From: Peter Freddolino (
Date: Fri Sep 28 2007 - 16:39:56 CDT

Hi Jan,
I noticed that you moved a lot of useful functions from paratool to
util; in addition, did you change the interfaces on some of them (such
as, say, bondedsel)? A lot of my code that relied on these functions is
now broken, and it's hard to tell from the comments exactly what changed.