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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