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src/m/d/MDAnalysis-0.8.1/examples/rmsd.py   MDAnalysis(Download)
        a = ref_coordinates.T.astype('float64')
        b = traj_coordinates.T.astype('float64')
        rmsd[k] = qcp.CalcRMSDRotationalMatrix(a,b,natoms,R,None)
 
        print "%5d  %8.3f A" % (k, rmsd[k])