Hi, Welcome to the CDK community.
Atom types can be determined with AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule); If you do this before detecting aromaticity, the exception should go away. Best wishes Uli On Thu, Oct 12, 2023 at 3:02 AM Velusamy Velu <vv...@peruselab.com> wrote: > Hi > > I'm a new user of CDK. It's a great tool and I'm learning a lot. I'm > currently trying to use the aromaticity detection tool, the Aromaticity. In > a test I built a benzene molecule, an instance of the IAtomContainer. This > was successful and I was able to create an image of it in the SVG format. > Then I went on to try to detect aromaticity using the following code > snippet. > > Aromaticity a = new Aromaticity(ElectronDonation.cdk(), Cycles.all()); > a.apply(molecule); > > The aromaticity.apply call throws the following error. > > java.lang.NullPointerException: atom has unset atom type > at java.util.Objects.requireNonNull(Objects.java:228) > at > org.openscience.cdk.aromaticity.AtomTypeModel.contribution(AtomTypeModel.java:112) > > I trace the error back to this line of code in AtomTypeModel.java > Objects.requireNonNull(atom.getAtomTypeName(), "atom has unset atom type"); > > Am I supposed to programmatically set the AtomTypeName? If the answer is > yes, then why so? Is there a simpler way to set the atom type name? > > I will greatly appreciate your help. > > Thanks > > Velusamy K. Velu > (614) 323-9649 > <https://peruselab.com> <https://www.linkedin.com/company/peruselab/> > <https://twitter.com/PeruseLab> <https://www.facebook.com/PeruseLab/> > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user >
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