Species-class: SBML type "Species"

In rsbml: R support for SBML, using libsbml

Description

A participant in an SBML model.

Instantiation

Objects can be created by calls of the form new("Species", ...).

Slots

id:

Object of class "character" uniquely identifying this component.

name:

Object of class "character" naming this component.

compartment:

Object of class "character" identifying the compartment in which this species is located.

initialAmount:

Object of class "numeric" indicating the initial amount for this species (mutually exclusive with initialConcentration).

initialConcentration:

Object of class "numeric" indicating the initial concentration for this species (mutually exclusive with initialAmount).

substanceUnits:

Object of class "character" identifying the units for the amount of this species or the numerator of the concentration.

spatialSizeUnits:

Object of class "character" identifying the units for the denominator of the species concentration.

hasOnlySubstanceUnits:

Object of class "logical" indicating whether the quantity of this species is specified as an amount or a concentration.

boundaryCondition:

Object of class "logical". If TRUE, indicates that the quantity of this species cannot be changed by a reaction.

charge:

Object of class "integer" indicating the electrical charge of this species.

constant:

Object of class "logical" indicating whether the quantity of this species can change.

units:

Object of class "character", deprecated.

metaId:

Object of class "character" that is an XML ID "described" by an RDF resource. This links an SBML element to an RDF resource. RDF may appear anywhere in an SBML element, but is usually placed inside the annotation element.

notes:

Object of class "character" containing user-readable XHTML notes about an element.

annotation:

Object of class "character" containing additional machine-readable information about an element, usually as RDF, such as BioPAX. This is where application-specific data belongs.

cvTerms:

Object of class "list" containing instances of CVTerm associated with this element.

sboTerm:

Object of class "integer" identifying a term in the Systems Biology Ontology (SBO).

Extends

Class "SBase", directly.

Methods

id

signature(object = "Species"): gets the id slot

id<-

signature(object = "Species"): sets the id slot

name

signature(object = "Species"): gets the name slot

name<-

signature(object = "Species"): sets the name slot

boundaryCondition

signature(object = "Species"): gets the boundaryCondition slot

boundaryCondition<-

signature(object = "Species"): sets the boundaryCondition slot

charge

signature(object = "Species"): gets the charge slot

charge<-

signature(object = "Species"): sets the charge slot

compartment

signature(object = "Species"): gets the compartment slot

compartment<-

signature(object = "Species"): sets the compartment slot

constant

signature(object = "Species"): gets the constant slot

constant<-

signature(object = "Species"): sets the constant slot

units

signature(object = "Species"): gets the constant slot

units<-

signature(object = "Species"): sets the constant slot

hasOnlySubstanceUnits

signature(object = "Species"): gets the hasOnlySubstanceUnits slot

hasOnlySubstanceUnits<-

signature(object = "Species"): sets the hasOnlySubstanceUnits slot

initialAmount

signature(object = "Species"): gets the initialAmount slot

initialAmount<-

signature(object = "Species"): sets the initialAmount slot

initialConcentration

signature(object = "Species"): gets the initialConcentration slot

initialConcentration<-

signature(object = "Species"): sets the initialConcentration slot

spatialSizeUnits

signature(object = "Species"): gets the spatialSizeUnits slot

spatialSizeUnits<-

signature(object = "Species"): sets the spatialSizeUnits slot

substanceUnits

signature(object = "Species"): gets the substanceUnits slot

substanceUnits<-

signature(object = "Species"): sets the substanceUnits slot

Author(s)

Michael Lawrence

References

http://sbml.org/documents/

rsbml documentation built on Nov. 8, 2020, 8:09 p.m.