String fileName = outFile.toString();
if (!fileName.endsWith(".cdk")) {
fileName += ".cdk";
outFile = new File(fileName);
}
cow = new CDKSourceCodeWriter(new FileWriter(outFile));
if (cow != null && askIOSettings())
{
cow.addChemObjectIOListener(new SwingGUIListener(jcpPanel, IOSetting.Importance.HIGH));
}
Iterator containers = ChemModelManipulator.getAllAtomContainers(model).iterator();