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))