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I'm trying to display some molecules in rdkit and save them as png files. Simple enough. However, when I display them, most of them are drawn at a weird angle (shown below) or even completely upside down. I tried using this section to correct this but no luck. I've looked through similar issues people had but none of them have been properly resolved as far as I can tell.
Does anybody have a solution to this?
Thank you !
You can use SetPreferCoordGen(True)
from rdkit import Chem
from rdkit.Chem import rdDepictor
rdDepictor.SetPreferCoordGen(True)
mol = Chem.MolFromSmiles('Fc1ccc2ncccc2c1')
mol
