In my last post, I doubted the accuracy of fingerprint based substructure search and pointed out sometimes fingerprint loosed hits. In fact, something went wrong in my code. As I was reading from SDF directly, while IteratingMDLReader does not percieve atom type or detect aromaticity automatically. This cause the incorrect matchings of UniversalIsomorphismTester, sorry for the incorrect post. I’ve run the test again, using the SMILES provided by Guha as input. The groovy script is also attached here.
|#||Query||Subgraph Isomorphism||Entended CDK||Missing||Extra|
Well, CDK fingerprint is OK.