outFile = new File(fileName);
}
cow = new SMILESWriter(new FileWriter(outFile));
if (cow != null && askIOSettings())
{
cow.addChemObjectIOListener(new SwingGUIListener(jcpPanel, IOSetting.Importance.HIGH));
}
Iterator<IAtomContainer> containers = ChemModelManipulator.getAllAtomContainers(model).iterator();
IAtomContainerSet som = model.getBuilder().newInstance(IAtomContainerSet.class);
while (containers.hasNext()) {
//Clone() is here because the SMILESWriter sets valencies and we don't