Clean3D Java snippet

Partner Extensions
1

Hi,

I would like to build a node that will run the Clean3D function on a molecule that I feed into it. I have found some sample code at https://www.chemaxon.com/forum/ftopic8409.html which I have adapted and entered into the 'Method body' pane of a Java snippet node. In the code below, $Molecule$ is the name of the column in which the structure is specified. The code is:

Dreiding d = new Dreiding();
d.init($Molecule$);
GradientOptimization g = new GradientOptimization(d);
g.setGradientRMSLimit(1e-3);
g.run();
if (!g.isOptimizationConverged()) {
  throw new IllegalStateException("Optimization was not converged");
}
return d.getMoleculeWithLastUsedCoordinates();
 

The node won't compile though, because it cannot resolve the Dreiding and GradientOptimization data types.

How can I make these available to the Java snippet? I have tried adding knime-marvin.jar and jchemlib.jar to the list of additional libraries, to no avail.

Any help would be gratefully received.

Thanks in advance,

Chris

2

First of all you need to specify the complete class names including packages since there are not automatic imports. However, even then it won't work because you cannot return a molecule from the Java Snippet node. Only primitive data types are supported.

3

Hi thor,

Thanks for your reply. I had wondered whether returning the atomic coordinates as a string in e.g. MOL format, followed by a subsequent conversion into molecule format might work.

I think it might be easier to create a new KNIME node using the Eclipse IDE to do this job, rather than using a snippet. This would enable me to return the data in molecule format.

Many thanks,

Chris

4

Is there a reason not to use the Clean3D step from the Standardizer node ?

5

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