code: protected boolean canDraw(IAtom atom, IAtomContainer container, RendererModel model) {
          // don't draw atoms without coordinates
          if (!hasCoordinates(atom)) {
              return false;
          }
  
          // don't draw invisible hydrogens
          if (invisibleHydrogen(atom, model)) {
              return false;
          }
  
          // don't draw invisible carbons
          if (invisibleCarbon(atom, container, model)) {
              return false;
          }
  
          return true;
      }
docs: Checks an atom to see if it should be drawn. There are three reasons
  not to draw an atom - a) no coordinates, b) an invisible hydrogen or
  c) an invisible carbon.
  
  @param atom the atom to check
  @param container the atom container the atom is part of
  @param model the renderer model
  @return true if the atom should be drawn