Hi Leon,
There's not really a "right" answer to your question - it depends on what
you want to calculate.
I personally think it makes more sense to use the heavy atom RMSD (which is
what you get if you remove Hs before calculating the RMSD), particularly if
you are comparing to experiment.
Note that AllChem.GetConformerRMSMatrix() does not take symmetry into
account, so you may not get the correct results.
I just opened a ticket to fix this, but in the meantime if you have
molecules with symmetry-equivalent atoms you are probably better off
generating the conformer RMS matrix manually using GetBestRMS().
Best,
-greg
On Wed, Nov 13, 2019 at 5:17 PM topgunhaides . <sunzhi....@gmail.com> wrote:
> Hi guys,
>
> I am new to RDKit, and have a question about adding and removing Hs.
>
> As recommended in the documentation, hydrogen atoms should be added for
> generating conformers, optimization, etc.
>
> However, for clustering, should the Hs be removed first, before generating
> the conformer RMS matrix? For instance:
>
>
> from rdkit import Chem
> from rdkit.Chem import AllChem, TorsionFingerprints
>
> suppl = Chem.SDMolSupplier('molecule.sdf')
>
> for mol in suppl:
> mh = Chem.AddHs(mol)
> cids = AllChem.EmbedMultipleConfs(mh, numConfs=5, maxAttempts=1000,
> pruneRmsThresh=0.5, numThreads=0,
> randomSeed=1)
> m = Chem.RemoveHs(mh)
> # RMS matrix
> rmsmat = AllChem.GetConformerRMSMatrix(m, prealigned=False)
> # TFD matrix
> tfdmat = TorsionFingerprints.GetTFDMatrix(m)
> print(rmsmat)
> print(tfdmat)
>
>
> Note I remove the Hs before getting RMS and TFD matrices. Both resulting
> matrices are different if I do not remove Hs. The RMS without Hs, in
> general, tend to be smaller than the RMS with Hs. This will in turn affect
> the subsequent clustering result.
>
> Could you guys give me some suggestions? Thank you!
>
> Best,
> Leon
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
