Rajarshi,
the CDK-Jmol bridge code needs some maintainance...
I will update the code examples shortly...
Comments below...
> Hi, I have some code that returns a IMolecule object
> I am interfacing it to some Jmol code which expects a Molecule
> When running the code I get an error:
>
> java.lang.ClassCastException: org.openscience.cdk.Molecule
>
> (It's not more informative since this is running from within R)
Clear enough...
> I am using code like below:
>
> public class ViewMolecule3D {
> JmolPanel jmolPanel;
>
> Molecule molecule = null;
Make this:
IMolecule molecule = null;
> String filename = null;
>
> final static String strScript = "";
>
> public ViewMolecule3D(IMolecule molecule) {
> this.molecule =(Molecule)molecule;
> }
>
> is it correct to coerce an IMolecule to Molecule?
I assume you use the CdkJmolAdapter class at some point... you will need
to update that code too.
If you have the need to convert a IMolecule into a Molecule, you can take
this code (say your IMolecule instance is imol):
Molecule mol = DefaultChemObjectBuilder.getInstance().newMolecule(imol);
Egon
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