On 18/04/2020 11:56, Paolo Tosco wrote:
Hi Tim,
mol.GetSubstructMatch(query) will give you indices in mol that match
query.
Yes, I can re-calculate it, but the fact that it's getting highlighted
in Jupyter suggests that the mol already has that info so it shouldn't
need recalculating. But I can't find it.
Also note that |rdFMCS.||MCSResult| has a |queryMol |property that
encode the MCS query, so you don't need to rebuild the query molecule
out of the SMARTS pattern.
Good. I'll use that.
p.
On 18/04/2020 10:27, Tim Dudgeon wrote:
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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