def test_calculate_interface(self): atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPErec.pdb') receptor = Complex(chains, atoms) atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPElig.pdb') ligand = Complex(chains, atoms) adapter = DFIREAdapter(receptor, ligand) receptor_residue_indexes, ligand_residue_indexes, dist_matrix, atom_indexes = get_interface_residues( adapter.receptor_model, adapter.ligand_model, max_cutoff=1.) receptor_residues = [] for residue_index in receptor_residue_indexes: residue = receptor.residues[residue_index] receptor_residues.append("%s.%d" % (residue.name, residue.number)) ligand_residues = [] for residue_index in ligand_residue_indexes: residue = ligand.residues[residue_index] ligand_residues.append("%s.%d" % (residue.name, residue.number)) # Checked according to UCSF chimera expected_receptor = ['SER.61', 'ALA.56', 'TYR.59', 'TYR.94', 'GLY.62', 'ILE.63', 'MET.104', 'ILE.106'] expected_ligand = ['LEU.7', 'LEU.8', 'GLU.24', 'HIS.25', 'GLY.26', 'TYR.27', 'CYS.28'] assert len(set(expected_receptor) & set(receptor_residues)) == 8 assert len(set(expected_ligand) & set(ligand_residues)) == 7
def test_calculate_FastDFIRE_1AY7(self): atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1AY7rec.pdb') receptor = Complex(chains, atoms) atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1AY7lig.pdb') ligand = Complex(chains, atoms) adapter = DFIREAdapter(receptor, ligand) assert_almost_equal(-20.7459619159, self.dfire(adapter.receptor_model, adapter.receptor_model.coordinates[0], adapter.ligand_model, adapter.ligand_model.coordinates[0]))
def test_calculate_TOBI_1AY7(self): atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1AY7rec.pdb') #@UnusedVariable receptor = Complex(chains, atoms) atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1AY7lig.pdb') #@UnusedVariable ligand = Complex(chains, atoms) adapter = TOBIAdapter(receptor, ligand) assert_almost_equal(2.34, self.tobi(adapter.receptor_model, adapter.receptor_model.coordinates[0], adapter.ligand_model, adapter.ligand_model.coordinates[0]))
def setup(self): self.golden_data_path = os.path.normpath(os.path.dirname(os.path.realpath(__file__))) + '/golden_data/' atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPErec.pdb') self.receptor = Complex(chains, atoms) atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPElig.pdb') self.ligand = Complex(chains, atoms) self.adapter = MJ3hAdapter(self.receptor, self.ligand) self.scoring_function = MJ3h()
def test_calculate_PyDockDNA_3MFK_with_hydrogens(self): atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '3mfk_homodimer.pdb.H') receptor = Complex(chains, atoms, structure_file_name=(self.golden_data_path + '3mfk_homodimer.pdb.H')) atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '3mfk_dna.pdb') ligand = Complex(chains, atoms, structure_file_name=(self.golden_data_path + '3mfk_dna.pdb')) adapter = CPyDockDNAAdapter(receptor, ligand) assert_almost_equal(688.1703668834168, self.dna(adapter.receptor_model, adapter.receptor_model.coordinates[0], adapter.ligand_model, adapter.ligand_model.coordinates[0]))
def test_calculate_starting_points(self): atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPE_rec.pdb') receptor = Complex(chains, atoms) atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPE_lig.pdb') ligand = Complex(chains, atoms) starting_points, rec_diameter, lig_diameter = calculate_surface_points(receptor, ligand, 10, 0.5) create_pdb_from_points(self.test_path+'points.pdb', starting_points) assert filecmp.cmp(self.golden_data_path+'starting_points.pdb', self.test_path+'points.pdb')
def test_calculate_DFIRE2_1EAW(self): atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1EAWrec.pdb') receptor = Complex(chains, atoms) atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1EAWlig.pdb') ligand = Complex(chains, atoms) adapter = DFIRE2Adapter(receptor, ligand) assert_almost_equal(-488.34640492000244, self.dfire(adapter.receptor_model, adapter.receptor_model.coordinates[0], adapter.ligand_model, adapter.ligand_model.coordinates[0]))
def test_calculate_DFIRE2_1PPE(self): atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPErec.pdb') receptor = Complex(chains, atoms) atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPElig.pdb') ligand = Complex(chains, atoms) adapter = DFIRE2Adapter(receptor, ligand) assert_almost_equal(-398.7303561600074, self.dfire(adapter.receptor_model, adapter.receptor_model.coordinates[0], adapter.ligand_model, adapter.ligand_model.coordinates[0]))
def test_calculate_phi_psi(self): atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPElig.pdb') protein = Complex(chains, atoms) # psi: angle #0:1@n,ca,c #0:2@n # phi: angle #0:1@c #0:2@n,ca,c phi_angles = [-105.92428251619579, -134.402235889132, -58.32268858533758, -85.62997439535678, -129.666484600813, -77.00076813772478, -142.09891098624075, -82.10672119029674, -163.14606891327375, -109.37900096123484, -138.72905680654182, -59.09699793329797, -60.06774387010816, -74.41030551527874, -99.82766540256617, -92.6495110068149, 54.969041241310705, -104.60151419194615, -67.57074855137641, -123.83574594954692, -85.90313254423194, -87.7781803331676, -66.345484249271, -64.51513795752882, 108.23656098935888, -129.62530277139578, -71.90658189461674, -170.4460918036806] psi_angles = [138.38576328505278, 105.22472788100255, 106.42882930892199, 150.65572151747787, 72.08329638522976, 130.19890858175336, 115.48238807519739, 132.48041144914038, 163.35191386073618, 151.17756189538443, -28.310569696143393, 162.66293554938997, -32.25480696024475, -20.28436719199857, -11.444789534534305, 163.38578466073147, 150.2534549328882, -128.53524744082424, 20.01260634937939, 151.96710290169335, 159.55519588393594, 115.07091589216549, 152.8911959270869, -24.04765297807205, -14.890186424782046, 15.86273088398991, 152.7552784042674, 146.11762131430552] for i in range(1, len(protein.residues)): phi, psi = calculate_phi_psi(protein.residues[i], protein.residues[i - 1]) assert_almost_equals(phi_angles[i - 1], math.degrees(phi)) assert_almost_equals(psi_angles[i - 1], math.degrees(psi))
def test_parse_complex_from_file(self): atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPE_l_u.pdb') assert 224 == len(atoms) assert 31 == len(residues) assert 2 == len(chains) assert 29 == len(chains[0].residues) assert 2 == len(chains[1].residues)
def test_calculate_chi_angles(self): # Command in chimera: angle #0:28@n,ca,cb,sg atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPElig.pdb') protein = Complex(chains, atoms) for residue in protein.residues: if residue.name == 'ARG' and residue.number == 1: chi_angles = calculate_chi_angles(residue) for key, value in chi_angles.iteritems(): if value: if key == 'x1': # angle #0:1@n,ca,cb,cg assert_almost_equals(-173.216, round(math.degrees(value), 3)) if key == 'x2': # angle #0:1@ca,cb,cg,cd assert_almost_equals(171.375, round(math.degrees(value), 3)) if key == 'x3': # angle #0:1@cb,cg,cd,ne assert_almost_equals(62.852, round(math.degrees(value), 3)) if key == 'x4': # angle #0:1@cg,cd,ne,cz assert_almost_equals(100.22, round(math.degrees(value), 2)) if residue.name == 'VAL' and residue.number == 2: # angle #0:2@n,ca,cb,cg1 chi_angles = calculate_chi_angles(residue) for key, value in chi_angles.iteritems(): if value: if key == 'x1': # angle #0:1@n,ca,cb,cg assert_almost_equals(-173.629, round(math.degrees(value), 3)) if residue.name == 'CYS' and residue.number == 28: chi_angles = calculate_chi_angles(residue) for key, value in chi_angles.iteritems(): if value: if key == 'x1': assert_almost_equals(-60.2554, round(math.degrees(value), 4))
def read_input_structure(pdb_file_name, ignore_oxt=True): """Reads the input structure. The arguments pdb_file_name can be a PDB file or a file containing a list of PDB files. ignore_oxt flag avoids saving OXT atoms. """ atoms_to_ignore = [] if ignore_oxt: atoms_to_ignore.append('OXT') structures = [] file_names = [] file_name, file_extension = os.path.splitext(pdb_file_name) if file_extension == DEFAULT_LIST_EXTENSION: file_names.extend(get_pdb_files(pdb_file_name)) else: file_names.append(pdb_file_name) for file_name in file_names: log.info("Reading structure from %s PDB file..." % file_name) atoms, residues, chains = parse_complex_from_file(file_name, atoms_to_ignore) structures.append({'atoms': atoms, 'residues': residues, 'chains': chains, 'file_name': file_name}) log.info("%s atoms, %s residues read." % (len(atoms), len(residues))) # Representatives are now the first structure, but this could change in the future structure = Complex.from_structures(structures) return structure
def test_write_pdb_to_file(self): atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPE_l_u.pdb') protein = Complex(chains) assert atoms == protein.atoms write_pdb_to_file(protein, self.test_path + '1PPE_l_u.pdb.parsed', protein.atom_coordinates[0]) assert filecmp.cmp(self.golden_data_path + '1PPE_l_u.pdb.parsed', self.test_path + '1PPE_l_u.pdb.parsed')
def calculate_membrane_height(parsed_receptor_file, restraints): atoms, residues, chains = parse_complex_from_file(parsed_receptor_file) receptor = Complex(chains, atoms) z_coord = [] for restraint in restraints: chain_id, residue_name, residue_number = restraint.split(".") residue = receptor.get_residue(chain_id, residue_name, residue_number) ca = residue.get_calpha() z_coord.append(ca.z) return min(z_coord)
def test_LightDockGSOBuilder_using_FromFileInitializer(self): builder = LightdockGSOBuilder() number_of_glowworms = 5 atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPErec.pdb') receptor = Complex(chains, atoms) atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPElig.pdb') ligand = Complex(chains, atoms) adapter = MJ3hAdapter(receptor, ligand) scoring_function = MJ3h() gso = builder.create_from_file(number_of_glowworms, self.random_number_generator, self.gso_parameters, [adapter], [scoring_function], self.bounding_box, self.golden_data_path+'initial_positions_1PPE.txt', 0.5, 0.5, 0.5, False, 10, 10) assert 5 == gso.swarm.get_size() gso.report(self.test_path + 'report.out') assert filecmp.cmp(self.golden_data_path + 'report_lightdockbuilder.out', self.test_path + 'report.out')
def test_evaluate_objective_function_rotation_y_axis_180_translation_10(self): atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPElig.pdb') ligand = Complex(chains, atoms) adapter = MJ3hAdapter(self.receptor, ligand) scoring_function = MJ3h() coordinates = Coordinates([10.,0.,0.,0.,0.,1.,0.]) landscape_position = DockingLandscapePosition(scoring_function, coordinates, adapter.receptor_model, adapter.ligand_model) assert_almost_equal(6.39, landscape_position.evaluate_objective_function())
def test_get_restraints(self): input_file = os.path.join(self.golden_data_path, '2UUY_lig.pdb') atoms, residues, chains = parse_complex_from_file(input_file) structure = Complex(chains) restraints = {'active':['B.ALA.21'], 'passive':['B.GLY.75'], 'blocked':[]} residues = get_restraints(structure, restraints) assert len(residues['active']) == 1 and len(residues['passive']) == 1 assert residues['active'][0].name == 'ALA' and residues['active'][0].number == 21 assert residues['passive'][0].name == 'GLY' and residues['passive'][0].number == 75
def test_calculate_PyDock_1AY7(self): atoms, residues, chains = parse_complex_from_file( self.golden_data_path + '1AY7_rec.pdb.H') receptor = Complex(chains, atoms, structure_file_name=(self.golden_data_path + '1AY7_rec.pdb.H')) atoms, residues, chains = parse_complex_from_file( self.golden_data_path + '1AY7_lig.pdb.H') ligand = Complex(chains, atoms, structure_file_name=(self.golden_data_path + '1AY7_lig.pdb.H')) adapter = CPyDockAdapter(receptor, ligand) assert_almost_equal( -15.923994756, self.pydock(adapter.receptor_model, adapter.receptor_model.coordinates[0], adapter.ligand_model, adapter.ligand_model.coordinates[0]))
def test_calculate_DNA_3MFK_with_hydrogens(self): atoms, residues, chains = parse_complex_from_file( self.golden_data_path + '3mfk_homodimer.pdb.H') receptor = Complex(chains, atoms, structure_file_name=(self.golden_data_path + '3mfk_homodimer.pdb.H')) atoms, residues, chains = parse_complex_from_file( self.golden_data_path + '3mfk_dna.pdb') ligand = Complex(chains, atoms, structure_file_name=(self.golden_data_path + '3mfk_dna.pdb')) adapter = DNAAdapter(receptor, ligand) assert_almost_equal( 688.1703668834168, self.dna(adapter.receptor_model, adapter.receptor_model.coordinates[0], adapter.ligand_model, adapter.ligand_model.coordinates[0]))
def test_read_write(self): pdb_file = self.golden_data_path / 'nm_dna' / '1DIZ_lig.pdb.H' _, _, chains = parse_complex_from_file(pdb_file) molecule = Complex(chains) nmodes = calculate_nmodes(pdb_file, n_modes=10, molecule=molecule) write_nmodes(nmodes, self.test_path / 'test_nm') expected_nmodes = read_nmodes(self.golden_data_path / 'nm_dna' / 'lightdock_lig.nm.npy') other_nmodes = read_nmodes(self.test_path / 'test_nm.npy') assert np.allclose(expected_nmodes, other_nmodes)
def test_parse_pdb_noh(self): atoms_to_ignore = ['H'] atoms, _, chains = parse_complex_from_file( self.golden_data_path / '1PPE_lig.pdb.H', atoms_to_ignore) protein = Complex(chains) assert atoms == protein.atoms write_pdb_to_file(protein, self.test_path / 'parsed_1PPE_lig.pdb.H', protein.atom_coordinates[0]) assert filecmp.cmp(self.golden_data_path / 'parsed_1PPE_lig.pdb.H', self.test_path / 'parsed_1PPE_lig.pdb.H')
def test_repr(self): atoms, _, chains = parse_complex_from_file(self.golden_data_path / '1PPElig.pdb') ligand = Complex(chains, atoms) adapter = MJ3hAdapter(self.receptor, ligand) scoring_function = MJ3h() coordinates = Coordinates([0., 0., 0., 1., 0., 0., 0.]) landscape_position = DockingLandscapePosition(scoring_function, coordinates, adapter.receptor_model, adapter.ligand_model) expected = "( 0.0000000, 0.0000000, 0.0000000, 1.0000000, 0.0000000, 0.0000000, 0.0000000) 0 0" assert expected == str(landscape_position)
def test_distance2_same_landscape_position(self): atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPElig.pdb') ligand = Complex(chains, atoms) adapter = MJ3hAdapter(self.receptor, ligand) scoring_function = MJ3h() coordinates = Coordinates([0., 0., 0., 1., 0., 0., 0.]) landscape_position1 = DockingLandscapePosition(scoring_function, coordinates, adapter.receptor_model, adapter.ligand_model) landscape_position2 = DockingLandscapePosition(scoring_function, coordinates, adapter.receptor_model, adapter.ligand_model) assert_almost_equal(0.0, landscape_position1.distance2(landscape_position2))
def test_calculate_anm_dna(self): pdb_file = os.path.join(self.golden_data_path, 'nm_dna', '1DIZ_lig.pdb.H') atoms, residues, chains = parse_complex_from_file(pdb_file) molecule = Complex(chains) nmodes = calculate_nmodes(pdb_file, n_modes=10, molecule=molecule) expected_nmodes = read_nmodes( os.path.join(self.golden_data_path, 'nm_dna', 'lightdock_lig.nm.npy')) assert np.allclose(expected_nmodes, nmodes)
def test_distance2_same_landscape_position(self): atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPElig.pdb') ligand = Complex(chains, atoms) adapter = MJ3hAdapter(self.receptor, ligand) scoring_function = MJ3h() coordinates = Coordinates([0., 0., 0., 1., 0., 0., 0.]) landscape_position1 = DockingLandscapePosition(scoring_function, coordinates, adapter.receptor_model, adapter.ligand_model) landscape_position2 = DockingLandscapePosition(scoring_function, coordinates, adapter.receptor_model, adapter.ligand_model) assert_almost_equal(0.0, landscape_position1.distance2(landscape_position2))
def test_get_restraints_with_error(self): input_file = self.golden_data_path / '2UUY_lig.pdb' _, _, chains = parse_complex_from_file(input_file) structure = Complex(chains) restraints = { 'active': ['B.VAL.21'], 'passive': ['B.GLY.75'], 'blocked': [] } residues = get_restraints(structure, restraints) assert residues is not None
def test_get_restraints_with_error(self): input_file = os.path.join(self.golden_data_path, '2UUY_lig.pdb') atoms, residues, chains = parse_complex_from_file(input_file) structure = Complex(chains) restraints = { 'active': ['B.VAL.21'], 'passive': ['B.GLY.75'], 'blocked': [] } residues = get_restraints(structure, restraints) assert False
def test_evaluate_objective_function_no_movement(self): """The result of this test must be the same value as testing the MJ3h function. Translation is 0 and Quaternion [1,0,0,0] means no rotation. """ atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPElig.pdb') ligand = Complex(chains, atoms) adapter = MJ3hAdapter(self.receptor, ligand) scoring_function = MJ3h() coordinates = Coordinates([0.,0.,0.,1.,0.,0.,0.]) landscape_position = DockingLandscapePosition(scoring_function, coordinates, adapter.receptor_model, adapter.ligand_model) assert_almost_equal(2.02, landscape_position.evaluate_objective_function())
def test_evaluate_objective_function_rotation_y_axis_180(self): atoms, residues, chains = parse_complex_from_file( self.golden_data_path + '1PPElig.pdb') ligand = Complex(chains, atoms) adapter = MJ3hAdapter(self.receptor, ligand) scoring_function = MJ3h() coordinates = Coordinates([0., 0., 0., 0., 0., 1., 0.]) landscape_position = DockingLandscapePosition(scoring_function, coordinates, adapter.receptor_model, adapter.ligand_model) assert_almost_equal(-1.4, landscape_position.evaluate_objective_function())
def test_evaluate_objective_function_no_movement(self): """The result of this test must be the same value as testing the MJ3h function. Translation is 0 and Quaternion [1,0,0,0] means no rotation. """ atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPElig.pdb') ligand = Complex(chains, atoms) adapter = MJ3hAdapter(self.receptor, ligand) scoring_function = MJ3h() coordinates = Coordinates([0.,0.,0.,1.,0.,0.,0.]) landscape_position = DockingLandscapePosition(scoring_function, coordinates, adapter.receptor_model, adapter.ligand_model) assert_almost_equal(2.02, landscape_position.evaluate_objective_function())
def test_calculate_starting_points_no_need_to_minimize(self): atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPE_rec.pdb') receptor = Complex(chains, atoms) atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPE_lig.pdb') ligand = Complex(chains, atoms) # Move structures to origin receptor_center = receptor.center_of_coordinates() ligand_center = ligand.center_of_coordinates() receptor_translation = [-1.*c for c in receptor_center] ligand_translation = [-1.*c for c in ligand_center] receptor.translate(receptor_translation) ligand.translate(ligand_translation) poses = FTDockCoordinatesParser.get_list_of_poses(self.golden_data_path + '1PPE.ftdock', ligand_center) assert 10000 == len(poses) for i in range(5): assert self.quaternions[i] == poses[i].q for j in range(3): assert_almost_equal(self.translations[i][j], poses[i].translation[j])
def test_LightDockGSOBuilder_using_FromFileInitializer(self): builder = LightdockGSOBuilder() number_of_glowworms = 5 atoms, residues, chains = parse_complex_from_file( self.golden_data_path + '1PPErec.pdb') receptor = Complex(chains, atoms) atoms, residues, chains = parse_complex_from_file( self.golden_data_path + '1PPElig.pdb') ligand = Complex(chains, atoms) adapter = MJ3hAdapter(receptor, ligand) scoring_function = MJ3h() gso = builder.create_from_file( number_of_glowworms, self.random_number_generator, self.gso_parameters, [adapter], [scoring_function], self.bounding_box, self.golden_data_path + 'initial_positions_1PPE.txt', 0.5, 0.5, 0.5, False, 10, 10) assert 5 == gso.swarm.get_size() gso.report(self.test_path + 'report.out') assert filecmp.cmp( self.golden_data_path + 'report_lightdockbuilder.out', self.test_path + 'report.out')
def test_move_step_rot_full_step_trans_full(self): atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPElig.pdb') ligand = Complex(chains, atoms) adapter = MJ3hAdapter(self.receptor, ligand) scoring_function = MJ3h() coordinates1 = Coordinates([0.,0.,0.,1.,0.,0.,0.]) landscape_position1 = DockingLandscapePosition(scoring_function, coordinates1, adapter.receptor_model, adapter.ligand_model, step_translation=10.0) adapter2 = MJ3hAdapter(self.receptor, ligand) coordinates2 = Coordinates([10.,0.,0.,1.,0.,0.,0.]) landscape_position2 = DockingLandscapePosition(scoring_function, coordinates2, adapter2.receptor_model, adapter2.ligand_model) landscape_position1.move(landscape_position2) assert landscape_position1 == landscape_position2
def test_move_step_rot_full_step_trans_full(self): atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPElig.pdb') ligand = Complex(chains, atoms) adapter = MJ3hAdapter(self.receptor, ligand) scoring_function = MJ3h() coordinates1 = Coordinates([0.,0.,0.,1.,0.,0.,0.]) landscape_position1 = DockingLandscapePosition(scoring_function, coordinates1, adapter.receptor_model, adapter.ligand_model, step_translation=10.0) adapter2 = MJ3hAdapter(self.receptor, ligand) coordinates2 = Coordinates([10.,0.,0.,1.,0.,0.,0.]) landscape_position2 = DockingLandscapePosition(scoring_function, coordinates2, adapter2.receptor_model, adapter2.ligand_model) landscape_position1.move(landscape_position2) assert landscape_position1 == landscape_position2
def test_clone(self): atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPElig.pdb') ligand = Complex(chains, atoms) adapter = MJ3hAdapter(self.receptor, ligand) scoring_function = MJ3h() coordinates = Coordinates([0.,0.,0.,1.,0.,0.,0.]) landscape_position_1 = DockingLandscapePosition(scoring_function, coordinates, adapter.receptor_model, adapter.ligand_model) landscape_position_2 = landscape_position_1.clone() assert landscape_position_1.translation.all() == landscape_position_2.translation.all() assert landscape_position_1.rotation == landscape_position_2.rotation landscape_position_2.translation[0] = 5.0 assert_almost_equal(5.0, landscape_position_2.translation[0]) assert_almost_equal(0.0, landscape_position_1.translation[0])
def calculate_sasa(pdb_file): # Read PDB structure atoms, residues, chains = parse_complex_from_file(pdb_file) molecule = Complex(chains, atoms, structure_file_name=pdb_file) # Load parameters parameters = DesolvationParameters() x = [] y = [] z = [] atom_names = [] atom_radius = [] for atom in molecule.atoms: x.append(atom.x) y.append(atom.y) z.append(atom.z) atom_names.append("%-4s" % atom.name) if atom.residue_name == 'CYX': atom.residue_name = 'CYS' atom_radius.append(parameters.radius_per_atom[atom.residue_name + "-" + atom.name]) x = np.array(x) y = np.array(y) z = np.array(z) num_residues = len(molecule.residues) num_atoms = len(molecule.atoms) residue_ids = [residue.number for residue in molecule.residues] num_atoms_per_residue = [ len(residue.atoms) for residue in molecule.residues ] # Calculate SASA with ACCESS start_time = timeit.default_timer() res_atmarea, res_area, res_scarea = access.access1(num_residues, num_atoms, residue_ids, num_atoms_per_residue, atom_names, x, y, z, atom_radius, 1) elapsed = timeit.default_timer() - start_time return sum(res_atmarea), elapsed
def test_calculate_chi_angles(self): # Command in chimera: angle #0:28@n,ca,cb,sg atoms, residues, chains = parse_complex_from_file( self.golden_data_path + '1PPElig.pdb') protein = Complex(chains, atoms) for residue in protein.residues: if residue.name == 'ARG' and residue.number == 1: chi_angles = calculate_chi_angles(residue) for key, value in chi_angles.items(): if value: if key == 'x1': # angle #0:1@n,ca,cb,cg assert_almost_equals(-173.216, round(math.degrees(value), 3)) if key == 'x2': # angle #0:1@ca,cb,cg,cd assert_almost_equals(171.375, round(math.degrees(value), 3)) if key == 'x3': # angle #0:1@cb,cg,cd,ne assert_almost_equals(62.852, round(math.degrees(value), 3)) if key == 'x4': # angle #0:1@cg,cd,ne,cz assert_almost_equals(100.22, round(math.degrees(value), 2)) if residue.name == 'VAL' and residue.number == 2: # angle #0:2@n,ca,cb,cg1 chi_angles = calculate_chi_angles(residue) for key, value in chi_angles.items(): if value: if key == 'x1': # angle #0:1@n,ca,cb,cg assert_almost_equals(-173.629, round(math.degrees(value), 3)) if residue.name == 'CYS' and residue.number == 28: chi_angles = calculate_chi_angles(residue) for key, value in chi_angles.items(): if value: if key == 'x1': assert_almost_equals(-60.2554, round(math.degrees(value), 4))
def read_input_structure(pdb_file_name, ignore_oxt=True, ignore_hydrogens=False, verbose_parser=False): """Reads the input structure. The arguments pdb_file_name can be a PDB file or a file containing a list of PDB files. ignore_oxt flag avoids saving OXT atoms. """ atoms_to_ignore = [] if ignore_oxt: atoms_to_ignore.append('OXT') log.info('Ignoring OXT atoms') if ignore_hydrogens: atoms_to_ignore.append('H') log.info('Ignoring Hydrogen atoms') structures = [] file_names = [] file_name, file_extension = os.path.splitext(pdb_file_name) if file_extension == DEFAULT_LIST_EXTENSION: file_names.extend(get_pdb_files(pdb_file_name)) else: file_names.append(pdb_file_name) for file_name in file_names: log.info("Reading structure from %s PDB file..." % file_name) atoms, residues, chains = parse_complex_from_file( file_name, atoms_to_ignore, verbose_parser) structures.append({ 'atoms': atoms, 'residues': residues, 'chains': chains, 'file_name': file_name }) log.info("%s atoms, %s residues read." % (len(atoms), len(residues))) # Representatives are now the first structure, but this could change in the future structure = Complex.from_structures(structures) return structure
def test_distance2_minus_10A_translation_y(self): atoms, _, chains = parse_complex_from_file(self.golden_data_path / '1PPElig.pdb') ligand = Complex(chains, atoms) adapter = MJ3hAdapter(self.receptor, ligand) scoring_function = MJ3h() coordinates = Coordinates([0., 0., 0., 1., 0., 0., 0.]) landscape_position1 = DockingLandscapePosition(scoring_function, coordinates, adapter.receptor_model, adapter.ligand_model) adapter2 = MJ3hAdapter(self.receptor, ligand) adapter2.ligand_model.translate([0.0, -10.0, 0.0]) landscape_position2 = DockingLandscapePosition(scoring_function, coordinates, adapter2.receptor_model, adapter2.ligand_model) assert_almost_equal(100.0, landscape_position1.distance2(landscape_position2)) assert_almost_equal(10.0, landscape_position1.distance(landscape_position2))
def test_move_step_rot_full_step_trans_half(self): atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPElig.pdb') ligand = Complex(chains, atoms) adapter = TOBIAdapter(self.receptor, ligand) scoring_function = TOBI() coordinates1 = Coordinates([0.,0.,0.,1.,0.,0.,0.]) landscape_position1 = DockingLandscapePosition(scoring_function, coordinates1, adapter.receptor_model, adapter.ligand_model, step_translation=5.0) adapter2 = TOBIAdapter(self.receptor, ligand) coordinates2 = Coordinates([10.,0.,0.,1.,0.,0.,0.]) landscape_position2 = DockingLandscapePosition(scoring_function, coordinates2, adapter2.receptor_model, adapter2.ligand_model) landscape_position1.move(landscape_position2) expected_translation = np.array([5.,0.,0.]) expected_rotation = Quaternion() assert (expected_translation == landscape_position1.translation).all() assert expected_rotation == landscape_position1.rotation
def test_move_step_rot_full_step_trans_half(self): atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPElig.pdb') ligand = Complex(chains, atoms) adapter = TOBIAdapter(self.receptor, ligand) scoring_function = TOBI() coordinates1 = Coordinates([0.,0.,0.,1.,0.,0.,0.]) landscape_position1 = DockingLandscapePosition(scoring_function, coordinates1, adapter.receptor_model, adapter.ligand_model, step_translation=5.0) adapter2 = TOBIAdapter(self.receptor, ligand) coordinates2 = Coordinates([10.,0.,0.,1.,0.,0.,0.]) landscape_position2 = DockingLandscapePosition(scoring_function, coordinates2, adapter2.receptor_model, adapter2.ligand_model) landscape_position1.move(landscape_position2) expected_translation = np.array([5.,0.,0.]) expected_rotation = Quaternion() assert (expected_translation == landscape_position1.translation).all() assert expected_rotation == landscape_position1.rotation
def test_calculate_phi_psi(self): atoms, residues, chains = parse_complex_from_file( self.golden_data_path + '1PPElig.pdb') protein = Complex(chains, atoms) # psi: angle #0:1@n,ca,c #0:2@n # phi: angle #0:1@c #0:2@n,ca,c phi_angles = [ -105.92428251619579, -134.402235889132, -58.32268858533758, -85.62997439535678, -129.666484600813, -77.00076813772478, -142.09891098624075, -82.10672119029674, -163.14606891327375, -109.37900096123484, -138.72905680654182, -59.09699793329797, -60.06774387010816, -74.41030551527874, -99.82766540256617, -92.6495110068149, 54.969041241310705, -104.60151419194615, -67.57074855137641, -123.83574594954692, -85.90313254423194, -87.7781803331676, -66.345484249271, -64.51513795752882, 108.23656098935888, -129.62530277139578, -71.90658189461674, -170.4460918036806 ] psi_angles = [ 138.38576328505278, 105.22472788100255, 106.42882930892199, 150.65572151747787, 72.08329638522976, 130.19890858175336, 115.48238807519739, 132.48041144914038, 163.35191386073618, 151.17756189538443, -28.310569696143393, 162.66293554938997, -32.25480696024475, -20.28436719199857, -11.444789534534305, 163.38578466073147, 150.2534549328882, -128.53524744082424, 20.01260634937939, 151.96710290169335, 159.55519588393594, 115.07091589216549, 152.8911959270869, -24.04765297807205, -14.890186424782046, 15.86273088398991, 152.7552784042674, 146.11762131430552 ] for i in range(1, len(protein.residues)): phi, psi = calculate_phi_psi(protein.residues[i], protein.residues[i - 1]) assert_almost_equals(phi_angles[i - 1], math.degrees(phi)) assert_almost_equals(psi_angles[i - 1], math.degrees(psi))
def test_move_step_rot_half_step_trans_half_and_anm(self): atoms, _, chains = parse_complex_from_file(self.golden_data_path / '1PPElig.pdb') ligand = Complex(chains, atoms) adapter = MJ3hAdapter(self.receptor, ligand) scoring_function = MJ3h() coordinates1 = Coordinates( [0., 0., 0., 1., 0., 0., 0., 1., 1., 1., 1.]) landscape_position1 = DockingLandscapePosition(scoring_function, coordinates1, adapter.receptor_model, adapter.ligand_model, step_translation=5.0, step_rotation=0.5, step_nmodes=0.5, num_rec_nmodes=2, num_lig_nmodes=2) adapter2 = MJ3hAdapter(self.receptor, ligand) coordinates2 = Coordinates( [10., 0., 0., 0., 0., 1., 0., 0., 0., 0., 0.]) landscape_position2 = DockingLandscapePosition(scoring_function, coordinates2, adapter2.receptor_model, adapter2.ligand_model, num_rec_nmodes=2, num_lig_nmodes=2) landscape_position1.move(landscape_position2) expected_translation = np.array([5., 0., 0.]) expected_rotation = Quaternion(0.707106781, 0.0, 0.707106781, 0.0) expected_anm = np.array([0.64644661, 0.64644661]) assert np.allclose(expected_translation, landscape_position1.translation) assert expected_rotation == landscape_position1.rotation assert np.allclose(expected_anm, landscape_position1.rec_extent) assert np.allclose(expected_anm, landscape_position1.lig_extent)
def test_calculate_min_volume_ellipsoid(self): atoms, _, chains = parse_complex_from_file(self.golden_data_path + '1PPE_l_u.pdb') protein = Complex(chains, atoms) ellipsoid = MinimumVolumeEllipsoid( protein.atom_coordinates[0].coordinates) assert_almost_equal(5.79979144, ellipsoid.center[0]) assert_almost_equal(13.30609275, ellipsoid.center[1]) assert_almost_equal(6.28378695, ellipsoid.center[2]) assert_almost_equal(11.51000999, ellipsoid.radii[0]) assert_almost_equal(17.41300089, ellipsoid.radii[1]) assert_almost_equal(25.1317681, ellipsoid.radii[2]) assert_almost_equal(-0.64868458, ellipsoid.rotation[0][0]) assert_almost_equal(-0.43420895, ellipsoid.rotation[0][1]) assert_almost_equal(0.62503673, ellipsoid.rotation[0][2]) assert_almost_equal(0.75208829, ellipsoid.rotation[1][0]) assert_almost_equal(-0.49144928, ellipsoid.rotation[1][1]) assert_almost_equal(0.43913643, ellipsoid.rotation[1][2]) assert_almost_equal(0.11649688, ellipsoid.rotation[2][0]) assert_almost_equal(0.75494384, ellipsoid.rotation[2][1]) assert_almost_equal(0.64535903, ellipsoid.rotation[2][2]) expected_poles = [ [13.266157381855532, 18.303842059830465, -0.91039204503235993], [-1.6665744987943629, 8.3083434397316651, 13.477965942387469], [-7.296322648355452, 21.863699498711949, -1.3628961564119457], [18.89590553141662, 4.7484860008501819, 13.930470053767054], [2.8720188105117521, -5.6669806736857815, -9.9352265853089641], [8.7275640725494164, 32.279166173247916, 22.502800482664075] ] assert np.allclose(expected_poles, ellipsoid.poles, ERROR_TOLERANCE)
from lightdock.pdbutil.PDBIO import parse_complex_from_file from lightdock.structure.complex import Complex from lightdock.rotamer.predictor import get_interface_residues, calculate_chi_angles, steric_energy from lightdock.rotamer.library import InterfaceSurfaceLibrary def usage(): print("Usage: %s receptor.pdb ligand.pdb" % sys.argv[0]) if __name__ == "__main__": if len(sys.argv[1:]) != 2: usage() raise SystemExit('Wrong command line') atoms, residues, chains = parse_complex_from_file(sys.argv[1]) receptor = Complex(chains, atoms) atoms, residues, chains = parse_complex_from_file(sys.argv[2]) ligand = Complex(chains, atoms) adapter = DFIREAdapter(receptor, ligand) # 5A of cutoff to be in the same line as the ASA value used in the original paper receptor_residue_indexes, ligand_residue_indexes, dist_matrix, atom_indexes = get_interface_residues( adapter.receptor_model, adapter.ligand_model, max_cutoff=5.) rotamer_library = InterfaceSurfaceLibrary() print("%d receptor interface residues" % len(receptor_residue_indexes)) receptor_residues = [] for residue_index in receptor_residue_indexes: residue = receptor.residues[residue_index] chi_angles = calculate_chi_angles(residue)
def setUp(self): self.path = os.path.dirname(os.path.realpath(__file__)) self.golden_data_path = os.path.normpath(os.path.dirname(os.path.realpath(__file__))) + '/golden_data/' atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1PPErec.pdb') self.receptor = Complex(chains, atoms)
args = parse_command_line() atoms_to_ignore = [] if args.noxt: atoms_to_ignore.append('OXT') structures = [] file_names = [] file_name, file_extension = os.path.splitext(args.structure) if file_extension == DEFAULT_LIST_EXTENSION: file_names.extend(get_pdb_files(args.structure)) else: file_names.append(args.structure) for file_name in file_names: log.info("Reading %s PDB file..." % file_name) atoms, residues, chains = parse_complex_from_file( file_name, atoms_to_ignore) structures.append({ 'atoms': atoms, 'residues': residues, 'chains': chains, 'file_name': file_name }) log.info("%s atoms, %s residues read." % (len(atoms), len(residues))) molecule = Complex.from_structures(structures) try: ellipsoid = MinimumVolumeEllipsoid( molecule.atom_coordinates[0].coordinates) except MinimumVolumeEllipsoidError as e: log.error(
if len(coord) > 7: nm_rec = np.array( [float(x) for x in coord[7:7 + DEFAULT_NMODES_REC]]) nm_lig = np.array( [float(x) for x in coord[7:7 + DEFAULT_NMODES_LIG]]) return translation, q, nm_rec, nm_lig return None if __name__ == "__main__": # Parse arguments glowworm_id, num_steps, receptor_pdb, ligand_pdb = parse_command_line() # Read receptor log.info("Reading %s receptor PDB file..." % receptor_pdb) atoms, residues, chains = parse_complex_from_file(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..." % ligand_pdb) atoms, residues, chains = parse_complex_from_file(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(receptor_pdb)) nmodes_rec = read_nmodes( os.path.join(nm_path, DEFAULT_REC_NM_FILE + '.npy')) except: nmodes_rec = None
parser.add_argument("scoring_function", help="scoring function") parser.add_argument("receptor", help="PDB receptor") parser.add_argument("ligand", help="PDB ligand") script_args = parser.parse_args() return script_args if __name__ == "__main__": args = parse_command_line() try: scoring_function_module = "lightdock.scoring.%s.driver" % args.scoring_function module = importlib.import_module(scoring_function_module) except ImportError: raise SystemExit("Scoring function not found or not available") atoms, residues, chains = parse_complex_from_file(args.receptor) receptor = Complex(chains, atoms, structure_file_name=args.receptor) atoms, residues, chains = parse_complex_from_file(args.ligand) ligand = Complex(chains, atoms, structure_file_name=args.ligand) CurrentScoringFunction = getattr(module, "DefinedScoringFunction") CurrentModelAdapter = getattr(module, "DefinedModelAdapter") adapter = CurrentModelAdapter(receptor, ligand) scoring_function = CurrentScoringFunction() energy = scoring_function(adapter.receptor_model, adapter.receptor_model.coordinates[0], adapter.ligand_model, adapter.ligand_model.coordinates[0]) print(args.scoring_function, ': ', energy)
args = parse_command_line() atoms_to_ignore = [] if args.noxt: atoms_to_ignore.append('OXT') structures = [] file_names = [] file_name, file_extension = os.path.splitext(args.structure) if file_extension == DEFAULT_LIST_EXTENSION: file_names.extend(get_pdb_files(args.structure)) else: file_names.append(args.structure) for file_name in file_names: log.info("Reading %s PDB file..." % file_name) atoms, residues, chains = parse_complex_from_file(file_name, atoms_to_ignore) structures.append({'atoms': atoms, 'residues': residues, 'chains': chains, 'file_name': file_name}) log.info("%s atoms, %s residues read." % (len(atoms), len(residues))) molecule = Complex.from_structures(structures) try: ellipsoid = MinimumVolumeEllipsoid(molecule.atom_coordinates[0].coordinates) except MinimumVolumeEllipsoidError, e: log.error("Impossible to calculate minimum volume ellipsoid. Reason: %s" % str(e)) raise SystemExit("%s finished with error" % script_name) output_file_name = molecule.structure_file_names[0] + DEFAULT_REFERENCE_POINTS_EXTENSION with open(output_file_name, 'w') as output: for point in ellipsoid.poles: output.write(get_point_respresentation(point) + os.linesep) output.write(get_point_respresentation(ellipsoid.center) + os.linesep)
""" 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.")
starting_file = sys.argv[1] 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)
def test_parse_multi_model_from_file(self): atoms, residues, chains = parse_complex_from_file( self.golden_data_path / 'multi_model.pdb') assert len(atoms) == 11 assert len(residues) == 1 assert len(chains) == 1
""" 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.")
try: pdb_structure = sys.argv[1] n_modes = int(sys.argv[2]) factor = float(sys.argv[3]) except: usage() raise SystemExit("Wrong command line") protein = parsePDB(pdb_structure) ca_atoms = protein.select('name CA') protein_anm = ANM('protein ca') protein_anm.buildHessian(ca_atoms) protein_anm.calcModes(n_modes=n_modes) print 'Normal modes calculated' atoms, residues, chains = parse_complex_from_file(pdb_structure) lightdock_structures = [{'atoms': atoms, 'residues': residues, 'chains': chains, 'file_name': pdb_structure}] lightdock_structure = Complex.from_structures(lightdock_structures) print 'Structure read by lightdock' num_atoms_prody = len(protein.protein) num_atoms_lightdock = len(atoms) if num_atoms_prody != num_atoms_lightdock: raise SystemExit("Number of atoms is different") protein_anm_ext, protein_all = extendModel(protein_anm, ca_atoms, protein, norm=True) modes = [] for i in range(n_modes): nm = protein_anm_ext.getEigvecs()[:, i].reshape((num_atoms_lightdock, 3))
def test_parse_multi_model_from_file(self): atoms, residues, chains = parse_complex_from_file(self.golden_data_path + 'multi_model.pdb') assert 11 == len(atoms) assert 1 == len(residues) assert 1 == len(chains)
parser.add_argument("scoring_function", help="scoring function") parser.add_argument("receptor", help="PDB receptor") parser.add_argument("ligand", help="PDB ligand") script_args = parser.parse_args() return script_args if __name__ == "__main__": args = parse_command_line() try: scoring_function_module = "lightdock.scoring.%s.driver" % args.scoring_function module = importlib.import_module(scoring_function_module) except ImportError: raise SystemExit("Scoring function not found or not available") atoms, residues, chains = parse_complex_from_file(args.receptor) receptor = Complex(chains, atoms, structure_file_name=args.receptor) atoms, residues, chains = parse_complex_from_file(args.ligand) ligand = Complex(chains, atoms, structure_file_name=args.ligand) CurrentScoringFunction = getattr(module, "DefinedScoringFunction") CurrentModelAdapter = getattr(module, "DefinedModelAdapter") adapter = CurrentModelAdapter(receptor, ligand) scoring_function = CurrentScoringFunction() energy = scoring_function(adapter.receptor_model, adapter.receptor_model.coordinates[0], adapter.ligand_model, adapter.ligand_model.coordinates[0]) print args.scoring_function, ': ', energy
from lightdock.pdbutil.PDBIO import parse_complex_from_file from lightdock.structure.complex import Complex from lightdock.rotamer.predictor import get_interface_residues, calculate_chi_angles, steric_energy from lightdock.rotamer.library import InterfaceSurfaceLibrary def usage(): print "Usage: %s receptor.pdb ligand.pdb" % sys.argv[0] if __name__ == "__main__": if len(sys.argv[1:]) != 2: usage() raise SystemExit('Wrong command line') atoms, residues, chains = parse_complex_from_file(sys.argv[1]) receptor = Complex(chains, atoms) atoms, residues, chains = parse_complex_from_file(sys.argv[2]) ligand = Complex(chains, atoms) adapter = DFIREAdapter(receptor, ligand) # 5A of cutoff to be in the same line as the ASA value used in the original paper receptor_residue_indexes, ligand_residue_indexes, dist_matrix, atom_indexes = get_interface_residues(adapter.receptor_model, adapter.ligand_model, max_cutoff=5.) rotamer_library = InterfaceSurfaceLibrary() print "%d receptor interface residues" % len(receptor_residue_indexes) receptor_residues = [] for residue_index in receptor_residue_indexes: residue = receptor.residues[residue_index]
try: pdb_structure = sys.argv[1] n_modes = int(sys.argv[2]) factor = float(sys.argv[3]) except: usage() raise SystemExit("Wrong command line") protein = parsePDB(pdb_structure) ca_atoms = protein.select('name CA') protein_anm = ANM('protein ca') protein_anm.buildHessian(ca_atoms) protein_anm.calcModes(n_modes=n_modes) print('Normal modes calculated') atoms, residues, chains = parse_complex_from_file(pdb_structure) lightdock_structures = [{'atoms': atoms, 'residues': residues, 'chains': chains, 'file_name': pdb_structure}] lightdock_structure = Complex.from_structures(lightdock_structures) print('Structure read by lightdock') num_atoms_prody = len(protein.protein) num_atoms_lightdock = len(atoms) if num_atoms_prody != num_atoms_lightdock: raise SystemExit("Number of atoms is different") protein_anm_ext, protein_all = extendModel(protein_anm, ca_atoms, protein, norm=True) modes = [] for i in range(n_modes): nm = protein_anm_ext.getEigvecs()[:, i].reshape((num_atoms_lightdock, 3))