Hi Greg,
I'm very glad, too :).
That would be great as it would be faithful to the notion of a single
coordination bond between the metal atom and the ligand (as opposed to
several coordination bonds to individual atoms of the ligand).
Best,
Michal
On Fri, 14 Sep 2018 at 11:03, Greg Landrum
That's more or less what the current code does: dative bonds from an atom
to a metal do not affect the perceived valence of the source atom:
In [13]: m = Chem.MolFromSmiles('[Fe]<-N(C)(C)C')
In [14]: m.Debug()
Atoms:
0 26 Fe chg: 0 deg: 1 exp: 1 imp: 0 hyb: 4 arom?: 0 chi: 0
1 7
I would suggest that all coordination bonds to metal that exceed the
accepted valence of an atom could be mark as zero-ordered. This is what
happens in recent PDB reader changes and fixed a lot of problems with
sanitization.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
Here’s a modest step in the right direction
https://www.wildcardconsulting.dk/useful-information/how-to-solve-problems-with-coordinate-bonds-in-rdkit/
Best regards, Jan
On 13 Sep 2018, at 15:14, Greg Landrum
mailto:greg.land...@gmail.com>> wrote:
Hi Michal,
Though the RDKit theoretically has
... and yet another example, bis-mu-dichloro-bis(allyl)dipalladium(II),
drawn according to ChemAxon's instructions:
https://docs.chemaxon.com/display/docs/How+to+draw+coordination+compounds
Michal
On Thu, 13 Sep 2018 at 14:45, Michal Krompiec
wrote:
> Hi Greg,
> Thanks for your fast reply.
Hi Greg,
Thanks for your fast reply. I've got two examples of ferrocene MOLfiles,
generated by MarvinSketch in KNIME, from ferrocene.cdxml (found somewhere
in the rdkit github repo), the other one from the ferrocene template in
Marvin. But actually they are almost the same.
The third example is
Hi Michal,
Though the RDKit theoretically has many of the infrastructure pieces
required to handle organometallics (though there's not a lot you can do
with them once you've loaded them), the difficult part almost always ends
up being finding input files that have reasonably machine-readable
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