Re: [Rdkit-discuss] rdkit can not read sodium hexaflourophosphate molfile

[Contact <co...@hj...>]

From: Contact [mailto:co...@hj...] 
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:gre...@gm...] 
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

 

-greg

 

 

On Tue, May 19, 2015 at 3:25 PM, Contact <co...@hj... <mailto:co...@hj...> > 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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