"SBMLDocument" from libsbml

Description

Low-level libsbml document structure.

Instantiation

A virtual Class: No objects may be created from it.

Extends

Class "oldClass", directly.

Methods

rsbml_check

signature(object = "SBMLDocument"): rsbml_check(object, quiet = FALSE, verbose = FALSE): semantically validates the document. If quiet is TRUE, emits warnings describing errors and fatal failures encountered when the document was parsed. If verbose is also TRUE, reports less critical warnings about problems in the model, such as internal inconsistencies.

rsbml_dom

signature(doc = "SBMLDocument"): Constructs an S4 object model from a libsbml document.

rsbml_graph

signature(doc = "SBMLDocument"): Converts a libsbml document to a graph.

rsbml_problems

signature(object = "SBMLDocument"): reports problems encountered during parsing and/or validation.

rsbml_write

signature(object = "SBMLDocument"): writes this document to a file as SBML.

rsbml_xml

signature(object = "SBMLDocument"): converts this document to a string as SBML.

simulate

signature(object = "SBMLDocument"): simulate(object, nsim = 10, seed, ...): a shortcut for simulating the model in this document using the SBML ODE Solver library. Arguments in ... should match slots of SOSProtocol. See simulate for more details.

Author(s)

Michael Lawrence

References

http://sbml.org/documents/

Examples

  # Read a document into an R DOM
  dom <- rsbml_read(system.file("sbml", "GlycolysisLayout.xml", package
= "rsbml"))
  
  # Convert to a graph
  graph <- rsbml_graph(dom)
  
  # Write it out to a file
  ## Not run: rsbml_write(dom, "my.xml")
  
  # Or convert it to a string of XML
  rsbml_xml(dom)

  # Read into external libsbml data structure
  doc <- rsbml_read(system.file("sbml", "GlycolysisLayout.xml", package
= "rsbml"), dom = FALSE)
  
  # Convert it explicitly to an S4 DOM
  dom <- rsbml_dom(doc)