Question

The following code supposed to read a file containing a set of molecular structures, then add a bunch of JPanels (equal to the number of molecules) and create a molecule on each panel. I get the right no of panels at the runtime. However only the first molecule is drawn on the first panel?

Answer 1

The drawMolViewPanel() function seems a little overengineered. For one, the panes list seems to be mostly temporary (you add objects to it, then from that list, add them to the MolTable‘s own panel collection; I don’t think you need it). If I understand the function correctly, this does the same thing and makes more sense to me:

public void drawMolViewPanel(String sdf) throws FileNotFoundException, CDKException
{
    ReadSDF(sdf);
    this.removeAll();

    for (int i = 0; i < this.fragments.size(); i++)
    {    
        MolViewer mv = new MolViewer();
        mv.setMolecule((Molecule)this.fragments.get(i));
        this.add(mv);
    }

    this.revalidate();
    this.repaint();
}

I’m not entirely sure that’s your issue, unfortunately.