Hi Hao,
The RDKit's extensions to SMARTS are documented here:
https://www.rdkit.org/docs/RDKit_Book.html#smarts-support-and-extensions
There is not an extension for "N_lp" and what the translation should be is
VERY highly dependent on what the authors meant by "lone pair".
For example: does the N involved in an amide bond have a lone pair by the
authors' definition?
-greg
On Wed, Jun 2, 2021 at 8:50 AM hwang929 wrote:
> Hi,
> I'm a student from the school of chemistry and molecular engineering, East
> China Normal University. I have some questions about smarts.
>
> I used the self defined smart writing method in this article(Torsion
> Library Reloaded: A New Version of Expert-Derived SMARTS Rules for
> Assessing Conformations of Small Molecules).
> For example, [*:1]~[*^3:2]!@[*^3:3]~[*:4] Here a "^3" denotes an sp3
> hybridized atom. In the same way，"^2" denotes an sp2 hybridized atom."^１"
> denotes an sp hybridized atom. But '^' symbol is not found in daylight, to
> my surprise I found that it can be read in and find the corresponding
> structure in rdkit. I don't know whether rdkit has a specific method to
> identify or what? If not correctly identified, how to express it(
> [*:1]~[*^3:2]!@[*^3:3]~[*:4])
>
> The second question: Another kind of smarts containing N_lp(eg:
> [CX4:1][CX4H2:2]!@[NX3;N_lp:3][CX4:4])
> N_lp explicitly requires a trivalent nitrogen with a lone pair. for
> example sulfonamides .It is not recognized by rdkit. Do I have any way to
> express it? What can I replace with N_lp.
>
> Thanks
> Kind regards,
> Hao Wang
>
>
>
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