def test_move_step_rot_half_step_trans_half(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=5.0,
step_rotation=0.5)
adapter2 = MJ3hAdapter(self.receptor, ligand)
coordinates2 = Coordinates([10., 0., 0., 0., 0., 1., 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(0.707106781, 0.0, 0.707106781, 0.0)
assert (expected_translation == landscape_position1.translation).all()
assert expected_rotation == landscape_position1.rotation
def test_distance2_10A_translation_x(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)
adapter2 = MJ3hAdapter(self.receptor, ligand)
adapter2.ligand_model.translate([10.0, 0.0, 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_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 __init__(self):
self.path = Path(__file__).absolute().parent
self.golden_data_path = self.path / 'golden_data'
atoms, _, chains = parse_complex_from_file(self.golden_data_path /
'1PPErec.pdb')
self.receptor = Complex(chains, atoms)
atoms, _, 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_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_repr(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 = 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 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_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_MJ3h_1AY7(self):
atoms, _, chains = parse_complex_from_file(self.golden_data_path /
'1AY7rec.pdb')
receptor = Complex(chains, atoms)
atoms, _, chains = parse_complex_from_file(self.golden_data_path /
'1AY7lig.pdb')
ligand = Complex(chains, atoms)
adapter = MJ3hAdapter(receptor, ligand)
assert_almost_equal(
-12.92,
self.mj3h(adapter.receptor_model,
adapter.receptor_model.coordinates[0],
adapter.ligand_model,
adapter.ligand_model.coordinates[0]))
def test_create_adapter(self):
atoms, _, chains = parse_complex_from_file(self.golden_data_path /
'1PPErec.pdb')
receptor = Complex(chains, atoms)
atoms, _, chains = parse_complex_from_file(self.golden_data_path /
'1PPElig.pdb')
ligand = Complex(chains, atoms)
adapter = MJ3hAdapter(receptor, ligand)
assert adapter.receptor_model.coordinates[0].coordinates.shape == (223,
3)
assert adapter.ligand_model.coordinates[0].coordinates.shape == (29, 3)
assert len(adapter.receptor_model.objects) == 223
assert len(adapter.ligand_model.objects) == 29
def test_calculate_MJ3h_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 = MJ3hAdapter(receptor, ligand)
assert_almost_equal(
-4.22,
self.mj3h(adapter.receptor_model,
adapter.receptor_model.coordinates[0],
adapter.ligand_model,
adapter.ligand_model.coordinates[0]))
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_distance2_same_landscape_position(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)
landscape_position2 = DockingLandscapePosition(scoring_function,
coordinates,
adapter.receptor_model,
adapter.ligand_model)
assert_almost_equal(0.0,
landscape_position1.distance2(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 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')