I'm just starting to use CDK, so may not be doing things right, but it
seems to me like the first property in a SD file is missing.
I have code like this:
InputStream ins = new FileInputStream(filename);
MDLReader reader = new MDLReader(ins);
ChemFile chemFile = (ChemFile) reader.read((ChemObject) new ChemFile());
List<IAtomContainer> containersList =
ChemFileManipulator.getAllAtomContainers(chemFile);
IMolecularDescriptor descriptor = new WienerNumbersDescriptor();
for (IAtomContainer mol : containersList) {
System.out.println(mol.getProperties());
}
The SD file properties bit of my file looks like this:
M END
> <mr_id>
4358263
> <SMI>
Oc1cccc(c1)c2nc(N3CCOCC3)c4oc5ncccc5c4n2
$$$$
But what gets written out by CDK is this:
{SMI=OC(=O)c1ccc(Nc2ncc3CN=C(c4c(F)cccc4F)c5cc(Cl)ccc5-c3n2)cc1}
The first property (mr_id) is missing.
This happens with 2 different files.
Tim
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