public static double getNormalizationFactor(IAtomContainer container) {
 double bondlength = 0.0;
 double ratio;
 <sep> 
 Desired bond length for storing structures in MDL mol files This
 should probably be set externally (from system wide settings)
 <sep>
 double desiredBondLength = 1.5;
<sep> loop over all bonds and determine the mean bond distance <sep>
 int counter = 0;
 for (IBond bond : container.bonds()) {
<sep> only consider two atom bonds into account <sep>
 if (bond.getAtomCount() == 2) {
 counter++;
 IAtom atom1 = bond.getBegin();
 IAtom atom2 = bond.getEnd();
 bondlength += Math.sqrt(Math.pow(atom1.getPoint2d().x - atom2.getPoint2d().x, 2)
 + Math.pow(atom1.getPoint2d().y - atom2.getPoint2d().y, 2));
 }
 }
 bondlength = bondlength / counter;
 ratio = desiredBondLength / bondlength;
 return ratio;
 }
