There are a number of classes in IMP.core which have been marked as deprecated for a while. I would be good to get rid of them entirely before the first public release. I propose that after the first marked stable version (a concept which will be explained in a forthcoming email from Ben), I remove them from SVN.

So please check your code to make sure you don't use them and if you do, start migrating to the replacement classes. You can find a list of such classes at https://salilab.org/imp/doc/doxygen/deprecated.html and you code should spit out warning messages whenever you create an instance of such a class.