Re: [Rdkit-discuss] organometallics?

[Michal Krompiec]

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  wrote:

> 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 
>> 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 
 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  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
>> 

Re: [Rdkit-discuss] organometallics?

[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 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 
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 
> 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  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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>>
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>>
>


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Re: [Rdkit-discuss] organometallics?

[Maciek Wójcikowski]

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 
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  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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>
>
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Re: [Rdkit-discuss] organometallics?

[Jan Halborg Jensen]

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 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 
mailto: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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Re: [Rdkit-discuss] organometallics?

[Michal Krompiec]

... 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. 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 Pd(dba)2 (also from Marvin's template library). As
> you can see, the attachment is made via a dummy atom placed where the bond
> is drawn (middle of Cp ring or middle of double bond).
> Best regards,
> Michal
>
>
> On Thu, 13 Sep 2018 at 14:14, Greg Landrum  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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Re: [Rdkit-discuss] organometallics?

[Michal Krompiec]

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 Pd(dba)2 (also from Marvin's template library). As you
can see, the attachment is made via a dummy atom placed where the bond is
drawn (middle of Cp ring or middle of double bond).
Best regards,
Michal


On Thu, 13 Sep 2018 at 14:14, Greg Landrum  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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Description: Binary data


fecp_from_cdx.sdf
Description: Binary data
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Re: [Rdkit-discuss] organometallics?

[Greg Landrum]

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 
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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