I've had some problems using MDLReader.read() with
various SDF files. In particular, files that are terminated
with '$$$$' while syntactically correct raise an exception
as does calling read() with a StringReader (because
input.ready() on a StringReader is always true).
Currently, when an exception is caught, readMolecule()
returns null. This in turn causes readChemFile() to fail.
As some errors (those described above) are not
terminal, it is more appropriate to display a warning and
skip the molecule. A simple patch is attached that
implements this workaround.