Hi Bruce,
setting fpSize to 4096 or 8192 leads to fingerprints with a few 0s
(although still a very high bit density). The same is true when I reduce
the maximum path length.
I do not see the same kind of behaviour with a different path-oriented
fingerprint implementation (ChemAxon), which made me wonder whether these
complex macrocycles could somehow confuse RDKit fingerprinter (or whether I
am seeing ghosts...).
Cheers,
Nils
On Thu, Jun 1, 2017 at 4:51 PM, Bruce Milne <bfmi...@gmail.com> wrote:
> Hi,
>
> Did you try setting the length of the fingerprint (fpSize) to a higher
> value than the default 2048 to see if you can get one with 0's?
>
> Cheers,
> Bruce
> >
> > Message: 2
> > Date: Thu, 1 Jun 2017 16:28:40 +0200
> > From: Nils Weskamp <nils.wesk...@gmail.com>
> > To: Rdkit-discuss@lists.sourceforge.net
> > Subject: [Rdkit-discuss] RDKit-fingerprints set all bits for complex
> > molecules?
> > Message-ID:
> > <CAPVmmo5E0GtzAXa8bJ5=8=r+5RL4Zmgtox7onSx2tJY0e=XbpQ@
> mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > 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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