abc.
The most relevant interface methods for the Chemical Development Kit (CDK) library are available in the joelib/util/cdk/CDKTools.java helper class.
The most relevant interface methods for the Weka data mining library library are available in the joelib/algo/weka/InstancesHelper.java helper class. For using Weka you should modify the constructors in weka.core.Attributes from 'protected' to 'public' and use the recompiled Weka sources.