Hi, The problem seems to be in src/fingerprints/finger3.cpp:
//Each bit represents a single substructure; no need for confirmation when substructure searching virtual unsigned int Flags() { return FPT_UNIQUEBITS;}; This confuses me. It's not because a the substructures are present in the queried molecule that the queried molecule is a superstructure of the query. So an isomorphism search is still needed to confirm the hit. When I change the Flags() function to return 0, I still don't get the expected results though. With my query there should be 46 hits but FP3 gives 26, FP4 25 and MACCS only 12. Is there something I'm missing here. If the bits simply represent a substructure, the fingerprint screening should return all possible molecules containing the query. Thanks in advance, Tim On Sun, Jul 22, 2012 at 11:48 PM, Tim Vandermeersch <tim.vandermeer...@gmail.com> wrote: > 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? > > Tim ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel