def toXMLString(self, enzmldoc):
'''
Converts EnzymeMLDocument to XML string.
Args:
EnzymeMLDocument enzmldoc: Previously created instance of an EnzymeML document
'''
doc = SBMLDocument()
doc.setLevelAndVersion(enzmldoc.getLevel(), enzmldoc.getVersion())
model = doc.createModel()
model.setName(enzmldoc.getName())
model.setId(enzmldoc.getName())
# Add references
self.__addRefs(model, enzmldoc)
# Add units
self.__addUnits(model, enzmldoc)
# Add Vessel
self.__addVessel(model, enzmldoc)
# Add protein
self.__addProteins(model, enzmldoc)
# Add reactants
self.__addReactants(model, enzmldoc)
# Add reactions
self.__addReactions(model, enzmldoc, csv=False)
# Write to EnzymeML
writer = SBMLWriter()
return writer.writeToString(doc)
def toSBML(self, enzmldoc):
'''
Returns libSBML model.
Args:
EnzymeMLDocument enzmldoc: Previously created instance of an EnzymeML document
'''
doc = SBMLDocument()
doc.setLevelAndVersion(enzmldoc.getLevel(), enzmldoc.getVersion())
model = doc.createModel()
model.setName(enzmldoc.getName())
model.setId(enzmldoc.getName())
# Add references
self.__addRefs(model, enzmldoc)
# Add units
self.__addUnits(model, enzmldoc)
# Add Vessel
self.__addVessel(model, enzmldoc)
# Add protein
self.__addProteins(model, enzmldoc)
# Add reactants
self.__addReactants(model, enzmldoc)
# Add reactions
self.__addReactions(model, enzmldoc, csv=False)
return doc
def toFile(self, enzmldoc, path):
'''
Writes EnzymeMLDocument object to an .omex container
Args:
EnzymeMLDocument enzmldoc: Previously created instance of an EnzymeML document
String path: EnzymeML file is written to this destination
'''
self.path = path + '/' + enzmldoc.getName()
try:
os.makedirs(self.path + '/data')
except FileExistsError:
pass
doc = SBMLDocument()
doc.setLevelAndVersion(enzmldoc.getLevel(), enzmldoc.getVersion())
model = doc.createModel()
model.setName(enzmldoc.getName())
model.setId(enzmldoc.getName())
# Add references
self.__addRefs(model, enzmldoc)
# Add units
self.__addUnits(model, enzmldoc)
# Add Vessel
self.__addVessel(model, enzmldoc)
# Add protein
self.__addProteins(model, enzmldoc)
# Add reactants
self.__addReactants(model, enzmldoc)
# Add reactions
self.__addReactions(model, enzmldoc)
# Write to EnzymeML
writer = SBMLWriter()
writer.writeSBMLToFile(doc, self.path + '/experiment.xml')
# Write to OMEX
self.__createArchive(enzmldoc, doc)
os.remove(self.path + '/experiment.xml')
os.remove(self.path + '/data/data.csv')
os.rmdir(self.path + '/data')
