Hi Greg, Thanks, molfile you attached shows how the problem can be solved for neutral pi-alkene ligands. I just tried and you can draw this in MarvinSketch in KNIME, and pass (as MOL) to RDKit nodes without problems! pi-allyl and cyclopentadienyl also worked when I drew them as Lewis structures with an explicit negative charge and coordinate bonds to all carbon atoms (see attached). Their 2D depiction perhaps isn't beautiful but it is not a problem for me. Best, Michal
On Fri, 14 Sep 2018 at 08:07, Greg Landrum <greg.land...@gmail.com> wrote:
> 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 N chg: 0 deg: 4 exp: 3 imp: 0 hyb: 5 arom?: 0 chi: 0
> 2 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
> 3 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
> 4 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
> Bonds:
> 0 1->0 order: 17 conj?: 0 aromatic?: 0
> 1 1->2 order: 1 conj?: 0 aromatic?: 0
> 2 1->3 order: 1 conj?: 0 aromatic?: 0
> 3 1->4 order: 1 conj?: 0 aromatic?: 0
>
>
> For what it's worth, if you draw coordinate bonds from atoms to the metal
> in the MOL file, you get something sensible back from the RDKit.
> I've attached a tweaked version of one of Michal's example files showing
> how to do this.
>
> Dealing with the dummy atoms directly is tricky because we'd need to
> figure out which atoms they are associated with. I think that there's a way
> to do it, but that's not handled in the .mol file you sent
>
> Best,
> -greg
>
>
>
>
> On Thu, Sep 13, 2018 at 6:51 PM Maciek Wójcikowski <mac...@wojcikowski.pl>
> wrote:
>
>> 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
>> mac...@wojcikowski.pl
>>
>>
>> czw., 13 wrz 2018 o 18:16 Jan Halborg Jensen <jhjen...@chem.ku.dk>
>> napisał(a):
>>
>>> 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 <greg.land...@gmail.com> wrote:
>>>
>>> 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
>>> structures in them.
>>>
>>> If you have some examples you can share, I'd be happy to take a look to
>>> see if I can suggest ways to read them in.
>>>
>>> Best,
>>> -greg
>>>
>>>
>>> On Wed, Sep 12, 2018 at 10:30 PM Michal Krompiec <
>>> michal.kromp...@gmail.com> wrote:
>>>
>>>> Hello,
>>>> I've been asked to analyze a dataset of organometallic compounds
>>>> (provided in SDF), but it turns out that most of them are not compatible
>>>> with RDKit (due to having pi-alkene, pi-allyl, cyclopentadienyl et al.
>>>> ligands). The structures can be correctly represented in Marvin, though.
>>>> Can anybody point me to a toolkit (or RDKit hack) that can handle these?
>>>> Best,
>>>> Michal
>>>>
>>>> ====
>>>> Dr. Michal Krompiec
>>>> Adjunct Professor
>>>> School of Chemistry, University of Southampton
>>>> Highfield, Southampton SO17 1BJ, UK
>>>>
>>>> and
>>>> Head of Computational Modelling | Performance Materials | Early
>>>> Research and Business Development
>>>> Merck
>>>> _______________________________________________
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>>
pd_cl_allyl_new.sdf
Description: Binary data
fecp_new.sdf
Description: Binary data
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