On Thu, Nov 14, 2019 at 11:24 PM Webster Homer <
webster.ho...@milliporesigma.com> wrote:
> I have a database which contains these three molecules.
>
> N[C@H](Cc1ccc(B(O)O)cc1)C(=O)O
>
> N[C@@H](Cc1ccc(B(O)O)cc1)C(=O)O
>
> NC(Cc1ccc(B(O)O)cc1)C(=O)O
>
>
>
> It seems that the exact search does not respect the rdkit.do_chiral_sss
>
> # select * from rdk.mols where m@=
> mol_from_smiles('NC(Cc1ccc(B(O)O)cc1)C(=O)O');
>
> structure_id | m
>
> --------------+----------------------------
>
> 29303328 | NC(Cc1ccc(B(O)O)cc1)C(=O)O
>
> (1 row)
>
> With do_chiral_sss set to false I would expect that all three would be
> found! Instead the @= will only find the those with matching
> stereochemistry.
>
> The @> operator does return all three, but it also returns hits that
> contain more than what I want.
>
> Moreover the semantics of the operators seem arbitrary.
>
>
>
> I think it would be better if chiral searching was done with an option to
> the operator rather than a session variable, but at least chiral searching
> should be consistent!
>
Yep, I agree. This is a bug and we'll fix it (
https://github.com/rdkit/rdkit/issues/2790)
Unfortunately, there's not really a straightforward work around to this one
until that bug is fixed.
-greg
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