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"]):
Reactions_Dict[rxn]["notes"].append("HB")
Update_Reactions += 1
if (Update_Reactions > 0):
if (compounds_dict[cpd]['linked_compound'] == 'null'):
print(
"Warning: missing linked compound for obsolete compound: "
+ cpd)
continue
lnkd_cpd = sorted(
compounds_dict[cpd]['linked_compound'].split(';'))[0]
# Replace cpd with lnkd_cpd in reaction fields:
# code, compound_ids, equation, stoichiometry
old_stoichiometry = reactions_dict[rxn]["stoichiometry"]
rxn_cpds_array = reactions_helper.parseStoich(old_stoichiometry)
reactions_helper.replaceCompound(rxn_cpds_array, cpd, lnkd_cpd)
new_stoichiometry = reactions_helper.buildStoich(rxn_cpds_array)
reactions_helper.rebuildReaction(reactions_dict[rxn],
new_stoichiometry)
print("Replacting obsolete " + cpd + " with " + lnkd_cpd + " in " +
rxn)
Update_Reactions += 1
# if(Update_Reactions>0):
# break
if (Update_Reactions > 0):
print("Saving replacement of " + str(Update_Reactions) +
" obsolete compounds in reactions")
reactions_helper.saveReactions(reactions_dict)