[Rdkit-discuss] AllChem.GetConformerRMSD: this is not RMSD between two conformers but an upper bound of it

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

Re: [Rdkit-discuss] Clustering

Following up on myself, On Jun 6, 2017, at 04:00, Andrew Dalke wrote: > I've fleshed out that algorithm so it's a command-line program that can be > used for benchmarking purposes. It's available from > http://dalkescientific.com/writings/taylor_butina.py . > > If