I am currently working on a project where i am examining two sdf files full of chemicals and comparing their fingerprints. I am doing this for several files, so I wasn't too surprised to see there was no exact matches in this particular data set. It happens. However, my boss wanted me to look at how close the nearest similarites were.
The top 3 hits are all exactly 5.0 for similarity. One of hitslooks to be a perfect match based on the SMILEs and everything else we can see. I can only assume there is some odd bug that is capping the threshold at 5.0 for this specific test. However, other tests using the same files do not show this, nor can I find any obvious difference in the Similarity Search node.