I'm glad to hear that things work. :-)
I noticed that there is information about the atoms associated with a
linkage point in the bond records of those v3000 SDFs:
M V30 39 9 38 37 ENDPTS=(2 20 21) ATTACH=ALL
I need to do a bit more looking, but it may be possible to add the ability
to directly parse and interpret this information; that would make things
easier and the drawings would be less crappy.
-greg
On Fri, Sep 14, 2018 at 10:55 AM Michal Krompiec <michal.kromp...@gmail.com>
wrote:
> 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
>>>>> _______________________________________________
>>>>> Rdkit-discuss mailing list
>>>>> Rdkit-discuss@lists.sourceforge.net
>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>>
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