def getInstanceRate(self, math, compartmentList, reversible, rReactant,
rProduct):
#remove compartments from expression
math = self.getPrunnedTree(math, compartmentList)
if reversible:
if math.getCharacter() == '-' and math.getNumChildren() > 1:
rateL, nl = (self.removeFactorFromMath(
math.getLeftChild().deepCopy(), rReactant, rProduct))
rateR, nr = (self.removeFactorFromMath(
math.getRightChild().deepCopy(), rProduct, rReactant))
else:
rateL, nl = self.removeFactorFromMath(math, rReactant,
rProduct)
rateL = "if({0} >= 0 ,{0},0)".format(rateL)
rateR, nr = self.removeFactorFromMath(math, rReactant,
rProduct)
rateR = "if({0} < 0 ,-({0}),0)".format(rateR)
nl, nr = 1, 1
else:
rateL, nl = (self.removeFactorFromMath(math.deepCopy(), rReactant,
rProduct))
rateR, nr = '0', '-1'
if reversible:
pass
return rateL, rateR
def removeFactorFromMath(self, math, reactants, products):
remainderPatterns = []
highStoichoiMetryFactor = 1
for x in reactants:
highStoichoiMetryFactor *= factorial(x[1])
y = [i[1] for i in products if i[0] == x[0]]
y = y[0] if len(y) > 0 else 0
#TODO: check if this actually keeps the correct dynamics
# this is basically there to address the case where theres more products
#than reactants (synthesis)
if x[1] > y:
highStoichoiMetryFactor /= comb(int(x[1]), int(y))
for counter in range(0, int(x[1])):
remainderPatterns.append(x[0])
#for x in products:
# highStoichoiMetryFactor /= math.factorial(x[1])
#remainderPatterns = [x[0] for x in reactants]
math = self.getPrunnedTree(math, remainderPatterns)
rateR = libsbml.formulaToString(math)
for element in remainderPatterns:
rateR = 'if({0} >0,({1})/{0} ,0)'.format(element, rateR)
if highStoichoiMetryFactor != 1:
rateR = '{0}*{1}'.format(rateR, int(highStoichoiMetryFactor))
return rateR, math.getNumChildren()
def getPrunnedTree(self, math, remainderPatterns):
'''
removes the remainderPatterns leafs from the math tree
'''
while (math.getCharacter() == '*'
or math.getCharacter() == '/') and len(remainderPatterns) > 0:
if libsbml.formulaToString(
math.getLeftChild()) in remainderPatterns:
remainderPatterns.remove(
libsbml.formulaToString(math.getLeftChild()))
math = math.getRightChild()
elif libsbml.formulaToString(
math.getRightChild()) in remainderPatterns:
remainderPatterns.remove(
libsbml.formulaToString(math.getRightChild()))
math = math.getLeftChild()
else:
if (math.getLeftChild().getCharacter()) == '*':
math.replaceChild(
0,
self.getPrunnedTree(math.getLeftChild(),
remainderPatterns))
if (math.getRightChild().getCharacter()) == '*':
math.replaceChild(
math.getNumChildren() - 1,
self.getPrunnedTree(math.getRightChild(),
remainderPatterns))
break
return math
def removeFactorFromMath(self, math, reactants, products):
remainderPatterns = []
highStoichoiMetryFactor = 1
for x in reactants:
highStoichoiMetryFactor *= factorial(x[1])
y = [i[1] for i in products if i[0] == x[0]]
y = y[0] if len(y) > 0 else 0
#TODO: check if this actually keeps the correct dynamics
# this is basically there to address the case where theres more products
#than reactants (synthesis)
if x[1] > y:
highStoichoiMetryFactor /= comb(int(x[1]), int(y))
for counter in range(0, int(x[1])):
remainderPatterns.append(x[0])
#for x in products:
# highStoichoiMetryFactor /= math.factorial(x[1])
#remainderPatterns = [x[0] for x in reactants]
math = self.getPrunnedTree(math,remainderPatterns)
rateR = libsbml.formulaToString(math)
for element in remainderPatterns:
rateR = 'if({0} >0,({1})/{0} ,0)'.format(element,rateR)
if highStoichoiMetryFactor != 1:
rateR = '{0}*{1}'.format(rateR, int(highStoichoiMetryFactor))
return rateR,math.getNumChildren()
def getInstanceRate(self,math,compartmentList, reversible,rReactant,rProduct):
#remove compartments from expression
math = self.getPrunnedTree(math, compartmentList)
if reversible:
if math.getCharacter() == '-' and math.getNumChildren() > 1:
rateL, nl = (self.removeFactorFromMath(
math.getLeftChild().deepCopy(), rReactant, rProduct))
rateR, nr = (self.removeFactorFromMath(
math.getRightChild().deepCopy(), rProduct, rReactant))
else:
rateL, nl = self.removeFactorFromMath(math, rReactant,
rProduct)
rateL = "if({0} >= 0 ,{0},0)".format(rateL)
rateR, nr = self.removeFactorFromMath(math, rReactant,
rProduct)
rateR = "if({0} < 0 ,-({0}),0)".format(rateR)
nl, nr = 1,1
else:
rateL, nl = (self.removeFactorFromMath(math.deepCopy(),
rReactant,rProduct))
rateR, nr = '0', '-1'
if reversible:
pass
return rateL,rateR
def add_missing_params(self, model, math):
if model is None or math is None:
return
if math.getType() == libsbml.AST_NAME:
id = math.getName()
param = model.getElementBySId(id)
if param is None:
param = model.createParameter()
param.setId(id)
param.setValue(1)
for i in range(math.getNumChildren()):
self.add_missing_params(model, math.getChild(i))
def getPrunnedTree(self,math,remainderPatterns):
'''
removes the remainderPatterns leafs from the math tree
'''
while (math.getCharacter() == '*' or math.getCharacter() == '/') and len(remainderPatterns) > 0:
if libsbml.formulaToString(math.getLeftChild()) in remainderPatterns:
remainderPatterns.remove(libsbml.formulaToString(math.getLeftChild()))
math = math.getRightChild()
elif libsbml.formulaToString(math.getRightChild()) in remainderPatterns:
remainderPatterns.remove(libsbml.formulaToString(math.getRightChild()))
math = math.getLeftChild()
else:
if(math.getLeftChild().getCharacter()) == '*':
math.replaceChild(0, self.getPrunnedTree(math.getLeftChild(), remainderPatterns))
if(math.getRightChild().getCharacter()) == '*':
math.replaceChild(math.getNumChildren() - 1,self.getPrunnedTree(math.getRightChild(), remainderPatterns))
break
return math
def readSBML(self,filename):
document = libsbml.readSBML(filename)
if (document.getNumErrors() > 0):
document.printErrors();
return(1);
model = document.getModel();
if (model == None):
print("The model is empty." + "\n");
return(1);
if model.getNumCompartments()==0:
print("There is no compartment in the model." + "\n");
return(1);
for cc in range(model.getNumCompartments()):
try:
self.add_compartment(model.getCompartment(cc).getId(),model.getCompartment(cc).getSize())
except:
print("Could not add the compartment number %d."%cc)
return(1);
if model.getNumSpecies()==0:
print("There is no species in the model." + "\n");
return(1);
for mm in range(model.getNumSpecies()):
try:
met_name = model.getSpecies(mm).getId()
isConstant = model.getSpecies(mm).getConstant()
compart = model.getSpecies(mm).getCompartment()
quantity = model.getSpecies(mm).getInitialAmount()
if quantity ==0 :
concentration = model.getSpecies(mm).getInitialConcentration()
met = self.addMetabolite(met_name,compart,concentration=concentration)
else:
met = self.addMetabolite(met_name,compart,quantity=quantity)
if model.getSpecies(mm).getName() is not "":
met.longName = model.getSpecies(mm).getName()
met.isConstant = isConstant
if isConstant:
met.exchangeCarbon = False
annotation = model.getSpecies(mm).getAnnotationString()
compoundID = re.search("C\d{5}",annotation)
chebiID = re.search("CHEBI.(\d{5})",annotation)
if compoundID is not None:
compoundID = compoundID.group(0)
met.compoundID = compoundID
if chebiID is not None:
met.chebiID = chebiID.group(1)
except:
import pdb;pdb.set_trace()
print("Could not add the metabolite number %d."%mm)
return(1);
for pp in range(model.getListOfParameters().size()):
try:
param = model.getListOfParameters().get(pp)
pname = param.getName()
pid = param.getId()
if pname == "":
pname = pid
param = self.addParameter(pname,param.getValue(),None)
param.id = pid
self.globalParameters.append(param)
except:
print("Could not add the global parameter number %d."%pp)
if model.getNumReactions()==0:
print("There is no species in the model." + "\n");
return(1);
this_dir, this_filename = os.path.split(__file__)
DATA_PATH = os.path.join(this_dir, "knownUnrenderedMathML")
knownUnrenderedMathML = []
for line in open(DATA_PATH).read().split("\n"):
if line is not "":
knownUnrenderedMathML.append(UnrenderedMathML(line))
for ff in range(model.getNumFunctionDefinitions()):
isComputable = True
try:
fd = model.getFunctionDefinition(ff)
math = fd.getMath()
arguments = [(math.getChild(n)).getName() for n in range ( math.getNumChildren()-1)]
math = math.getChild(math.getNumChildren() - 1)
formula = libsbml.formulaToString(math)
nameFd = fd.getId()
for unknown in knownUnrenderedMathML:
if unknown.identify(formula):
formula = unknown.replace(formula)
func = self.addFunctionDefinition(nameFd,formula,arguments)
isComputable = bool(func.isComputable())
# if not isComputable:
# # import pdb;pdb.set_trace()
# assert(isComputable)
except:
if not bool(func.isComputable()):
print("Function number %s is not computable."%ff)
print("Could not add the function definition number %d."%ff)
return(1);
for rr in range(model.getNumReactions()):
theSBMLreac = model.getReaction(rr)
reac_name = theSBMLreac.getId()
metabolite_names = []
stoichiometry = []
try:
for mm in range(theSBMLreac.getNumReactants()):
metabolite_names.append(theSBMLreac.getReactant(mm).getSpecies())
stoichiometry.append(-theSBMLreac.getReactant(mm).getStoichiometry())
for mm in range(theSBMLreac.getNumModifiers()):
metabolite_names.append(theSBMLreac.getModifier(mm).getSpecies())
stoichiometry.append(0)
for mm in range(theSBMLreac.getNumProducts()):
metabolite_names.append(theSBMLreac.getProduct(mm).getSpecies())
stoichiometry.append(theSBMLreac.getProduct(mm).getStoichiometry())
kineticLaw = theSBMLreac.getKineticLaw()
kineticLawMath = libsbml.formulaToString(kineticLaw.getMath())
for unknown in knownUnrenderedMathML:
if unknown.identify(kineticLawMath):
kineticLawMath = unknown.replace(kineticLawMath)
reac = self.addReaction(reac_name,metabolite_names,stoichiometry,kineticLawMath)
reac.longName = theSBMLreac.getName()
for pp in range(kineticLaw.getListOfParameters().size()):
param = kineticLaw.getListOfParameters().get(pp)
pname = param.getName()
if pname == "":
pname = param.getId()
self.addParameter(pname,param.getValue(),reac)
funcDef = re.findall("(\w+)\([,\s\w]+?\)",kineticLawMath)
for ff in funcDef:
func_result = self.functionDefinitions[getNames(self.functionDefinitions).index(ff)]
reac.functionDefinitions.append(func_result)
func_result.reactions.append(reac)
except:
print("Could not add the reaction number %d."%rr)
return(1);
