Dear all,
I'm faced to a strange behavior using the MDLV2000Reader to read a
simple SDF file containing properties.
When I use the reader to read a single IMolecule from a file (or a
String: same issue), the properties are missing when I call the
getProperties for this molecule.
Yet, if I ask the reader to read a ChemFile instead of reading a
molecule, the properties are read correctly.
I suspect this is a bug; please confirm this so I could send a bug
report. Here is a small snippet of code illustrating the problem:
public static void main(String [] args) throws Exception {
File f = new File("benzene.sdf");
MDLV2000Reader reader = new MDLV2000Reader(new FileReader(f));
// Working...
// ChemFile chemFile = (ChemFile)reader.read((ChemObject)new
ChemFile());
// List<IAtomContainer> containersList =
ChemFileManipulator.getAllAtomContainers(chemFile);
//
// IAtomContainer m = containersList.get(0);
// Not working...
IMolecule m = (IMolecule) reader.read(new Molecule());
reader.close();
System.out.println("Props: "+m.getProperties());
}
Here is the content of the benzene file:
Marvin 07240915192D
6 6 0 0 0 0 999 V2000
-6.0991 3.9777 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.8136 3.5652 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.8136 2.7402 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.0991 2.3277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.3846 2.7402 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.3846 3.5652 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 6 2 0 0 0 0
2 3 2 0 0 0 0
3 4 1 0 0 0 0
4 5 2 0 0 0 0
5 6 1 0 0 0 0
M END
> <molecule_name>
benzene
> <foo_prop>
1.5684
$$$$
The same behavior occurs with various CDK-git version, which I
retrieve from http://pele.farmbio.uu.se/nightly-jcp/, and also with
the lastest stable version 1.2.7.
Cheers :)
Vincent
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