def antimonyToSBML(self, sb_str, SBO=False):
""" Converts an Antimony string to raw SBML.
:param sb_str: The raw Antimony string
:returns: A 2-tuple (module_name, raw_sbml)
"""
import antimony as sb
if not SBO:
sbo_parser = antimonySBOParser(sb_str)
try:
sb_str = sbo_parser.elideSBOTerms()
except:
pass
# try to load the Antimony code`
code = sb.loadAntimonyString(sb_str)
# if errors, bail
if self.checkAntimonyReturnCode(code):
errors = sb.getLastError()
raise RuntimeError('Errors encountered when trying to load model into Antimony:\n{}'.format(errors))
module = sb.getMainModuleName()
sbml = sb.getSBMLString(module)
if not SBO:
sbml = sbo_parser.addSBOsToSBML(sbml)
return (module, sbml)
def antimonyToSBML(self, sb_str, SBO=False):
""" Converts an Antimony string to raw SBML.
:param sb_str: The raw Antimony string
:returns: A 2-tuple (module_name, raw_sbml)
"""
import antimony as sb
if not SBO:
sbo_parser = antimonySBOParser(sb_str)
try:
sb_str = sbo_parser.elideSBOTerms()
except:
pass
# try to load the Antimony code`
code = sb.loadAntimonyString(sb_str)
# if errors, bail
if self.checkAntimonyReturnCode(code):
errors = sb.getLastError()
raise RuntimeError(
'Errors encountered when trying to load model into Antimony:\n{}'
.format(errors))
module = sb.getMainModuleName()
sbml = sb.getSBMLString(module)
if not SBO:
sbml = sbo_parser.addSBOsToSBML(sbml)
return (module, sbml)
def loada(sbstr):
import antimony as sb
r = sb.loadAntimonyString(sbstr)
if r < 0:
raise RuntimeError('Failed to load Antimony model: {}'.format(
sb.getLastError()))
return roadrunner.RoadRunner(sb.getSBMLString(sb.getModuleNames()[-1]))
def _checkAntimonyReturnCode(code):
""" Helper for checking the antimony response code.
Raises Exception if error in antimony.
:param code: antimony response
:type code: int
"""
if code < 0:
raise Exception("Antimony: {}".format(antimony.getLastError()))
def cellmlStrToAntimony(CellMLStr):
"""Convert a cellml string into the
equivalent antimony string:
ant = cellMLStrToAntimony('mymodel.cellml')
"""
if antimony.loadCellMLFile(CellMLStr) < 0:
raise Exception("Error calling cellMLStrToAntimony" + antimony.getLastError())
return antimony.getAntimonyString(None)
def cellmlStrToSBML(CellMLStr):
"""Convert a cellml string into the
equivalent SBML string:
sbmlStr = cellMLStrToSBML('mymodel.cellml')
"""
if antimony.loadCellMLFile(CellMLStr) < 0:
raise Exception("Error calling cellMLStrToSBML" + antimony.getLastError())
return antimony.getSBMLString(None)
def _checkAntimonyReturnCode(code):
""" Helper for checking the antimony response code.
Raises Exception if error in antimony.
:param code: antimony response
:type code: int
"""
if code < 0:
raise Exception('Antimony: {}'.format(antimony.getLastError()))
def cellmlFileToSBML(CellMLFileName):
"""Load a cellml file and return the
equivalent SBML string:
sbmlStr = cellMLToSBML('mymodel.cellml')
"""
if antimony.loadCellMLFile(CellMLFileName) < 0:
raise Exception("Error calling loadCellMLFile" + antimony.getLastError())
return antimony.getSBMLString(None)
def sbmlToAntimony(str):
"""Convert a SBML string into Antimony:
sbmlStr = sbmlToAntimony (antimonyStr)
"""
err = antimony.loadSBMLString(str)
if err < 0:
raise Exception("Antimony: " + antimony.getLastError())
return antimony.getAntimonyString(None)
def AntimonyTranslatorError(self, getAntimonyMessage=False, *args, **kwrds):
import inspect
line = inspect.stack()[1][2]
call = inspect.stack()[1][4]
error_string = 'AntimonyTranslatorError line :' + str(line) + ' call:' + str(call)
if getAntimonyMessage:
error_message = antimony.getLastError()
error_string = error_string + ' Antimony returned an error with the following messages: \n' + error_message
else:
error_string = error_string + ' Trying to access one of the Antimony translator methods but Antimony libraries (e.g. libAntimony) has not been installed with your CompuCell3D package'
raise AttributeError(error_string)
def antimonyTosbml(antStr):
"""Convert an antimony string into SBML:
sbmlStr = antimonyTosbml (antimonyStr)
"""
err = antimony.loadAntimonyString(antStr)
if err < 0:
raise Exception("Antimony: " + antimony.getLastError())
Id = antimony.getMainModuleName()
return antimony.getSBMLString(Id)
def loadAntimonyModel(antStr):
"""Load an Antimony string:
r = loadAntModel (antimonyStr)
"""
err = antimony.loadAntimonyString(antStr)
if err < 0:
raise Exception("Antimony: " + antimony.getLastError())
Id = antimony.getMainModuleName()
sbmlStr = antimony.getSBMLString(Id)
rr = roadrunner.RoadRunner(sbmlStr)
antimony.clearPreviousLoads()
return rr
def cellmlFileToAntimony(self, sbml_path):
""" Converts a CellML file to Antimony source.
:param sbml_path: The path to the CellML file
:returns: A 2-tuple (module_name, antimony_source)
"""
import antimony as sb
# try to load the Antimony code`
code = sb.loadCellMLFile(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)
return (module, sb_source)
def cellmlFileToAntimony(self, sbml_path):
""" Converts a CellML file to Antimony source.
:param sbml_path: The path to the CellML file
:returns: A 2-tuple (module_name, antimony_source)
"""
import antimony as sb
# try to load the Antimony code`
code = sb.loadCellMLFile(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)
return (module, sb_source)
def antimonyToSBML(self, sb_str):
""" Converts an Antimony string to raw SBML.
:param sb_str: The raw Antimony string
:returns: A 2-tuple (module_name, raw_sbml)
"""
import antimony as sb
# try to load the Antimony code`
code = sb.loadAntimonyString(sb_str)
# 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()
sbml = sb.getSBMLString(module)
return (module, sbml)
def sbmlToAntimony(self, sbml, addSBO=False):
""" Converts a raw SBML string to Antimony source.
:param sbml: The raw SBML string
:returns: A 2-tuple (module_name, antimony_source)
"""
import antimony as sb
# try to load the Antimony code`
code = sb.loadSBMLString(sbml)
# 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_str=sbml)
return (module, sb_source)
def sbmlToAntimony(self, sbml, addSBO=False):
""" Converts a raw SBML string to Antimony source.
:param sbml: The raw SBML string
:returns: A 2-tuple (module_name, antimony_source)
"""
import antimony as sb
# try to load the Antimony code`
code = sb.loadSBMLString(sbml)
# 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_str=sbml)
return (module, sb_source)
def __check_antimony_return_code(code):
if code < 0:
raise Exception('Antimony: {}'.format(antimony.getLastError()))
import antimony
with open('../model/rnadecay.sb') as f:
sb = f.read()
print(sb)
res = antimony.loadString(sb)
if res < 0:
print(antimony.getLastError())
print(res)
print(antimony.getModuleNames())
print(antimony.getModuleNames()[-1])
sbml = antimony.getSBMLString(antimony.getModuleNames()[-1])
with open('../model/rnadecay_sbml.xml', 'w') as f:
f.write(sbml)
import antimony
with open('transcription.sb') as f:
sb = f.read()
#print(sb)
res = antimony.loadString(sb)
if res < 0:
print(antimony.getLastError())
#print(res)
#print(antimony.getModuleNames())
#print(antimony.getModuleNames()[-1])
sbml = antimony.getSBMLString(antimony.getModuleNames()[-1])
with open('transcription_sbml.xml', 'w') as f:
f.write(sbml)
plotlegend = True #Legende plotten?
verbose = 2 #Verbose level: 0 = garnicht, 1 = Statistik 1x je outerLoop, 2 = Statistik nach jedem N, 3 = +Schleifenzaehler (Haengt sich die Simulation auf?)
Nscale = 100
#Produkt der naechsten 3 Variablen ist die Anzahl der insg. simulierten Pfade
outerLoop = 1 #Anzahl Wiederholungen festlegen (multipliziert sich mit AnzahlPfade zur Anzahl der simulierten Pfade je N)
Nrange = range(
3
) #Bereich von N festlegen. range(5) == 0,1,2,3,4. Daher Multiplikator N = (N+1)*Nscale
AnzahlPfade = 40 #Anzahl Wiederholungen festlegen (multipliziert sich mit outerLoop). Fuer schoene Plots hier Wert 40-100. Fuer grosse N: doplot=False, hier 1, dafuer bei outerLoop gewuenschte Werte eintragen.
#--------------stay-above-this-line----- #Modell laden, kann auch URL sein z.B. von www.biomodels.net---------
if os.path.isfile(antStr): #----------- start copy&paste from tellurium.py
code = antimony.loadAntimonyFile(antStr)
else:
code = antimony.loadAntimonyString(antStr)
if code < 0:
raise Exception('Antimony: {}'.format(antimony.getLastError()))
mid = antimony.getMainModuleName()
sbml = antimony.getSBMLString(mid)
r = roadrunner.RoadRunner(sbml) #----------- end copy&paste from tellurium.py
#----------------the-next-three-lines-should-be-user-adapted--------
r.setIntegrator(
'gillespie') #Integrator auswaehlen. Andere unterstuetzen z.B. ODEs
r.getIntegrator().setValue(
'variable_step_size', True
) #Parameter fuer Integrator setzen, anderer Integrator unterstuetzt andere Parameter
Config.setValue(Config.MAX_OUTPUT_ROWS, pow(
10, 7)) #bei 64-bit pow(10,11) oder weniger bei wenig Arbeitsspeicher
#-----------end-user-parameters-----------
Reactions = 0
start_time = time.time()
selectToSave = ['N'] + selectToPlot
tEnd = 3.01
doplot = True #plotten?
plotlegend = True #Legende plotten?
verbose = 2 #Verbose level: 0 = garnicht, 1 = Statistik 1x je outerLoop, 2 = Statistik nach jedem N, 3 = +Schleifenzaehler (Haengt sich die Simulation auf?)
Nscale=100
#Produkt der naechsten 3 Variablen ist die Anzahl der insg. simulierten Pfade
outerLoop = 1 #Anzahl Wiederholungen festlegen (multipliziert sich mit AnzahlPfade zur Anzahl der simulierten Pfade je N)
Nrange= range(3) #Bereich von N festlegen. range(5) == 0,1,2,3,4. Daher Multiplikator N = (N+1)*Nscale
AnzahlPfade = 40 #Anzahl Wiederholungen festlegen (multipliziert sich mit outerLoop). Fuer schoene Plots hier Wert 40-100. Fuer grosse N: doplot=False, hier 1, dafuer bei outerLoop gewuenschte Werte eintragen.
#--------------stay-above-this-line----- #Modell laden, kann auch URL sein z.B. von www.biomodels.net---------
if os.path.isfile(antStr): #----------- start copy&paste from tellurium.py
code = antimony.loadAntimonyFile(antStr)
else:
code = antimony.loadAntimonyString(antStr)
if code < 0:
raise Exception('Antimony: {}'.format(antimony.getLastError()))
mid = antimony.getMainModuleName()
sbml = antimony.getSBMLString(mid)
r = roadrunner.RoadRunner(sbml) #----------- end copy&paste from tellurium.py
#----------------the-next-three-lines-should-be-user-adapted--------
r.setIntegrator('gillespie') #Integrator auswaehlen. Andere unterstuetzen z.B. ODEs
r.getIntegrator().setValue('variable_step_size', True) #Parameter fuer Integrator setzen, anderer Integrator unterstuetzt andere Parameter
Config.setValue(Config.MAX_OUTPUT_ROWS,pow(10,7)) #bei 64-bit pow(10,11) oder weniger bei wenig Arbeitsspeicher
#-----------end-user-parameters-----------
Reactions = 0
start_time = time.time()
selectToSave = ['N'] + selectToPlot
form=(1,len(selectToSave))
r.selections = selectToSave
simuliertePfade = 0
PfadeGesamt=outerLoop*AnzahlPfade*len(Nrange)
