Hi Greg, I have an SDFile at hand (see attached). Lookup of SureChEMBL-structures is possible via
https://www.surechembl.org/chemical/SCHEMBL16257312 (although we can argue whether that page is convenient...). Thanks for your help, Nils On Thu, Jun 1, 2017 at 6:05 PM, Greg Landrum <greg.land...@gmail.com> wrote: > 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 >> >> ------------------------------------------------------------ >> ------------------ >> 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 >> >> >
complex_molecules_with_all_bits_set.sdf.gz
Description: GNU Zip compressed data
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