Re: [Rdkit-discuss] assigning bond orders from reference: problems with COOH group

[Paolo T. <pao...@gm...>]

Hi Mariana,

if you modify your Jupyter notebook as in

https://gist.github.com/ptosco/d807c64df9f277e92284bc5a7cecbc1d

then it should work also in the presence of graph isomorphisms.

Cheers,
p.


On 12/13/18 12:18, Mariana Assmann wrote:
> Hi all,
>
> I have docking poses (from AutoDockVina) in a format that does not 
> provide bond information, and there is no information on hydrogens 
> atoms unless they are important for hydrogens bonds. I was assigning 
> the bond orders from the original reference structure or it's smiles 
> string using the methods in 
> https://gist.github.com/ptosco/4844d3635cf14d11e5e14381993915c1 using 
> AllChem.AssignBondOrdersFromTemplate() and adding the original 
> hydrogens back on. This approach does not work well when I have -COOH 
> groups present. In AssignBondOrdersFromTemplate, the substructure 
> match almost always assigns the oxygens the opposite way so that my 
> resulting structure is -C(OH)=OH which can't be sanitized in the end. 
> I would like to keep the configuration of the docking output.
>
> Is there a way to correct that in an automated way? I have quite a few 
> poses with that problem and can't do that manually.
>
> I have uploaded a gist with an example problem here: 
> https://gist.github.com/c4asma/b338321238d1924cc2964612ed278e9e
> Here, oxygen with atom number 46 has the hydrogen, and number 45 
> should be assigned a double bond (input 7). But, after 
> AllChem.AssignBondOrdersFromTemplate() oxygen 46 is assigned the 
> double bond (input 15)
>
> Thank you,
> Mariana
>
>
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