Re: [Rdkit-discuss] Problem with depicting reaction SMARTS
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
Sent: 08 February 2022 21:48
To: Mark Mackey
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
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 , int
width, int height)
{
try
{
std::string text = reaction.toStdString();
std::unique_ptr
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 )
{
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:1]>>[o:1]” works fine, as does
“[c,n:1]>>[O:1]”, but doing “[c,n:1]>>[o:1]” fails (as does the equivalent
“[c,nH1:1]>>[o:1]”):
Exception in ChemicalReactionsCalculation::toSvg on "[c,n: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,
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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> wrote:
> Hi all,
>
>
>
> I’m trying to generate an SVG from reaction SMARTS. The code looks like
> this:
>
>
>
> QByteArray ChemicalReactionsCalculation::toSvg(const QString ,
> int width, int height)
>
> {
>
> try
>
> {
>
> std::string text = reaction.toStdString();
>
>
>
> std::unique_ptr
> 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 )
>
> {
>
> 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:1]>>[o:1]” works fine, as does
> “[c,n:1]>>[O:1]”, but doing “[c,n:1]>>[o:1]” fails (as does the
> equivalent “[c,nH1:1]>>[o:1]”):
>
>
>
> Exception in ChemicalReactionsCalculation::toSvg on "[c,n: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 Web: 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
[Rdkit-discuss] Problem with depicting reaction SMARTS
Hi all,
I'm trying to generate an SVG from reaction SMARTS. The code looks like this:
QByteArray ChemicalReactionsCalculation::toSvg(const QString , int
width, int height)
{
try
{
std::string text = reaction.toStdString();
std::unique_ptr
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 )
{
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:1]>>[o:1]" works fine, as does
"[c,n:1]>>[O:1]", but doing "[c,n:1]>>[o:1]" fails (as does the equivalent
"[c,nH1:1]>>[o:1]"):
Exception in ChemicalReactionsCalculation::toSvg on "[c,n: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 Web:
www.cresset-group.com
