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
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On Mon, Jan 15, 2024 at 11:09 AM Tim Dudgeon <[email protected]> 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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