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 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 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 __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 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(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 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)
"""
Create the SBML model.
"""
import antimony
model_id = 'vanderpol'
# ----------------------------
model_str = '''
model {}
var species x = -2;
var species y = 0;
const mu = 1;
J1: -> x; y
J2: -> y; mu *(1-x^2)*y - x
end
'''.format(model_id)
# ----------------------------
antimony.setBareNumbersAreDimensionless(True)
antimony.loadAntimonyString(model_str)
model_file = './vanderpol-sbml.xml'
antimony.writeSBMLFile(model_file, model_id)
print(model_file)
def generateNetworkFromAntimony(ant_str):
"""
Generate network matrix from Antimony string
:param ant_str: Antimony string
:rtype: array
"""
import antimony
import tellurium as te
antimony.clearPreviousLoads()
antimony.loadAntimonyString(ant_str)
module = antimony.getModuleNames()[-1]
num_rxn = int(antimony.getNumReactions(module))
rct = antimony.getReactantNames(module)
rct = [list(i) for i in rct]
rct_flat = [item for sublist in rct for item in sublist]
prd = antimony.getProductNames(module)
prd = [list(i) for i in prd]
prd_flat = [item for sublist in prd for item in sublist]
ratelaw = antimony.getReactionRates(module)
r = te.loada(ant_str)
bnd = r.getBoundarySpeciesIds()
flt = r.getFloatingSpeciesIds()
s_arr = np.array(sorted(bnd + flt))
ref_list = generateCombinationOfSpecies(s_arr)
net_mat = np.zeros([len(ref_list), len(ref_list)])
for i in range(num_rxn):
if len(rct[i]) == 1 and len(prd[i]) == 1:
r_s = rct[i][0]
p_s = prd[i][0]
r_s_i = ref_list.index(r_s)
p_s_i = ref_list.index(p_s)
net_mat[r_s_i][p_s_i] = 1
elif len(rct[i]) == 2 and len(prd[i]) == 1:
r_s1 = rct[i][0]
r_s2 = rct[i][1]
p_s = prd[i][0]
r_s_i = ref_list.index(tuple(sorted((r_s1, r_s2))))
p_s_i = ref_list.index(p_s)
net_mat[r_s_i][p_s_i] = 1
elif len(rct[i]) == 1 and len(prd[i]) == 2:
r_s = rct[i][0]
p_s1 = prd[i][0]
p_s2 = prd[i][1]
r_s_i = ref_list.index(r_s)
p_s_i = ref_list.index(tuple(sorted((p_s1, p_s2))))
net_mat[r_s_i][p_s_i] = 1
elif len(rct[i]) == 2 and len(prd[i]) == 2:
r_s1 = rct[i][0]
r_s2 = rct[i][1]
p_s1 = prd[i][0]
p_s2 = prd[i][1]
r_s_i = ref_list.index(tuple(sorted((r_s1, r_s2))))
p_s_i = ref_list.index(tuple(sorted((p_s1, p_s2))))
if '/' in ratelaw[i]: # Inhibition
net_mat[r_s_i][p_s_i] = 2
else:
net_mat[r_s_i][p_s_i] = 1
antimony.clearPreviousLoads()
return net_mat, ref_list
timePoints = [1.0, 2.0, 3.0] #zu welchen Zeitpunkten soll die Konfiguration gespeichert werden?
tStart = 0 #Start- und Endzeit der Simulation
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
# 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 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]:
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
#model combined
# #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;
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)
