def constructGenericBinding(self):
#### FORWARD
# let rxn =
# "Far1(MAPK_site,T306~none) + Fus3(target_site,T180~PO4,Y182~PO4) -> \Far1(MAPK_site!1,T306~none).Fus3(target_site!1,T180~PO4,Y182~PO4) kon_Fus3pTpY_Far1"
# Then this function should return (("Far1", "MAPK_site"), ("Fus3, "target_site"))
# This is the "generic binding that is formed.
#### DECOMPOSITION
# Let rxn =
# "Far1(MAPK_site!1,T306~none).Fus3(target_site!1,T180~PO4,Y182~PO4) -> Far1(MAPK_site,T306~none) + Fus3(target_site,T180~PO4,Y182~PO4) koff_Fus3pTpY_Far1"
# Then this function should return (("Far1", "MAPK_site"), ("Fus3, "target_site")).
#### MODIFICATION
# Let rxn = "Dig1(PO4_site~PO4) -> Dig1(PO4_site~none) kcat_nonspecific_dephosph"
# Should return (Dig1, PO4_site, PO4), I *think*.
if self.modificationRxn:
self.genericBinding = util.calculateSignificantModificationSite(self.reactants, self.products)
return self.genericBinding
elif self.dimerizationRxn:
self.genericBinding = util.calculateSignificantBinding(self.reactants, self.products)
elif self.decompositionRxn:
self.genericBinding = util.calculateSignificantBinding(self.products, self.reactants)
else:
raise ValueError
self.genericBinding = list(self.genericBinding)
self.genericBinding.sort()
self.genericBinding = tuple(self.genericBinding)
return self.genericBinding
def constructGenericBinding(self):
#### FORWARD
# let rxn =
# "Far1(MAPK_site,T306~none) + Fus3(target_site,T180~PO4,Y182~PO4) -> \Far1(MAPK_site!1,T306~none).Fus3(target_site!1,T180~PO4,Y182~PO4) kon_Fus3pTpY_Far1"
# Then this function should return (("Far1", "MAPK_site"), ("Fus3, "target_site"))
# This is the "generic binding that is formed.
#### DECOMPOSITION
# Let rxn =
# "Far1(MAPK_site!1,T306~none).Fus3(target_site!1,T180~PO4,Y182~PO4) -> Far1(MAPK_site,T306~none) + Fus3(target_site,T180~PO4,Y182~PO4) koff_Fus3pTpY_Far1"
# Then this function should return (("Far1", "MAPK_site"), ("Fus3, "target_site")).
#### MODIFICATION
# Let rxn = "Dig1(PO4_site~PO4) -> Dig1(PO4_site~none) kcat_nonspecific_dephosph"
# Should return (Dig1, PO4_site, PO4), I *think*.
if self.modificationRxn:
self.genericBinding = util.calculateSignificantModificationSite(
self.reactants, self.products)
return self.genericBinding
elif self.dimerizationRxn:
self.genericBinding = util.calculateSignificantBinding(
self.reactants, self.products)
elif self.decompositionRxn:
self.genericBinding = util.calculateSignificantBinding(
self.products, self.reactants)
else:
raise ValueError
self.genericBinding = list(self.genericBinding)
self.genericBinding.sort()
self.genericBinding = tuple(self.genericBinding)
return self.genericBinding
def initialize(self):
if len(self.reactantList) == 1 and len(self.productList) == 2:
self.decomposition, self.dimerization, self.modificationReaction = True, False, False
elif len(self.reactantList) == 2 and len(self.productList) == 1:
self.decomposition, self.dimerization, self.modificationReaction = False, True, False
elif len(self.reactantList) == 1 and len(self.productList) == 1:
self.decomposition, self.dimerization, self.modificationReaction = False, False, True
else:
raise ValueError, "Reaction not properly formed in MatchObject initializer..."
if self.modificationReaction:
self.significantBinding = util.calculateSignificantModificationSite(self.reactantList, self.productList)
else:
try:
self.significantBinding = util.calculateSignificantBinding(self.reactantList, self.productList)
except:
# Whoops bad reaction thingy.
print "Poorly formed reaction..."
def initialize(self):
if len(self.reactantList) == 1 and len(self.productList) == 2:
self.decomposition, self.dimerization, self.modificationReaction = True, False, False
elif len(self.reactantList) == 2 and len(self.productList) == 1:
self.decomposition, self.dimerization, self.modificationReaction = False, True, False
elif len(self.reactantList) == 1 and len(self.productList) == 1:
self.decomposition, self.dimerization, self.modificationReaction = False, False, True
else:
raise ValueError, "Reaction not properly formed in MatchObject initializer..."
if self.modificationReaction:
self.significantBinding = util.calculateSignificantModificationSite(
self.reactantList, self.productList)
else:
try:
self.significantBinding = util.calculateSignificantBinding(
self.reactantList, self.productList)
except:
# Whoops bad reaction thingy.
print "Poorly formed reaction..."
