Re: [Rdkit-discuss] Chem.AddHs() doesn't care about compound layout

[Sereina <ser...@gm...>]

Dear Michal,

Chem.AddHs() has the option “addCoords” which is normally set to False.
So, using

mol = Chem.AddHs(mol, addCoords=True)

should solve your problem.

Best,
Sereina



On 20 Aug 2014, at 19:07, Michał Nowotka <mm...@gm...> wrote:

> Hello,
> 
> Imagine I have a compound with some 2D coordinates I really like:
> 
>    mol
> 
> Now I would like to add hydrogens to it:
> 
>     mol = Chem.AddHs(mol)
> 
> The problem is, all new hydrogen atoms will have (0,0,0) coordinates,
> which doesn't look to good...
> 
> I could force recomputing 2D coords for the whole compound:
> 
>    AllChem.Compute2dCoords(mol)
> 
> But this will ruin my beautiful layout of the original, non-hydrogen part...
> 
> Is it possible to layout hydrogens around my compound after I add them?
> 
> Regards,
> Michał Nowotka
> 
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