Re: [Rdkit-discuss] sanitization removes Hs - is this expected?

[Christos K. <chr...@gm...>]

Hi Michal,

It doesn't actually removes them, to be more precise it hides them.
You actually explicit define a hydrogen as ([H]), but if you omit it it
still exists.
You can use Chem.AddHs(...) to add the hydrogens in a molecule and
Chem.RemoveHs(..) to hide them.

Best,
Christos


On 24 February 2014 15:48, Michal Krompiec <mic...@gm...>wrote:

> Hello, I have just noticed this:
> >>> Chem.MolToSmiles(Chem.MolFromSmiles("[H]c1c([H])sc([H])c1[H]"))
> 'c1ccsc1'
> >>>
> Chem.MolToSmiles(Chem.MolFromSmiles("[H]c1c([H])sc([H])c1[H]",sanitize=False))
> '[H]c1sc([H])c([H])c1[H]'
> >>>
> Chem.MolToSmiles(Chem.RemoveHs(Chem.MolFromSmiles("[H]c1c([H])sc([H])c1[H]",sanitize=False)))
> 'c1ccsc1'
> >>> Chem.MolToSmiles(Chem.MolFromSmiles("[H]c1cscc1[H]"))
> 'c1ccsc1'
> >>> Chem.MolToSmiles(Chem.MolFromSmiles("[H]c1cscc1[H]",sanitize=False))
> '[H]c1cscc1[H]'
>
> Is it the expected behaviour? Why does sanitization remove hydrogens?
> Is it controlled by any of the SanitizeFlags?
>
> Best wishes,
> Michal
>
>
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Christos Kannas
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