Hi Paul,

Regarding your second question:

> On 25 Oct 2017, at 18:36, Paul Hawkins <phawk...@eyesopen.com> wrote:
> Also, once I generate the conformers what is best way to cluster them by RMSD 
> so that each conformer has a minimum RMSD to all the others in the set?

I think the function AllChem.GetConformerRMSMatrix() might do (parts of) what 
you want.

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