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 2.42.0 Index]