From: Contact [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]
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 <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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