def test_calculate_PISA_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 = PISAAdapter(receptor, ligand)
assert_almost_equal(
-0.2097,
round(
self.pisa(adapter.receptor_model,
adapter.receptor_model.coordinates[0],
adapter.ligand_model,
adapter.ligand_model.coordinates[0]), 4))
def __init__(self):
self.path = Path(__file__).absolute().parent
self.test_path = self.path / 'scratch_docking_landscape'
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)
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)
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)
parameters = DesolvationParameters()
# Lightdock structure to freesasa structure
structure = Structure()
for atom in molecule.atoms:
structure.addAtom(atom.name, atom.residue_name, atom.residue_number,
atom.chain_id, atom.x, atom.y, atom.z)
atom_names = []
atom_radius = []
for atom in molecule.atoms:
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])
structure.setRadii(atom_radius)
start_time = timeit.default_timer()
result = freesasa.calc(structure)
elapsed = timeit.default_timer() - start_time
return result.totalArea(), elapsed
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_null_rotation(self):
protein = Complex(chains=self.chains2)
q = Quaternion()
protein.rotate(q)
write_pdb_to_file(protein, self.test_path + 'rotated.pdb',
protein.atom_coordinates[0])
assert filecmp.cmp(self.golden_data_path + 'two_residues.pdb',
self.test_path + 'rotated.pdb')
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)
def test_calculate_initial_poses(self):
atoms, residues, chains = parse_complex_from_file(
os.path.join(self.golden_data_path, '3p0g',
'receptor_membrane.pdb'))
receptor = Complex(chains)
atoms, residues, chains = parse_complex_from_file(
os.path.join(self.golden_data_path, '3p0g', 'ligand.pdb'))
ligand = Complex(chains)
rec_translation = receptor.move_to_origin()
lig_translation = ligand.move_to_origin()
num_swarms = 10
num_glowworms = 10
seed = 324324
restraints = parse_restraints_file(
os.path.join(self.golden_data_path, '3p0g', 'restraints.list'))
receptor_restraints = get_restraints(receptor, restraints['receptor'])
ligand_restraints = get_restraints(ligand, restraints['ligand'])
rec_restraints = receptor_restraints['active'] + receptor_restraints[
'passive']
lig_restraints = ligand_restraints['active'] + ligand_restraints[
'passive']
positions_files = calculate_initial_poses(receptor,
ligand,
num_swarms,
num_glowworms,
seed,
rec_restraints,
lig_restraints,
rec_translation,
lig_translation,
dest_folder=self.test_path,
is_membrane=True)
assert filecmp.cmp(
positions_files[0],
os.path.join(self.golden_data_path, '3p0g', 'init',
'initial_positions_0.dat'))
assert filecmp.cmp(
positions_files[1],
os.path.join(self.golden_data_path, '3p0g', 'init',
'initial_positions_1.dat'))
def test_calculate_starting_points(self):
# Receptor
file_name = self.golden_data_path / '1PPE_rec.pdb'
atoms, _, chains = parse_complex_from_file(file_name)
receptor = Complex(chains, atoms, structure_file_name=file_name)
# Ligand
file_name = self.golden_data_path / '1PPE_lig.pdb'
atoms, _, chains = parse_complex_from_file(file_name)
ligand = Complex(chains, atoms, structure_file_name=file_name)
starting_points, rec_diameter, lig_diameter = calculate_surface_points(receptor, ligand, 50, [0.,0.,0.], 50.)
assert_almost_equal(rec_diameter, 50.213210831413676)
assert_almost_equal(lig_diameter, 27.855559534857672)
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_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_calculate_anm_dna(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)
expected_nmodes = read_nmodes(self.golden_data_path / 'nm_dna' / 'lightdock_lig.nm.npy')
assert np.allclose(expected_nmodes, nmodes)
def test_calculate_anm_protein_2(self):
pdb_file = self.golden_data_path / 'nm_prot' / '2UUY_rec.pdb'
_, _, chains = parse_complex_from_file(pdb_file)
molecule = Complex(chains)
nmodes = calculate_nmodes(pdb_file, n_modes=10, molecule=molecule)
expected_nmodes = read_nmodes(self.golden_data_path / 'nm_prot' / 'lightdock_rec.nm.npy')
assert np.allclose(expected_nmodes, nmodes)
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_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_DNA_3MFK(self):
atoms, _, chains = parse_complex_from_file(self.golden_data_path /
'3mfk_homodimer.pdb')
receptor = Complex(chains,
atoms,
structure_file_name=(self.golden_data_path /
'3mfk_homodimer.pdb'))
atoms, _, 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(
-2716.68018700585,
self.dna(adapter.receptor_model,
adapter.receptor_model.coordinates[0],
adapter.ligand_model,
adapter.ligand_model.coordinates[0]))
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 test_calculate_DNA_3MFK_with_hydrogens(self):
atoms, _, 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, _t, 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_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_create_complex_only_with_chains(self):
protein = Complex(chains=self.chains)
expected_coordinates = np.array([[1, 1, 1], [2, 2, 2], [1.1, 1.2, 1.3],
[2.9, 2.8, 2.7]])
assert 4 == protein.num_atoms
assert 2 == protein.num_residues
assert (expected_coordinates == protein.atom_coordinates).all()
for expected_index, atom in enumerate(protein.atoms):
assert expected_index == atom.index
def test_write_pdb_to_file(self):
atoms, _, 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 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_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_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_translate(self):
atom1 = Atom(2, 'C', '', 'A', 'ALA', x=2., y=2., z=2.)
atom2 = Atom(2, 'C', '', 'A', 'ALA', x=0., y=0., z=0.)
residue = Residue('ALA', 1, [atom1, atom2])
chains = [Chain('A', [residue])]
protein = Complex(chains)
com = protein.center_of_mass()
protein.translate([c * -1 for c in com])
expected_coordinates = np.array([[1, 1, 1], [-1, -1, -1]])
assert (expected_coordinates == protein.atom_coordinates).all()
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_rotation_180_degrees_y_axis_origin_is_0(self):
"""Expected file has been generated with Chimera fixing the rotation to the
center of coordinates and modifying the column of atom name to have the
same padding as the write_pdb_file function.
"""
protein = Complex(chains=self.chains2)
q = Quaternion(0, 0.0, 1.0, 0)
protein.rotate(q)
write_pdb_to_file(protein, self.test_path + 'rotated.pdb',
protein.atom_coordinates[0])
assert filecmp.cmp(self.golden_data_path + 'two_residues_y_180.pdb',
self.test_path + 'rotated.pdb')
def test_move_to_origin(self):
atom1 = Atom(2, 'C', '', 'A', 'ALA', x=0., y=0., z=0.)
atom2 = Atom(2, 'C', '', 'A', 'ALA', x=2., y=2., z=2.)
atom3 = Atom(2, 'C', '', 'A', 'ALA', x=4., y=4., z=4.)
residue = Residue('ALA', 1, [atom1, atom2, atom3])
chains = [Chain('A', [residue])]
protein = Complex(chains)
protein.move_to_origin()
expected_coordinates = np.array([[-2., -2., -2.], [0, 0, 0],
[2., 2., 2.]])
assert (expected_coordinates == protein.atom_coordinates).all()
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_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')
