diff --git a/selfies/utils/encoding_utils.py b/selfies/utils/encoding_utils.py
index 411c353..05d31c1 100644
--- a/selfies/utils/encoding_utils.py
+++ b/selfies/utils/encoding_utils.py
@@ -47,9 +47,18 @@ def selfies_to_encoding(
         selfies += "[nop]" * (pad_to_len - len_selfies(selfies))
 
     # integer encode
-    char_list = split_selfies(selfies)
-    integer_encoded = [vocab_stoi[char] for char in char_list]
-
+    integer_encoded = []
+    for char in split_selfies(selfies):
+        if (char == ".") and ("." not in vocab_stoi):
+            raise KeyError(
+                "The SELFIES string contains two unconnected molecules "
+                "(given by the '.' character), but vocab_stoi does not "
+                "contain the '.' key. Please add it to the vocabulary "
+                "or separate the molecules."
+            )
+
+        integer_encoded.append(vocab_stoi[char])
+        
     if enc_type == "label":
         return integer_encoded