cleanup

rs/reaction_system_with_concentrations_param.py

@@ -4,9 +4,11 @@ from colour import *
 from rs.reaction_system import ReactionSystem
 
 class ParameterSet(object):
+
     def __init__(self, name):
         self.name = name
 
+
 class ReactionSystemWithConcentrationsParam(ReactionSystem):
 
     def __init__(self):
@@ -24,12 +26,13 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
         name = ""
         def_max_conc = -1
         if type(e) is tuple and len(e) == 2:
-            name,def_max_conc = e
+            name, def_max_conc = e
         elif type(e) is str:
             name = e
             print("\nWARNING: no maximal concentration level specified for:", e, "\n")
         else:
-            raise RuntimeError("Bad entity type when adding background set element")
+            raise RuntimeError(
+                "Bad entity type when adding background set element")
 
         self.assume_not_in_bgset(name)
         self.background_set.append(name)
@@ -73,7 +76,8 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
 
     def has_non_zero_concentration(self, elem):
         if elem[1] < 1:
-            raise RuntimeError("Unexpected concentration level in state: " + str(elem))
+            raise RuntimeError(
+                "Unexpected concentration level in state: " + str(elem))
 
     def process_rip(self, R, I, P, ignore_empty_R=False):
         """Chcecks concentration levels and converts entities names into their ids"""
@@ -85,26 +89,26 @@ class ReactionSystemWithConcentrationsParam(ReactionSystem):
         for r in R:
             self.is_valid_entity_with_concentration(r)
             self.has_non_zero_concentration(r)
-            entity,level = r
-            reactants.append((self.get_entity_id(entity),level))
+            entity, level = r
+            reactants.append((self.get_entity_id(entity), level))
             if self.max_concentration < level:
                 self.max_concentration = level
         inhibitors = []
         for i in I:
             self.is_valid_entity_with_concentration(i)
             self.has_non_zero_concentration(i)
-            entity,level = i
-            inhibitors.append((self.get_entity_id(entity),level))
+            entity, level = i
+            inhibitors.append((self.get_entity_id(entity), level))
             if self.max_concentration < level:
                 self.max_concentration = level
         products = []
         for p in P:
             self.is_valid_entity_with_concentration(p)
             self.has_non_zero_concentration(p)
-            entity,level = p
-            products.append((self.get_entity_id(entity),level))
+            entity, level = p
+            products.append((self.get_entity_id(entity), level))
 
-        return reactants,inhibitors,products
+        return reactants, inhibitors, products
 
     def add_reaction(self, R, I, P):
         """Adds a reaction