Hi James,
Thanks for reporting this.
Here's a somewhat more compact reproducible showing the problem:
http://nbviewer.ipython.org/gist/greglandrum/dda2bffd0ba128d1decb
The corresponding gist is here:
https://gist.github.com/greglandrum/dda2bffd0ba128d1decb
And here's the issue:
https://github.com/rdkit/rdkit/issues/385
-greg
On Fri, Nov 14, 2014 at 10:03 PM, James Davidson <j.david...@vernalis.com>
wrote:
> Dear All,
>
>
>
> I am finding differences when I align multiple conformers to a reference
> molecule depending on if I (a) first convert the conformers to a list of
> individual RDKit mol objects; or (b) work directly with the multi-conformer
> mol. In the second case I always find that conformer 0 gives the best
> alignment score(!)
>
>
>
> If anyone can see what I am doing wrong (or – much less likely – what the
> toolkit is doing wrong) then it would be greatly appreciated.
>
> I have (hopefully) attached an IPython notebook (in .ipnb and .html
> formats) with a sanitised example (ie with ‘dummy’ molecules, and not ‘real
> work’ structures) to illustrate the point.
>
>
>
> Kind regards
>
>
>
> James
>
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