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 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 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 __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 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 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 antimonyToCellML(ant):
""" Convert Antimony to CellML string.
:param ant: Antimony string or file
:type ant: str | file
:return: CellML
:rtype: str
"""
if os.path.isfile(ant):
code = antimony.loadAntimonyFile(ant)
else:
code = antimony.loadAntimonyString(ant)
_checkAntimonyReturnCode(code)
mid = antimony.getMainModuleName()
return antimony.getCellMLString(mid)
def __init__(self, model_contents: str, content_type: str) -> None:
if content_type == "ModelString":
er_code = sb.loadAntimonyString(model_contents)
elif content_type == "ModelFile":
er_code = sb.loadAntimonyFile(model_contents)
else:
raise KeyError(f"Unsupported content_type: {content_type}")
self.er_code = er_code
if self.er_code == -1:
error_msg = "Error while parsing model. Model variable names "
error_msg += "might be antimony keywords (see docs at https://"
error_msg += "cayenne.readthedocs.io/en/latest/tutorial.html)."
raise ModelError(error_msg)
self.sb_module = sb.getMainModuleName()
self._parse_model()
def antimonyToCellML(ant):
""" Convert Antimony to CellML string.
:param ant: Antimony string or file
:type ant: str | file
:return: CellML
:rtype: str
"""
if os.path.isfile(ant):
code = antimony.loadAntimonyFile(ant)
else:
code = antimony.loadAntimonyString(ant)
_checkAntimonyReturnCode(code)
mid = antimony.getMainModuleName()
return antimony.getCellMLString(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(ant):
""" Convert Antimony to SBML string.
:param ant: Antimony string or file
:type ant: str | file
:return: SBML
:rtype: str
"""
try:
isfile = os.path.isfile(ant)
except ValueError:
isfile = False
if isfile:
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
"""
try:
isfile = os.path.isfile(ant)
except ValueError:
isfile = False
if isfile:
code = antimony.loadAntimonyFile(ant)
else:
code = antimony.loadAntimonyString(ant)
_checkAntimonyReturnCode(code)
mid = antimony.getMainModuleName()
return antimony.getSBMLString(mid)
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 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 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)
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)
if os.path.isfile(path+name): #Header in CSV-Datei automatisch erzeugen, falls Datei noch nicht existiert
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))
import tellurium as te
import tempfile
# load model
r = te.loada('S1 -> S2; k1*S1; k1 = 0.1; S1 = 10')
# file for export
f_matlab = tempfile.NamedTemporaryFile(suffix=".m")
# export current model state
r.exportToMatlab(f_matlab.name)
# to export the initial state when the model was loaded
# set the current argument to False
r.exportToMatlab(f_matlab.name, current=False)
# The string representations of the current model are available via
str_matlab = r.getCurrentMatlab()
# and of the initial state when the model was loaded via
str_matlab = r.getMatlab()
print(str_matlab)
# In[5]:
import antimony
antimony.loadAntimonyString('''S1 -> S2; k1*S1; k1 = 0.1; S1 = 10''')
ant_str = antimony.getCellMLString(antimony.getMainModuleName())
print(ant_str)
# In[6]:
# file for export
f_matlab = tempfile.NamedTemporaryFile(suffix=".m")
# export current model state
r.exportToMatlab(f_matlab.name)
# to export the initial state when the model was loaded
# set the current argument to False
r.exportToMatlab(f_matlab.name, current=False)
# The string representations of the current model are available via
str_matlab = r.getCurrentMatlab()
# and of the initial state when the model was loaded via
str_matlab = r.getMatlab()
print(str_matlab)
# In[5]:
import antimony
antimony.loadAntimonyString('''S1 -> S2; k1*S1; k1 = 0.1; S1 = 10''')
ant_str = antimony.getCellMLString(antimony.getMainModuleName())
print(ant_str)
# In[6]:
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)
