def read_clustering(filename):
    """ Read the clustering in

    :param filename:
        The cluster file to read
    :returns:
        A list of lists of active site numbers
    """

    clusters = []
    cluster = []

    with open(filename, 'r') as fp:
        for line in fp:
            line = line.strip()
            if line == '':
                continue
            if line.startswith('---'):
                continue

            if line.startswith('Cluster'):
                if len(cluster) > 0:
                    clusters.append(cluster)
                cluster = []
            else:
                cluster.append(int(line))
    if len(cluster) > 0:
        clusters.append(cluster)
    return clusters