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> 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 > 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
