I think I tracked it down.
If I use 'bondCompare=rdFMCS.BondCompare.CompareOrderExact' for the
FindMCS() function then it seem to find the right MCS.
Seems like by default it matches aromatic and aliphatic rings, and by
doing so in my example it finds a bigger MCS so uses it.
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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