Hi John,
Thank you the fast response. I am using another viewer, which could have
brought the confusion. This just means the issue in my code might come from
somewhere else.
Thanks,
Yannick
On Tue, Jun 6, 2017 at 3:25 AM, John Mayfield <john.wilkinson...@gmail.com>
wrote:
> Hi Yannick,
>
> Please, please, please don't "add hydrogens" like this! The hydrogens are
> already there and don't need to be added - this is just wasted effort and
> worst of all the atom typing *might* change your structures valence!! If
> for some reason you want to make hydrogens explicit just call this method
> directly:
>
> AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule);
>
>
> Anyways why do you think the stereochemistry is different? All your SMILES
> are the same and the stereochemistry is preserved correctly - paste them in
> here to see: https://cdkdepict-openchem.rhcloud.com/depict.html
>
>
> [image: Inline images 1]
>
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