Thanks for your help Daniel, that was just what I needed!
I'm having a strange problem though, when I import the jmarvin.jar file and try to use tautomerization plugin the method and field names are all alphabetic instead of corresponding to the names in the examples. Are the JAR files protected in some way? Am I using them incorrectly? I'm sorry if I'm being a bit dense, I've tried to find a tutorial on how to use the MarvinBeans packages but I haven't been able to find anything.
The autocomplete I am getting in eclipse (I confirmed the methods with reflection so this isn't an Eclipse issue):