continue
#Parse old stoichiometry into array
old_stoichiometry = Reactions_Dict[rxn]["stoichiometry"]
Rxn_Cpds_Array = ReactionsHelper.parseStoich(old_stoichiometry)
#Don't adjust reactions that only have water
if (len(Rxn_Cpds_Array) == 1):
continue
Water_Adjustment = 1
if ("-1" in Reactions_Dict[rxn]["status"]):
Water_Adjustment = -1
#Adjust for water
ReactionsHelper.adjustCompound(Rxn_Cpds_Array, "cpd00001",
float(Water_Adjustment))
#Recompute new status and stoichiometry
new_status = ReactionsHelper.balanceReaction(Rxn_Cpds_Array)
new_stoichiometry = ReactionsHelper.buildStoich(Rxn_Cpds_Array)
if (new_status != Reactions_Dict[rxn]['status']):
status_file.write(rxn + "\t" + Reactions_Dict[rxn]['status'] + "\t" +
new_status + "\n")
if (new_stoichiometry != old_stoichiometry):
print "Rebuilding reaction :", rxn
ReactionsHelper.rebuildReaction(Reactions_Dict[rxn], new_stoichiometry)
Reactions_Dict[rxn]["status"] = new_status
if ("WB" not in Reactions_Dict[rxn]["notes"]):
if (Reactions_Dict[rxn]["notes"] == ""
elements = block.split("/")
#only making adjustments if mass imbalance is a single element,
#and the element is hydrogen
if (len(elements) > 1 or not elements[0].startswith("H:")):
continue
(element, number) = elements[0].split(":")
#print("Adjusting: "+rxn,element,number)
#Parse old stoichiometry into array
old_stoichiometry = Reactions_Dict[rxn]["stoichiometry"]
Rxn_Cpds_Array = ReactionsHelper.parseStoich(old_stoichiometry)
#Adjust for protons
ReactionsHelper.adjustCompound(Rxn_Cpds_Array, "cpd00067",
float(number))
#Recompute new status and stoichiometry
new_status = ReactionsHelper.balanceReaction(Rxn_Cpds_Array)
new_stoichiometry = ReactionsHelper.buildStoich(Rxn_Cpds_Array)
if (new_status != Reactions_Dict[rxn]['status']):
status_file.write(rxn + "\t" + Reactions_Dict[rxn]['status'] +
"\t" + new_status + "\n")
if (new_stoichiometry != old_stoichiometry):
print("Rebuilding reaction :", rxn)
ReactionsHelper.rebuildReaction(Reactions_Dict[rxn],
new_stoichiometry)
Reactions_Dict[rxn]["status"] = new_status
if ("HB" not in Reactions_Dict[rxn]["notes"]):
if (rxn_code in reactions_codes):
matched_rxn = sorted(list(reactions_codes[rxn_code]))[0]
#Because we adjust for water a posterior
#We need to include water when matching codes, in case
if (matched_rxn is None):
#Find statuses that only have water imbalance
new_status = reactions_helper.balanceReaction(new_rxn_cpds_array)
if (new_status == "MI:H:2/O:1" or new_status == "MI:H:-2/O:-1"):
Water_Adjustment = 1
if ("-1" in new_status):
Water_Adjustment = -1
#Adjust for water
reactions_helper.adjustCompound(new_rxn_cpds_array, "cpd00001",
float(Water_Adjustment))
rxn_code = reactions_helper.generateCode(new_rxn_cpds_array)
if (rxn_code in reactions_codes):
matched_rxn = sorted(list(reactions_codes[rxn_code]))[0]
if (matched_rxn is not None):
#Add Names, EC and Alias
#Regardless of match-type, add new names
#NB at this point, names shouldn't match _anything_ already in the database
#Names are saved separately as part of the aliases at the end of the script
for name in rxn['NAMES'].split('|'):
if (name not in All_Names):
#Possible for there to be no names in biochemistry?
if (matched_rxn not in Names_Dict):
Names_Dict[matched_rxn] = list()
Names_Dict[matched_rxn].append(name)