or the hydrogens are poor on the 5-membered ring, and the
two hydrogens on the NH2 are superimposed.
(In practise I'm starting from a 3D SDF and trying to generate 2D coords for
it, hence the need for CoordGen).
What am I doing wrong?
Regards,
Mark
--
Mark Mackey
Chief Scientific Offic
Hi all,
After further offline discussion with Paolo, it turns out that the behaviour I
was seeing was due to a bug, which has now been fixed by Paolo and accepted.
Thanks Paolo for sorting this out!
Regards,
Mark
From: Paolo Tosco
Sent: 27 August 2020 23:08
To: Mark Mackey
Cc: rdkit-discuss
ldn’t be that much of a net win. As a result, take all
of the above with a grain of salt 😊.
Regards,
Mark
--
Mark Mackey
Chief Scientific Officer
Cresset
New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG8 0SS, UK
tel: +44 (0)1223 858890mobile: +44 (0)7595 099165fax
he code looked clean enough but it was slow. Unfortunately from the
RDKit point of view it's LGPL so can't be used as the basis of an RDKit shape
algorithm.
Regards,
Mark
From: Chris Swain
Sent: 04 November 2020 15:56
To: rdkit-discuss@lists.sourceforge.net; Mark Mackey
Subject: Re:
Hi Paolo,
Hmmm, I think this is displaying a bug (or at the very least unexpected
behaviour) in the aromaticity code. The issue isn’t the aromaticity of the
imidazole/dihydroimidazole, but the aromaticity of the pyridyl. Alexis’ second
molecule is identical to the first except that one bond in
I believe it's not possible to represent the chirality of the attached
molecule's ring fusion carbons without using an explicit H.
Regards,
Mark
--
Mark Mackey
Chief Scientific Officer
Cresset
New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG8 0SS, UK
tel: +
, b2) in B, break all bonds in
B except b1 and b2. Keep the fragment containing b1 only if it also contains b2.
Regards,
Mark
--
Mark Mackey
Chief Scientific Officer
Cresset
New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG8 0SS, UK
tel: +44 (0)1223 858890mobile: +44 (0
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 Off
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
quivalent
"[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?
Regar
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...@cres
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