Jan,
Do you want to do a supervised alignment (i.e. you specify which atoms in
the fragment map to which atoms in the molecule) or unsupervised alignment
(where the algorithm needs to figure this out)/
It sounds like you're interested in the first; this blog post may be useful
http://rdkit.blogspot.it/2016/07/using-ipywidgets-and-py3dmol-to-browse.html
-greg
On Fri, Nov 17, 2017 at 11:17 AM, Jan Halborg Jensen <jhjen...@chem.ku.dk>
wrote:
>
> Is there a way to rigidly align a 3D molecule to a fragment?
>
> I want to compare several conformations by aligning a rigid part of the
> molecule
>
> Best regards, Jan
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