See this commit if you want to know how it has been fixed in the development
code.
https://github.com/rdkit/rdkit/commit/672f8ea2008ca88ee66664c9dc91eab74894916a
<https://github.com/rdkit/rdkit/commit/672f8ea2008ca88ee66664c9dc91eab74894916a>
-David
> On May 21, 2015, at 4:26 AM, Contact <cont...@hjhimmler.de> wrote:
>
> From: Contact [mailto:cont...@hjhimmler.de <mailto:cont...@hjhimmler.de>]
> Sent: Wednesday, May 20, 2015 10:16 AM
> To: 'Greg Landrum'
> Subject: RE: [Rdkit-discuss] rdkit can not read sodium hexaflourophosphate
> molfile
>
> HI Greg,
>
> thanks for the answer.
> Since I am not very familiar with the internals of rdkit-
> What exactly do you mean with ‘.. adding the extra allowed valence for P..’ ?
> Does that mean there exists some kind of ‘ptable’ and I can add an extra
> valence there ? If yes, where is that ptable located ?
> If not, how do I add the extra valence otherwise ?
>
> Would appreciate you let me know.
> Best regards
> Hans-Juergen
>
> From: Greg Landrum [mailto:greg.land...@gmail.com
> <mailto:greg.land...@gmail.com>]
> Sent: Wednesday, May 20, 2015 4:53 AM
> To: Contact
> Cc: RDKit Discuss
> Subject: Re: [Rdkit-discuss] rdkit can not read sodium hexaflourophosphate
> molfile
>
> 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
> <https://github.com/rdkit/rdkit/issues/510>
>
> -greg
>
>
> On Tue, May 19, 2015 at 3:25 PM, Contact <cont...@hjhimmler.de
> <mailto: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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