2D clean not producing good images.

I'm trying to generate 2D pictures for 3D molecules. The code I am using is this:





JChemMolecule molecule = cloneJChemMolecule();


dearomatize();


hydrogenize(false);


molecule.clean(2,"");


return (Image) molecule.toObject(IMAGE_FORMAT);





Most images look fine, except for molecules such as heme (see attached sdf). In the picture, bonds are crossed, and the molecule isn't recognizable. Are there other options I can use to make better images?





Thanks,


Joe

Joe,


We are developing template-based cleaning, which will be an option in Standardizer


We will probably solve the problem by adding a heme template. Users will also be able to add their own templates.