[Cdk-devel] Error when parsin Mol2 files

[Thorsten M. <Tho...@un...>]

Hi,

When parsing Mol2 files with the Mol2Reader and the
NoNotificationChemObjectBuilder

IChemModel model =
(IChemModel)reader.read(NoNotificationChemObjectBuilder.getInstance().newChemModel());

I get a lot of exceptions like this:

org.openscience.cdk.exception.NoSuchAtomTypeException: The AtomType Cl
could not be found
        at
org.openscience.cdk.config.AtomTypeFactory.getAtomType(AtomTypeFactory.java:279)
        at
org.openscience.cdk.io.Mol2Reader.readMolecule(Mol2Reader.java:223)
        at org.openscience.cdk.io.Mol2Reader.read(Mol2Reader.java:139)

This also happens for N.ar, S.3, S.2, N.am and many others. I'm using
the latest trunk-code.

Regards,

Thorsten

-- 
Thorsten Meinl                        room: Z813
ALTANA Chair for Bioinformatics       fax: +49 (0)7531 88-5132
and Information Mining                phone: +49 (0)7531 88-5016
Box M712, 78457 Konstanz, Germany