diff --git a/.gitignore b/.gitignore
index 39aa9026..f9bf9c80 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,3 +10,5 @@ temp_testing/*
 build
 dist
 Issues/rule_keywords/test_DeleteMolecules_changed.bngl
+.jules/
+__pycache__/
diff --git a/bionetgen/atomizer/atomizer/analyzeSBML.py b/bionetgen/atomizer/atomizer/analyzeSBML.py
index 928d3bc4..b9eab4b5 100644
--- a/bionetgen/atomizer/atomizer/analyzeSBML.py
+++ b/bionetgen/atomizer/atomizer/analyzeSBML.py
@@ -283,7 +283,6 @@ def analyzeSpeciesModification(self, baseElement, modifiedElement, partialAnalys
                 distance = self.distanceToModification(
                     particle, comparisonElement, translationKeys[0]
                 )
-                score = difflib.ndiff(particle, modifiedElement)
             else:
                 # FIXME: make sure we only do a search on those variables that are viable
                 # candidates. this is once again fuzzy string matchign. there should
@@ -299,15 +298,14 @@ def analyzeSpeciesModification(self, baseElement, modifiedElement, partialAnalys
                     distance = self.distanceToModification(
                         particle, comparisonElement, translationKeys[0]
                     )
-                    score = difflib.ndiff(particle, modifiedElement)
-                # FIXME:tis is just an ad-hoc parameter in terms of how far a mod is from a species name
+                # TODO: 4 is just an ad-hoc parameter in terms of how far a mod is from a species name
                 # use something better
-            if distance < 4:
+
+            max_modification_distance = 4
+            if distance < max_modification_distance:
                 scores.append([particle, distance])
         if len(scores) > 0:
-            winner = scores[[x[1] for x in scores].index(min([x[1] for x in scores]))][
-                0
-            ]
+            winner = min(scores, key=lambda x: x[1])[0]
         else:
             winner = None
         if winner: