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_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_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)