Core libSBML

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.

Data Structures
class	AlgebraicRule_t
class	AssignmentRule_t
class	ASTNode_t
class	Compartment_t
class	CompartmentType_t
class	Constraint_t
class	ConversionOption_t
class	ConversionProperties_t
class	CVTerm_t
class	Date_t
class	DefinitionURLRegistry_t
class	Delay_t
class	ElementFilter_t
class	Event_t
class	EventAssignment_t
class	ExpressionAnalyser_t
class	FormulaTokenizer_t
	@_tstruct_t _tFormulaTokenizer_t_t @_tsbmlbrief_t{_tcore_t} _tTracks_t _tthe_t _tstate_t _tof_t _ttokenizing_t _ta_t _tformula_t _tstring_t. More...
class	FunctionDefinition_t
class	InitialAssignment_t
class	KineticLaw_t
class	L3ParserSettings_t
class	List_t
class	ListOf_t
class	ListOfCompartments_t
class	ListOfCompartmentTypes_t
class	ListOfConstraints_t
class	ListOfEventAssignments_t
class	ListOfEvents_t
class	ListOfFunctionDefinitions_t
class	ListOfInitialAssignments_t
class	ListOfLocalParameters_t
class	ListOfParameters_t
class	ListOfReactions_t
class	ListOfRules_t
class	ListOfSpecies_t
class	ListOfSpeciesReferences_t
class	ListOfSpeciesTypes_t
class	ListOfUnitDefinitions_t
class	ListOfUnits_t
class	LocalParameter_t
class	Model_t
class	ModelCreator_t
class	ModelHistory_t
class	ModifierSpeciesReference_t
class	Parameter_t
class	Priority_t
class	RateRule_t
class	RDFAnnotationParser_t
class	Reaction_t
class	Rule_t
class	SBase_t
class	SBaseExtensionPoint_t
class	SBasePlugin_t
class	SBasePluginCreator_t
class	SBasePluginCreatorBase_t
class	SBMLConstructorException_t
class	SBMLConverter_t
class	SBMLConverterRegistry_t
class	SBMLDocument_t
class	SBMLDocumentPlugin_t
class	SBMLDocumentPluginNotRequired_t
class	SBMLError_t
class	SBMLErrorLog_t
class	SBMLExtension_t
class	SBMLExtensionException_t
class	SBMLExtensionNamespaces_t
class	SBMLExtensionRegister_t
class	SBMLExtensionRegistry_t
class	SBMLFunctionDefinitionConverter_t
class	SBMLIdConverter_t
class	SBMLInferUnitsConverter_t
class	SBMLInitialAssignmentConverter_t
class	SBMLInternalValidator_t
class	SBMLLevel1Version1Converter_t
class	SBMLLevelVersionConverter_t
class	SBMLLocalParameterConverter_t
class	SBMLNamespaces_t
class	SBMLRateOfConverter_t
class	SBMLRateRuleConverter_t
class	SBMLReactionConverter_t
class	SBMLReader_t
class	SBMLRuleConverter_t
class	SBMLStripPackageConverter_t
class	SBMLUnitsConverter_t
class	SBMLValidator_t
class	SBMLVisitor_t
class	SBMLWriter_t
class	SBO_t
class	SimpleSpeciesReference_t
class	Species_t
class	SpeciesReference_t
class	SpeciesType_t
class	StoichiometryMath_t
class	SyntaxChecker_t
class	Trigger_t
class	Unit_t
class	UnitDefinition_t
class	Validator_t
class	VConstraint_t
class	XMLAttributes_t
class	XMLConstructorException_t
class	XMLError_t
class	XMLErrorLog_t
class	XMLInputStream_t
class	XMLLogOverride_t
class	XMLNamespaces_t
class	XMLNode_t
class	XMLOutputStream_t
class	XMLToken_t
class	XMLTriple_t

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Data Structure Documentation

AlgebraicRule_t

class AlgebraicRule_t

AssignmentRule_t

class AssignmentRule_t

ASTNode_t

class ASTNode_t

Compartment_t

class Compartment_t

CompartmentType_t

class CompartmentType_t

Constraint_t

class Constraint_t

ConversionOption_t

class ConversionOption_t

ConversionProperties_t

class ConversionProperties_t

CVTerm_t

class CVTerm_t

Date_t

class Date_t

DefinitionURLRegistry_t

class DefinitionURLRegistry_t

Delay_t

class Delay_t

ElementFilter_t

class ElementFilter_t

Event_t

class Event_t

EventAssignment_t

class EventAssignment_t

ExpressionAnalyser_t

class ExpressionAnalyser_t

FormulaTokenizer_t

class FormulaTokenizer_t

Data Fields
char *	formula	Field used to store the formula string.
unsigned int	pos	Field used to store the current parsing position.

FunctionDefinition_t

class FunctionDefinition_t

InitialAssignment_t

class InitialAssignment_t

KineticLaw_t

class KineticLaw_t

L3ParserSettings_t

class L3ParserSettings_t

List_t

class List_t

ListOf_t

class ListOf_t

ListOfCompartments_t

class ListOfCompartments_t

ListOfCompartmentTypes_t

class ListOfCompartmentTypes_t

ListOfConstraints_t

class ListOfConstraints_t

ListOfEventAssignments_t

class ListOfEventAssignments_t

ListOfEvents_t

class ListOfEvents_t

ListOfFunctionDefinitions_t

class ListOfFunctionDefinitions_t

ListOfInitialAssignments_t

class ListOfInitialAssignments_t

ListOfLocalParameters_t

class ListOfLocalParameters_t

ListOfParameters_t

class ListOfParameters_t

ListOfReactions_t

class ListOfReactions_t

ListOfRules_t

class ListOfRules_t

ListOfSpecies_t

class ListOfSpecies_t

ListOfSpeciesReferences_t

class ListOfSpeciesReferences_t

ListOfSpeciesTypes_t

class ListOfSpeciesTypes_t

ListOfUnitDefinitions_t

class ListOfUnitDefinitions_t

ListOfUnits_t

class ListOfUnits_t

LocalParameter_t

class LocalParameter_t

Model_t

class Model_t

ModelCreator_t

class ModelCreator_t

ModelHistory_t

class ModelHistory_t

ModifierSpeciesReference_t

class ModifierSpeciesReference_t

Parameter_t

class Parameter_t

Priority_t

class Priority_t

RateRule_t

class RateRule_t

RDFAnnotationParser_t

class RDFAnnotationParser_t

Reaction_t

class Reaction_t

Rule_t

class Rule_t

SBase_t

class SBase_t

SBaseExtensionPoint_t

class SBaseExtensionPoint_t

SBasePlugin_t

class SBasePlugin_t

SBasePluginCreator_t

class SBasePluginCreator_t

SBasePluginCreatorBase_t

class SBasePluginCreatorBase_t

SBMLConstructorException_t

class SBMLConstructorException_t

SBMLConverter_t

class SBMLConverter_t

SBMLConverterRegistry_t

class SBMLConverterRegistry_t

SBMLDocument_t

class SBMLDocument_t

SBMLDocumentPlugin_t

class SBMLDocumentPlugin_t

SBMLDocumentPluginNotRequired_t

class SBMLDocumentPluginNotRequired_t

SBMLError_t

class SBMLError_t

SBMLErrorLog_t

class SBMLErrorLog_t

SBMLExtension_t

class SBMLExtension_t

SBMLExtensionException_t

class SBMLExtensionException_t

SBMLExtensionNamespaces_t

class SBMLExtensionNamespaces_t

SBMLExtensionRegister_t

class SBMLExtensionRegister_t

SBMLExtensionRegistry_t

class SBMLExtensionRegistry_t

SBMLFunctionDefinitionConverter_t

class SBMLFunctionDefinitionConverter_t

SBMLIdConverter_t

class SBMLIdConverter_t

SBMLInferUnitsConverter_t

class SBMLInferUnitsConverter_t

SBMLInitialAssignmentConverter_t

class SBMLInitialAssignmentConverter_t

SBMLInternalValidator_t

class SBMLInternalValidator_t

SBMLLevel1Version1Converter_t

class SBMLLevel1Version1Converter_t

SBMLLevelVersionConverter_t

class SBMLLevelVersionConverter_t

SBMLLocalParameterConverter_t

class SBMLLocalParameterConverter_t

SBMLNamespaces_t

class SBMLNamespaces_t

SBMLRateOfConverter_t

class SBMLRateOfConverter_t

SBMLRateRuleConverter_t

class SBMLRateRuleConverter_t

SBMLReactionConverter_t

class SBMLReactionConverter_t

SBMLReader_t

class SBMLReader_t

SBMLRuleConverter_t

class SBMLRuleConverter_t

SBMLStripPackageConverter_t

class SBMLStripPackageConverter_t

SBMLUnitsConverter_t

class SBMLUnitsConverter_t

SBMLValidator_t

class SBMLValidator_t

SBMLVisitor_t

class SBMLVisitor_t

SBMLWriter_t

class SBMLWriter_t

SBO_t

class SBO_t

SimpleSpeciesReference_t

class SimpleSpeciesReference_t

Species_t

class Species_t

SpeciesReference_t

class SpeciesReference_t

SpeciesType_t

class SpeciesType_t

StoichiometryMath_t

class StoichiometryMath_t

SyntaxChecker_t

class SyntaxChecker_t

Trigger_t

class Trigger_t

Unit_t

class Unit_t

UnitDefinition_t

class UnitDefinition_t

Validator_t

class Validator_t

VConstraint_t

class VConstraint_t

XMLAttributes_t

class XMLAttributes_t

XMLConstructorException_t

class XMLConstructorException_t

XMLError_t

class XMLError_t

XMLErrorLog_t

class XMLErrorLog_t

XMLInputStream_t

class XMLInputStream_t

XMLLogOverride_t

class XMLLogOverride_t

XMLNamespaces_t

class XMLNamespaces_t

XMLNode_t

class XMLNode_t

XMLOutputStream_t

class XMLOutputStream_t

XMLToken_t

class XMLToken_t

XMLTriple_t

class XMLTriple_t