Hi, I'm wanting to depict a molecule without sterochemistry, but the
DepictionGenerator stubbornly seems to add it back.
What is the way to do this? In the example below a squiggle bond is
displayed even though all bonds have been set to Stereo.NONE and I have
already layed out the molecule.
void "no stereo"() {
IAtomContainer mol = ChemUtils.readSmiles("c1ccc(N=C2SCCN2c2ccccc2)cc1")
StructureDiagramGenerator sdg =new StructureDiagramGenerator();
sdg.setMolecule(mol);
sdg.generateCoordinates(new Vector2d(0,1));
mol = sdg.getMolecule();
for (IBond bond : mol.bonds()) {
bond.setStereo(IBond.Stereo.NONE);
}
DepictionGenerator g =new DepictionGenerator()
Depiction d = g.depict(mol)
when:
def img = d.toImg()
ByteArrayOutputStream out =new ByteArrayOutputStream();
ImageIO.write(img,"png", out);
out.close();
byte[] png = out.toByteArray();
Files.write(java.nio.file.Paths.get("/tmp/myimage5.png"), png)
then:
png !=null png.length > 0 }
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