code: protected Color getAtomColor(IAtom atom, RendererModel model) {
          Color atomColor = model.get(AtomColor.class);
          if ((Boolean) model.get(ColorByType.class)) {
              atomColor = ((IAtomColorer) model.get(AtomColorer.class)).getAtomColor(atom);
          }
          return atomColor;
      }
docs: Returns the drawing color of the given atom. An atom is colored as
  highlighted if highlighted. The atom is color marked if in a
  substructure. If not, the color from the CDK2DAtomColor is used (if
  selected). Otherwise, the atom is colored black.