Backing up and restore tokudb files on a new mysql installation

In reference to my this post Is looks like I have to restore the whole tokudb. Is there any way I can disabled innodb? So I am going to yum remove the current mysql and reinstall again. In the meantime I still have my current db directory with all the tokudb data files. So once I create the refresh installation I just create a new database and can I replace in those files and restore my db via this method?