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.

`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

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.

coerce

  `signature(from = "SBML", to = "graph")`: converts the S4 object model to a graph.

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.

rsbml\_graph

  `signature(object = "SBML")`: converts this document to a graph object.

rsbml\_check

  `signature(object = "SBML")`: perform consistency checks, see `rsbml_check`.

simulate

  `signature(object = "SBML")`: converts this document to an internal `SBMLDocument` and calls `simulate` on it.

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
      dom <- rsbml_read(system.file("sbml", "GlycolysisLayout.xml", package = "rsbml"))

      # 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 2.44.0 Index]