__init__.py 文件源码

def wrmsd(X, Y, w):
    """
    Calculate the weighted root mean squared deviation (wRMSD) using Kabsch'
    formula.

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

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

    @param w: input weights
    @type w: numpy array

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

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

    ## normalize weights

    w = w / w.sum()

    X = X - dot(w, X)
    Y = Y - dot(w, Y)

    R_x = sum(X.T ** 2 * w)
    R_y = sum(Y.T ** 2 * w)

    L = svd(dot(Y.T * w, X))[1]

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