#74 NullPointerException when validating SMIRKS transformation output

[jorro]

We are using the Ambit SMIRKS library in our application, SMIRKS are used to transform structures, and on certain transformation products, we get a NullPointerExceptuion when validating the compound using CDK. I attached an example code where this happens. I think CDK should avoid this and not throw a NullPointer, but there seems to be something wrong with the IAtomContainer which is produced by the SMIRKS library. The Exception is:

Exception in thread "main" java.lang.NullPointerException
at org.openscience.cdk.validate.BasicValidator.validateHydrogenCount(BasicValidator.java:162)
at org.openscience.cdk.validate.BasicValidator.validateAtom(BasicValidator.java:58)
at org.openscience.cdk.validate.ValidatorEngine.validateAtom(ValidatorEngine.java:94)
at org.openscience.cdk.validate.ValidatorEngine.validateAtomContainer(ValidatorEngine.java:113)
at Test.main(Test.java:38)

This happens in both Version 2.4.2 and Version 2.5.1.

I attached an example class which can be used to reproduce the problem. If you get the SMILES from the structure and create a new IAtomContainer, the validation works.

[Nina Jeliazkova]

The newly created atoms by Ambit-SMIRKS did not have implicit H atoms set which causes this bug.
Since SVN rev 5042 the newly created atoms implicit H should be initialized with a non null object.

Deployed at Maven repository as 2.5.2-SNAPSHOT

[Nina Jeliazkova]

I would propose to revert the fix setting implicit hydrogens to Integer[0], as this might not be the correct chemistry.

Instead, provide an optional function (as below) to set the correct atom parameters (implicit H is only one of the parameters which are not set correctly after applying the transformation).

for (IAtomContainer ac : products.atomContainers()) {
    for (IAtom atom: ac.atoms()) {
        atom.setFormalNeighbourCount((Integer) CDKConstants.UNSET);
    atom.setAtomTypeName((String) CDKConstants.UNSET);
    atom.setMaxBondOrder((IBond.Order) CDKConstants.UNSET);
    atom.setBondOrderSum((Double) CDKConstants.UNSET);
    atom.setHybridization((IAtomType.Hybridization) CDKConstants.UNSET);
    atom.setFlag(CDKConstants.ISAROMATIC, false);
    }
    for (IBond bond : ac.bonds()) {
    bond.setFlag(CDKConstants.ISAROMATIC, false);
    }
    //once unset, perceive the correct atom types. This will set all the atom parameters
     AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(ac);
}