__init__.py 文件源码

def rmsd(X, Y):
    """
    Calculate the root mean squared deviation (RMSD) using Kabsch' formula.

    @param X: (n, d) input vector
    @type X: numpy array

    @param Y: (n, d) input vector
    @type Y: numpy array

    @return: rmsd value between the input vectors
    @rtype: float
    """

    from numpy import sum, dot, sqrt, clip, average
    from numpy.linalg import svd, det

    X = X - X.mean(0)
    Y = Y - Y.mean(0)

    R_x = sum(X ** 2)
    R_y = sum(Y ** 2)

    V, L, U = svd(dot(Y.T, X))

    if det(dot(V, U)) < 0.:
        L[-1] *= -1

    return sqrt(clip(R_x + R_y - 2 * sum(L), 0., 1e300) / len(X))