Dear Greg,
It seems that all examples I found are in fact incorrect (due to an
error during conversion of SDF produced by ISIS Draw with OpenBabel)
and contain this bit:
c1(sc(c2c1nsn2)) which was meant to be: c1scc2N=S=Nc12.
By the way, ChemSketch understands c1(sc(c2c1nsn2)) as N1SNc2cscc12.
So it is not a bug in your code, unless you consider the fused
thiadiazole ring aromatic.
Best wishes,
Michal
On 5 December 2013 12:19, Greg Landrum greg.land...@gmail.com wrote:
Hi Michal,
On Thu, Dec 5, 2013 at 11:52 AM, Michal Krompiec michal.kromp...@gmail.com
wrote:
Hello,
Is it possible to suppress kekulization by SDWriter? I get the
following error on a call to SDWriter.write:
ValueError: Sanitization error: Can't kekulize mol
But some molecules can't be kekulized using RDKit's algorithm, even
though they are otherwise 'correct'.
hmm, I'd love to see examples of those if you can share them.
I browsed the sources and it seems that SDWriter calls MolToMolBlock
with the default parameter kekulize=True. Can this parameter be
exposed in SDWriter?
Yep, I'll get it in for the next release.
-greg
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