SBML-class {rsbml} | R Documentation

## SBML type "SBML"

### Description

The root element of an SBML document. An actual SBML `Model` may be retrieved from an instance of this class.

### Instantiation

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

### Slots

`level`:
  Object of class `"integer"` indicating the level of the SBML standard (currently at 2).
`ver`:
  Object of class `"integer"` indicating the version of the level (currently at 2 for level 2).
`model`:
  Object of class `"Model"` the SBML model itself.
`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.

### Extends

Class `"SBase"`, directly.

### Methods

coerce
  `signature(from = "SBMLDocument", to = "SBML")`: constructs the S4 object model from a low-level libsbml document.
coerce
  `signature(from = "SBML", to = "SBMLDocument")`: converts the S4 object model to a low-level libsbml document.
level
  `signature(object = "SBML")`: gets the `level` slot
level<-
  `signature(object = "SBML")`: sets the `level` slot
model
  `signature(object = "SBML")`: gets the `model` slot
model<-
  `signature(object = "SBML")`: sets the `model` slot
rsbml_doc
  `signature(model = "SBML")`: converts the S4 object model to a low-level libsbml document.
rsbml_write
  `signature(object = "SBML")`: writes this document to a file as SBML.
rsbml_xml
  `signature(object = "SBML")`: converts this document to a string as SBML.
ver
  `signature(object = "SBML")`: gets the `ver` slot
ver<-
  `signature(object = "SBML")`: sets the `ver` slot

### Author(s)

Michael Lawrence

### References

http://sbml.org/documents/

### Examples

      # Get a DOM
      doc <- rsbml_read(system.file("sbml", "GlycolysisLayout.xml", package = "rsbml"))
      dom <- rsbml_dom(doc)

      # Get the species ID's
      sapply(species(model(dom)), id)

      # Convert DOM back to a low-level document for checking
      doc <- rsbml_doc(dom)
      rsbml_check(doc)

      # Write a DOM to a file
      ## Not run: rsbml_write(dom, "my.xml")

[Package rsbml version 1.4.0 Index]