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#1288 AtomTypeManipulator error is not sufficiently descriptive (IAtomType was null)

cdk-1.4.x
open
nobody
IAtomType (1) assignment (1) typer (1)
1
2016-08-10
2013-01-06
Joerg Kurt Wegner
No

AtomTypeManipulator:62 throws IllegalArgumentException("The IAtomType was null.").
Potentially AtomContainerManipulator is not sufficient.
A test file with 256 molecules from ChEMBL where this issue occurs is attached.

Any way to clarify why? Which atoms are not assigned? Anything helping with drilling down?

1 Attachments
cdk_issues.sdf

Discussion

  • John May

    John May - 2013-01-06

    Hi Joerg,

    How are you using the code? That error makes sense if you're calling it directly.

    :::java
IAtom atom = ...; // non-null instance
AtomTypeManipulator.configure(atom, null); // exception -> atom type was null

    The AtomTypeManipulator is probably a bit low level for usual atom typing try the AtomContainerMaipulator. The following works without error for me on the test molecules from ChEMBL.

    Note: IteratingSDFReader = IteratingMDLReader on 1.4.x

    :::java

IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
String path = "/Users/johnmay/Downloads/cdk_issues.sdf";

IteratingSDFReader sdf = new IteratingSDFReader(new FileReader(path),
                                                builder,
                                                true); 
while (sdf.hasNext()) {
    IAtomContainer container = sdf.next();
    AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(container);
}
     

  • Egon Willighagen

    Egon Willighagen - 2016-08-10

    Joerg, you can discover that in your code with a try/catch... just see what the value of the passed atom was?