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 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()
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()
class Core2interfaces(object):
"""
Defines interfaces for translating PySCeS model objects into and from other formats.
"""
core = None
sbml = None
core2sbml = None
core2psc = None
sbml2core = None
sbml_level = 2
sbml_version = 1
def __buildPscComponents__(self):
"""
Builds the PSC file
"""
self.core2psc.setHeader()
self.core2psc.setFixed()
self.core2psc.setCompartments()
self.core2psc.setFunctions()
self.core2psc.setReactions()
self.core2psc.setAssignmentRules()
self.core2psc.setRateRules()
self.core2psc.setEvents()
self.core2psc.setSpecies()
self.core2psc.setParameters()
self.core2psc.setNotes()
def __buildSbmlComponents__(self):
"""
The SBML file build commands
"""
self.core2sbml.createModel()
self.core2sbml.setDescription()
self.core2sbml.setUnits()
self.core2sbml.setCompartments()
self.core2sbml.setSpecies()
self.core2sbml.setParameters()
self.core2sbml.setReactions()
self.core2sbml.setEvents()
self.core2sbml.setRules()
def writeMod2PSC(self, mod, filename=None, directory=None, iValues=True, getstrbuf=False):
"""
Writes a PySCeS model object to a PSC file.
- *filename*: writes <filename>.psc or <model_name>.psc if None
- *directory*: (optional) an output directory
- *iValues*: if True then the models initial values are used (or the current values if False).
- *getstrbuf*: if True a StringIO buffer is returned instead of writing to disk
"""
self.core = NewCore(mod, iValues=iValues)
assert self.core != None, "\nPlease set a PySCeS model or Core2 object"
self.core2psc = CoreToPsc(self.core)
if not iValues:
self.core2psc.SPECIES_CURRENT_VALUE = True
self.core2psc.FIXED_SPECIES_CURRENT_VALUE = True
self.core2psc.PARAMETER_CURRENT_VALUE = True
self.__buildPscComponents__()
if filename == None: filename = self.core.name
if filename[-4:] != '.psc': filename += '.psc'
if not getstrbuf:
self.core2psc.write(filename, directory, getstrbuf)
else:
return self.core2psc.write(filename, directory, getstrbuf)
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 readSBMLToCore(self, filename, directory=None):
"""
Reads the SBML file specified with filename and converts it into
a core2 object pysces.interface.core
- *filename*: the SBML file
- *directory*: (optional) the SBML file directory None means try the current working directory
"""
if directory != None:
fpath = os.path.join(directory, filename)
assert os.path.exists(fpath), "\nFile \"%s\" does not exist!" % fpath
self.sbml2core = SbmlToCore()
self.sbml2core.getSbmlStringFromDisk(filename, Dir=directory)
self.sbml2core.getSbmlModel()
self.sbml2core.getParsedModel()
self.sbml2core.getUnits()
self.core = NewCore(self.sbml2core)
def readMod2Core(self, mod, iValues=True):
"""
Convert a PySCeS model object to core2
- *iValues*: if True then the models initial values are used (or the current values if False).
"""
self.core = NewCore(mod, iValues=iValues)
def writeCore2PSC(self, filename=None, directory=None, getstrbuf=False):
"""
Writes a Core2 object to a PSC file.
- *filename*: writes <filename>.xml or <model_name>.xml if None
- *directory*: (optional) an output directory
- *getstrbuf*: if True a StringIO buffer is returned instead of writing to disk
"""
assert self.core != None, "\nPlease set a PySCeS model or Core2 object"
## print 'Using existing self.core'
self.core2psc = CoreToPsc(self.core)
self.__buildPscComponents__()
if filename == None: filename = self.core.name
if filename[-4:] != '.psc': filename += '.psc'
if not getstrbuf:
self.core2psc.write(filename, directory, getstrbuf)
else:
return self.core2psc.write(filename, directory, getstrbuf)
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()
def convertSBML2PSC(self, sbmlfile, sbmldir=None, pscfile=None, pscdir=None):
"""
Convert an SBML file to a PySCeS MDL input file.
- *sbmlfile*: the SBML file name
- *sbmldir*: the directory of SBML files (if None current working directory is assumed)
- *pscfile*: the output PSC file name (if None *sbmlfile*.psc is used)
- *pscdir*: the PSC output directory (if None the pysces.model_dir is used)
"""
if sbmldir == None or not os.path.exists(sbmldir):
sbmldir = os.getcwd()
if not os.path.exists(os.path.join(sbmldir,sbmlfile)):
raise RuntimeError, '\nSBML file \"%s\" does not exist!' % os.path.join(sbmldir,sbmlfile)
if pscdir == None or not os.path.exists(pscdir):
pscdir = model_dir
if pscfile == None:
pscfile = '%s.psc' % sbmlfile
self.readSBMLToCore(filename=sbmlfile, directory=sbmldir)
self.writeCore2PSC(filename=pscfile, directory=pscdir, getstrbuf=False)
print '\nSBML2PSC\nin : %s\nout: %s' % (os.path.join(sbmldir,sbmlfile),os.path.join(pscdir,pscfile))
class Core2interfaces(object):
"""
Defines interfaces for translating PySCeS model objects into and from other formats.
"""
core = None
sbml = None
core2sbml = None
core2psc = None
sbml2core = None
sbml_level = 2
sbml_version = 1
def __buildPscComponents__(self):
"""
Builds the PSC file
"""
self.core2psc.setHeader()
self.core2psc.setFixed()
self.core2psc.setCompartments()
self.core2psc.setFunctions()
self.core2psc.setReactions()
self.core2psc.setAssignmentRules()
self.core2psc.setRateRules()
self.core2psc.setEvents()
self.core2psc.setSpecies()
self.core2psc.setParameters()
self.core2psc.setNotes()
def __buildSbmlComponents__(self):
"""
The SBML file build commands
"""
self.core2sbml.createModel()
self.core2sbml.setDescription()
self.core2sbml.setUnits()
self.core2sbml.setCompartments()
self.core2sbml.setSpecies()
self.core2sbml.setParameters()
self.core2sbml.setReactions()
self.core2sbml.setEvents()
self.core2sbml.setRules()
def writeMod2PSC(self,
mod,
filename=None,
directory=None,
iValues=True,
getstrbuf=False):
"""
Writes a PySCeS model object to a PSC file.
- *filename*: writes <filename>.psc or <model_name>.psc if None
- *directory*: (optional) an output directory
- *iValues*: if True then the models initial values are used (or the current values if False).
- *getstrbuf*: if True a StringIO buffer is returned instead of writing to disk
"""
self.core = NewCore(mod, iValues=iValues)
assert self.core != None, "\nPlease set a PySCeS model or Core2 object"
self.core2psc = CoreToPsc(self.core)
if not iValues:
self.core2psc.SPECIES_CURRENT_VALUE = True
self.core2psc.FIXED_SPECIES_CURRENT_VALUE = True
self.core2psc.PARAMETER_CURRENT_VALUE = True
self.__buildPscComponents__()
if filename == None: filename = self.core.name
if filename[-4:] != '.psc': filename += '.psc'
if not getstrbuf:
self.core2psc.write(filename, directory, getstrbuf)
else:
return self.core2psc.write(filename, directory, getstrbuf)
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 readSBMLToCore(self, filename, directory=None):
"""
Reads the SBML file specified with filename and converts it into
a core2 object pysces.interface.core
- *filename*: the SBML file
- *directory*: (optional) the SBML file directory None means try the current working directory
"""
if directory != None:
fpath = os.path.join(directory, filename)
assert os.path.exists(
fpath), "\nFile \"%s\" does not exist!" % fpath
self.sbml2core = SbmlToCore()
self.sbml2core.getSbmlStringFromDisk(filename, Dir=directory)
self.sbml2core.getSbmlModel()
self.sbml2core.getParsedModel()
self.sbml2core.getUnits()
self.core = NewCore(self.sbml2core)
def readMod2Core(self, mod, iValues=True):
"""
Convert a PySCeS model object to core2
- *iValues*: if True then the models initial values are used (or the current values if False).
"""
self.core = NewCore(mod, iValues=iValues)
def writeCore2PSC(self, filename=None, directory=None, getstrbuf=False):
"""
Writes a Core2 object to a PSC file.
- *filename*: writes <filename>.xml or <model_name>.xml if None
- *directory*: (optional) an output directory
- *getstrbuf*: if True a StringIO buffer is returned instead of writing to disk
"""
assert self.core != None, "\nPlease set a PySCeS model or Core2 object"
## print 'Using existing self.core'
self.core2psc = CoreToPsc(self.core)
self.__buildPscComponents__()
if filename == None: filename = self.core.name
if filename[-4:] != '.psc': filename += '.psc'
if not getstrbuf:
self.core2psc.write(filename, directory, getstrbuf)
else:
return self.core2psc.write(filename, directory, getstrbuf)
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()
def convertSBML2PSC(self,
sbmlfile,
sbmldir=None,
pscfile=None,
pscdir=None):
"""
Convert an SBML file to a PySCeS MDL input file.
- *sbmlfile*: the SBML file name
- *sbmldir*: the directory of SBML files (if None current working directory is assumed)
- *pscfile*: the output PSC file name (if None *sbmlfile*.psc is used)
- *pscdir*: the PSC output directory (if None the pysces.model_dir is used)
"""
if sbmldir == None or not os.path.exists(sbmldir):
sbmldir = os.getcwd()
if not os.path.exists(os.path.join(sbmldir, sbmlfile)):
raise RuntimeError, '\nSBML file \"%s\" does not exist!' % os.path.join(
sbmldir, sbmlfile)
if pscdir == None or not os.path.exists(pscdir):
pscdir = model_dir
if pscfile == None:
pscfile = '%s.psc' % sbmlfile
self.readSBMLToCore(filename=sbmlfile, directory=sbmldir)
self.writeCore2PSC(filename=pscfile, directory=pscdir, getstrbuf=False)
print '\nSBML2PSC\nin : %s\nout: %s' % (os.path.join(
sbmldir, sbmlfile), os.path.join(pscdir, pscfile))