libSBML C API
libSBML 5.8.0 C API
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Implementation of SBML Level 2's SpeciesType construct.
The term species type refers to reacting entities independent of location. These include simple ions (e.g., protons, calcium), simple molecules (e.g., glucose, ATP), large molecules (e.g., RNA, polysaccharides, and proteins), and others.
SBML Level 2 Versions 2–4 provide an explicit SpeciesType class of object to enable Species objects of the same type to be related together. SpeciesType is a conceptual construct; the existence of SpeciesType objects in a model has no effect on the model's numerical interpretation. Except for the requirement for uniqueness of species/species type combinations located in compartments, simulators and other numerical analysis software may ignore SpeciesType definitions and references to them in a model.
There is no mechanism in SBML Level 2 for representing hierarchies of species types. One SpeciesType object cannot be the subtype of another SpeciesType object; SBML provides no means of defining such relationships.
As with other major structures in SBML, SpeciesType has a mandatory attribute, "id", used to give the species type an identifier. The identifier must be a text string conforming to the identifer syntax permitted in SBML. SpeciesType also has an optional "name" attribute, of type string
. The "id" and "name" must be used according to the guidelines described in the SBML specification (e.g., Section 3.3 in the Level 2 Version 4 specification).
SpeciesType was introduced in SBML Level 2 Version 2. It is not available in SBML Level 1 nor in Level 3.