added method to generate reaction config

src/box_model.py

@@ -3,6 +3,8 @@
 from music_box_evolving_conditions import EvolvingConditions
 from music_box_reaction_list import ReactionList
 from music_box_reaction import Reaction
+from music_box_reactant import Reactant
+from music_box_product import Product
 from music_box_species_list import SpeciesList
 from music_box_species import Species
 from music_box_model_options import BoxModelOptions
@@ -63,7 +65,11 @@ def generateConfig(self):
         speciesConfig = self.generateSpeciesConfig()
         print(speciesConfig)
 
+        reactionConfig = self.generateReactionConfig()
+        print(reactionConfig)
+
         pass
+
     def generateSpeciesConfig(self):
         """
         Generate a JSON configuration for the species in the box model.
@@ -72,14 +78,14 @@ def generateSpeciesConfig(self):
             str: A JSON-formatted string representing the species configuration.
         """
 
-        #Established relative tolerance
-        relTolerance = {
-            "type" : "RELATIVE_TOLERANCE",
-            "value" : self.species_list.relative_tolerance
-        }
-
         speciesArray = []
-        speciesArray.append(relTolerance)
+
+        #Adds relative tolerance if value is set
+        if(self.species_list.relative_tolerance != None):
+            relativeTolerance = {}
+            relativeTolerance["Type"] = "RELATIVE_TOLERANCE"
+            relativeTolerance["value"] = self.species_list.relative_tolerance
+            speciesArray.append(relativeTolerance)
 
         #Adds species to config
         for species in self.species_list.species:
@@ -115,4 +121,69 @@ def generateSpeciesConfig(self):
 
         return json.dumps(species_json)
 
+
+    def generateReactionConfig(self):
+        """
+        Generate a JSON configuration for the reactions in the box model.
+
+        Returns:
+            str: A JSON-formatted string representing the reaction configuration.
+        """
+        reacList = {}
+
+        #Add mechanism name if value is set
+        if self.reaction_list.name != None:
+            reacList["name"] = self.reaction_list.name
+
+        reacList["type"] = "MECHANISM"
+
+        reactionsArray = []
+
+        #Adds reaction to config
+        for reaction in self.reaction_list.reactions:
+            reac = {}
+
+            #Adds reaction name if value is set
+            if(reaction.reaction_type != None):
+                reac["type"] = reaction.reaction_type
+
+            reactants = {}
+
+            #Adds reactants
+            for reactant in reaction.reactants:
+                quantity = {}
+
+                #Adds reactant quantity if value is set
+                if reactant.quantity != None:
+                    quantity["quantity"] = reactant.quantity
+                reactants[reactant.name] = quantity
+
+            reac["reactants"] = reactants
+
+            products = {}
+
+            #Adds products
+            for product in reaction.products:
+                yield_value = {}
+
+                 #Adds product yield if value is set
+                if product.yield_value != None:
+                    yield_value["yield"] = product.yield_value
+                products[product.name] = yield_value
+
+            reac["products"] = products
+
+             #Adds reaction name if value is set
+            if(reaction.name != None):
+                reac["MUSICA name"] = reaction.name
+
+            reactionsArray.append(reac)
+
+        reacList["reactions"] = reactionsArray
+
+        reactionsJson = {
+            "camp-data" : [reacList]
+        }
+
+        return json.dumps(reactionsJson)
 

src/music_box_product.py

@@ -8,7 +8,7 @@ class Product:
         yield_value (float): The yield of the product.
     """
 
-    def __init__(self, species, yield_value):
+    def __init__(self, species, yield_value=None):
         """
         Initializes a new instance of the Product class.
 

src/music_box_reactant.py

@@ -7,7 +7,7 @@ class Reactant:
         quantity (float): The quantity of the reactant.
     """
 
-    def __init__(self, species, quantity):
+    def __init__(self, species, quantity=None):
         """
         Initializes a new instance of the Reactant class.
 

src/music_box_reaction_list.py

@@ -8,13 +8,15 @@ class ReactionList:
         reactions (List[Reaction]): A list of Reaction instances.
     """
 
-    def __init__(self, reactions=None):
+    def __init__(self, name=None, reactions=None):
         """
         Initializes a new instance of the ReactionList class.
 
         Args:
             reactions (List[Reaction]): A list of Reaction instances. Default is an empty list.
         """
+
+        self.name = name
         self.reactions = reactions if reactions is not None else []
 
     def add_reaction(self, reaction):