for index in union_set:
    loc = np.where(indices==index)
    dist = distances[loc]
    weight_array = np.zeros(len(indices))
    dist_array = np.zeros(len(indices))
    np.put(dist_array, loc[0], dist)
    np.put(weight_array, loc[0], weights[loc[0]])
    np.dot(weight_array, dist_array)

>>> indices = np.array([[3,6,9], [4, 3, 8], [7, 3, 3]])
>>> distances = np.array([[0.1, 0.2, 0.3], [0.2, 0.5, 0.8], [0.3, 0.4, 0.5]])
>>> weights = np.array([0.6, 0.4, 0.9])
>>> weight_array = np.zeros(len(indices))
>>> dist_array = np.zeros(len(indices))
>>> loc = np.where(indices==7)
>>> loc
(array([2]), array([0]))
>>> dist = distances[loc]
>>> dist
array([0.3])
>>> np.put(dist_array, loc[0], dist)
>>> dist_array
array([0. , 0. , 0.3])
>>> np.put(weight_array, loc[0], weights[loc[0]])
>>> weight_array
array([0. , 0. , 0.9])

>>> indices = np.array([[1,2,3], [2, 5, 9]])
>>> distances = np.array([[0.1, 0.2, 0.3], [0.2, 0.4, 0.6]])
>>> np.where(np.in1d(indices, 1))
(array([0]),)
>>> np.where(np.in1d(indices, 2))
(array([1, 3]),)
>>> np.where(np.in1d(indices, 9))
(array([5]),)
>>> distances.ravel()[np.where(np.in1d(indices, 9))]
array([0.6])
>>> distances.ravel()[np.where(np.in1d(indices, 2))]
array([0.2, 0.2])

>>> union_set = np.array(list(set().union(*indices)), dtype=np.uint32)
>>> union_set
array([1, 2, 3, 5, 9], dtype=uint32)
>>> distances.ravel()[np.where(np.in1d(indices, union_set))]
array([0.1, 0.2, 0.3, 0.2, 0.4, 0.6])