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
>>> _______________________________________________
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
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>
pd_dba2.dative.mol
Description: Binary data
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