diff --git a/src/main/org/openscience/cdk/fingerprint/Fingerprinter.java b/src/main/org/openscience/cdk/fingerprint/Fingerprinter.java
index <HASH>..<HASH> 100644
--- a/src/main/org/openscience/cdk/fingerprint/Fingerprinter.java
+++ b/src/main/org/openscience/cdk/fingerprint/Fingerprinter.java
@@ -204,7 +204,7 @@ public class Fingerprinter implements IFingerprinter {
             }
         }
         // now lets clean stuff up
-        List<String> cleanPath = new ArrayList<String>();
+        Set<String> cleanPath = new HashSet<String>();
         for (StringBuffer s : allPaths) {
             if (cleanPath.contains(s.toString()) || cleanPath.contains(s.reverse().toString())) continue;
             else cleanPath.add(s.toString());
[jonalv-fingerprint-<I>.x] first optimization brings down fingerprinting time to about <I>% of what it was before

git-svn-id: <URL>