sys.path.append('../../Libs/Python')
from BiochemPy import Reactions
ReactionsHelper = Reactions()
Reactions_Dict = ReactionsHelper.loadReactions()
Update_Reactions = 0
status_file = open("Status_Changes.txt", 'w')
for rxn in sorted(Reactions_Dict.keys()):
if (Reactions_Dict[rxn]["status"] == "EMPTY"):
continue
Rxn_Cpds_Array = ReactionsHelper.parseStoich(
Reactions_Dict[rxn]["stoichiometry"])
new_status = ReactionsHelper.balanceReaction(Rxn_Cpds_Array)
old_status = Reactions_Dict[rxn]["status"]
#Need to handle reactions with polymers
if (new_status == "Duplicate reagents"):
new_status = "NB"
continue
if (new_status != old_status and "CK" not in old_status):
print("Changing Status for " + rxn + " from " + old_status + " to " +
new_status)
status_file.write(rxn + "\t" + old_status + "\t" + new_status + "\n")
Reactions_Dict[rxn]["status"] = new_status
Update_Reactions += 1
if (Update_Reactions > 0):
rxn_code = reactions_helper.generateCode(new_rxn_cpds_array)
matched_rxn = None
if (len(new_rxn_cpds_array) == 0):
matched_rxn = Empty_Rxn_ID
else:
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