Hi Greg, Argh, I’d missed that we hadn’t done the ring calculation on the reagents, and had been led astray by Googling the exception message. Adding the ring calculation does the trick - thanks very much for the help.
Regards, Mark Dr Mark Mackey Chief Scientific Officer Cresset From: Greg Landrum <greg.land...@gmail.com> Sent: 14 September 2021 06:01 To: Mark Mackey <m...@cresset-group.com> Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Reaction SMARTS ring properties Hi Mark, You haven't shown how the molecules in reagentsRdMolList are constructed, but from the error message I guess that they have been created without running any of the sanitization code. The example transformation you show includes ring information, so it will generate errors if the molecules you run through the reaction don't have the ring information pre-computed. If you don't care about ring size information, the fastest way to get the required info is to call MolOps::fastFindRings() on the molecules in reagentsRdMolList before passing them to rxn->runReactants(). If you include ring size (or ring count) information in your transformations, then using MolOps::symmetrizeSSSR() is a better idea. I hope that helps, -greg On Tue, Sep 14, 2021 at 12:33 AM Mark Mackey via Rdkit-discuss <rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>> wrote: Hi all, I’m trying to run some chemical reactions using the C++ API. Doing something like text = “ [cH1:1]1:[c:2](-[CH2:7]-[CH2:8]-[NH2:9]):[c:3]:[c:4]:[c:5]:[c:6]:1.[#6:11]-[CH1;R0:10]=[OD1]>>[c:1]12:[c:2](-[CH2:7]-[CH2:8]-[NH1:9]-[C:10]-2(-[#6:11])):[c:3]:[c:4]:[c:5]:[c:6]:1c1cc(CCN)ccc1”; auto rxn =RDKit::RxnSmartsToChemicalReaction(text, nullptr, false); rxn->initReactantMatchers(); auto reactionProducts = rxn->runReactants(reagentsRdMolList, 0); works fine for trivial transformations, but throws “RingInfo not initialized” for anything more complex. Googling has shown that the problem is that the ring information is not automatically calculated for the SMARTS molecules, but I’m failing to work out what I need to call RDKit::MolOps::findSSSR on and when. All pointers appreciated. Regards, Mark Dr Mark Mackey Chief Scientific Officer Cresset This email has been sent from Cresset BioMolecular Discovery Limited, registered in England and Wales, Company Number: 04151475. The information in this email and any attachments are confidential and may be privileged. It is intended solely for the addressee and access to this email by anyone else is unauthorised. If an addressing or transmission error has misdirected this email, please notify the author by replying to this email. If you are not the intended recipient you must not use, disclose, distribute, store or copy the information in any medium. Although this e-mail and any attachments are believed to be free from any virus or other defect which might affect any system into which they are opened or received, it is the responsibility of the recipient to check that they are virus-free and that they will in no way affect systems and data. No responsibility is accepted by Cresset BioMolecular Discovery Limited for any loss or damage arising in any way from their receipt, opening or use. Privacy notice<https://www.cresset-group.com/privacy/> _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
