Species-class {rsbml} | R Documentation

## SBML type "Species"

### 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/

[Package rsbml version 2.2.1 Index]