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 flattenMotif(combined):
#flatten the combined model by converting it to sbml and then converting back to Antimony
antimony.clearPreviousLoads()
code = antimony.loadAntimonyString(combined)
if code <= 0:
textfile = open('combined.txt', 'w')
textfile.write(combined)
textfile.close()
raise AssertionError(
'combined model is not flattenable. Are you using the right species names? '
+ 'Combined model saved as: ' + str(os.getcwd()) +
'\\combined.txt')
sbmlStr = antimony.getSBMLString('combined')
antimony.loadSBMLString(sbmlStr)
flatComb = antimony.getAntimonyString('combined')
####TODO
#Delete extraneous mRNA -> Protein reactions at P_c connections
#look for p_c#, regex
#delete second equation with occurance of p_c#curr, regex
#todo: remove extraneous species + parameters in the removed equation
####TODO
return (flatComb)
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 translate_to_sbml_string(self, model_file: str = '', model_string: str = ''):
"""
Returns string of SBML model specification translated from Antimony or CellML model specification file or string
:param model_file: relative path to model specification file
:param model_string: model specification string
:return {str,str}: string of SBML model specification, string of main module name
"""
# Just to be sure, call clear previous loads
antimony.clearPreviousLoads()
# Loading from model string or file?
if model_file == '':
res_load = antimony.loadString(model_string)
else:
model_path_normalized = self.normalize_path(model_file)
res_load = antimony.loadFile(model_path_normalized)
if res_load == -1:
AntimonyTranslatorError(self, getAntimonyMessage=True)
# Get main loaded module
main_module_name = antimony.getMainModuleName()
if not main_module_name:
AntimonyTranslatorError(self, getAntimonyMessage=True)
# Return string of SBML model specification
translated_model_string = antimony.getSBMLString(main_module_name)
if not translated_model_string:
AntimonyTranslatorError(self, getAntimonyMessage=True)
else:
return translated_model_string, main_module_name
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 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 __antimony_to_sbml(ant):
try:
isfile = os.path.isfile(ant)
except ValueError:
isfile = False
if isfile:
code = antimony.loadAntimonyFile(ant)
else:
code = antimony.loadAntimonyString(ant)
__check_antimony_return_code(code)
mid = antimony.getMainModuleName()
return antimony.getSBMLString(mid)
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 cellmlToSBML(cellml):
""" Convert CellML to SBML string.
:param cellml: CellML string or file
:type cellml: str | file
:return: SBML
:rtype: str
"""
if os.path.isfile(cellml):
code = antimony.loadCellMLFile(cellml)
else:
code = antimony.loadCellMLString(cellml)
_checkAntimonyReturnCode(code)
return antimony.getSBMLString(None)
def cellmlToSBML(cellml):
""" Convert CellML to SBML string.
:param cellml: CellML string or file
:type cellml: str | file
:return: SBML
:rtype: str
"""
if os.path.isfile(cellml):
code = antimony.loadCellMLFile(cellml)
else:
code = antimony.loadCellMLString(cellml)
_checkAntimonyReturnCode(code)
return antimony.getSBMLString(None)
def antimonyToSBML(ant):
""" Convert Antimony to SBML string.
:param ant: Antimony string or file
:type ant: str | file
:return: SBML
:rtype: str
"""
if os.path.isfile(ant):
code = antimony.loadAntimonyFile(ant)
else:
code = antimony.loadAntimonyString(ant)
_checkAntimonyReturnCode(code)
mid = antimony.getMainModuleName()
return antimony.getSBMLString(mid)
def antimonyToSBML(ant):
""" Convert Antimony to SBML string.
:param ant: Antimony string or file
:type ant: str | file
:return: SBML
:rtype: str
"""
if os.path.isfile(ant):
code = antimony.loadAntimonyFile(ant)
else:
code = antimony.loadAntimonyString(ant)
_checkAntimonyReturnCode(code)
mid = antimony.getMainModuleName()
return antimony.getSBMLString(mid)
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 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)
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)
if os.path.isfile(path+name): #Header in CSV-Datei automatisch erzeugen, falls Datei noch nicht existiert
f=open(path+name,'ab')
import antimony
ant = '''
model stoch()
species A,B,C,D,E
A -> B; k1
B -> C; k2
C -> D; k3
D -> C; k4
E -> C; k5
A = 100000
B = 1000
C = 1000
D = 1000
E = 100000
k1 = 0.2
k2 = 0.05
k3 = 0.1
k4 = 0.01
k5 = 0.05
end
'''
antimony.loadAntimonyString(ant)
sbmlstr = antimony.getSBMLString(antimony.getMainModuleName())
#print(sbmlstr)
with open('stoch_l3.xml', 'w') as f:
f.write(sbmlstr)
# #repeat for n-1 modules
# #!!module names have to be identical to model names from imported models!!
# A : model1();
# B : model2();
# #repeat for all models I have
# #specify a global input node
# var species p_c;
# A.p_input is p_c;
# B.p_output is p_c;
# #repeat for n-1 modules
# end
# '''
#properly flatten the combined model
antimony.loadAntimonyString(combined)
sbmlstr = antimony.getSBMLString('combined')
antimony.loadSBMLString(sbmlstr)
flatcomb = antimony.getAntimonyString('combined')
r = te.loada(flatcomb)
r.exportToAntimony('combined.txt')
r.draw(layout='dot')
#combined = reads + '''
#model combined
# var species p_c;
# #!!module names have to be identical to model names from imported models!!
# A : ffl1();
# B : ffl1();
# A.p_input is p_c;
# B.p_output is p_c;
def getSBMLStr(self):
antimony.clearPreviousLoads()
antimony.loadString(self.getRawStr())
return antimony.getSBMLString(antimony.getModuleNames()[-1])
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)
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
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)
