def __construct_reaction(self, rname, ko, reac, arrow, prod, mname):
""" Code to parse and construct a reaction"""
# Step 1. split reactants.
rname = str(rname)
mname = str(mname)
r = Reaction(rname)
left_coef, left_comp = self.__get_coef_and_name(reac)
right_coef, right_comp = self.__get_coef_and_name(prod)
r.substrates.extend(left_comp)
r.products.extend(right_comp)
for i in xrange(len(left_coef)):
r.stoichiometry[left_comp[i]] = left_coef[i]
for i in xrange(len(right_coef)):
r.stoichiometry[right_comp[i]] = right_coef[i]
r.reversible = arrow
r.arrow = arrow
if ko == True:
r.ko = True
elif ko == False:
r.ko = False
elif 'false' in ko:
# elif type(ko) == type("") and ko.lower() == "false":
r.ko = False
else:
r.ko = True
r.metabolism = mname
r.active = True
return r
def __construct_reaction_from_reactionlst(self, reaction, rid, reversible):
substrates = []
products = []
stoichiometry = {}
longname_map = {}
r = Reaction(rid)
substrates = self.reactiondb.get_stoichiometry(rid, "_substrates_")
products = self.reactiondb.get_stoichiometry(rid, "_products_")
if substrates == "None":
return None
for sub in substrates:
stoichiometry[ sub ] = self.reactiondb.get_stoichiometry(rid, sub)
longname_map[ sub ] = self.reactiondb.get_long_name(sub)
for prod in products:
stoichiometry[ prod ] = self.reactiondb.get_stoichiometry(rid, prod)
longname_map[ prod ] = self.reactiondb.get_long_name( prod )
r.substrates = substrates
r.products = products
r.stoichiometry = stoichiometry
r.reversible = reversible
r.longname_map = longname_map
return r
def __construct_reaction_from_reactionlst(self, reaction, rid, reversible):
substrates = []
products = []
stoichiometry = {}
longname_map = {}
r = Reaction(rid)
substrates = self.reactiondb.get_stoichiometry(rid, "_substrates_")
products = self.reactiondb.get_stoichiometry(rid, "_products_")
# print "Get RID", rid
# print "sub is", substrates
if substrates == "None":
return None
for sub in substrates:
stoichiometry[sub] = self.reactiondb.get_stoichiometry(rid, sub)
longname_map[sub] = self.reactiondb.get_long_name(sub)
# print sub, self.reactiondb.get_long_name(sub)
# print
for prod in products:
# print '"' + prod + '"', '"'+ self.reactiondb.get_long_name(prod)+'"'
stoichiometry[prod] = self.reactiondb.get_stoichiometry(rid, prod)
longname_map[prod] = self.reactiondb.get_long_name(prod)
# print
# print "===="
r.substrates = substrates
r.products = products
r.stoichiometry = stoichiometry
r.reversible = reversible
r.longname_map = longname_map
return r
def __construct_reaction(self, rname, ko, reac, arrow, prod, mname):
""" Code to parse and construct a reaction"""
# Step 1. split reactants.
rname = str(rname)
mname = str(mname)
r = Reaction(rname)
left_coef, left_comp = self.__get_coef_and_name(reac)
right_coef, right_comp = self.__get_coef_and_name(prod)
r.substrates.extend(left_comp)
r.products.extend(right_comp)
print "[Add pathway] The substrates are ", r.substrates
print "[Add pathway] The products are ", r.products
for i in xrange(len(left_coef)):
r.stoichiometry[left_comp[i]] = left_coef[i]
for i in xrange(len(right_coef)):
r.stoichiometry[right_comp[i]] = right_coef[i]
print "[Add pathway] r.stoichiometry is ", r.stoichiometry
print "Get external arrow is ", arrow
r.reversible = arrow
r.arrow = arrow
if ko == "false":
r.ko = False
else:
r.ko = True
r.metabolism = mname
r.active = True
return r
def __construct_reaction(self, rname, ko, reac, arrow, prod, mname):
""" Code to parse and construct a reaction"""
# Step 1. split reactants.
rname = str(rname)
mname = str(mname)
r = Reaction(rname)
left_coef, left_comp = self.__get_coef_and_name(reac)
right_coef, right_comp = self.__get_coef_and_name(prod)
r.substrates.extend(left_comp)
r.products.extend(right_comp)
print "[Add pathway] The substrates are ", r.substrates
print "[Add pathway] The products are ", r.products
for i in xrange(len(left_coef)):
r.stoichiometry[left_comp[i]] = left_coef[i]
for i in xrange(len(right_coef)):
r.stoichiometry[right_comp[i]] = right_coef[i]
print "[Add pathway] r.stoichiometry is ", r.stoichiometry
print "Get external arrow is ", arrow
r.reversible = arrow
r.arrow = arrow
if ko == "false":
r.ko = False
else:
r.ko = True
r.metabolism = mname
r.active = True
return r
def __construct_reaction_from_reactionlst(self, reaction, rid, reversible):
substrates = []
products = []
stoichiometry = {}
longname_map = {}
r = Reaction(rid)
substrates = self.reactiondb.get_stoichiometry(rid, "_substrates_")
products = self.reactiondb.get_stoichiometry(rid, "_products_")
# print "Get RID", rid
# print "sub is", substrates
if substrates == "None":
return None
for sub in substrates:
stoichiometry[ sub ] = self.reactiondb.get_stoichiometry(rid, sub)
longname_map[ sub ] = self.reactiondb.get_long_name(sub)
# print sub, self.reactiondb.get_long_name(sub)
# print
for prod in products:
# print '"' + prod + '"', '"'+ self.reactiondb.get_long_name(prod)+'"'
stoichiometry[ prod ] = self.reactiondb.get_stoichiometry(rid, prod)
longname_map[ prod ] = self.reactiondb.get_long_name( prod )
# print
# print "===="
r.substrates = substrates
r.products = products
r.stoichiometry = stoichiometry
r.reversible = reversible
r.longname_map = longname_map
return r
def __construct_reaction_from_kgml(self, reaction, rid, reversible):
substrates = []
products = []
stoichiometry = {}
for sub in reaction.getiterator('substrate'):
name = remove_comma(sub.get('name'))
substrates.append(name)
stoichiometry[ name ] = self.reactiondb.get_stoichiometry(rid, name)
for prod in reaction.getiterator('product'):
name = remove_comma(prod.get('name'))
products.append(name)
stoichiometry[ name ] = self.reactiondb.get_stoichiometry(rid, name)
r = Reaction(rid)
r.substrates = substrates
r.products = products
r.stoichiometry = stoichiometry
r.reversible = reversible
return r
def __construct_reaction_from_kgml(self, reaction, rid, reversible):
substrates = []
products = []
stoichiometry = {}
for sub in reaction.getiterator('substrate'):
name = remove_comma(sub.get('name'))
substrates.append(name)
stoichiometry[name] = self.reactiondb.get_stoichiometry(rid, name)
for prod in reaction.getiterator('product'):
name = remove_comma(prod.get('name'))
products.append(name)
stoichiometry[name] = self.reactiondb.get_stoichiometry(rid, name)
r = Reaction(rid)
r.substrates = substrates
r.products = products
r.stoichiometry = stoichiometry
r.reversible = reversible
return r
