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
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