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 >
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