Thanks Paolo – we’ll give that a try. Regards, Mark
Dr Mark Mackey Chief Scientific Officer Cresset New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG8 0SS, UK Tel: +44 (0)1223 858890 Mobile: +44 (0)7595099165 Email: m...@cresset-group.com<mailto:m...@cresset-group.com> Web: www.cresset-group.com<http://www.cresset-group.com/> From: Paolo Tosco <paolo.tosco.m...@gmail.com> Sent: 08 February 2022 21:48 To: Mark Mackey <m...@cresset-group.com> Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Problem with depicting reaction SMARTS Hi Mark, I believe the bug is caused by the fact that isAtomListQuery() returns true for a query that is actually a complex query, and that subsequently getAtomListQueryVals() (called by getAtomListText()) fails to parse. The following patch seems to solve the problem: $ git diff diff --git a/Code/GraphMol/QueryOps.cpp b/Code/GraphMol/QueryOps.cpp index a80d8f5..ea28ad3 100644 --- a/Code/GraphMol/QueryOps.cpp +++ b/Code/GraphMol/QueryOps.cpp @@ -812,8 +812,9 @@ bool _atomListQueryHelper(const T query) { return false; } } + return true; } - return true; + return false; } } // namespace bool isAtomListQuery(const Atom *a) { Cheers, p. On Tue, Feb 8, 2022 at 8:29 PM Mark Mackey via Rdkit-discuss <rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>> wrote: Hi all, I’m trying to generate an SVG from reaction SMARTS. The code looks like this: QByteArray ChemicalReactionsCalculation::toSvg(const QString &reaction, int width, int height) { try { std::string text = reaction.toStdString(); std::unique_ptr<RDKit::ChemicalReaction> rxn(RDKit::RxnSmartsToChemicalReaction(text)); if (rxn) { RDKit::MolDraw2DSVG drawer(width, height); drawer.drawReaction(*rxn); drawer.finishDrawing(); auto svg = drawer.getDrawingText(); return QByteArray::fromStdString(svg); } } catch (const std::exception &e) { qWarning() << "Exception in ChemicalReactionsCalculation::toSvg on" << reaction << ":" << e.what(); } return QByteArray(); } This works fine for most reaction SMARTS strings, but throws an exception at “drawer.drawReaction” when the SMARTS string has a combination of Boolean operators in it. For example, “[n&H1:1]>>[o:1]” works fine, as does “[c,n:1]>>[O:1]”, but doing “[c,n&H1:1]>>[o:1]” fails (as does the equivalent “[c,nH1:1]>>[o:1]”): Exception in ChemicalReactionsCalculation::toSvg on "[c,n&H1:1]>>[o:1]" : bad query type1 This happens for pretty much any combination of “,” and “&” operators inside the square brackets. Any ideas? Regards, Mark Dr Mark Mackey Chief Scientific Officer Cresset New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG8 0SS, UK Tel: +44 (0)1223 858890 Mobile: +44 (0)7595099165 Email: m...@cresset-group.com<mailto:m...@cresset-group.com> Web: www.cresset-group.com<http://www.cresset-group.com/> 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
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