The function you want is GetBestRMS, note that you can set the conformer idx
for the probe and ref.
http://www.rdkit.org/Python_Docs/rdkit.Chem.AllChem-module.html#GetBestRMS
----
Brian Kelley
> On Jun 15, 2017, at 5:30 AM, Francois BERENGER
> <beren...@bioreg.kyushu-u.ac.jp> wrote:
>
> Hello,
>
> I am afraid that in AllChem.GetConfomerRMSD: one doesn't get the RMSD
> between the two conformers but an upper bound of it.
>
> I understand from the doc that if they are aligned, they are aligned
> to the first conformer of the molecule.
>
> To get the real RMSD between two conformers, they must
> be superimposed together, not to a third conformer.
>
> Please tell me if I'm wrong.
>
> Regards,
> F.
>
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