Core libSBML

SBML Level 3 introduced a modular architecture, in which SBML Level 3 Core is usable in its own right (much like SBML Levels 1 and 2 before it), and optional SBML Level 3 Packages add features to this Core. To support this architecture, libSBML is itself divided into a core libSBML and optional extensions.

Differences between core libSBML and extensions to libSBML

Core libSBML corresponds to the features of SBML Levels 1 to 3 Core; they are always available, and require applications to understand only the SBML core specifications. The classes listed on the rest of this page constitute libSBML's implementation of SBML Levels 1–3, without any SBML Level 3 packages.

By contrast, the libSBML extensions are plug-ins that each implement support for a given SBML Level 3 package. Separate pages of this API manual describe the libSBML extensions for those SBML Level 3 packages that are supported at this time. They are grouped under the section titled Level 3 Extensions. The stable releases of libSBML only include extensions for officially-released package specifications; additional, experimental extensions may be available for other Level 3 packages that may not yet have been finalized by the SBML community. You can find copies of these experimental extensions at the download site for libSBML on SourceForge.net.

Summary of core SBML objects implemented in libSBML

Each type of component in a plain SBML model (i.e., one that does not use any SBML packages) is described using a specific type of SBML data object that organizes the relevant information. The top level of an SBML model definition consists of lists of these components, with every list being optional. The next table enumerates the lists and objects defined by core SBML; also shown are the SBML Level+Version combinations for which they are valid.

SBML components and corresponding libSBML objects.

Level & Version	LibSBML container object	LibSBML data object(s)
Level 2 Version 1 and higher	ListOfFunctionDefinitions	FunctionDefinition
Level 2 Version 1 and higher	ListOfUnitDefinitions	UnitDefinition
Level 2 Versions 2–5	ListOfCompartmentTypes	CompartmentType
Level 1 and higher	ListOfCompartments	Compartment
Level 2 Versions 2–5	ListOfSpeciesTypes	SpeciesType
Level 1 and higher	ListOfSpecies	Species
Level 1 and higher	ListOfParameters	Parameter
Level 2 Version  and higher	ListOfInitialAssignments	InitialAssignment
Level 1 and higher	ListOfRules	AssignmentRule, AlgebraicRule, RateRule
Level 2 Version  and higher	ListOfConstraints	Constraint
Level 1 and higher	ListOfReactions	Reaction
Level 2 Version 1 and higher	ListOfEvents	Event

The list of classes below constitutes the public API of core libSBML. The list includes classes that are not defined in any SBML specification; these utility classes are provided by libSBML to implement various kinds of functionality useful in the context of working with SBML content. More...

Classes
class	AlgebraicRule
class	AssignmentRule
class	ASTNode
class	Compartment
class	CompartmentType
class	Constraint
class	ConversionOption
class	ConversionProperties
class	CVTerm
class	Date
class	DefinitionURLRegistry
class	Delay
class	ElementFilter
class	Event
class	EventAssignment
class	ExpressionAnalyser
struct	FormulaTokenizer_t
class	FunctionDefinition
class	InitialAssignment
class	KineticLaw
class	L3ParserSettings
class	List
class	ListOf
class	ListOfCompartments
class	ListOfCompartmentTypes
class	ListOfConstraints
class	ListOfEventAssignments
class	ListOfEvents
class	ListOfFunctionDefinitions
class	ListOfInitialAssignments
class	ListOfLocalParameters
class	ListOfParameters
class	ListOfReactions
class	ListOfRules
class	ListOfSpecies
class	ListOfSpeciesReferences
class	ListOfSpeciesTypes
class	ListOfUnitDefinitions
class	ListOfUnits
class	LocalParameter
class	Model
class	ModelCreator
class	ModelHistory
class	ModifierSpeciesReference
class	Parameter
class	Priority
class	RateRule
class	RDFAnnotationParser
class	Reaction
class	RenderLayoutConverter
class	Rule
class	SBase
class	SBaseExtensionPoint
class	SBasePlugin
class	SBasePluginCreator< SBasePluginType, SBMLExtensionType >
class	SBasePluginCreatorBase
class	SBMLConstructorException
class	SBMLConverter
class	SBMLConverterRegistry
class	SBMLDocument
class	SBMLDocumentPlugin
class	SBMLDocumentPluginNotRequired
class	SBMLError
class	SBMLErrorLog
class	SBMLExtension
class	SBMLExtensionException
class	SBMLExtensionNamespaces< SBMLExtensionType >
class	SBMLExtensionRegister< SBMLExtensionType >
class	SBMLExtensionRegistry
class	SBMLFunctionDefinitionConverter
class	SBMLIdConverter
class	SBMLInferUnitsConverter
class	SBMLInitialAssignmentConverter
class	SBMLInternalValidator
class	SBMLLevel1Version1Converter
class	SBMLLevelVersionConverter
class	SBMLLocalParameterConverter
class	SBMLNamespaces
class	SBMLRateOfConverter
class	SBMLRateRuleConverter
class	SBMLReactionConverter
class	SBMLReader
class	SBMLRuleConverter
class	SBMLStripPackageConverter
class	SBMLUnitsConverter
class	SBMLValidator
class	SBMLVisitor
class	SBMLWriter
class	SBO
class	SimpleSpeciesReference
class	Species
class	SpeciesReference
class	SpeciesType
class	StoichiometryMath
class	SyntaxChecker
struct	Token_t
class	Trigger
class	Unit
class	UnitDefinition
class	Validator
class	VConstraint
class	XMLAttributes
class	XMLConstructorException
class	XMLError
class	XMLErrorLog
class	XMLInputStream
class	XMLLogOverride
class	XMLNamespaces
class	XMLNode
class	XMLOutputStream
class	XMLToken
class	XMLTriple

Detailed Description

SBML Level 3 introduced a modular architecture, in which SBML Level 3 Core is usable in its own right (much like SBML Levels 1 and 2 before it), and optional SBML Level 3 Packages add features to this Core. To support this architecture, libSBML is itself divided into a core libSBML and optional extensions.

Differences between core libSBML and extensions to libSBML

Core libSBML corresponds to the features of SBML Levels 1 to 3 Core; they are always available, and require applications to understand only the SBML core specifications. The classes listed on the rest of this page constitute libSBML's implementation of SBML Levels 1–3, without any SBML Level 3 packages.

By contrast, the libSBML extensions are plug-ins that each implement support for a given SBML Level 3 package. Separate pages of this API manual describe the libSBML extensions for those SBML Level 3 packages that are supported at this time. They are grouped under the section titled Level 3 Extensions. The stable releases of libSBML only include extensions for officially-released package specifications; additional, experimental extensions may be available for other Level 3 packages that may not yet have been finalized by the SBML community. You can find copies of these experimental extensions at the download site for libSBML on SourceForge.net.

Summary of core SBML objects implemented in libSBML

Each type of component in a plain SBML model (i.e., one that does not use any SBML packages) is described using a specific type of SBML data object that organizes the relevant information. The top level of an SBML model definition consists of lists of these components, with every list being optional. The next table enumerates the lists and objects defined by core SBML; also shown are the SBML Level+Version combinations for which they are valid.

SBML components and corresponding libSBML objects.

Level & Version	LibSBML container object	LibSBML data object(s)
Level 2 Version 1 and higher	ListOfFunctionDefinitions	FunctionDefinition
Level 2 Version 1 and higher	ListOfUnitDefinitions	UnitDefinition
Level 2 Versions 2–5	ListOfCompartmentTypes	CompartmentType
Level 1 and higher	ListOfCompartments	Compartment
Level 2 Versions 2–5	ListOfSpeciesTypes	SpeciesType
Level 1 and higher	ListOfSpecies	Species
Level 1 and higher	ListOfParameters	Parameter
Level 2 Version  and higher	ListOfInitialAssignments	InitialAssignment
Level 1 and higher	ListOfRules	AssignmentRule, AlgebraicRule, RateRule
Level 2 Version  and higher	ListOfConstraints	Constraint
Level 1 and higher	ListOfReactions	Reaction
Level 2 Version 1 and higher	ListOfEvents	Event

The list of classes below constitutes the public API of core libSBML. The list includes classes that are not defined in any SBML specification; these utility classes are provided by libSBML to implement various kinds of functionality useful in the context of working with SBML content.