Hi JW,
On Wed, Dec 21, 2016 at 11:57 PM, JW Feng <f...@dnli.com> wrote:
>
> I am using AllChem.EmbedMultipleConfs to generate conformers. I noticed
> that conformers in the result set are very similar to each other. I wrote
> a test script to calculate RMS for the conformers and may have found a
> bug. Looks like AllChem.EmbedMultipleConfs is calculating RMS using all
> atoms, including Hs, when pruning. The documents says pruning is based on
> heavy atoms RMS.
>
You're absolutely correct. The code uses all atoms, but the documentation
says it only uses heavy atoms.
So there's either a bug in the documentation or in the code. Here's the
github entry: https://github.com/rdkit/rdkit/issues/1227
I believe the right thing to do is change the code, which will lead to
different results from the embedding, but I will hold off on making the fix
to see if any discussion materializes either here or on github.
> Attached is my test script and an input file that illustrates the
> problem. In this script, 50 conformers are generated and pruneRmsThresh is
> 0.5. Pairwise RMS between conformers are >0.5 when H atoms are included.
> Pairwise RMS are <0.5 for many conformers when only heavy atoms are
> included.
>
Thanks for the detailed report and script to reproduce the problem!
-greg
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