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