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_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