[IMP-dev] Various small changes

Add operator[] to Vector3D as that is kind of customary in C++

Add a few methods to randomize particles in the XYZdecorator

Use the inactive particle exception in particle.h

Make some clarifications in the documents about what show and other things should do. And remove the name from the Optimization state since it is never used. We may want to put the name into object so that everything has it, but the current system with a few random objects having it is kind of awkward.

Add a singleton score function that applies a unary function to the value of a single attribute.