import protocol
protocol.loadPDB("model.pdb",deleteUnknownAtoms=True)
tol=1e-4

import trace
trace.suspend()
xplor.simulation.disableOutput()

xplor.command("flags exclude * include VDW end")
xplor.command("set print=off end")

numAtoms=xplor.simulation.numAtoms()
for idi in range(1,numAtoms+1):
    for idj in range(idi+1,numAtoms+1):
        xplor.command("constr inte (id %d) (id %d) end" %(idi, idj))
        vdwEnergy = float(xplor.command("energy end",("ENER",))[0])
        if abs(vdwEnergy) > tol:
            atomi = xplor.simulation.atomByID(idi-1).string()
            atomj = xplor.simulation.atomByID(idj-1).string()
            print "(%s) (%s) %.5f" % (atomi,atomj,vdwEnergy)