def writeMod2SBML(self,
mod,
filename=None,
directory=None,
iValues=True,
getdocument=False,
getstrbuf=False):
"""
Writes a PySCeS model object to an SBML file.
- *filename*: writes <filename>.xml or <model_name>.xml if None
- *directory*: (optional) an output directory
- *iValues*: if True then the models initial values are used (or the current values if False).
- *getdocument*: if True an SBML document object is returned instead of writing to disk or
- *getstrbuf*: if True a StringIO buffer is returned instead of writing to disk
"""
self.core = NewCore(mod, iValues=iValues)
## assert os.sys.platform != 'win32', '\nSBML translation currently only supported on Linux (Mac?)'
assert self.core != None, "\nPlease set a PySCeS model or Core2 object"
self.core2sbml = CoreToSBML(self.core)
self.core2sbml.level = self.sbml_level
self.core2sbml.version = self.sbml_version
assert self.core2sbml.SBML != None, "\nProblems loading SBML/Python interface"
self.__buildSbmlComponents__()
if filename == None: filename = self.core.name
if filename[-4:] != '.xml': filename += '.xml'
if getdocument:
return self.core2sbml.getSBMLdocument()
elif getstrbuf:
return self.core2sbml.getSBMLFileAsStrBuf()
else:
self.core2sbml.writeSBML2file(filename, directory)
def writeCore2SBML(self, filename=None, directory=None, getdocument=False):
"""
Writes Core2 object to an SBML file.
- *filename*: writes <filename>.xml or <model_name>.xml if None
- *directory*: (optional) an output directory
- *getdocument*: if True an SBML document object is returned instead of writing to disk or
"""
assert self.core != None, "\nPlease set a PySCeS model or Core2 object"
## print 'Using existing self.core'
self.core2sbml = CoreToSBML(self.core)
self.core2sbml.level = self.sbml_level
self.core2sbml.version = self.sbml_version
assert self.core2sbml.SBML != None, "\nProblems loading SBML/Python interface"
self.__buildSbmlComponents__()
if filename == None: filename = self.core.name
if filename[-4:] != '.xml': filename += '.xml'
if not getdocument:
self.core2sbml.writeSBML2file(filename, directory)
else:
return self.core2sbml.getSBMLdocument()
