Hi Greg and Sereina,

Thanks for confirming the bug.  I also vote for changing the code to use
only heavy atoms.  Is symmetry taken into consideration when calculating
RMS during the pruning step?

Best,

JW

___________________
JW Feng, Ph.D.
Denali Therapeutics Inc.
151 Oyster Point Blvd, 2nd Floor, South San Francisco, CA 94080 | (650)
270-0628

On Thu, Dec 22, 2016 at 7:02 AM, Sereina <sereina.rini...@gmail.com> wrote:

> 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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