Hi Nils,
Can you please send me the SMILES for those structures (or point me to an
easy way to lookup a SCHEMBL id)?
I will take a look at these, but I don't currently have a convenient copy
of SCHEMBL.
-greg
On Thu, Jun 1, 2017 at 4:28 PM, Nils Weskamp <nils.wesk...@gmail.com> wrote:
> Dear RDKitters,
>
> I just calculated RDKit "Daylight-like" fingerprints for a number of
> public compound databases and found quite a number of examples where the
> resulting fingerprints have *all* bits set to 1. This happens in both KNIME
> 3.2.1 (1024/1/7) and also via the command line (2048/1/7/4) for RDKit
> 2016.03.
>
> Examples include (from SureChEMBL):
>
> SCHEMBL5141968
>
> SCHEMBL13916889
>
> SCHEMBL16257315
>
> SCHEMBL16257310
>
> SCHEMBL16257297
>
> SCHEMBL16257215
>
> SCHEMBL16257169
>
> SCHEMBL8232906
>
> SCHEMBL16257312
>
> SCHEMBL13011081
>
> SCHEMBL12570100
>
> SCHEMBL14524878
>
> SCHEMBL6370886
>
> SCHEMBL15305169
>
> SCHEMBL16912871
>
> SCHEMBL13290179
>
>
> Now, these are obviously some very large and complex molecules, so I would
> expect that they contain many features and thus set many bits - but all of
> them?
>
> So, in short: Are these compounds so ugly that it is normal for the
> fingerprints to have all bits set or are they so ugly that they trigger
> some rare bug in RDKit?
>
> Any ideas / suggestions / comments?
>
> Thanks a lot,
> Nils
>
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