The problem was with forgetting to add writer.close()
It fixed the problem.
public static void writeSDF() throws IOException, CDKException, Exception
{
String filename = "/Users/lochana/Desktop/test.sdf";
SDFWriter writer = new SDFWriter(new FileWriter(new File(filename)));
for (IAtomContainer ac : compounds) {
writer.write(ac);
}
writer.close();
System.out.println("Done!");
}------------------------------------------------------------------------------
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