Could not find the main class: chemaxon.fragmenter.Fragmente

Dear all,

i am trying to perform a fragmentation with a python script using this command: commands.getstatusoutput("/home/user/ChemAxon/JChem/bin/fragment -c /home/user/ChemAxon/JChem/bin/FragmenterRecap.xml %s -i MoleculeID -f sdf:-a -o frags.sdf"%(file))

I've got the script from a colleague where it worked perfectly. Unfortunately I am getting the following error:

Exception in thread "main" java.lang.NoClassDefFoundError: chemaxon/fragmenter/Fragmenter
Caused by: java.lang.ClassNotFoundException: chemaxon.fragmenter.Fragmenter
    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.fragmenter.Fragmenter.  Program will exit.

I am using a Linux Ubuntu 14.04 LTS machine and JChem 16.2.1. Java version 1.7.0_95

Any suggestions?

Best regards,

Janette

Fragmenter is a discontinued product, and it is not included in the JChem release any more.

You can install an old release which includes Fragmenter (e.g. JChem 6.3.x), and keep using it.