I also updated the Jupyter notebook with the solution.
Out of interest, I now need to get the atom indices of the part of the
molecule that matched.
As Jupyter is nicely highlighting this that must already be present in
the molecule somehow, but I can't find out how.
I look at molecule and atom properties but can't find anything that
suggests "highlight me".
How is this encoded?
Tim
On 17/04/2020 19:02, Paolo Tosco wrote:
Hi Tim,
I’ll take a look later and get back to you.
Cheers,
p.
On 17 Apr 2020, at 18:55, Tim Dudgeon <tdudgeon...@gmail.com> wrote:
I'm wanting to use AllChem.ConstrainedEmbed() to generate a conformer of a
molecule tethered to a molecule that should always have some MCS. I found some
code on the internet that mostly works, but I don't fully understand.
It generally works as planned, but for a small number of examples it fails.
Can someone guide me to what is wrong. Here is an example (good and bad):
https://github.com/tdudgeon/jupyter_mpro/blob/master/tethering.ipynb
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