[Cod-bugs] Optimade API returns empty results for SMILES query, while web interface works properly for the same SMILES value

[Mehmet Giritli - STFC UKRI]

Thank you Andrius.

Best,
Mehmet.
________________________________
From: Andrius Merkys <andrius.merkys at gmail.com>
Sent: 23 May 2025 15:47
To: Giritli, Mehmet (STFC,RAL,SC) <mehmet.giritli at stfc.ac.uk>
Cc: Aileen Day <A.E.Day at soton.ac.uk>; Poulter, Gemma (STFC,RAL,SC) <gemma.poulter at stfc.ac.uk>; cod-bugs at ibt.lt <cod-bugs at ibt.lt>
Subject: Re: [Cod-bugs] Optimade API returns empty results for SMILES query, while web interface works properly for the same SMILES value

Dear Mehmet,

On 2025-05-23 13:51, Mehmet Giritli - STFC UKRI wrote:
> We'd like to report an issue we are facing with the COD's Optimade API.
>
> Using a SMILES string to search with COD website interface works fine:
>
> https://www.crystallography.net/cod/search.php
> <https://www.crystallography.net/cod/search.php>
> SMILES: c1ccccc1
>
> However, when the same SMILES value is used to query through Optimade
> API, we get no results back (and no errors either). Here is how we are
> searching with Optimade:
>
> https://www.crystallography.net/cod/optimade/structures?filter=_cod_smiles=%22c1ccccc1%22 <https://www.crystallography.net/cod/optimade/structures?filter=_cod_smiles=%22c1ccccc1%22>
>
> Please let me know if you need any further information.

You are right to observe that search by SMILES does not work in the
current COD OPTIMADE interface. It is not implemented yet, and as such
it should return an error. We will either implement the search or emit a
proper error message in the next COD website update.

Please mind that, when implemented, search by SMILES in COD OPTIMADE
interface will not perform substructure search as is done in regular
search interface. Most likely this will be string comparison instead,
due to the complexity of substructure search.

Best wishes,
Andrius

--
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7
LT-10257 Vilnius, Lithuania

-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.crystallography.net/pipermail/cod-bugs/attachments/20250523/73fddfe3/attachment.htm>