the ownership semantics of sip/PyQt changed between versions. Object
which were previously staying in memory are now garbage collected.
Event handlers associated with these objects were then removed.
The fix presented in this patch is rather ugly. We store references to
the objects inside the _Init* functions. Ideally, these types of hacks
would not be required, but I could not find another way to approach
the problem.

The code becomes much simpler, cleaner and fixes as weird crash
with Qt 4.8

Commited patched file by mistake

Thanks Tobias for diagnosing the problem

distance to check

in the structure_analysis.py module.

This is used to make functions written at the CoordFrame level
accesible to analyze both entities and trajectories.

Conflicts:

	modules/mol/alg/src/filter_clashes.cc

Non-error output of lddt all to stdout
Removed from usage text an option that has been removed from the program

Conflicts:

	modules/mol/alg/src/filter_clashes.cc