Merge pull request ModelSEED#93 from ModelSEED/rebalancing_reactions

Implemented removal of reagents of zero coefficient

Author: JamesJeffryes

Libs/Python/BiochemPy/Reactions.py

@@ -227,6 +227,7 @@ def balanceReaction(self, rgts_array):
 
     def adjustCompound(self, rxn_cpds_array, compound, adjustment,
                        compartment=0):
+
         if (adjustment == 0):
             return rxn_cpds_array
 
@@ -238,11 +239,14 @@ def adjustCompound(self, rxn_cpds_array, compound, adjustment,
 
         # Check to see if it already exists
         cpd_exists = 0
+        cpd_remove = {}
         for rgt in rxn_cpds_array:
             if (rgt["compound"] == compound and
                         rgt["compartment"] == compartment):
                 rgt["coefficient"] -= adjustment
                 cpd_exists = 1
+                if(rgt["coefficient"] == 0):
+                    cpd_remove=rgt
 
         if (cpd_exists != 1):
             rgt_id = compound + "_" + str(compartment) + "0"
@@ -253,6 +257,10 @@ def adjustCompound(self, rxn_cpds_array, compound, adjustment,
                  "name": self.Compounds_Dict[compound]["name"],
                  "formula": self.Compounds_Dict[compound]["formula"],
                  "charge": self.Compounds_Dict[compound]["charge"]})
+
+        if(len(cpd_remove.keys())>0):
+            rxn_cpds_array.remove(cpd_remove)
+
         return
 
     def rebuildReaction(self, reaction_dict, stoichiometry):

Scripts/Biochemistry/Adjust_Protons.py …/Biochemistry/Adjust_Reaction_Protons.pyScripts/Biochemistry/Adjust_Protons.py renamed to Scripts/Biochemistry/Adjust_Reaction_Protons.py Scripts/Biochemistry/Adjust_Protons.py renamed to Scripts/Biochemistry/Adjust_Reaction_Protons.py

@@ -11,6 +11,9 @@
 
 Update_Reactions=0
 for rxn in sorted(Reactions_Dict.keys()):
+#    if(rxn != "rxn00013"):
+#        continue
+
     if(Reactions_Dict[rxn]["status"] == "EMPTY"):
         continue
 
@@ -36,7 +39,9 @@
 
         old_stoichiometry=Reactions_Dict[rxn]["stoichiometry"]
         Rxn_Cpds_Array=ReactionsHelper.parseStoich(old_stoichiometry)
+        print "1: ",Rxn_Cpds_Array
         ReactionsHelper.adjustCompound(Rxn_Cpds_Array,"cpd00067",float(number))
+        print "2: ",Rxn_Cpds_Array
         new_status = ReactionsHelper.balanceReaction(Rxn_Cpds_Array)
         new_stoichiometry = ReactionsHelper.buildStoich(Rxn_Cpds_Array)
 
@@ -49,8 +54,8 @@
                     Reactions_Dict[rxn]["notes"]="HB"
                 else:
                     Reactions_Dict[rxn]["notes"]+="|HB"
-            Update_Reactions=1
+            Update_Reactions+=1
 
-if(Update_Reactions==1):
-    print "Saving reactions";
+if(Update_Reactions>0):
+    print "Saving adjusted protons for "+str(Update_Reactions)+" reactions";
     ReactionsHelper.saveReactions(Reactions_Dict)

Scripts/Biochemistry/Rebalance_Reactions.py

@@ -11,22 +11,25 @@
 
 Update_Reactions=0
 for rxn in sorted(Reactions_Dict.keys()):
+#    if(rxn != "rxn00013"):
+#        continue
+
     if(Reactions_Dict[rxn]["status"] == "EMPTY"):
         continue
 
     Rxn_Cpds_Array=ReactionsHelper.parseStoich(Reactions_Dict[rxn]["stoichiometry"])
-    Status = ReactionsHelper.balanceReaction(Rxn_Cpds_Array)
+    new_status = ReactionsHelper.balanceReaction(Rxn_Cpds_Array)
 
     #Need to handle reactions with polymers
-    if("ERROR" in Status):
+    if("ERROR" in new_status):
         continue
 
     old_status=Reactions_Dict[rxn]["status"]
-    if(Status != old_status and "CK" not in old_status):
-        print "Changing Status for "+rxn+" from "+old_status+" to "+Status
-        Reactions_Dict[rxn]["status"]=Status
-        Update_Reactions=1
+    if(new_status != old_status and "CK" not in old_status):
+        print "Changing Status for "+rxn+" from "+old_status+" to "+new_status
+        Reactions_Dict[rxn]["status"]=new_status
+        Update_Reactions=+1
 
-if(Update_Reactions==1):
-    print "Saving reactions";
+if(Update_Reactions>0):
+    print "Saving updated statuses for "+str(Update_Reactions)+" reactions";
     ReactionsHelper.saveReactions(Reactions_Dict)

Scripts/Biochemistry/Rebuild_Reactions.py

@@ -18,7 +18,7 @@
     Stoichiometry=ReactionsHelper.buildStoich(Rxn_Cpds_Array)
     if(Stoichiometry != Reactions_Dict[rxn]["stoichiometry"]):
         ReactionsHelper.rebuildReaction(Reactions_Dict[rxn],Stoichiometry)
-        Update_Reactions=1
+        Update_Reactions+=1
 
-print "Saving reactions";
+print "Saving rebuilt equations for "+str(Update_Reactions)+" reactions";
 ReactionsHelper.saveReactions(Reactions_Dict)