libSBML C++ API  5.18.0
Multistate, Multicomponent and Multicompartment Species

The libSBML “multi” extension implements support for the SBML Level 3 Multistate, Multicomponent and Multicompartment Species package.

Introduction

The SBML Level 3 Multistate, Multicomponent and Multicompartment Species (multi) package provides an extension of SBML Level 3 that supports encoding models with molecular complexes that have multiple components and can exist in multiple states and in multiple compartments. One of its goals also is to provide a platform for sharing models based on the specifications of bimolecular interactions and the rules governing such interactions. In addition, this specification includes features to support multicompartment species (species that are described as residing in more than one compartment).

Authors

The primary authors of the SBML Level 3 Multistate, Multicomponent and Multicompartment Species specification are Fenkgai Zhang and Martin Meier-Schellersheim.

The specification for this SBML package

This API documentation for libSBML does not provide a complete explanation of the SBML Level 3 Multistate, Multicomponent and Multicompartment Species package (whose nickname is “multi”). If you are developing software that uses “multi”, 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 the SBML Level 3 Multistate, Multicomponent and Multicompartment Species package, current at the time of this libSBML release (5.18.0). Note: an Internet connection is required to access these documents.
Specification (in PDF format) Known issues
Multistate, Multicomponent and Multicompartment Species package, Version 1 Release 1 Errata page
More...

Classes

class  BindingSiteSpeciesType
 multi Extension of MultiSpeciesType to define a binding site. More...
 
class  CompartmentReference
 multi Child of a Compartment that references a different Compartment. More...
 
class  InSpeciesTypeBond
 multi Defines a bond within a MultiSpeciesType. More...
 
class  IntraSpeciesReaction
 multi A subclass of Reaction for changes of an internal species bond. More...
 
class  ListOfCompartmentReferences
 multi A list of CompartmentReference objects. More...
 
class  ListOfInSpeciesTypeBonds
 multi A list of InSpeciesTypeBond objects. More...
 
class  ListOfMultiSpeciesTypes
 multi A list of MultiSpeciesType objects. More...
 
class  ListOfOutwardBindingSites
 multi A list of OutwardBindingSite objects. More...
 
class  ListOfPossibleSpeciesFeatureValues
 multi A list of PossibleSpeciesFeatureValue objects. More...
 
class  ListOfSpeciesFeatures
 multi A list of SpeciesFeature objects. More...
 
class  ListOfSpeciesFeatureTypes
 multi A list of SpeciesFeatureType objects. More...
 
class  ListOfSpeciesFeatureValues
 multi A list of SpeciesFeatureValue objects. More...
 
class  ListOfSpeciesTypeComponentIndexes
 multi A list of SpeciesTypeComponentIndex objects. More...
 
class  ListOfSpeciesTypeComponentMapInProducts
 multi A list of SpeciesTypeComponentMapInProduct objects. More...
 
class  ListOfSpeciesTypeInstances
 multi A list of SpeciesTypeInstance objects. More...
 
class  MultiASTPlugin
 multi Extension of ASTBasePlugin. More...
 
class  MultiCompartmentPlugin
 multi Extension of Compartment for the "multi" package. More...
 
class  MultiExtension
 multi Base extension class for the package. More...
 
class  MultiListOfReactionsPlugin
 multi Extension of ListOfReactions for the "multi" package. More...
 
class  MultiModelPlugin
 multi Extension of Model. More...
 
class  MultiPkgNamespaces
 multi SBMLNamespaces extension for the "multi" package. More...
 
class  MultiSBMLDocumentPlugin
 multi Extension of SBMLDocument for the "multi" package. More...
 
class  MultiSimpleSpeciesReferencePlugin
 multi Extension of SimpleSpeciesReference for the "multi" package. More...
 
class  MultiSpeciesPlugin
 multi Extension of Species for the "multi" package. More...
 
class  MultiSpeciesReferencePlugin
 multi Extension of SpeciesReference for the "multi" package. More...
 
class  MultiSpeciesType
 multi A type of Species in SBML Level 3 "multi" More...
 
class  MultiValidator
 multi Entry point for package validation. More...
 
class  OutwardBindingSite
 multi Defines a outward-facing binding site for a MultiSpeciesType. More...
 
class  PossibleSpeciesFeatureValue
 multi Defines one value of a SpeciesFeature. More...
 
class  SpeciesFeature
 multi Defines a feature of a multi Species. More...
 
class  SpeciesFeatureType
 multi Defines a template for referencing SpeciesFeature objects. More...
 
class  SpeciesFeatureValue
 multi Defines a particular value for a SpeciesFeature. More...
 
class  SpeciesTypeComponentIndex
 multi Identifies a component within a MultiSpeciesType. More...
 
class  SpeciesTypeComponentMapInProduct
 multi Distinguishes between components in reactants versus products. More...
 
class  SpeciesTypeInstance
 multi Allows construction of structured MultiSpeciesType objects. More...
 
class  SubListOfSpeciesFeatures
 multi Defines a set of SpeciesFeature objects. More...
 

Detailed Description

The libSBML “multi” extension implements support for the SBML Level 3 Multistate, Multicomponent and Multicompartment Species package.

Introduction

The SBML Level 3 Multistate, Multicomponent and Multicompartment Species (multi) package provides an extension of SBML Level 3 that supports encoding models with molecular complexes that have multiple components and can exist in multiple states and in multiple compartments. One of its goals also is to provide a platform for sharing models based on the specifications of bimolecular interactions and the rules governing such interactions. In addition, this specification includes features to support multicompartment species (species that are described as residing in more than one compartment).

Authors

The primary authors of the SBML Level 3 Multistate, Multicomponent and Multicompartment Species specification are Fenkgai Zhang and Martin Meier-Schellersheim.

The specification for this SBML package

This API documentation for libSBML does not provide a complete explanation of the SBML Level 3 Multistate, Multicomponent and Multicompartment Species package (whose nickname is “multi”). If you are developing software that uses “multi”, 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 the SBML Level 3 Multistate, Multicomponent and Multicompartment Species package, current at the time of this libSBML release (5.18.0). Note: an Internet connection is required to access these documents.
Specification (in PDF format) Known issues
Multistate, Multicomponent and Multicompartment Species package, Version 1 Release 1 Errata page