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 <alexis.parenty.h...@gmail.com>
wrote:
> 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(CCCN(C1)C(C)=O)N")
>
> print(mol_structure.HasSubstructMatch(mol_frag, useChirality=True))
> ==> False
>
>
> worst, the other isomeric fragment matches when it should not:
>
> mol_frag = Chem.MolFromSmarts("C[C@@]1CCCN(C1)C(C)=O")
> mol_structure = Chem.MolFromSmiles("C[C@]1(CCCN(C1)C(C)=O)N")
>
> print(mol_structure.HasSubstructMatch(mol_frag, useChirality=True))
> ==> True
>
> Am I missing something?
>
> Many thanks,
>
> Alexis
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