One often transforms a collection of particles into a standard orientation before performing calculations on them. Usually you do this to hide the fact that your code is not rotationally invariant and/or translationally invariant.
Some examples of standard orientations are:
1. Place the origin at the center of mass and then rotate the system so that the moments of inertia are aligned with the axes of the coordinate system.
2. Place the origin at the center of nuclear charge and then rotate the system so that the moments of inertia are parallel to the axes of the coordinate system.
If you are doing this, you probably shouldn't be. You should be fixing your code. ;)