I would expect the problem here is kekulization. The SMARTS is pattern
matching using the kekule structure (i.e. double and single bonds, non
aromatic atoms) and is not sanitized whereas the SMILES after parsing and
sanitization has aromatic bonds and aromatic atoms. Try what happens when
you do a SMARTS match with the SMILES with aromatic atoms:
`[2H]c1cc([3H])cc(C2=N[C@](C)([37Cl])CC2)c1`
best wishes
wim
On Thu, Jun 27, 2024 at 10:56 AM pgchem pgchem <pgc...@tuschehund.de> wrote:
> Hello all,
>
> if every valid SMILES is also a valid SMARTS, why does:
>
> select substruct('[2H]C1=CC([3H])=CC(=C1)C1=N[C@](C)([37Cl])CC1'::mol,
> '[2H]C1=CC([3H])=CC(=C1)C1=N[C@](C)([37Cl])CC1'::mol)
>
> yield "True", but:
>
> select substruct('[2H]C1=CC([3H])=CC(=C1)C1=N[C@](C)([37Cl])CC1'::mol,
> '[2H]C1=CC([3H])=CC(=C1)C1=N[C@](C)([37Cl])CC1'::qmol)
>
> is "False"? The same is observed when using the @> operator.
>
> RDKit 2024.03.3 built from source + PostgreSQL 16.3.
>
> best regards
>
> Ernst-Georg
>
>
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