rsbml (version 2.30.0)

SBMLDocument-class: "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, strict = FALSE, consistency = TRUE): Check for problems with the document and signal R conditions if any errors are detected. If strict is TRUE, libsbml warnings will be emitted as R warnings (these are often too pedantic). If consistency is also TRUE, reports problems regarding internal model inconsistencies. This can be time consuming.

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.

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)