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=x...@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 > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > ------------------------------ > > End of Rdkit-discuss Digest, Vol 116, Issue 3 > ********************************************* ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
