SBML-class {rsbml} | R Documentation |
The root element of an SBML document. An actual SBML
Model
may be retrieved from an instance of this class.
Objects can be created by calls of the form new("SBML", ...)
.
level
:"integer"
indicating the
level of the SBML standard (currently at 2). ver
:"integer"
indicating the
version of the level (currently at 2 for level 2). model
:"Model"
the SBML model itself. metaId
:"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
:"character"
containing user-readable XHTML notes about an element. annotation
:"character"
containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.cvTerms
:"list"
containing
instances of CVTerm
associated with this
element.sboTerm
:"integer"
identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase"
, directly.
signature(from = "SBMLDocument", to = "SBML")
:
constructs the S4 object model from a low-level libsbml document.signature(from = "SBML", to = "SBMLDocument")
:
converts the S4 object model to a low-level libsbml document. signature(from = "SBML", to = "graph")
:
converts the S4 object model to a graph. signature(object = "SBML")
: gets the level
slot signature(object = "SBML")
: sets the level
slot signature(object = "SBML")
: gets the model
slot signature(object = "SBML")
: sets the model
slot signature(model = "SBML")
: converts the S4 object model
to a low-level libsbml document.signature(object = "SBML")
: writes this document
to a file as SBML.signature(object = "SBML")
: converts this document
to a string as SBML.signature(object = "SBML")
: converts this
document to a graph object. signature(object = "SBML")
: converts this
document to an internal SBMLDocument
and
calls simulate
on it.signature(object = "SBML")
: gets the ver
slot signature(object = "SBML")
: sets the ver
slot Michael Lawrence
# 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")