Hello all, I'm having problems reading CML files into CDK. The problem appears to be that all aromatic bonds are assigned a bond order of '1'.
I read in a CML file like this:
<code>
InputStream stream = new ByteArrayInputStream(completeCml.getBytes());
CMLReader reader = new CMLReader(stream);
IMolecule fakeMol = null;
try
{
ChemFile chemFile = (ChemFile) reader.read((ChemObject) new
ChemFile());
IChemSequence seq = chemFile.getChemSequence(0);
IChemModel chemModel = seq.getChemModel(0);
IMoleculeSet set = chemModel.getMoleculeSet();
fakeMol = set.getMolecule(0);
}
catch (Exception e)
{
LOG.error(e.toString());
}
</code>
Upon examination of the new molecule, there are no aromatic bonds. How can
I fix this?
--Steve
attached is a sample CML file, so you know what I'm working with.
test.cml
Description: Binary data
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