if (myBondingRadius == 0)
continue;
float searchRadius = myBondingRadius + maxBondingRadius + bondTolerance;
initializeBspt(modelIndex);
CubeIterator iter = bspf.getCubeIterator(modelIndex);
iter.initialize(atom, searchRadius, true);
while (iter.hasMoreElements()) {
Atom atomNear = (Atom) iter.nextElement();
if (atomNear == atom || atomNear.isDeleted())
continue;
int atomIndexNear = atomNear.index;