Hello Paolo,
Many thanks for your detailed explanation. I think it is all clear now. I
was not aware that a C with a single @ would always be tagged as CCW in a
Smarts due to the missing implicit H. Pity I cannot add a H to get the
correct CW tag since it would no longer match the superstructure..
Hi Alexis,
The chiral substructure match does not look at the CIP labels, but rather
at the atom parities, as you expected.
In the examples below I have reordered your mol_structure as it makes
things easier to understand.
Let's work with a fragment constructed from SMILES rather than from SMART
Hi Shani,
Many thanks for your response. Good observation! I did not realise that the
stereoisomer nomenclature had swap on removing the amine. However, is it
the intended behaviour of the method?
To me, in that case, the S stereoisomer fragment should match the R
stereoisomer super structure but i
Hi Alexis,
I think that the reason for this is because in the first case you are
comparing S and R stereoisomer and hence it is false while in the second
you are comparing R and R.
best,
Shani
[image: q.gif]
On Tue, Jan 4, 2022 at 1:22 PM Alexis Parenty
wrote:
> Hi everyone,
>
> Why is it that
Hi everyone,
Why is it that the following smarts C[C@]1CCCN(C1)C(C)=O does not match the
following structure C[C@]1(CCCN(C1)C(C)=O)N when using the chirality
argument in the HasSubstructMatch method?
mol_frag = Chem.MolFromSmarts("C[C@]1CCCN(C1)C(C)=O")
mol_structure = Chem.MolFromSmiles("C[C@]1
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