Beispiel #1
0
    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)
Beispiel #2
0
    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()