Overlap checker

[pckroon]

It may be a nice idea to add a processor at the end of the pipeline that checks for overlaps/clashes. I think the relevant data should come from FF variables (or whatevers, we need to revisit the fileformat anyway). It would be nice to be able to set debug/info/warning messages based on different distance criteria. Is there any other functionality that should be exposed? For example, exclude certain atoms (name? type? pairs?) from the comparison.