def compareModels(sbmlModel, antModel):
'''
This code needs to be rewritten.
'''
import roadrunner, pylab, antimony
sbmlModel = "00001-sbml-l2v4.xml"
antModel = sbmlModel.replace(sbmlModel[-3:], "ant")
# Make a round trip to and from Antimony
antimony.loadSBMLFile(sbmlModel)
antimony.writeAntimonyFile(antModel, antimony.getModuleNames()[1])
antimony.loadAntimonyFile(antModel)
antimony.writeSBMLFile("test.xml", antimony.getModuleNames()[1])
rr1 = roadrunner.RoadRunner(sbmlModel)
rr2 = roadrunner.RoadRunner("test.xml")
result1 = rr1.simulate(0, 10, 101)
result2 = rr2.simulate(0, 10, 101)
result = result1 - result2
pylab.plot(result[:, 0], result[:, 1:])
pylab.show()
def convertSBML2Antimony(filename):
if filename[-3:] == "xml":
model_name = filename.replace(filename[-3:], "ant")
antimony.loadSBMLFile(filename)
antimony.writeAntimonyFile(model_name, antimony.getMainModuleName())
elif filename[-3:] == "ant":
model_name = filename.replace(filename[-3:], "xml")
antimony.loadAntimonyFile(filename)
antimony.writeSBMLFile(model_name, antimony.getMainModuleName())
else:
print("Error, input file not SBML '*.xml' or Antimony '*.ant' ")
def translate_sbml(cls, sbml_file: str):
"""
Translate SBML file to Antimony model specification.
cayenne's model specification is loosely based on Antimony's model
specification.
"""
er_code = sb.loadSBMLFile(sbml_file)
if er_code == -1:
raise ModelError("Error while parsing model")
sb_module = sb.getMainModuleName()
sb_string = sb.getAntimonyString(sb_module)
return sb_string
def sbmlToCellML(sbml):
""" Convert SBML to CellML string.
:param sbml: SBML string or file
:type sbml: str | file
:return: CellML
:rtype: str
"""
if os.path.isfile(sbml):
code = antimony.loadSBMLFile(sbml)
else:
code = antimony.loadSBMLString(sbml)
_checkAntimonyReturnCode(code)
return antimony.getCellMLString(None)
def sbmlToCellML(sbml):
""" Convert SBML to CellML string.
:param sbml: SBML string or file
:type sbml: str | file
:return: CellML
:rtype: str
"""
if os.path.isfile(sbml):
code = antimony.loadSBMLFile(sbml)
else:
code = antimony.loadSBMLString(sbml)
_checkAntimonyReturnCode(code)
return antimony.getCellMLString(None)
def sbmlToAntimony(sbml):
""" Convert SBML to antimony string.
:param sbml: SBML string or file
:type sbml: str | file
:return: Antimony
:rtype: str
"""
isfile = False
try:
isfile = os.path.isfile(sbml)
except:
pass
if isfile:
code = antimony.loadSBMLFile(sbml)
else:
code = antimony.loadSBMLString(str(sbml))
_checkAntimonyReturnCode(code)
return antimony.getAntimonyString(None)
def sbmlToAntimony(sbml):
""" Convert SBML to antimony string.
:param sbml: SBML string or file
:type sbml: str | file
:return: Antimony
:rtype: str
"""
isfile = False
try:
isfile = os.path.isfile(sbml)
except:
pass
if isfile:
code = antimony.loadSBMLFile(sbml)
else:
code = antimony.loadSBMLString(str(sbml))
_checkAntimonyReturnCode(code)
return antimony.getAntimonyString(None)
def sbmlFileToAntimony(self, sbml_path, addSBO=False):
""" Converts a SBML file to Antimony source.
:param sbml_path: The path to the SBML file
:returns: A 2-tuple (module_name, antimony_source)
"""
import antimony as sb
# try to load the Antimony code`
code = sb.loadSBMLFile(sbml_path)
# if errors, bail
if self.checkAntimonyReturnCode(code):
errors = sb.getLastError()
raise RuntimeError('Errors encountered when trying to load model:\n{}'.format(errors))
module = sb.getMainModuleName()
sb_source = sb.getAntimonyString(module)
if addSBO:
sb_source = self.tryAddSBOTerms(sb_source, sbml_file=sbml_path)
return (module, sb_source)
def sbmlFileToAntimony(self, sbml_path, addSBO=False):
""" Converts a SBML file to Antimony source.
:param sbml_path: The path to the SBML file
:returns: A 2-tuple (module_name, antimony_source)
"""
import antimony as sb
# try to load the Antimony code`
code = sb.loadSBMLFile(sbml_path)
# if errors, bail
if self.checkAntimonyReturnCode(code):
errors = sb.getLastError()
raise RuntimeError('Errors encountered when trying to load model:\n{}'.format(errors))
module = sb.getMainModuleName()
sb_source = sb.getAntimonyString(module)
if addSBO:
sb_source = self.tryAddSBOTerms(sb_source, sbml_file=sbml_path)
return (module, sb_source)