SBML-class: SBML type "SBML"

In rsbml: R support for SBML, using libsbml

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")

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