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 it does not. The R stereoisomer fragment
matches the R stereoisomer super structure when It should not. What do you
think?
Best,
Alexis
On Tue, 4 Jan 2022 at 12:42, Shani Zev <levishan...@gmail.com> wrote:
> 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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>
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