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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