I should have included the query. It looks like RD Kit is ignoring the H atom The user put in an explicit H ===========MOL file after this aldehyde query MJ192500
4 3 0 0 0 0 0 0 0 0999 V2000 -2.8123 1.5508 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5267 1.1383 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2412 1.5508 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5267 0.3133 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 0 0 0 0 2 4 2 0 0 0 0 2 3 1 0 0 0 0 M END =================MOL file above this From: Greg Landrum <greg.land...@gmail.com> Sent: Friday, July 16, 2021 11:38 PM To: Webster Homer <webster.ho...@milliporesigma.com> Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Substructure search for an aldehyde returns ketones and acids [WARNING – EXTERNAL EMAIL] Do not open links or attachments unless you recognize the sender of this email. If you are unsure please click the button "Report suspicious email" Hi Webster, Without seeing an actual query I am inclined to believe that it’s not a bug. The problem is more likely a query which has not been drawn explicitly or an easily made mistake in the way the cartridge is being used. Assuming that the aldehyde queries have been drawn with an explicit H atom connected to the C (apologies for not showing this, I’m on my phone and don’t have a sketcher available), you should be calling the cartridge function qmol_from_ctab(), not mol_from_ctab(), before doing the query. qmol_from_ctab() will use the H to help define the query. If you’re doing this and still seeing incorrect search results, please share a query and the way you’re doing the search and we can try to help (or diagnose the bug if there is one) Best, -greg On Fri, 16 Jul 2021 at 17:53, Webster Homer <webster.ho...@milliporesigma.com<mailto:webster.ho...@milliporesigma.com>> wrote: We use RDKit Postgresql cartridge as our substructure searcher. When a user sketches an aldehyde and submits the mol fle as the query. RD Kit returns aldehydes, but also returns ketones and acids. Is this a bug? This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith. Click merckgroup.com/disclaimer<https://www.merckgroup.com/en/legal-disclaimer/mail-disclaimer.html> to access the German, French, Spanish, Portuguese, Turkish, Polish and Slovak versions of this disclaimer. Please find our Privacy Statement information by clicking here merckgroup.com/en/privacy-statement.html<https://www.merckgroup.com/en/privacy-statement.html> _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith. Click merckgroup.com/disclaimer<https://www.merckgroup.com/en/legal-disclaimer/mail-disclaimer.html> to access the German, French, Spanish, Portuguese, Turkish, Polish and Slovak versions of this disclaimer. Please find our Privacy Statement information by clicking here merckgroup.com/en/privacy-statement.html<https://www.merckgroup.com/en/privacy-statement.html>
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