You can also use a different electron donation model which doesn’t need atom types.

- John

On 12 Oct 2023, at 02:07, Uli Fechner <u...@pending.ai> wrote:


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
     
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