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

[Greg L. <gre...@gm...>]

Hi Michal,

On Mon, Feb 24, 2014 at 4:48 PM, 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?
>

 It is the expected behavior. When sanitization is turned on, the SMILES
parser actually calls "RemoveHs"; this removes the hydrogens from the graph
and then sanitizes the molecule.

If you do not want the Hs removed, you can tell MolFromSmiles to skip the
sanitization (which also skips the RemoveHs) and then sanitize yourself::

In [3]: m=Chem.MolFromSmiles("[H]c1c([H])sc([H])c1[H]",sanitize=False)

In [4]: Chem.SanitizeMol(m)
Out[4]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE

In [5]: print Chem.MolToSmiles(m)
[H]c1sc([H])c([H])c1[H]

I hope this helps,
-greg