Could not find the main class: chemaxon.clustering.ward

I am trying to perform a ward clustering.   The command:

java -cp "/home/rwharper/ChemAxon/JChem/lib/jchem.jar:home/rwharper/ChemAxon/JChem/lib/jchem:/usr/share/java" chemaxon.clustering.ward -f 1024 -x -y -z -c 1000 -g -i rocs_egfr_src_q2_results.fp -o rocs_q2_clustered.out

Gives the following error:

Exception in thread "main" java.lang.NoClassDefFoundError: chemaxon/clustering/ward
Caused by: java.lang.ClassNotFoundException: chemaxon.clustering.ward
    at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
Could not find the main class: chemaxon.clustering.ward.  Program will exit.

I the class not really there, or do I not have the path right?

Dick

Dear Dick,

 

The executable class name is chemaxon.clustering.Ward (instead of
chemaxon.clustering.ward).

Command line tool 'ward' calls this class; it is recommended to use instead of java directly.

 

Regards,

Gabor

Thanks, Gabor.  The reason I called directly through java is that I had a memory problem with the previous job.

Also - I have the smiles and an identifier in the input file.  Is there a way to get the clustering program to use the identifier in the output file?

 

Thanks again,

Dick

Dear Dick,

 

Sorry for the late answer. Currently it is not possible. We recommend to work around by reattaching the identifier using linux shell tools.

 

regards,

Gabor