I tried MarvinSketch before I posted that and all the same there too.. let
me know if you still think there is a problem.
On 7 June 2017 at 18:13, Yannick .Djoumbou <y.djoum...@gmail.com> wrote:
> 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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