To give some context, it's not that we're trying to sample a diverse set of conformers (and find something close to the experimental). In this case, we're generating initial geometries - to assess Naruki's fragment-based builder in Open Babel.
But you raise an excellent point - by picking only one random conformer (as we're doing), we'll absolutely going to have a higher RMSD than sampling 50 conformers per compound and picking the best. We'll try a quick test to be safe, but thanks for the suggestion. -Geoff On Mon, Feb 25, 2019 at 3:55 PM Greg Landrum <greg.land...@gmail.com> wrote: > > Hi Naruki, > > You're only generating a single conformer per molecule; I wouldn't expect > that to do particularly well. It's generally better to call > EmbedMultipleConfs(). > > As an aside: I've looked at the platinum set too, it might be worth checking > out this RDKit blog post: > http://rdkit.blogspot.com/2017/05/looking-at-platinum-dataset.html > > -greg > > > On Mon, Feb 25, 2019 at 11:53 AM Naruki Yoshikawa > <naruki.yoshik...@gmail.com> wrote: >> >> Dear all, >> >> I'm evaluating ETKDG method implemented in RDKit using the Platinum >> Dataset introduced in a benchmark paper >> https://pubs.acs.org/doi/abs/10.1021/acs.jcim.7b00505/ >> SMILES generated from the dataset is served as input and a 3D >> conformer is generated. >> We evaluate RMSD between generated structure and experimental structure. >> >> Although the author of the benchmark paper reported the mean RMSD to >> be below 1.0 angstrom, my evaluation code reports around 1.5 angstrom. >> I can't figure out why such a big difference occurs. >> >> My evaluation code is here: >> https://gist.github.com/n-yoshikawa/0ba04a1b0c718c4cc8d83702f3759afa >> There is a link to data in this gist. >> >> Thanks, >> Naruki >> >> >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
