class GeometryTools {

    public static double getBondLengthMedian(final IAtomContainer container) {
        if (container.getBondCount() == 0) throw new IllegalArgumentException("Container has no bonds.");
        double[] lengths = new double[container.getBondCount()];
        for (int i = 0; i < container.getBondCount(); i++) {
            final IBond bond = container.getBond(i);
            final IAtom atom1 = bond.getBegin();
            final IAtom atom2 = bond.getEnd();
            if (atom1.getPoint2d() == null || atom2.getPoint2d() == null)
                throw new IllegalArgumentException("An atom has no 2D coordinates.");
            lengths[i] = getLength2D(bond);
        }
        Arrays.sort(lengths);
        return lengths[lengths.length / 2];
    }

}