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_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_PyDock_1AY7(self):
atoms, _, 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, _, 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_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 test_calculate_DNA_1AZP(self):
atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1azp_prot.pdb')
receptor = Complex(chains, atoms, structure_file_name=(self.golden_data_path + '1azp_prot.pdb'))
atoms, residues, chains = parse_complex_from_file(self.golden_data_path + '1azp_dna.pdb')
ligand = Complex(chains, atoms, structure_file_name=(self.golden_data_path + '1azp_dna.pdb'))
adapter = DDNAAdapter(receptor, ligand)
assert_almost_equal(6.915295143021656, self.dna(adapter.receptor_model, adapter.receptor_model.coordinates[0],
adapter.ligand_model, adapter.ligand_model.coordinates[0]))
def test_calculate_PISA_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 = PISAAdapter(receptor, ligand)
assert_almost_equal(-0.2141, round(self.pisa(adapter.receptor_model, adapter.receptor_model.coordinates[0],
adapter.ligand_model, adapter.ligand_model.coordinates[0]), 4))
def test_calculate_DFIRE2_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 = DFIRE2Adapter(receptor, ligand)
assert_almost_equal(-283.19129030999665, 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_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 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 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 __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_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_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_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_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_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_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_DFIRE_1EAW(self):
atoms, _, chains = parse_complex_from_file(self.golden_data_path /
'1EAWrec.pdb')
receptor = Complex(chains, atoms)
atoms, _, chains = parse_complex_from_file(self.golden_data_path /
'1EAWlig.pdb')
ligand = Complex(chains, atoms)
adapter = DFIREAdapter(receptor, ligand)
assert_almost_equal(
-16.2182794457,
self.dfire(adapter.receptor_model,
adapter.receptor_model.coordinates[0],
adapter.ligand_model,
adapter.ligand_model.coordinates[0]))
def test_calculate_TOBI_1EAW(self):
atoms, _, chains = parse_complex_from_file(self.golden_data_path /
'1EAWrec.pdb')
receptor = Complex(chains, atoms)
atoms, _, chains = parse_complex_from_file(self.golden_data_path /
'1EAWlig.pdb')
ligand = Complex(chains, atoms)
adapter = TOBIAdapter(receptor, ligand)
assert_almost_equal(
-11.22,
self.tobi(adapter.receptor_model,
adapter.receptor_model.coordinates[0],
adapter.ligand_model,
adapter.ligand_model.coordinates[0]))
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_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 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_calculate_FastDFIRE_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 = 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_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 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_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 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 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 __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_clone_complex(self):
protein1 = Complex(chains=self.chains)
protein2 = protein1.clone()
assert protein1.num_atoms == protein2.num_atoms
assert protein1.num_residues == protein2.num_residues
for atom1, atom2 in zip(protein1.atoms, protein2.atoms):
assert atom1 == atom2
assert protein1.atom_coordinates == protein2.atom_coordinates
for residue1, residue2 in zip(protein1.residues, protein2.residues):
assert residue1 == residue2
protein2.atoms[0].name = 'C'
for atom1, atom2 in zip(protein1.atoms[1:], protein2.atoms[1:]):
assert atom1 == atom2
assert protein1.atoms[0] != protein2.atoms[0]
def test_clone_complex(self):
protein1 = Complex(chains=self.chains)
protein2 = protein1.clone()
assert protein1.num_atoms == protein2.num_atoms
assert protein1.num_residues == protein2.num_residues
for atom1, atom2 in zip(protein1.atoms, protein2.atoms):
assert atom1 == atom2
assert protein1.atom_coordinates == protein2.atom_coordinates
for residue1, residue2 in zip(protein1.residues, protein2.residues):
assert residue1 == residue2
protein2.atoms[0].name = 'C'
for atom1, atom2 in zip(protein1.atoms[1:], protein2.atoms[1:]):
assert atom1 == atom2
assert protein1.atoms[0] != protein2.atoms[0]
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_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_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])
setup = get_setup_from_file(args.setup_file) if args.setup_file else None
num_anm_rec = DEFAULT_NMODES_REC
num_anm_lig = DEFAULT_NMODES_LIG
if setup and setup['use_anm']:
num_anm_rec = setup['anm_rec']
num_anm_lig = setup['anm_lig']
# Receptor
structures = []
for structure in get_lightdock_structures(args.receptor_structures):
log.info("Reading %s receptor PDB file..." % structure)
atoms, residues, chains = parse_complex_from_file(structure)
structures.append({'atoms': atoms, 'residues': residues, 'chains': chains, 'file_name': structure})
log.info("%s atoms, %s residues read." % (len(atoms), len(residues)))
receptor = Complex.from_structures(structures)
# Ligand
structures = []
for structure in get_lightdock_structures(args.ligand_structures):
log.info("Reading %s ligand PDB file..." % structure)
atoms, residues, chains = parse_complex_from_file(structure)
structures.append({'atoms': atoms, 'residues': residues, 'chains': chains, 'file_name': structure})
log.info("%s atoms, %s residues read." % (len(atoms), len(residues)))
ligand = Complex.from_structures(structures)
# Output file
translations, rotations, receptor_ids, ligand_ids, \
rec_extents, lig_extents = parse_output_file(args.lightdock_output, num_anm_rec, num_anm_lig)
found_conformations = len(translations)
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)
log.info('Points written to %s' % output_file_name)
points = [point for point in ellipsoid.poles]
points.append(ellipsoid.center)
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))
modes.append(nm)
def test_center_of_mass_empty_complex(self):
protein = Complex([])
com = protein.center_of_mass()
assert_almost_equals(0., com[0])
assert_almost_equals(0., com[1])
assert_almost_equals(0., com[2])
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.")
def test_center_of_mass(self):
protein = Complex(chains=self.chains)
com = protein.center_of_mass()
assert_almost_equals(1.8037228011238935, com[0])
assert_almost_equals(1.7998854581864723, com[1])
assert_almost_equals(1.7960481152490517, com[2])
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 test_center_of_coordinates(self):
protein = Complex(chains=self.chains)
cc = protein.center_of_coordinates()
assert_almost_equals(1.75, cc[0])
assert_almost_equals(1.75, cc[1])
assert_almost_equals(1.75, cc[2])
def test_center_of_coordinates_zero_atoms(self):
protein = Complex(chains=[])
cc = protein.center_of_coordinates()
assert_almost_equals(0.0, cc[0])
assert_almost_equals(0.0, cc[1])
assert_almost_equals(0.0, cc[2])
