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src/m/d/MDAnalysis-0.8.1/MDAnalysis/analysis/rms.py   MDAnalysis(Download)
        a = a - numpy.average(a, axis=0, weights=weights)
        b = b - numpy.average(b, axis=0, weights=weights)
    return qcp.CalcRMSDRotationalMatrix(a.T.astype(numpy.float64),b.T.astype(numpy.float64),
                                        a.shape[0], None, relative_weights)
 
                # so that R acts **to the left** and can be broadcasted; we're saving
                # one transpose. [orbeckst])
                rmsd[k, 2] = qcp.CalcRMSDRotationalMatrix(ref_coordinates_T_64,
                                                          traj_coordinates.T.astype(numpy.float64),
                                                          natoms, rot, weight)
                # 2) calculate secondary RMSDs
                for igroup, (refpos, atoms) in enumerate(izip(groupselections_ref_coords_T_64, self.groupselections_atoms), 3):
                    rmsd[k, igroup] = qcp.CalcRMSDRotationalMatrix(refpos,
                                                                   atoms['mobile'].positions.T.astype(numpy.float64),
                                                                   atoms['mobile'].numberOfAtoms(), None, weight)
            else:
                # only calculate RMSD by setting the Rmatrix to None
                # (no need to carry out the rotation as we already get the optimum RMSD)
                rmsd[k, 2] = qcp.CalcRMSDRotationalMatrix(ref_coordinates_T_64,

src/m/d/MDAnalysis-0.8.1/MDAnalysis/analysis/align.py   MDAnalysis(Download)
        weights = numpy.asarray(weights)/numpy.mean(weights)
    rot = numpy.zeros(9, dtype=numpy.float64)
    rmsd = qcp.CalcRMSDRotationalMatrix(a.T.astype(numpy.float64), b.T.astype(numpy.float64),
                                        b.shape[0], rot, weights)
    return numpy.matrix(rot.reshape(3,3)), rmsd
        # so that R acts **to the left** and can be broadcasted; we're saving
        # one transpose. [orbeckst])
        rmsd[k] = qcp.CalcRMSDRotationalMatrix(ref_coordinates.T.astype(numpy.float64),
                                               traj_coordinates.T.astype(numpy.float64),
                                               natoms, rot, weight)

src/m/d/MDAnalysisTests-0.8.1/MDAnalysisTests/test_qcprot.py   MDAnalysisTests(Download)
 
    # Calculate rmsd and rotation matrix
    qcp_rmsd = qcp.CalcRMSDRotationalMatrix(frag_a,frag_b,N,rot,None)
 
    #print 'qcp rmsd = ',rmsd