Velusamy is correct. The primary storage of stereochemistry is via Stereo
elements.
The bond display only controls the bond display, your code would do what
you want if you generated the coordinates first and then cleared the bond
display/stereo info but since you didn't have the coordinates from the
SMILES these get automatically computed for you.
Best,
John
On Mon, 15 Jan 2024 at 18:26, Velusamy Velu <kool.v...@gmail.com> wrote:
> The 3rd line below works for me.
>
> final SmilesParser PARSER = new
> SmilesParser(SilentChemObjectBuilder.getInstance());
> IAtomContainer mol = PARSER.parseSmiles("C[C@@H](C(=O)O)N");
> mol.setStereoElements(new ArrayList<>());
>
> Thanks
>
> Velusamy K. Velu
> 614-323-9649
> <https://peruselab.com/> <https://www.linkedin.com/in/vkvelu/>
> <https://twitter.com/PeruseLab> <https://www.facebook.com/PeruseLab/>
>
>
> On Mon, Jan 15, 2024 at 11:09 AM Tim Dudgeon <tdudgeon...@gmail.com>
> wrote:
>
>> What is the best approach to clear stereochemistry from a molecule.
>> I think I was told to use:
>>
>> for (IBond bond : mol.bonds()) {
>> bond.setStereo(IBond.Stereo.NONE);
>> bond.setDisplay(IBond.Display.Solid);
>> }
>>
>> But if I use this for a molecule generated from SMILES it still is
>> depicted with a wedge bond.
>>
>> IAtomContainer mol = smilesParser.parseSmiles("C[C@@H](C(=O)O)N");
>>
>> for (IBond bond : mol.bonds()) {
>> bond.setStereo(IBond.Stereo.NONE);
>> bond.setDisplay(IBond.Display.Solid);
>> }
>> DepictionGenerator dg = new DepictionGenerator().withSize(512, 512)
>> .withAtomColors();
>> dg.depict(mol).writeTo("mol.png");
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