Hi Brian and thank you for your respons.
Yes, so Tversky with alpha parameter set to 1.0 and a cutoff for the
similarity at 1.0 (100 % of me in you) will equal substucture search, at
least at a theoretical level. I guess my question is, does imperfections in
the fp model likley to generate these kind of results? So I use ecfp4 with
2048 bits.

Regards
Axel
On Dec 12, 2016 6:57 PM, "Brian Kelley" <fustiga...@gmail.com> wrote:

> I'm not really sure what you mean by tversky searching in substructure
> mode.
>
> Fingerprinting methods do not guarantee the presence of an exact
> substructure.  You can think of tversky asking what percentage of me is in
> you and that percentage doesn't have to be a substructure.  However they
> are correlated in that a good screening fingerprint can throw out molecules
> that will never be a substructure match.  You still have to check the
> substructure match however.
>
> Using a screen fingerprint to filter out true negatives, I generally go
> from 5-10k substructure matches/sec to around 500-600k/sec in real world
> searches.  I'm happy to provide an example of this if you need it.
>
> I hope this helps.
>
> ----
> Brian Kelley
>
> On Dec 12, 2016, at 11:29 AM, Axel Rudling <axru6...@gmail.com> wrote:
>
> Hello all,
>
> Currently I'm doing a project with Tversky searching in substructure mode
> and use smiles for creating fingerprints.
>
> For most molecules I get the correct result but there are some molecules
> where I get an overflow of falsely predicted substructure molecules. In
> brief, I get a large amount of compounds as a result from the substructure
> search that are not actually substructures of the query compound. I'm not
> certain of why but it might have to do with the FP representation as these
> molecules have a very unusual curricular structure ex.:
>
> C1C[NH2+]CCC[NH2+]CCCNCCC[NH2+]C1
>
>
> I use 2048-bit ECFP4 fingerprints.
>
> tverskySim = DataStructs.TverskySimilarity(ffp1,ffp2,1.0,0.0)
>
> Does anyone have an idea?
>
>
> best
>
> Axel
>
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