Hi,
We have been using the CDK IteratingMDLReader quite successful for some
time now. But suddenly, it does not work anymore. I figured out that it
is due to changing stuff around the cdk code...so far so good. After
some time I noticed that the Stream I give to the IteratingMDLReader has
changed. The working one was a java.io.PushbackInputStream, the new one
is a org.restlet.engine.http.io.ChunkedInputStream. Both extend the
java.io.InputStream class. Another difference I noticed, is that calling
the available() method on the PushbackInputStream results in 1, on the
ChunkedInputStream it results in 0. That's the fact I figured out so
far. The code fragments around the Reader:
InputStream n = r.getStream();
// those statements made me figure out what changed:
System.out.println("[GET2] available: "+in.available());
System.out.println("[GET2] available: "+in.toString());
IteratingMDLReader sdfreader = new IteratingMDLReader(in,
DefaultChemObjectBuilder.getInstance());
try {
if(in != null){
while (sdfreader.hasNext()) {
IMolecule mol2store = (IMolecule)sdfreader.next();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol2store);
CDKHueckelAromaticityDetector.detectAromaticity(mol2store);
System.out.println("MolAtomCount: " + mol2store.getAtomCount());
mols.add(mol2store);
}
}
}catch(Exception e){
e.printStackTrace();
}finally{
sdfreader.close();
in.close();
}
The contents of the chunked stream seems to be fine...it works with
JOELIB2 (joelib2.io.BasicReader) and it works if I write the stream to a
file and then import it with the IteratingMDLReader.
Any clues? This is quite important for us to work. At the moment we have
a little workaround but I'd like to change that.
best regards,
Tobias
--
Dipl.-Bioinf. Tobias Girschick
Technische Universität München
Institut für Informatik
Lehrstuhl I12 - Bioinformatik
Bolzmannstr. 3
85748 Garching b. München, Germany
--
Tobias Girschick
mailto: [email protected]
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