Hi, I've created a fastsearch index using the FP2, FP3, FP4 & MACCS fingerprints. When I do a substructure search without fingerprints (in a 10K file), I get 647 hits. With FP2 I also get these hits. However with the other fingerprints I get more hits. These hits include molecules that do not have my query as substructure. It seems like no substructure search is done for the other fingerprints. This is using svn. Any ideas?
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