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 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 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 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
