def count_contacts(native_file, d_cutoff, min_seq_separation):
    (coords, resis) = read_PDB(native_file, 'CA')
    native_contacts = compute_contacts_matrix(coords, thresh=d_cutoff, min_seq_separation=min_seq_separation)
    return int(np.sum(native_contacts))
def count_contacts(native_file, d_cutoff, min_seq_separation):
    (coords, resis) = read_PDB(native_file, 'CA')
    native_contacts = compute_contacts_matrix(coords, thresh=d_cutoff, min_seq_separation=min_seq_separation)
    return int(np.sum(native_contacts))