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> 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
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>
>
>
>
>
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