How to use the lightdock.structure.complex.Complex function in lightdock

receptor_file = sys.argv[2]
    ligand_file = sys.argv[3]
    steps = int(sys.argv[4])
    configuration_file = sys.argv[5]

    log.info("Starting file: %s" % starting_file)
    log.info("Receptor: %s" % receptor_file)
    log.info("Ligand: %s" % ligand_file)
    log.info("Steps: %d" % steps)
    log.info("Configuration file: %s" % configuration_file)
    print

    # Read structures (already in the center)
    log.info("Reading %s receptor PDB file..." % receptor_file)
    atoms, residues, chains = parse_complex_from_file(receptor_file)
    receptor = Complex(chains, atoms)
    log.info("%s atoms, %s residues read." % (len(atoms), len(residues)))

    log.info("Reading %s ligand PDB file..." % ligand_file)
    atoms, residues, chains = parse_complex_from_file(ligand_file)
    ligand = Complex(chains, atoms)
    log.info("%s atoms, %s residues read." % (len(atoms), len(residues)))

    # Start from results positions
    log.info("Reading calculated data from %s" % starting_file)
    translations, rotations, luciferin, neighbors, vision_range, scoring = parse_output_file(starting_file)
    num_glowworms = len(translations)
    log.info("%d glowworms loaded" % num_glowworms)

    adapter = DFIREAdapter(receptor, ligand)
    scoring_function = DFIRE()
    log.info("Loaded DFIRE scoring function")

parser.add_argument("receptor_structure", help="receptor structure", type=valid_file, metavar="receptor_structure")
    # Ligand
    parser.add_argument("ligand_structure", help="ligand structure", type=valid_file, metavar="ligand_structure")
    # Lightdock output file
    parser.add_argument("lightdock_output", help="lightdock output file", type=valid_file, metavar="lightdock_output")
    # Solution to minimize
    parser.add_argument("glowworm", help="glowworm to minimize", type=valid_integer_number)
    # Scoring function
    parser.add_argument("-s", "--scoring_function", help="scoring function used", dest="scoring_function")
    args = parser.parse_args()

    # Read receptor structure
    structure = args.receptor_structure
    log.info("Reading %s receptor PDB file..." % structure)
    atoms, residues, chains = parse_complex_from_file(structure)
    receptor = Complex(chains, atoms, residues, structure_file_name=structure)
    log.info("%s atoms, %s residues read." % (len(atoms), len(residues)))

    # Read ligand structure
    structure = args.ligand_structure
    log.info("Reading %s ligand PDB file..." % structure)
    atoms, residues, chains = parse_complex_from_file(structure)
    ligand = Complex(chains, atoms, residues, structure_file_name=structure)
    log.info("%s atoms, %s residues read." % (len(atoms), len(residues)))

    # Output file
    translations, rotations, receptor_ids, ligand_ids, rec_extents, lig_extents = parse_output_file(args.lightdock_output)

    # Destination path is the same as the lightdock output
    destination_path = os.path.dirname(args.lightdock_output)

    # If normal modes used, need to read them

structures = []
    for structure in get_lightdock_structures(args.receptor_structures):
        log.info("Reading %s receptor PDB file..." % structure)
        atoms, residues, chains = parse_complex_from_file(structure)
        structures.append({'atoms': atoms, 'residues': residues, 'chains': chains, 'file_name': structure})
        log.info("%s atoms, %s residues read." % (len(atoms), len(residues)))
    receptor = Complex.from_structures(structures)

    # Ligand
    structures = []
    for structure in get_lightdock_structures(args.ligand_structures):
        log.info("Reading %s ligand PDB file..." % structure)
        atoms, residues, chains = parse_complex_from_file(structure)
        structures.append({'atoms': atoms, 'residues': residues, 'chains': chains, 'file_name': structure})
        log.info("%s atoms, %s residues read." % (len(atoms), len(residues)))
    ligand = Complex.from_structures(structures)

    # Output file
    translations, rotations, receptor_ids, ligand_ids, \
        rec_extents, lig_extents = parse_output_file(args.lightdock_output, num_anm_rec, num_anm_lig)

    found_conformations = len(translations)
    num_conformations = args.glowworms
    if num_conformations > found_conformations:
        log.warning("Number of conformations is bigger than found solutions (%s > %s)" % (num_conformations,
                                                                                          found_conformations))
        log.warning("Clipping number of conformations to %s" % found_conformations)
        num_conformations = found_conformations

    # Destination path is the same as the lightdock output
    destination_path = os.path.dirname(args.lightdock_output)

Parses command line arguments
    """
    parser = argparse.ArgumentParser(prog='surface_density')
    parser.add_argument("pdb1", help="PDB file for receptor structure")
    parser.add_argument("pdb2", help="PDB file for ligand structure")
    parser.add_argument("points", type=int, default=400, help="The number of points on the surface")
    args = parser.parse_args()
    return args


if __name__ == "__main__":
    args = parse_command_line()

    # Read receptor and calculate max radius
    atoms, residues, chains = parse_complex_from_file(args.pdb1)
    structure = Complex(chains, atoms, structure_file_name=args.pdb1)
    distances_matrix = spatial.distance.squareform(spatial.distance.pdist(structure.representative()))
    radius1 = np.max(distances_matrix)/2.

    # Read ligand and calculate max radius
    atoms, residues, chains = parse_complex_from_file(args.pdb2)
    structure = Complex(chains, atoms, structure_file_name=args.pdb2)
    distances_matrix = spatial.distance.squareform(spatial.distance.pdist(structure.representative()))
    radius2 = np.max(distances_matrix)/2.

    # Calculate the area of the sphere of radius (Rl + Rr)
    density_area = (4*np.pi*(radius1+radius2)**2)/args.points

    if density_area > MIN_SURFACE_DENSITY:
        log.warning("Surface density is below recommended, please increase the number of points on the surface.")

    print ';'.join([str(x) for x in [radius1, radius2, density_area]])

def from_structures(structures, representative_id=0):
        return Complex(structures[representative_id]['chains'],
                       structures[representative_id]['atoms'],
                       structures[representative_id]['residues'],
                       structures[representative_id]['file_name'],
                       structures, representative_id)

log = LoggingManager.get_logger('diameter')


def parse_command_line():
    parser = argparse.ArgumentParser(prog='calculate_diameter')
    parser.add_argument("pdb", help="PDB file for structure to calculate maximum diameter")
    args = parser.parse_args()
    return args


if __name__ == "__main__":
    args = parse_command_line()

    atoms, residues, chains = parse_complex_from_file(args.pdb)
    structure = Complex(chains, atoms, structure_file_name=args.pdb)
    distances_matrix = spatial.distance.squareform(spatial.distance.pdist(structure.representative()))
    ligand_max_diameter = np.max(distances_matrix)

    print ligand_max_diameter

num_anm_rec = DEFAULT_NMODES_REC
    num_anm_lig = DEFAULT_NMODES_LIG
    if setup and setup['use_anm']:
        num_anm_rec = setup['anm_rec']
        num_anm_lig = setup['anm_lig']
    
    # Read receptor
    log.info("Reading %s receptor PDB file..." % args.receptor_pdb)
    atoms, residues, chains = parse_complex_from_file(args.receptor_pdb)
    receptor = Complex(chains, atoms)
    log.info("%s atoms, %s residues read." % (len(atoms), len(residues)))
    
    # Read ligand
    log.info("Reading %s ligand PDB file..." % args.ligand_pdb)
    atoms, residues, chains = parse_complex_from_file(args.ligand_pdb)
    ligand = Complex(chains, atoms)
    log.info("%s atoms, %s residues read." % (len(atoms), len(residues)))

    try:
        nm_path = os.path.abspath(os.path.dirname(args.receptor_pdb))
        nmodes_rec = read_nmodes(os.path.join(nm_path, DEFAULT_REC_NM_FILE + '.npy'))
    except:
        nmodes_rec = None
    try:
        nm_path = os.path.abspath(os.path.dirname(args.ligand_pdb))
        nmodes_lig = read_nmodes(os.path.join(nm_path, DEFAULT_LIG_NM_FILE + '.npy'))
    except:
        nmodes_lig = None

    for step in xrange(0, args.steps+1):
        try:
            # Parse each stored step file

# Parse arguments
    args = parse_command_line()

    # Load setup configuration if provided
    setup = get_setup_from_file(args.setup_file) if args.setup_file else None

    num_anm_rec = DEFAULT_NMODES_REC
    num_anm_lig = DEFAULT_NMODES_LIG
    if setup and setup['use_anm']:
        num_anm_rec = setup['anm_rec']
        num_anm_lig = setup['anm_lig']
    
    # Read receptor
    log.info("Reading %s receptor PDB file..." % args.receptor_pdb)
    atoms, residues, chains = parse_complex_from_file(args.receptor_pdb)
    receptor = Complex(chains, atoms)
    log.info("%s atoms, %s residues read." % (len(atoms), len(residues)))
    
    # Read ligand
    log.info("Reading %s ligand PDB file..." % args.ligand_pdb)
    atoms, residues, chains = parse_complex_from_file(args.ligand_pdb)
    ligand = Complex(chains, atoms)
    log.info("%s atoms, %s residues read." % (len(atoms), len(residues)))

    try:
        nm_path = os.path.abspath(os.path.dirname(args.receptor_pdb))
        nmodes_rec = read_nmodes(os.path.join(nm_path, DEFAULT_REC_NM_FILE + '.npy'))
    except:
        nmodes_rec = None
    try:
        nm_path = os.path.abspath(os.path.dirname(args.ligand_pdb))
        nmodes_lig = read_nmodes(os.path.join(nm_path, DEFAULT_LIG_NM_FILE + '.npy'))