Hi,
Properly handing the hypervalent PF6- species has been on the RDKit todo
list for a while. There is a quick solution (adding the extra allowed
valence for P) and there's a "right" solution (revisiting the valence
model). Every time I start to do the first I think I should be doing the
second, but I don't have the time to dedicate to that, so it just sits.
Rather than continuing this, I'll just go ahead and add the extra valence.
:-)
Here's the github item:
https://github.com/rdkit/rdkit/issues/510
-greg
On Tue, May 19, 2015 at 3:25 PM, Contact <cont...@hjhimmler.de> wrote:
> HI,
>
>
>
> I did draw sodium hexaflourophosphate (using marvin) and saved the
> structure as molfile.
>
> I have a very simple knime workflow. The workflow consist of a molfile
> reader node and a rdkit ‘RDKit From Molecule’ node.
>
> The readmolfile node has no problems to read the molfile.
>
> The rdkit ‚RDKit From Molecule’ node can not read the molfile (i.e. the
> structure ends up in the ‘Erroneous input data’ output port.
>
> The structure is drawn correct i.e. positive charge on sodium, negative
> charge on the phosphor atom.
>
> The molfile is attached to the mail.
>
>
>
> Any idea why rdkit has problems with reading this molfile ?
>
>
>
> Any feedback or clarification is appreciated.
>
> Best
>
> Hans-Juergen
>
>
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