Hi Greg,
I would also vote for changing the code such that only heavy atoms are used in
the RMS calculation.
Best,
Sereina
On 22 Dec 2016, at 13:36, Greg Landrum <greg.land...@gmail.com> wrote:
> 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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