I have a follow up question on ConstrainedEmbed.
You pass the molecule to embed and the substructure core into this
function and get back the embedded and aligned molecule.
In rare cases there will be multiple substructure matches (e.g. in the
case of symmetry). How would one go about generating alignment for all
of these matches rather than (presumably) just the first?
Tim
On 18/04/2020 11:56, Paolo Tosco wrote:
Hi Tim,
mol.GetSubstructMatch(query) will give you indices in mol that match
query.
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.
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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