Dear Jean-Paul,
On Fri, Jan 27, 2012 at 4:57 AM, JP <[email protected]> wrote:
>
> I can read an SDF file (attached: test.sdf) using ForwardSDMolSupplier (with
> sanitization explicitly turned on) - but I cannot write the molecule back to
> a second SD file using SDWriter.
> Interestingly, upon writing it fails with a sanitization error (ValueError:
> "Sanitization error: Can't kekulize mol"). Note that the molecule is not
> null and I am not doing anything with the molecule.
That's a bug, thanks for pointing it out.
> My question is: how did the molecule pass the initial sanitization test
> (when it is read) but not the second (when it is written) ?
The CTAB format requires that bonds be written out as either single or
double,[1] so aromatic rings must be converted into the kekule form
before generating the CTAB. The RDKit is incapable of generating a
kekule form for this molecule because, I think, something is wrong
with the way it has done chemistry perception around the boron. You
can see this in the SMILES:
In [2]: ms = [x for x in Chem.SDMolSupplier('test.sdf')]
In [3]: Chem.MolToSmiles(ms[0])
Out[3]: 'Cc1n[n+](C)[bH2-](O)c2sccc12'
I believe that boron atom shouldn't have any explicit Hs.
-greg
[1] The actual wording of the specification says that aromatic bonds
should only be used for substructure queries
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