpecies objects. More...
 
def libsbml.Transition.__init__ (self, args)
 qual A transition of a QualitativeSpecies. More...
 
def libsbml.ListOfTransitions.__init__ (self, args)
 qual A list of Transition objects. More...
 
def libsbml.QualPkgNamespaces.clone (self)
 qual SBMLNamespaces extension for the package. More...
 
def libsbml.QualExtension.getPackageName ()
 qual Base extension class for the package. More...
 

Detailed Description

The libSBML “qual” extension implements support for the SBML Level 3 Qualitative Models package.

Introduction

Quantitative methods for modeling biological networks require an in-depth knowledge of the biochemical reactions and their stoichiometric and kinetic parameters. In many practical cases, this knowledge is missing. This has led to the development of several qualitative modeling methods using information such as gene expression data coming from functional genomic experiments.

The qualitative models contemplated in this SBML Level 3 package for Qualitative Models are essentially based on the definition of regulatory or influence graphs. The components of these models differ from the species and reactions used in current SBML models. For example, qualitative models typically associate discrete levels of activities with entity pools; the processes involving them cannot be described as reactions per se but rather as transitions between states. These systems can be viewed as reactive systems, whose dynamics are represented by means of state transition graphs (or other Kripke structures representing, in the form of a graph, which nodes are the reachable states and in which the edges are the state transitions). In this context, logical regulatory networks (Boolean or multi-valued) and standard Petri nets are the two formalisms mostly used in biology that give rise to such behaviors. Published models using these approaches cover, far from exhaustively, gene regulatory networks, signalling pathways and metabolic pathways.

Despite differences from traditional SBML models, it is desirable to bring these classes of models under a common format scheme. The purpose of this Qualitative Models package for SBML Level 3 is to support encoding qualitative models in SBML.

The specification for this SBML package

This API documentation for libSBML does not provide a complete explanation of the SBML Level 3 Qualitative Models (“qual”) package. If you are developing software that uses “qual”, you are strongly urged to read the actual specification for the package. A link to the specification document current is provided below, along with a link to the page of known issues (if any).

Specification for SBML Level 3 Qualitative Models, current at the time of this libSBML release (5.11.0). Note: an Internet connection is required to access these documents.
Specification (in PDF format) Known issues
Qualitative Models package, Version 1 Release 1 Errata page

Function Documentation

def libsbml.QualModelPlugin.__init__ (   self,
  args 
)

qual Extension of Model.

The extension of SBML Level 3 Core's Model class is relatively straightforward: the Qualitative Models Package adds two lists, one for holding qualitativeSpecies (ListOfQualitativeSpecies), and the other for holding transitions (ListOfTransitions). The Model element may contain at most one ListOfQualitativeSpecies, which must contain at least one QualitativeSpecies. It may also contain at most one ListOfTransitions which must contain at least one Transition.

This method has multiple variants; they differ in the arguments they accept.

__init__(string uri, string prefix, QualPkgNamespaces qualns)   QualModelPlugin
__init__(QualModelPlugin orig)   QualModelPlugin

Each variant is described separately below.


Method variant with the following signature:
QualModelPlugin(stringuri, stringprefix, QualPkgNamespaces qualns)

Constructor


Method variant with the following signature:
QualModelPlugin(QualModelPlugin orig)

Copy constructor. Creates a copy of this SBase object.

def libsbml.FunctionTerm.__init__ (   self,
  args 
)

qual A function term.

Each FunctionTerm is associated with a result and with a Boolean function inside a Math element that can be used to set the conditions under which this term is selected.

This method has multiple variants; they differ in the arguments they accept.

__init__(long level, long version, long pkgVersion)   FunctionTerm
__init__(long level, long version)   FunctionTerm
__init__(long level)   FunctionTerm
__init__()   FunctionTerm
__init__(QualPkgNamespaces qualns)   FunctionTerm
__init__(FunctionTerm orig)   FunctionTerm

Each variant is described separately below.


Method variant with the following signature:
FunctionTerm(QualPkgNamespaces qualns)

Creates a new FunctionTerm with the given QualPkgNamespaces object.

Parameters
qualnsthe QualPkgNamespaces object

Method variant with the following signature:
FunctionTerm(FunctionTerm orig)

Copy constructor for FunctionTerm.

Parameters
origthe FunctionTerm instance to copy.

Method variant with the following signature:
FunctionTerm(long level = QualExtension.getDefaultLevel(), long version = QualExtension.getDefaultVersion(), long pkgVersion = QualExtension.getDefaultPackageVersion())

Creates a new FunctionTerm with the given level, version, and package version.

Parameters
levela long integer, the SBML Level to assign to this FunctionTerm
versiona long integer, the SBML Version to assign to this FunctionTerm
pkgVersiona long integer, the SBML Qual Version to assign to this FunctionTerm
def libsbml.ListOfFunctionTerms.__init__ (   self,
  args 
)

qual A list of FunctionTerm objects.

The ListOfFunctionTerms is a container for the FunctionTerms of a Transition.

The various ListOf___ classes in SBML are merely containers used for organizing the main components of an SBML model. In libSBML's implementation, ListOf___ classes are derived from the intermediate utility class ListOf, which is not defined by the SBML specifications but serves as a useful programmatic construct. ListOf is itself is in turn derived from SBase, which provides all of the various ListOf___ classes with common features defined by the SBML specification, such as 'metaid' attributes and annotations.

The relationship between the lists and the rest of an SBML model is illustrated by the following (for SBML Level 2 Version 4):

Readers may wonder about the motivations for using the ListOf___ containers in SBML. A simpler approach in XML might be to place the components all directly at the top level of the model definition. The choice made in SBML is to group them within XML elements named after ListOfClassname, in part because it helps organize the components. More importantly, the fact that the container classes are derived from SBase means that software tools can add information about the lists themselves into each list container's 'annotation'.

See also
ListOfFunctionDefinitions
ListOfUnitDefinitions
ListOfCompartmentTypes
ListOfSpeciesTypes
ListOfCompartments
ListOfSpecies
ListOfParameters
ListOfInitialAssignments
ListOfRules
ListOfConstraints
ListOfReactions
ListOfEvents
Input

This method has multiple variants; they differ in the arguments they accept.

__init__(long level, long version, long pkgVersion)   ListOfFunctionTerms
__init__(long level, long version)   ListOfFunctionTerms
__init__(long level)   ListOfFunctionTerms
__init__()   ListOfFunctionTerms
__init__(QualPkgNamespaces qualns)   ListOfFunctionTerms
__init__(ListOfFunctionTerms orig)   ListOfFunctionTerms

Each variant is described separately below.


Method variant with the following signature:
ListOfFunctionTerms(QualPkgNamespaces qualns)

Creates a new ListOfFunctionTerms with the given QualPkgNamespaces object.

Parameters
qualnsthe QualPkgNamespaces object

Method variant with the following signature:
ListOfFunctionTerms(long level = QualExtension.getDefaultLevel(), long version = QualExtension.getDefaultVersion(), long pkgVersion = QualExtension.getDefaultPackageVersion())

Creates a new ListOfFunctionTerms with the given level, version, and package version.

Parameters
levela long integer, the SBML Level to assign to this ListOfFunctionTerms
versiona long integer, the SBML Version to assign to this ListOfFunctionTerms
pkgVersiona long integer, the SBML Qual Version to assign to this ListOfFunctionTerms

Method variant with the following signature:
ListOfFunctionTerms(ListOfFunctionTerms orig)
def libsbml.DefaultTerm.__init__ (   self,
  args 
)

qual The default result of a Transition.

The DefaultTerm defines the default result of a Transition. This term is used if there are no other FunctionTerm elements or if none of the Math elements of the FunctionTerm elements evaluates to True.

This method has multiple variants; they differ in the arguments they accept.

__init__(long level, long version, long pkgVersion)   DefaultTerm
__init__(long level, long version)   DefaultTerm
__init__(long level)   DefaultTerm
__init__()   DefaultTerm
__init__(QualPkgNamespaces qualns)   DefaultTerm
__init__(DefaultTerm orig)   DefaultTerm

Each variant is described separately below.


Method variant with the following signature:
DefaultTerm(QualPkgNamespaces qualns)

Creates a new DefaultTerm with the given QualPkgNamespaces object.

Parameters
qualnsthe QualPkgNamespaces object

Method variant with the following signature:
DefaultTerm(long level = QualExtension.getDefaultLevel(), long version = QualExtension.getDefaultVersion(), long pkgVersion = QualExtension.getDefaultPackageVersion())

Creates a new DefaultTerm with the given level, version, and package version.

Parameters
levela long integer, the SBML Level to assign to this DefaultTerm
versiona long integer, the SBML Version to assign to this DefaultTerm
pkgVersiona long integer, the SBML Qual Version to assign to this DefaultTerm

Method variant with the following signature:
DefaultTerm(DefaultTerm orig)

Copy constructor for DefaultTerm.

Parameters
origthe DefaultTerm instance to copy.
def libsbml.Input.__init__ (   self,
  args 
)

qual The input to a QualitativeSpecies.

Each Input refers to a QualitativeSpecies that participates in the corresponding Transition. In Petri nets, these are the input places of the transition. In logical models, they are the regulators of the species whose behaviour is defined by the transition.

This method has multiple variants; they differ in the arguments they accept.

__init__(long level, long version, long pkgVersion)   Input
__init__(long level, long version)   Input
__init__(long level)   Input
__init__()   Input
__init__(QualPkgNamespaces qualns)   Input
__init__(Input orig)   Input

Each variant is described separately below.


Method variant with the following signature:
Input(QualPkgNamespaces qualns)

Creates a new Input with the given QualPkgNamespaces object.

Parameters
qualnsthe QualPkgNamespaces object

Method variant with the following signature:
Input(long level = QualExtension.getDefaultLevel(), long version = QualExtension.getDefaultVersion(), long pkgVersion = QualExtension.getDefaultPackageVersion())

Creates a new Input with the given level, version, and package version.

Parameters
levela long integer, the SBML Level to assign to this Input
versiona long integer, the SBML Version to assign to this Input
pkgVersiona long integer, the SBML Qual Version to assign to this Input

Method variant with the following signature:
Input(Input orig)

Copy constructor for Input.

Parameters
origthe Input instance to copy.
def libsbml.ListOfInputs.__init__ (   self,
  args 
)

qual A list of Input objects.

The ListOfInputs is a container for the Inputs of a Transition.

The various ListOf___ classes in SBML are merely containers used for organizing the main components of an SBML model. In libSBML's implementation, ListOf___ classes are derived from the intermediate utility class ListOf, which is not defined by the SBML specifications but serves as a useful programmatic construct. ListOf is itself is in turn derived from SBase, which provides all of the various ListOf___ classes with common features defined by the SBML specification, such as 'metaid' attributes and annotations.

The relationship between the lists and the rest of an SBML model is illustrated by the following (for SBML Level 2 Version 4):

Readers may wonder about the motivations for using the ListOf___ containers in SBML. A simpler approach in XML might be to place the components all directly at the top level of the model definition. The choice made in SBML is to group them within XML elements named after ListOfClassname, in part because it helps organize the components. More importantly, the fact that the container classes are derived from SBase means that software tools can add information about the lists themselves into each list container's 'annotation'.

See also
ListOfFunctionDefinitions
ListOfUnitDefinitions
ListOfCompartmentTypes
ListOfSpeciesTypes
ListOfCompartments
ListOfSpecies
ListOfParameters
ListOfInitialAssignments
ListOfRules
ListOfConstraints
ListOfReactions
ListOfEvents
Input

This method has multiple variants; they differ in the arguments they accept.

__init__(long level, long version, long pkgVersion)   ListOfInputs
__init__(long level, long version)   ListOfInputs
__init__(long level)   ListOfInputs
__init__()   ListOfInputs
__init__(QualPkgNamespaces qualns)   ListOfInputs

Each variant is described separately below.


Method variant with the following signature:
ListOfInputs(QualPkgNamespaces qualns)

Creates a new ListOfInputs with the given QualPkgNamespaces object.

Parameters
qualnsthe QualPkgNamespaces object

Method variant with the following signature:
ListOfInputs(long level = QualExtension.getDefaultLevel(), long version = QualExtension.getDefaultVersion(), long pkgVersion = QualExtension.getDefaultPackageVersion())

Creates a new ListOfInputs with the given level, version, and package version.

Parameters
levela long integer, the SBML Level to assign to this ListOfInputs
versiona long integer, the SBML Version to assign to this ListOfInputs
pkgVersiona long integer, the SBML Qual Version to assign to this ListOfInputs
def libsbml.Output.__init__ (   self,
  args 
)

qual The output from a QualitativeSpecies.

Each Output refers to a QualitativeSpecies that participates in (is affected by) the corresponding Transition. In Petri net models these are the output places of the transition.

In a logical model, a QualitativeSpecies should be referenced in at most one ListOfOutputs, (that of the Transition defining the evolution of this species). When a Transition has several outputs, it is because the referenced species share the same regulators and the same logical rules.

This method has multiple variants; they differ in the arguments they accept.

__init__(long level, long version, long pkgVersion)   Output
__init__(long level, long version)   Output
__init__(long level)   Output
__init__()   Output
__init__(QualPkgNamespaces qualns)   Output
__init__(Output orig)   Output

Each variant is described separately below.


Method variant with the following signature:
Output(QualPkgNamespaces qualns)

Creates a new Output with the given QualPkgNamespaces object.

Parameters
qualnsthe QualPkgNamespaces object

Method variant with the following signature:
Output(long level = QualExtension.getDefaultLevel(), long version = QualExtension.getDefaultVersion(), long pkgVersion = QualExtension.getDefaultPackageVersion())

Creates a new Output with the given level, version, and package version.

Parameters
levela long integer, the SBML Level to assign to this Output
versiona long integer, the SBML Version to assign to this Output
pkgVersiona long integer, the SBML Qual Version to assign to this Output

Method variant with the following signature:
Output(Output orig)

Copy constructor for Output.

Parameters
origthe Output instance to copy.
def libsbml.ListOfOutputs.__init__ (   self,
  args 
)

qual A list of Output objects.

The ListOfOutputs is a container for the Output elements of a Transition.

The various ListOf___ classes in SBML are merely containers used for organizing the main components of an SBML model. In libSBML's implementation, ListOf___ classes are derived from the intermediate utility class ListOf, which is not defined by the SBML specifications but serves as a useful programmatic construct. ListOf is itself is in turn derived from SBase, which provides all of the various ListOf___ classes with common features defined by the SBML specification, such as 'metaid' attributes and annotations.

The relationship between the lists and the rest of an SBML model is illustrated by the following (for SBML Level 2 Version 4):

Readers may wonder about the motivations for using the ListOf___ containers in SBML. A simpler approach in XML might be to place the components all directly at the top level of the model definition. The choice made in SBML is to group them within XML elements named after ListOfClassname, in part because it helps organize the components. More importantly, the fact that the container classes are derived from SBase means that software tools can add information about the lists themselves into each list container's 'annotation'.

See also
ListOfFunctionDefinitions
ListOfUnitDefinitions
ListOfCompartmentTypes
ListOfSpeciesTypes
ListOfCompartments
ListOfSpecies
ListOfParameters
ListOfInitialAssignments
ListOfRules
ListOfConstraints
ListOfReactions
ListOfEvents
Output

This method has multiple variants; they differ in the arguments they accept.

__init__(long level, long version, long pkgVersion)   ListOfOutputs
__init__(long level, long version)   ListOfOutputs
__init__(long level)   ListOfOutputs
__init__()   ListOfOutputs
__init__(QualPkgNamespaces qualns)   ListOfOutputs

Each variant is described separately below.


Method variant with the following signature:
ListOfOutputs(QualPkgNamespaces qualns)

Creates a new ListOfOutputs with the given QualPkgNamespaces object.

Parameters
qualnsthe QualPkgNamespaces object

Method variant with the following signature:
ListOfOutputs(long level = QualExtension.getDefaultLevel(), long version = QualExtension.getDefaultVersion(), long pkgVersion = QualExtension.getDefaultPackageVersion())

Creates a new ListOfOutputs with the given level, version, and package version.

Parameters
levela long integer, the SBML Level to assign to this ListOfOutputs
versiona long integer, the SBML Version to assign to this ListOfOutputs
pkgVersiona long integer, the SBML Qual Version to assign to this ListOfOutputs
def libsbml.QualitativeSpecies.__init__ (   self,
  args 
)

qual Extension of Species.

Similarly to the Species in SBML, the components of qualitative models refer to pools of entities that are considered indistinguishable and are each located in a specific Compartment. However, here components are characterised by their qualitative influences rather than by taking part in reactions. Therefore, we define the QualitativeSpecies element to represent such pools of entities.

In a Petri net, qualitative species refer to the places of the model, while in a logical model, they refer to the variables of this model (i.e. nodes of the influence graph).

A QualitativeSpecies describes a pool of indistinguishable entities in a Compartment. It is associated with a level (an integer representing e.g. an activity state, or a functional level of concentration, etc.)

This method has multiple variants; they differ in the arguments they accept.

__init__(long level, long version, long pkgVersion)   QualitativeSpecies
__init__(long level, long version)   QualitativeSpecies
__init__(long level)   QualitativeSpecies
__init__()   QualitativeSpecies
__init__(QualPkgNamespaces qualns)   QualitativeSpecies
__init__(QualitativeSpecies orig)   QualitativeSpecies

Each variant is described separately below.


Method variant with the following signature:
QualitativeSpecies(QualPkgNamespaces qualns)

Creates a new QualitativeSpecies with the given QualPkgNamespaces object.

Parameters
qualnsthe QualPkgNamespaces object

Method variant with the following signature:
QualitativeSpecies(long level = QualExtension.getDefaultLevel(), long version = QualExtension.getDefaultVersion(), long pkgVersion = QualExtension.getDefaultPackageVersion())

Creates a new QualitativeSpecies with the given level, version, and package version.

Parameters
levela long integer, the SBML Level to assign to this QualitativeSpecies
versiona long integer, the SBML Version to assign to this QualitativeSpecies
pkgVersiona long integer, the SBML Qual Version to assign to this QualitativeSpecies

Method variant with the following signature:
QualitativeSpecies(QualitativeSpecies orig)

Copy constructor for QualitativeSpecies.

Parameters
origthe QualitativeSpecies instance to copy.
def libsbml.ListOfQualitativeSpecies.__init__ (   self,
  args 
)

qual A list of QualitativeSpecies objects.

The ListOfQualitativeSpecies is a container for the QualitativeSpecies elements of a Model.

The various ListOf___ classes in SBML are merely containers used for organizing the main components of an SBML model. In libSBML's implementation, ListOf___ classes are derived from the intermediate utility class ListOf, which is not defined by the SBML specifications but serves as a useful programmatic construct. ListOf is itself is in turn derived from SBase, which provides all of the various ListOf___ classes with common features defined by the SBML specification, such as 'metaid' attributes and annotations.

The relationship between the lists and the rest of an SBML model is illustrated by the following (for SBML Level 2 Version 4):

Readers may wonder about the motivations for using the ListOf___ containers in SBML. A simpler approach in XML might be to place the components all directly at the top level of the model definition. The choice made in SBML is to group them within XML elements named after ListOfClassname, in part because it helps organize the components. More importantly, the fact that the container classes are derived from SBase means that software tools can add information about the lists themselves into each list container's 'annotation'.

See also
ListOfFunctionDefinitions
ListOfUnitDefinitions
ListOfCompartmentTypes
ListOfSpeciesTypes
ListOfCompartments
ListOfSpecies
ListOfParameters
ListOfInitialAssignments
ListOfRules
ListOfConstraints
ListOfReactions
ListOfEvents
QualitativeSpecies

This method has multiple variants; they differ in the arguments they accept.

__init__(long level, long version, long pkgVersion)   ListOfQualitativeSpecies
__init__(long level, long version)   ListOfQualitativeSpecies
__init__(long level)   ListOfQualitativeSpecies
__init__()   ListOfQualitativeSpecies
__init__(QualPkgNamespaces qualns)   ListOfQualitativeSpecies

Each variant is described separately below.


Method variant with the following signature:
ListOfQualitativeSpecies(QualPkgNamespaces qualns)

Creates a new ListOfQualitativeSpecies with the given QualPkgNamespaces object.

Parameters
qualnsthe QualPkgNamespaces object

Method variant with the following signature:
ListOfQualitativeSpecies(long level = QualExtension.getDefaultLevel(), long version = QualExtension.getDefaultVersion(), long pkgVersion = QualExtension.getDefaultPackageVersion())

Creates a new ListOfQualitativeSpecies with the given level, version, and package version.

Parameters
levela long integer, the SBML Level to assign to this ListOfQualitativeSpecies
versiona long integer, the SBML Version to assign to this ListOfQualitativeSpecies
pkgVersiona long integer, the SBML Qual Version to assign to this ListOfQualitativeSpecies
def libsbml.Transition.__init__ (   self,
  args 
)

qual A transition of a QualitativeSpecies.

A Transition element contains at most one ListOfInputs and one ListOfOutputs and exactly one ListOfFunctionTerms.

A Transition defines the changes in level associated with the QualitativeSpecies that occur when a Transition is enabled.

In logical models, a Transition is used to specify the logical rule associated with a QualitativeSpecies (that appears as an Output of this Transition). For example, the rule 'if A > 1 : B = 2' would be encapsulated as a Transition with QualitativeSpecies 'A' as an Input and 'B' as an Output; the 'if A > 1' rule being encode by the math element of a FunctionTerm with the resultLevel attribute having a value '2'.

In Petri net models, a Transition is interpreted, using the common Petri net semantics, as events that might occur within the system causing tokens to be moved.

This method has multiple variants; they differ in the arguments they accept.

__init__(long level, long version, long pkgVersion)   Transition
__init__(long level, long version)   Transition
__init__(long level)   Transition
__init__()   Transition
__init__(QualPkgNamespaces qualns)   Transition
__init__(Transition orig)   Transition

Each variant is described separately below.


Method variant with the following signature:
Transition(QualPkgNamespaces qualns)

Creates a new Transition with the given QualPkgNamespaces object.

Parameters
qualnsthe QualPkgNamespaces object

Method variant with the following signature:
Transition(long level = QualExtension.getDefaultLevel(), long version = QualExtension.getDefaultVersion(), long pkgVersion = QualExtension.getDefaultPackageVersion())

Creates a new Transition with the given level, version, and package version.

Parameters
levela long integer, the SBML Level to assign to this Transition
versiona long integer, the SBML Version to assign to this Transition
pkgVersiona long integer, the SBML Qual Version to assign to this Transition

Method variant with the following signature:
Transition(Transition orig)

Copy constructor for Transition.

Parameters
origthe Transition instance to copy.
def libsbml.ListOfTransitions.__init__ (   self,
  args 
)

qual A list of Transition objects.

The ListOfTransitions is a container for the Transition elements of a Model.

The various ListOf___ classes in SBML are merely containers used for organizing the main components of an SBML model. In libSBML's implementation, ListOf___ classes are derived from the intermediate utility class ListOf, which is not defined by the SBML specifications but serves as a useful programmatic construct. ListOf is itself is in turn derived from SBase, which provides all of the various ListOf___ classes with common features defined by the SBML specification, such as 'metaid' attributes and annotations.

The relationship between the lists and the rest of an SBML model is illustrated by the following (for SBML Level 2 Version 4):

Readers may wonder about the motivations for using the ListOf___ containers in SBML. A simpler approach in XML might be to place the components all directly at the top level of the model definition. The choice made in SBML is to group them within XML elements named after ListOfClassname, in part because it helps organize the components. More importantly, the fact that the container classes are derived from SBase means that software tools can add information about the lists themselves into each list container's 'annotation'.

See also
ListOfFunctionDefinitions
ListOfUnitDefinitions
ListOfCompartmentTypes
ListOfSpeciesTypes
ListOfCompartments
ListOfSpecies
ListOfParameters
ListOfInitialAssignments
ListOfRules
ListOfConstraints
ListOfReactions
ListOfEvents
Transition

This method has multiple variants; they differ in the arguments they accept.

__init__(long level, long version, long pkgVersion)   ListOfTransitions
__init__(long level, long version)   ListOfTransitions
__init__(long level)   ListOfTransitions
__init__()   ListOfTransitions
__init__(QualPkgNamespaces qualns)   ListOfTransitions

Each variant is described separately below.


Method variant with the following signature:
ListOfTransitions(QualPkgNamespaces qualns)

Creates a new ListOfTransitions with the given QualPkgNamespaces object.

Parameters
qualnsthe QualPkgNamespaces object

Method variant with the following signature:
ListOfTransitions(long level = QualExtension.getDefaultLevel(), long version = QualExtension.getDefaultVersion(), long pkgVersion = QualExtension.getDefaultPackageVersion())

Creates a new ListOfTransitions with the given level, version, and package version.

Parameters
levela long integer, the SBML Level to assign to this ListOfTransitions
versiona long integer, the SBML Version to assign to this ListOfTransitions
pkgVersiona long integer, the SBML Qual Version to assign to this ListOfTransitions
def libsbml.QualPkgNamespaces.clone (   self)

qual SBMLNamespaces extension for the package.

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.

SBML Level 3 “packages” add features on top of SBML Level 3 Core. When a model definition uses an SBML package, it must declare the Level and Version of SBML Core and the Version of the package being used. The package name, the SBML Level and Version, and the package Version correspond uniquely to an XML namespace added to the XML encoding of the SBML model.

LibSBML Level 3 extensions are implementations of support for SBML Level 3 packages. Each package is implemented as a separate extension. To allow software applications to query the level and version information of an extension's package implementation, libSBML uses specialized object classes. For the extension implementing the SBML “qual” package, the object class is QualPkgNamespaces. (This class is a specialization of a common base class called SBMLExtensionNamespaces that is not exposed in the libSBML programming language interfaces other than C++.)

Objects of class QualPkgNamespaces can be passed to constructors of SBML components defined by “qual” in order to ensure that the correct component structure is created. This is necessary because different versions of an SBML Level 3 package may introduce differences in the definition of the components defined by the package. (For example, later editions of a package may introduce new attributes on a component that are not present in earlier editions of the package specification.)

See also
CompPkgNamespaces
FbcPkgNamespaces
LayoutPkgNamespaces

Creates and returns a deep copy of this SBMLExtensionNamespaces.

clone()   QualPkgNamespaces
Returns
a (deep) copy of this SBMLExtensionNamespaces.
def libsbml.QualExtension.getPackageName ( )

qual Base extension class for the package.

Returns the nickname of the SBML Level 3 package implemented by this libSBML extension.

getPackageName()   string
Returns
the package nickname, as a string.
Note
Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.