__init__.py 文件源码

def average_structure(X):
    """
    Calculate an average structure from an ensemble of structures
    (i.e. X is a rank-3 tensor: X[i] is a (N,3) configuration matrix).

    @param X: m x n x 3 input vector
    @type X: numpy array

    @return: average structure
    @rtype: (n,3) numpy.array
    """
    from numpy.linalg import eigh

    B = csb.numeric.gower_matrix(X)
    v, U = eigh(B)
    if numpy.iscomplex(v).any():
        v = v.real
    if numpy.iscomplex(U).any():
        U = U.real

    indices = numpy.argsort(v)[-3:]
    v = numpy.take(v, indices, 0)
    U = numpy.take(U, indices, 1)

    x = U * numpy.sqrt(v)
    i = 0
    while is_mirror_image(x, X[0]) and i < 2:
        x[:, i] *= -1
        i += 1
    return x