// the commented code below is functionally equal to a one-liner library call in the end
/*
double rmsd = 0;
for (int i = 0; i < size; i++) {
    Atom atomLeft = listLeft.get(i);
    Atom atomRight = listRight.get(i);

    double distance = calculateDistance(atomLeft, atomRight);
    rmsd += distance * distance;
}
rmsd /= size;
rmsd = Math.sqrt(rmsd);
*/
double rmsd = SVDSuperimposer.getRMS(atomSet1, atomSet2);