libSBML C++ API  5.13.0
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 ListOfFunctionDefinitionsFunctionDefinition
Level 2 Version 1 and higher ListOfUnitDefinitionsUnitDefinition
Level 2 Versions 2–5 ListOfCompartmentTypesCompartmentType
Level 1 and higher ListOfCompartmentsCompartment
Level 2 Versions 2–5 ListOfSpeciesTypesSpeciesType
Level 1 and higher ListOfSpeciesSpecies
Level 1 and higher ListOfParametersParameter
Level 2 Version  and higher ListOfInitialAssignmentsInitialAssignment
Level 1 and higher ListOfRulesAssignmentRule, AlgebraicRule, RateRule
Level 2 Version  and higher ListOfConstraintsConstraint
Level 1 and higher ListOfReactionsReaction
Level 2 Version 1 and higher ListOfEventsEvent

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
  An SBML algebraic rule representing 0 = f(W). More...
 
class  AssignmentRule
  An SBML assignment rule representing x = f(Y). More...
 
class  ASTNode
  Abstract Syntax Trees for mathematical expressions. More...
 
class  Compartment
  An SBML compartment, where species are located. More...
 
class  CompartmentType
  A compartment type in SBML Level 2. More...
 
class  Constraint
  An SBML constraint, for stating validity assumptions. More...
 
class  ConversionOption
  A single configuration setting for an SBML converter. More...
 
class  ConversionProperties
  Set of configuration option values for a converter. More...
 
class  CVTerm
  A MIRIAM-compliant controlled vocabulary term. More...
 
class  Date
  A MIRIAM-compliant date representation. More...
 
class  Delay
  A delay on the time of execution of an SBML event. More...
 
class  ElementFilter
  Base class for filter functions. More...
 
class  Event
  A discontinuous SBML event. More...
 
class  EventAssignment
  An assignment to a variable by an SBML event. More...
 
struct  FormulaTokenizer_t
  Tracks the state of tokenizing a formula string. More...
 
class  FunctionDefinition
  A user-defined function in an SBML model. More...
 
class  InitialAssignment
  An SBML initial assignment, evaluated once only. More...
 
class  KineticLaw
  The rate expression for an SBML reaction. More...
 
class  L3ParserSettings
  Controls the behavior of the Level 3 formula parser. More...
 
class  List
  Simple, plain, generic lists. More...
 
class  ListOf
  Parent class for libSBML's "ListOfXYZ" classes. More...
 
class  ListOfCompartments
  A list of Compartment objects. More...
 
class  ListOfCompartmentTypes
  A list of CompartmentType objects. More...
 
class  ListOfConstraints
  A list of Constraint objects. More...
 
class  ListOfEventAssignments
  A list of EventAssignment objects. More...
 
class  ListOfEvents
  A list of Event objects. More...
 
class  ListOfFunctionDefinitions
  A list of FunctionDefinition objects. More...
 
class  ListOfInitialAssignments
  A list of InitialAssignment objects. More...
 
class  ListOfLocalParameters
  A list of LocalParameter objects. More...
 
class  ListOfParameters
  A list of Parameter objects. More...
 
class  ListOfReactions
  A list of Reaction objects. More...
 
class  ListOfRules
  A list of Rule objects. More...
 
class  ListOfSpecies
  A list of Species objects. More...
 
class  ListOfSpeciesReferences
  A list of SpeciesReference objects. More...
 
class  ListOfSpeciesTypes
  A list of SpeciesType objects. More...
 
class  ListOfUnitDefinitions
  A list of UnitDefinition objects. More...
 
class  ListOfUnits
  A list of Unit objects. More...
 
class  LocalParameter
  A parameter inside an SBML reaction definition. More...
 
class  Model
  An SBML model. More...
 
class  ModelCreator
  MIRIAM-compliant data about a model's creator. More...
 
class  ModelHistory
  MIRIAM-compliant data about a model's history. More...
 
class  ModifierSpeciesReference
  A reference to an SBML modifier species. More...
 
class  Parameter
  An SBML parameter: a named symbol with a value. More...
 
class  Priority
  The priority of execution of an SBML event. More...
 
class  RateRule
  An SBML rate rule representing dx/dt = f(Y). More...
 
class  RDFAnnotationParser
  MIRIAM-compliant RDF annotation reader/writer. More...
 
class  Reaction
  An SBML reaction between species in an SBML model. More...
 
class  Rule
  Parent class for SBML rules in libSBML. More...
 
class  SBase
  SBML's SBase class, base class of most SBML objects. More...
 
class  SBaseExtensionPoint
  Base class for extending SBML components More...
 
class  SBasePlugin
  Base class for extending SBML objects in packages. More...
 
class  SBasePluginCreator< SBasePluginType, SBMLExtensionType >
  Template for SBasePlugin factory objects. More...
 
class  SBasePluginCreatorBase
  Base class of SBasePluginCreator. More...
 
class  SBMLConstructorException
  Exceptions thrown by some libSBML constructors. More...
 
class  SBMLConverter
  Base class for SBML converters. More...
 
class  SBMLConverterRegister< SBMLConversionType >
  Template for SBML converter registry registrations. More...
 
class  SBMLConverterRegistry
  Registry of all libSBML SBML converters. More...
 
class  SBMLDocument
  Overall SBML container object. More...
 
class  SBMLDocumentPlugin
  Base class for extending SBMLDocument in packages. More...
 
class  SBMLDocumentPluginNotRequired
  Base class for non-required Level 3 packages plug-ins. More...
 
class  SBMLError
  An error, warning or other diagnostic. More...
 
class  SBMLErrorLog
  Log of diagnostics reported during processing. More...
 
class  SBMLExtension
  Base class for SBML Level 3 package plug-ins. More...
 
class  SBMLExtensionException
  Exception used by package extensions More...
 
class  SBMLExtensionNamespaces< SBMLExtensionType >
  Set of SBML Level + Version + namespace triples. More...
 
class  SBMLExtensionRegister< SBMLExtensionType >
  Template class for extension package registration More...
 
class  SBMLExtensionRegistry
  Registry where package extensions are registered. More...
 
class  SBMLFunctionDefinitionConverter
  Converter to expand user-defined functions in-line. More...
 
class  SBMLIdConverter
  Converter for replacing object identifiers. More...
 
class  SBMLInferUnitsConverter
  Converter for inferring and setting parameter units. More...
 
class  SBMLInitialAssignmentConverter
  Converter that removes SBML initial assignments. More...
 
class  SBMLInternalValidator
  Basic SBML consistency checks and other validations. More...
 
class  SBMLLevel1Version1Converter
  Whole-document SBML Level/Version converter. More...
 
class  SBMLLevelVersionConverter
  Whole-document SBML Level/Version converter. More...
 
class  SBMLLocalParameterConverter
  Converter to turn local parameters into global ones. More...
 
class  SBMLNamespaces
  Set of SBML Level + Version + namespace triples. More...
 
class  SBMLReactionConverter
  Converter to replace reactions with SBML rate rules. More...
 
class  SBMLReader
  File and text-string SBML reader. More...
 
class  SBMLRuleConverter
  Converter that sorts SBML rules and assignments. More...
 
class  SBMLStripPackageConverter
  Converter that removes SBML Level 3 packages. More...
 
class  SBMLUnitsConverter
  Converts a model's existing units to SI units. More...
 
class  SBMLValidator
  Base class for SBML validators. More...
 
class  SBMLVisitor
  Support class for operations on SBML objects. More...
 
class  SBMLWriter
  File and text-string SBML writer. More...
 
class  SBO
  Facilities for using the Systems Biology Ontology. More...
 
class  SimpleSpeciesReference
  Abstract class for references to species in reactions. More...
 
class  Species
  An SBML species – a pool of entities. More...
 
class  SpeciesReference
  A reference to an SBML species in a reaction. More...
 
class  SpeciesType
  A species type in SBML Level 2. More...
 
class  StoichiometryMath
  Stochiometry expressions in SBML Level 2 reactions. More...
 
class  SyntaxChecker
  Methods for checking the validity of SBML identifiers. More...
 
struct  Token_t
  A token from FormulaTokenizer_nextToken(). More...
 
class  Trigger
  The trigger expression for an SBML event. More...
 
class  Unit
  A single unit referenced in an SBML unit definition. More...
 
class  UnitDefinition
  A definition of a unit used in an SBML model. More...
 
class  Validator
  Entry point for SBML validation rules in libSBML. More...
 
class  VConstraint
  Helper class for SBML validators. More...
 
class  XMLAttributes
  A list of attributes on an XML element. More...
 
class  XMLConstructorException
  Exceptions thrown by some libSBML constructors. More...
 
class  XMLError
  XML-level errors, warnings and other diagnostics. More...
 
class  XMLErrorLog
  Log of diagnostics reported during XML processing. More...
 
class  XMLInputStream
  An interface to an XML input stream. More...
 
class  XMLLogOverride
  Facility for temporarily overriding error severities. More...
 
class  XMLNamespaces
  An XML Namespace. More...
 
class  XMLNode
  A node in libSBML's XML document tree. More...
 
class  XMLOutputStream
  Interface to an XML output stream. More...
 
class  XMLToken
  A token in an XML stream. More...
 
class  XMLTriple
  A qualified XML name. More...
 

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 ListOfFunctionDefinitionsFunctionDefinition
Level 2 Version 1 and higher ListOfUnitDefinitionsUnitDefinition
Level 2 Versions 2–5 ListOfCompartmentTypesCompartmentType
Level 1 and higher ListOfCompartmentsCompartment
Level 2 Versions 2–5 ListOfSpeciesTypesSpeciesType
Level 1 and higher ListOfSpeciesSpecies
Level 1 and higher ListOfParametersParameter
Level 2 Version  and higher ListOfInitialAssignmentsInitialAssignment
Level 1 and higher ListOfRulesAssignmentRule, AlgebraicRule, RateRule
Level 2 Version  and higher ListOfConstraintsConstraint
Level 1 and higher ListOfReactionsReaction
Level 2 Version 1 and higher ListOfEventsEvent

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.