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
	An SBML algebraic rule representing 0 = f(W). More...
class	AssignmentRule_t
	An SBML assignment rule representing x = f(Y). More...
class	ASTNode_t
	Abstract Syntax Tree (AST) representation of a mathematical expression. More...
class	Compartment_t
	An SBML compartment, where species are located. More...
class	CompartmentType_t
	A compartment type in SBML Level 2. More...
class	Constraint_t
	An SBML constraint, for stating validity assumptions. More...
class	ConversionOption_t
	A single configuration setting for an SBML converter. More...
class	ConversionProperties_t
	Set of configuration option values for a converter. More...
class	CVTerm_t
	A MIRIAM-compliant controlled vocabulary term. More...
class	Date_t
	A MIRIAM-compliant date representation. More...
class	DefinitionURLRegistry_t
	Registry of all libSBML SBML DefinitionURLs. More...
class	Delay_t
	A delay on the time of execution of an SBML event. More...
class	ElementFilter_t
	Base class for filter functions. More...
class	Event_t
	A discontinuous SBML event. More...
class	EventAssignment_t
	An assignment to a variable by an SBML event. More...
struct	FormulaTokenizer_t
	Tokenizes a mathematical formula string in SBML Level 1 syntax. More...
class	FunctionDefinition_t
	A user-defined function in an SBML model. More...
class	InitialAssignment_t
	An SBML initial assignment, evaluated once only. More...
class	KineticLaw_t
	The rate expression for an SBML reaction. More...
class	L3ParserSettings_t
	Controls the behavior of the Level 3 formula parser. More...
class	List_t
	Simple, plain, generic lists. More...
class	ListOf_t
	Parent class for libSBML's "ListOfXYZ" classes. More...
class	ListOfCompartments_t
	A list of Compartment_t objects. More...
class	ListOfCompartmentTypes_t
	A list of CompartmentType_t objects. More...
class	ListOfConstraints_t
	A list of Constraint_t objects. More...
class	ListOfEventAssignments_t
	A list of EventAssignment_t objects. More...
class	ListOfEvents_t
	A list of Event_t objects. More...
class	ListOfFunctionDefinitions_t
	A list of FunctionDefinition_t objects. More...
class	ListOfInitialAssignments_t
	A list of InitialAssignment_t objects. More...
class	ListOfLocalParameters_t
	A list of LocalParameter_t objects. More...
class	ListOfParameters_t
	A list of Parameter_t objects. More...
class	ListOfReactions_t
	A list of Reaction_t objects. More...
class	ListOfRules_t
	A list of Rule_t objects. More...
class	ListOfSpecies_t
	A list of Species_t objects. More...
class	ListOfSpeciesReferences_t
	A list of SpeciesReference_t objects. More...
class	ListOfSpeciesTypes_t
	A list of SpeciesType_t objects. More...
class	ListOfUnitDefinitions_t
	A list of UnitDefinition_t objects. More...
class	ListOfUnits_t
	A list of Unit_t objects. More...
class	LocalParameter_t
	A parameter inside an SBML reaction definition. More...
class	Model_t
	An SBML model. More...
class	ModelCreator_t
	MIRIAM-compliant data about a model's creator. More...
class	ModelHistory_t
	MIRIAM-compliant data about a model's history. More...
class	ModifierSpeciesReference_t
	A reference to an SBML modifier species. More...
class	Parameter_t
	An SBML parameter: a named symbol with a value. More...
class	Priority_t
	The priority of execution of an SBML event. More...
class	RateRule_t
	An SBML rate rule representing dx/dt = f(Y). More...
class	RDFAnnotationParser_t
	MIRIAM-compliant RDF annotation reader/writer. More...
class	Reaction_t
	An SBML reaction between species in an SBML model. More...
class	RenderLayoutConverter_t
	Converts an SBML document with Layout_t and Render information between the Level 3 package version and the Level 2 annotation version. More...
class	Rule_t
	Parent class for SBML rules in libSBML. More...
class	SBase_t
	SBML's SBase class, base class of most SBML objects. More...
class	SBaseExtensionPoint_t
	Base class for extending SBML components More...
class	SBasePlugin_t
	Base class for extending SBML objects in packages. More...
class	SBasePluginCreator_t
	Template for SBasePlugin_t factory objects. More...
class	SBasePluginCreatorBase_t
	Base class of SBasePluginCreator. More...
class	SBMLConstructorException_t
	Exceptions thrown by some libSBML constructors. More...
class	SBMLConverter_t
	Base class for SBML converters. More...
class	SBMLConverterRegistry_t
	Registry of all libSBML SBML converters. More...
class	SBMLDocument_t
	Overall SBML container object. More...
class	SBMLDocumentPlugin_t
	Base class for extending SBMLDocument_t in packages. More...
class	SBMLDocumentPluginNotRequired_t
	Base class for non-required Level 3 packages plug-ins. More...
class	SBMLError_t
	An error, warning or other diagnostic. More...
class	SBMLErrorLog_t
	Log of diagnostics reported during processing. More...
class	SBMLExtension_t
	Base class for SBML Level 3 package plug-ins. More...
class	SBMLExtensionException_t
	Exception used by package extensions More...
class	SBMLExtensionNamespaces_t
	Set of SBML Level + Version + namespace triples. More...
class	SBMLExtensionRegister_t
	Template class for extension package registration More...
class	SBMLExtensionRegistry_t
	Registry where package extensions are registered. More...
class	SBMLFunctionDefinitionConverter_t
	Converter to expand user-defined functions in-line. More...
class	SBMLIdConverter_t
	Converter for replacing object identifiers. More...
class	SBMLInferUnitsConverter_t
	Converter for inferring and setting parameter units. More...
class	SBMLInitialAssignmentConverter_t
	Converter that removes SBML initial assignments. More...
class	SBMLInternalValidator_t
	Basic SBML consistency checks and other validations. More...
class	SBMLLevel1Version1Converter_t
	Whole-document SBML Level/Version converter. More...
class	SBMLLevelVersionConverter_t
	Whole-document SBML Level/Version converter. More...
class	SBMLLocalParameterConverter_t
	Converter to turn local parameters into global ones. More...
class	SBMLNamespaces_t
	Set of SBML Level + Version + namespace triples. More...
class	SBMLRateOfConverter_t
	Converter to inteerchange csymbol 'rateOf' with FunctionDefinition_t. More...
class	SBMLReactionConverter_t
	Converter to replace reactions with SBML rate rules. More...
class	SBMLReader_t
	File and text-string SBML reader. More...
class	SBMLRuleConverter_t
	Converter that sorts SBML rules and assignments. More...
class	SBMLStripPackageConverter_t
	Converter that removes SBML Level 3 packages. More...
class	SBMLUnitsConverter_t
	Converts a model's existing units to SI units. More...
class	SBMLValidator_t
	Base class for SBML validators. More...
class	SBMLVisitor_t
	Support class for operations on SBML objects. More...
class	SBMLWriter_t
	File and text-string SBML writer. More...
class	SBO_t
	Facilities for using the Systems Biology Ontology. More...
class	SimpleSpeciesReference_t
	Abstract class for references to species in reactions. More...
class	Species_t
	An SBML species – a pool of entities. More...
class	SpeciesReference_t
	A reference to an SBML species in a reaction. More...
class	SpeciesType_t
	A species type in SBML Level 2. More...
class	StoichiometryMath_t
	Stochiometry expressions in SBML Level 2 reactions. More...
class	SyntaxChecker_t
	Methods for checking the validity of SBML identifiers. More...
struct	Token_t
	Structure used to store a token returned by FormulaTokenizer_nextToken(). More...
union	Token_t.value
class	Trigger_t
	The trigger expression for an SBML event. More...
class	Unit_t
	A single unit referenced in an SBML unit definition. More...
class	UnitDefinition_t
	A definition of a unit used in an SBML model. More...
class	Validator_t
	Entry point for SBML validation rules in libSBML. More...
class	VConstraint_t
	Helper class for SBML validators. More...
class	XMLAttributes_t
	A list of attributes on an XML element. More...
class	XMLConstructorException_t
	Exceptions thrown by some libSBML constructors. More...
class	XMLError_t
	XML-level errors, warnings and other diagnostics. More...
class	XMLErrorLog_t
	Log of diagnostics reported during XML processing. More...
class	XMLInputStream_t
	An interface to an XML input stream. More...
class	XMLLogOverride_t
	Facility for temporarily overriding error severities. More...
class	XMLNamespaces_t
	An XML Namespace. More...
class	XMLNode_t
	A node in libSBML's XML document tree. More...
class	XMLOutputStream_t
	Interface to an XML output stream. More...
class	XMLToken_t
	A token in an XML stream. More...
class	XMLTriple_t
	A qualified XML name. More...

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Data Structure Documentation

class DefinitionURLRegistry_t

class ElementFilter_t

class ListOfConstraints_t

class ListOfUnits_t

class RenderLayoutConverter_t

class SBasePluginCreator_t

class SBasePluginCreatorBase_t

class SBMLConstructorException_t

class SBMLConverter_t

class SBMLConverterRegistry_t

class SBMLDocumentPluginNotRequired_t

class SBMLError_t

class SBMLErrorLog_t

class SBMLExtensionException_t

class SBMLExtensionRegister_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 SBMLRateOfConverter_t

class SBMLReactionConverter_t

class SBMLRuleConverter_t

class SBMLStripPackageConverter_t

class SBMLUnitsConverter_t

class SBMLValidator_t

class SBMLVisitor_t

class SBO_t

class SimpleSpeciesReference_t

struct Token_t

Data Fields
long	exponent	Secondary field used when the token is a real in e-notation.
TokenType_t	type	This token's type.
union Token_t	value	Value of the token.

union Token_t.value

Data Fields
char	ch	Member used when the token is a character.
long	integer	Member used when the token is an integer.
char *	name	Member used when the token is a symbol.
double	real	Member used when the token is a real.

class Validator_t

class VConstraint_t

class XMLConstructorException_t

class XMLLogOverride_t