sbml_exportEquationList: Write sbml model to filename

In dlill/petab: PEtab support for R

Write sbml model to filename

Description

Write sbml model to filename

Usage

sbml_exportEquationList(
  equationList,
  filename,
  modelname = "Model",
  unitInfo = getUnitInfo(),
  speciesInfo = getSpeciesInfo(equationList),
  parInfo = getParInfo(equationList, eventList = events),
  compartmentInfo = getCompartmentInfo(equationList),
  events = NULL
)

Arguments

equationList
filename
modelname
unitInfo
speciesInfo
parInfo
compartmentInfo

Value

NULL, called for side effect

Author(s)

Daniel Lill ([e-mail])

See Also

Other SBML export: eqnlist_addDefaultCompartment(), getCompartmentInfo(), getParInfo(), getReactionInfo(), getSpeciesInfo(), getUnitInfo(), sbml_addOneCompartment(), sbml_addOneEvent(), sbml_addOneParameter(), sbml_addOneReaction(), sbml_addOneSpecies(), sbml_addOneUnit(), sbml_initialize(), sbml_kineticLawAddParameters(), sbml_reactionAddKineticLaw(), sbml_reactionAddModifiers(), sbml_reactionAddProducts(), sbml_reactionAddReactants(), sbml_validateSBML()

Examples

equationList <- NULL
equationList <- addReaction(equationList, from = "E + S", to = "ES", rate = "(kon)*E*S",
                            description = "production of complex")
equationList <- addReaction(equationList, from = "ES", to = "E + S", rate = "koff*ES",
                            description = "decay of complex")
equationList <- addReaction(equationList, from = "ES", to = "E + P", rate = "kcat*ES",
                            description = "production of product")
equationList <- eqnlist_addDefaultCompartment(equationList, "cytoplasm")

filename <- modelname <- file.path(tempdir(), "model.xml")

parInfo <- data.table(tibble::tribble(
  ~parName, ~parValue, ~parUnit,
  "kon"   ,     0.10,"litre_per_mole_per_second" ,
  "koff"  ,     0.55,"per_second" ,
  "kcat"  ,     1.00,"per_second" ))
unitInfo <- getUnitInfo()
compartmentInfo <- getCompartmentInfo(equationList)
speciesInfo <- getSpeciesInfo(equationList)

# Eventlist 1 with values only
eventList <- eventlist(var = "E", time = 0, value = 1, root = NA, method = "replace")
eventList <- addEvent(eventList, var = "E", time = 1, value = 0, root = NA, method = "replace")
eventInfo <- getEventInfo(eventList)

# Eventlist 2 with parameters as well
eventList2 <- eventlist(var = "E", time = 0, value = "E_event1", root = NA, method = "replace")
eventList2 <- addEvent(eventList2, var = "E", time = 1, value = "E_event2", root = NA, method = "replace")
eventInfo2 <- getEventInfo(eventList2)
parInfo2 <- getParInfo(equationList, eventList2)


sbml_exportEquationList(equationList, filename, parInfo = parInfo)
sbml_exportEquationList(equationList, filename, parInfo = parInfo, eventList = eventList)
sbml_exportEquationList(equationList, filename, parInfo = parInfo2, eventList = eventList2) # don't know why this throws an error..

dlill/petab documentation built on Oct. 9, 2022, 3:07 p.m.