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
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/2
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 stru
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