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!

Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today.http://sdm.link/intel
Rdkit-discuss mailing list

Reply via email to