def test_rmsd():
# pick one molecule from docked poses
mols = list(
oddt.toolkit.readfile(
'sdf',
os.path.join(test_data_dir, 'data/dude/xiap/actives_docked.sdf')))
mols = list(filter(lambda x: x.title == '312335', mols))
res = {
'method=None': [
4.7536, 2.5015, 2.7942, 1.1282, 0.7444, 1.6257, 4.7625, 2.7168,
2.5504, 1.9304, 2.6201, 3.1742, 3.2254, 4.7785, 4.8035, 7.8963,
2.2385, 4.8625, 3.2037
],
'method=hungarian': [
0.9013, 1.0730, 1.0531, 1.0286, 0.7353, 1.4094, 0.5391, 1.3297,
1.0881, 1.7796, 2.6064, 3.1577, 3.2135, 0.8126, 1.2909, 2.5217,
2.0836, 1.8325, 3.1874
],
'method=min_symmetry': [
0.9013, 1.0732, 1.0797, 1.0492, 0.7444, 1.6257, 0.5391, 1.5884,
1.0935, 1.9304, 2.6201, 3.1742, 3.2254, 1.1513, 1.5206, 2.5361,
2.2385, 1.971, 3.2037
],
}
kwargs_grid = [{
'method': None
}, {
'method': 'hungarian'
}, {
'method': 'min_symmetry'
}]
for kwargs in kwargs_grid:
res_key = '_'.join('%s=%s' % (k, v) for k, v in sorted(kwargs.items()))
assert_array_almost_equal(
[rmsd(mols[0], mol, **kwargs) for mol in mols[1:]],
res[res_key],
decimal=4)
# test shuffled rmsd
for _ in range(5):
for kwargs in kwargs_grid:
# dont use method=None in shuffled tests
if kwargs['method'] is None:
continue
res_key = '_'.join('%s=%s' % (k, v)
for k, v in sorted(kwargs.items()))
assert_array_almost_equal([
rmsd(mols[0], shuffle_mol(mol), **kwargs) for mol in mols[1:]
],
res[res_key],
decimal=4)
def test_rmsd_errors():
mol = oddt.toolkit.readstring('smi', 'c1ccccc1')
mol.make3D()
mol.addh()
mol2 = next(oddt.toolkit.readfile('sdf', os.path.join(test_data_dir, 'data/dude/xiap/actives_docked.sdf')))
for method in [None, 'hungarian', 'min_symmetry']:
with pytest.raises(ValueError, match='Unequal number of atoms'):
rmsd(mol, mol2, method=method)
for _ in range(5):
with pytest.raises(ValueError, match='Unequal number of atoms'):
rmsd(shuffle_mol(mol), shuffle_mol(mol2), method=method)
def test_rmsd_errors():
mol = oddt.toolkit.readstring('smi', 'c1ccccc1')
mol.make3D()
mol.addh()
mol2 = next(
oddt.toolkit.readfile(
'sdf',
os.path.join(test_data_dir, 'data/dude/xiap/actives_docked.sdf')))
for method in [None, 'hungarian', 'min_symmetry']:
with pytest.raises(ValueError, match='Unequal number of atoms'):
rmsd(mol, mol2, method=method)
for _ in range(5):
with pytest.raises(ValueError, match='Unequal number of atoms'):
rmsd(shuffle_mol(mol), shuffle_mol(mol2), method=method)
def test_diverse_conformers():
# FIXME: make toolkit a module so we can import from it
diverse_conformers_generator = oddt.toolkit.diverse_conformers_generator
mol = oddt.toolkit.readstring(
"smi",
"CN1CCN(S(=O)(C2=CC=C(OCC)C(C3=NC4=C(N(C)N=C4CCC)C(N3)=O)=C2)=O)CC1")
mol.make3D()
if oddt.toolkit.backend == 'ob' and oddt.toolkit.__version__ < '2.4.0':
assert_raises(NotImplementedError, diverse_conformers_generator, mol)
return None # skip test for older OB
res = []
for conf in diverse_conformers_generator(mol, seed=123456):
res.append(rmsd(mol, conf))
assert_equal(len(res), 10)
if oddt.toolkit.backend == 'ob':
assert_array_almost_equal(res, [
0., 3.043712, 3.897143, 3.289482, 3.066374, 2.909683, 2.913927,
3.488244, 3.70603, 3.597467
])
# else:
# if oddt.toolkit.__version__ > '2016.03.9':
# assert_array_almost_equal(res, [1.237538, 2.346984, 0.900624,
# 3.469511, 1.886213, 2.128909,
# 2.852608, 1.312513, 1.291595,
# 1.326843])
# else:
# assert_array_almost_equal(res, [3.08995, 2.846358, 3.021795,
# 1.720319, 2.741972, 2.965332,
# 2.925344, 2.930157, 2.934049,
# 3.009545])
# check all implemented methods
if oddt.toolkit.backend == 'ob':
methods = ['ga', 'confab']
else:
methods = ['dg', 'etkdg', 'kdg', 'etdg']
for method in methods:
assert_equal(
len(
diverse_conformers_generator(mol,
seed=123456,
n_conf=5,
method=method)), 5)
assert_equal(
len(
diverse_conformers_generator(mol,
seed=123456,
n_conf=10,
method=method)), 10)
assert_equal(
len(
diverse_conformers_generator(mol,
seed=123456,
n_conf=20,
method=method)), 20)
def test_spatial():
"""Test spatial misc computations"""
mol = oddt.toolkit.readstring('smi', 'c1ccccc1')
mol.make3D()
mol2 = mol.clone
# Test rotation
assert_almost_equal(mol2.coords, rotate(mol2.coords, np.pi, np.pi, np.pi))
# Rotate perpendicular to ring
mol2.coords = rotate(mol2.coords, 0, 0, np.pi)
# RMSD
assert_almost_equal(rmsd(mol, mol2, method=None), 2.77, decimal=1)
# Hungarian must be close to zero (RDKit is 0.3)
assert_almost_equal(rmsd(mol, mol2, method='hungarian'), 0, decimal=0)
# Minimized by symetry must close to zero
assert_almost_equal(rmsd(mol, mol2, method='min_symmetry'), 0, decimal=0)
def test_spatial():
"""Test spatial misc computations"""
mol = oddt.toolkit.readstring('smi', 'c1ccccc1')
mol.make3D()
mol2 = mol.clone
# Test rotation
assert_almost_equal(mol2.coords, rotate(mol2.coords, np.pi, np.pi, np.pi))
# Rotate perpendicular to ring
mol2.coords = rotate(mol2.coords, 0, 0, np.pi)
# RMSD
assert_almost_equal(rmsd(mol, mol2, method=None), 2.77, decimal=1)
# Hungarian must be close to zero (RDKit is 0.3)
assert_almost_equal(rmsd(mol, mol2, method='hungarian'), 0, decimal=0)
# Minimized by symetry must close to zero
assert_almost_equal(rmsd(mol, mol2, method='min_symmetry'), 0, decimal=0)
def test_diverse_conformers():
# FIXME: make toolkit a module so we can import from it
diverse_conformers_generator = oddt.toolkit.diverse_conformers_generator
mol = oddt.toolkit.readstring(
'smi',
'CN1CCN(S(=O)(C2=CC=C(OCC)C(C3=NC4=C(N(C)N=C4CCC)C(N3)=O)=C2)=O)CC1')
mol.make3D()
res = []
for conf in diverse_conformers_generator(mol, seed=123456):
res.append(rmsd(mol, conf))
assert len(res) == 10
if oddt.toolkit.backend == 'ob':
if oddt.toolkit.__version__ < '0.3':
assert_array_almost_equal(res, [
0., 3.043712, 3.897143, 3.289482, 3.066374, 2.909683, 2.913927,
3.488244, 3.70603, 3.597467
])
else:
assert_array_almost_equal(res, [
0.0, 1.372770, 2.489789, 2.759941, 2.968366, 3.228773,
3.392191, 3.921166, 3.185065, 3.283915
])
# else:
# if oddt.toolkit.__version__ > '2016.03.9':
# assert_array_almost_equal(res, [1.237538, 2.346984, 0.900624,
# 3.469511, 1.886213, 2.128909,
# 2.852608, 1.312513, 1.291595,
# 1.326843])
# else:
# assert_array_almost_equal(res, [3.08995, 2.846358, 3.021795,
# 1.720319, 2.741972, 2.965332,
# 2.925344, 2.930157, 2.934049,
# 3.009545])
# check all implemented methods
if oddt.toolkit.backend == 'ob':
methods = ['ga', 'confab']
else:
methods = ['dg', 'etkdg', 'kdg', 'etdg']
for method in methods:
assert len(
diverse_conformers_generator(mol,
seed=123456,
n_conf=5,
method=method)) == 5
assert len(
diverse_conformers_generator(mol,
seed=123456,
n_conf=10,
method=method)) == 10
assert len(
diverse_conformers_generator(mol,
seed=123456,
n_conf=20,
method=method)) == 20
def test_rmsd():
# pick one molecule from docked poses
mols = list(oddt.toolkit.readfile('sdf', os.path.join(test_data_dir, 'data/dude/xiap/actives_docked.sdf')))
mols = list(filter(lambda x: x.title == '312335', mols))
res = {
'method=None':
[4.7536, 2.5015, 2.7942, 1.1282, 0.7444, 1.6257, 4.7625,
2.7168, 2.5504, 1.9304, 2.6201, 3.1742, 3.2254, 4.7785,
4.8035, 7.8963, 2.2385, 4.8625, 3.2037],
'method=hungarian':
[0.9013, 1.0730, 1.0531, 1.0286, 0.7353, 1.4094, 0.5391,
1.3297, 1.0881, 1.7796, 2.6064, 3.1577, 3.2135, 0.8126,
1.2909, 2.5217, 2.0836, 1.8325, 3.1874],
'method=min_symmetry':
[0.9013, 1.0732, 1.0797, 1.0492, 0.7444, 1.6257, 0.5391,
1.5884, 1.0935, 1.9304, 2.6201, 3.1742, 3.2254, 1.1513,
1.5206, 2.5361, 2.2385, 1.971, 3.2037],
}
kwargs_grid = [{'method': None},
{'method': 'hungarian'},
{'method': 'min_symmetry'}]
for kwargs in kwargs_grid:
res_key = '_'.join('%s=%s' % (k, v)
for k, v in sorted(kwargs.items()))
assert_array_almost_equal([rmsd(mols[0], mol, **kwargs)
for mol in mols[1:]],
res[res_key], decimal=4)
# test shuffled rmsd
for _ in range(5):
for kwargs in kwargs_grid:
# dont use method=None in shuffled tests
if kwargs['method'] is None:
continue
res_key = '_'.join('%s=%s' % (k, v)
for k, v in sorted(kwargs.items()))
assert_array_almost_equal([rmsd(mols[0],
shuffle_mol(mol),
**kwargs)
for mol in mols[1:]],
res[res_key], decimal=4)
def test_diverse_conformers():
# FIXME: make toolkit a module so we can import from it
diverse_conformers_generator = oddt.toolkit.diverse_conformers_generator
mol = oddt.toolkit.readstring(
'smi',
'CN1CCN(S(=O)(C2=CC=C(OCC)C(C3=NC4=C(N(C)N=C4CCC)C(N3)=O)=C2)=O)CC1'
)
mol.make3D()
if oddt.toolkit.backend == 'ob' and oddt.toolkit.__version__ < '2.4.0':
with pytest.raises(NotImplementedError):
diverse_conformers_generator(mol)
return None # skip test for older OB
res = []
for conf in diverse_conformers_generator(mol, seed=123456):
res.append(rmsd(mol, conf))
assert len(res) == 10
if oddt.toolkit.backend == 'ob':
assert_array_almost_equal(res, [0., 3.043712, 3.897143, 3.289482,
3.066374, 2.909683, 2.913927,
3.488244, 3.70603, 3.597467])
# else:
# if oddt.toolkit.__version__ > '2016.03.9':
# assert_array_almost_equal(res, [1.237538, 2.346984, 0.900624,
# 3.469511, 1.886213, 2.128909,
# 2.852608, 1.312513, 1.291595,
# 1.326843])
# else:
# assert_array_almost_equal(res, [3.08995, 2.846358, 3.021795,
# 1.720319, 2.741972, 2.965332,
# 2.925344, 2.930157, 2.934049,
# 3.009545])
# check all implemented methods
if oddt.toolkit.backend == 'ob':
methods = ['ga', 'confab']
else:
methods = ['dg', 'etkdg', 'kdg', 'etdg']
for method in methods:
assert len(diverse_conformers_generator(mol,
seed=123456,
n_conf=5,
method=method)) == 5
assert len(diverse_conformers_generator(mol,
seed=123456,
n_conf=10,
method=method)) == 10
assert len(diverse_conformers_generator(mol,
seed=123456,
n_conf=20,
method=method)) == 20
def test_spatial():
"""Test spatial misc computations"""
mol = oddt.toolkit.readstring('smi', 'c1ccccc1')
mol.make3D()
mol2 = mol.clone
# Test rotation
assert_almost_equal(mol2.coords, rotate(mol2.coords, np.pi, np.pi, np.pi))
# Rotate perpendicular to ring
mol2.coords = rotate(mol2.coords, 0, 0, np.pi)
# RMSD
assert_almost_equal(rmsd(mol, mol2, method=None), 2.77, decimal=1)
# Hungarian must be close to zero (RDKit is 0.3)
assert_almost_equal(rmsd(mol, mol2, method='hungarian'), 0, decimal=0)
# pick one molecule from docked poses
mols = list(
oddt.toolkit.readfile(
'sdf',
os.path.join(test_data_dir, 'data/dude/xiap/actives_docked.sdf')))
mols = list(filter(lambda x: x.title == '312335', mols))
assert_array_almost_equal([rmsd(mols[0], mol) for mol in mols[1:]], [
4.753552, 2.501487, 2.7941732, 1.1281863, 0.74440968, 1.6256877,
4.762476, 2.7167852, 2.5504358, 1.9303833, 2.6200771, 3.1741529,
3.225431, 4.7784939, 4.8035369, 7.8962774, 2.2385094, 4.8625236,
3.2036853
])
assert_array_almost_equal(
[rmsd(mols[0], mol, method='hungarian') for mol in mols[1:]], [
0.90126, 1.073049, 1.053131, 1.028578, 0.735297, 1.409403,
0.539091, 1.329666, 1.088053, 1.779618, 2.606429, 3.157684,
3.213502, 0.812635, 1.290902, 2.521703, 2.083612, 1.832457,
3.187363
])
def test_vs_docking():
"""VS docking (Vina) tests"""
vs = virtualscreening(n_cpu=1)
vs.load_ligands('sdf', xiap_crystal_ligand)
# bad docking engine
with pytest.raises(ValueError):
vs.dock('srina', 'prot.pdb')
vs.dock(engine='autodock_vina',
protein=xiap_protein,
auto_ligand=xiap_crystal_ligand,
exhaustiveness=1,
energy_range=6,
num_modes=7,
size=(20, 20, 20),
seed=0)
mols = list(vs.fetch())
assert len(mols) == 7
mol_data = mols[0].data
assert 'vina_affinity' in mol_data
assert 'vina_rmsd_lb' in mol_data
assert 'vina_rmsd_ub' in mol_data
if oddt.toolkit.backend == 'ob':
vina_scores = [-5.3, -4.0, -3.8, -3.7, -3.4, -3.4, -3.0]
else:
vina_scores = [-6.3, -6.0, -5.8, -5.8, -3.9, -3.0, -1.1]
assert_array_equal([float(m.data['vina_affinity']) for m in mols],
vina_scores)
# verify the SMILES of molecules
ref_mol = next(oddt.toolkit.readfile('sdf', xiap_crystal_ligand))
if oddt.toolkit.backend == 'ob':
# OB 2.3.2 will fail the following, since Hs are removed, etc.
# OB 2.4 recognizes the smiles chirality wrong
pass
else:
vina_rmsd = [
8.153314, 5.32554, 8.514586, 8.510169, 9.060128, 8.995098, 8.626776
]
assert_array_equal([mol.smiles for mol in mols],
[ref_mol.smiles] * len(mols))
assert_array_almost_equal(
[rmsd(ref_mol, mol, method='min_symmetry') for mol in mols],
vina_rmsd)
def test_vs_docking():
"""VS docking (Vina) tests"""
vs = virtualscreening(n_cpu=1)
vs.load_ligands('sdf', xiap_crystal_ligand)
# bad docking engine
with pytest.raises(ValueError):
vs.dock('srina', 'prot.pdb')
vs.dock(engine='autodock_vina',
protein=xiap_protein,
auto_ligand=xiap_crystal_ligand,
exhaustiveness=1,
energy_range=6,
num_modes=7,
size=(20, 20, 20),
seed=0)
mols = list(vs.fetch())
assert len(mols) == 7
mol_data = mols[0].data
assert 'vina_affinity' in mol_data
assert 'vina_rmsd_lb' in mol_data
assert 'vina_rmsd_ub' in mol_data
if oddt.toolkit.backend == 'ob':
vina_scores = [-5.3, -4.0, -3.8, -3.7, -3.4, -3.4, -3.0]
else:
vina_scores = [-6.3, -6.0, -5.8, -5.8, -3.9, -3.0, -1.1]
assert_array_equal([float(m.data['vina_affinity']) for m in mols], vina_scores)
# verify the SMILES of molecules
ref_mol = next(oddt.toolkit.readfile('sdf', xiap_crystal_ligand))
if oddt.toolkit.backend == 'ob':
# OB 2.3.2 will fail the following, since Hs are removed, etc.
# OB 2.4 recognizes the smiles chirality wrong
pass
else:
vina_rmsd = [8.153314, 5.32554, 8.514586, 8.510169, 9.060128, 8.995098,
8.626776]
assert_array_equal([mol.smiles for mol in mols],
[ref_mol.smiles] * len(mols))
assert_array_almost_equal([rmsd(ref_mol, mol, method='min_symmetry')
for mol in mols], vina_rmsd)
def test_spatial():
"""Test spatial computations"""
# Angles
assert_array_almost_equal(angle(np.array((1, 0, 0)),
np.array((0, 0, 0)),
np.array((0, 1, 0))), 90)
assert_array_almost_equal(angle(np.array((1, 0, 0)),
np.array((0, 0, 0)),
np.array((1, 1, 0))), 45)
mol = oddt.toolkit.readstring('smi', 'c1ccccc1')
mol.make3D()
# Check benzene ring angle
assert_array_almost_equal(angle(mol.coords[0],
mol.coords[1],
mol.coords[2]), 120, decimal=1)
# Dihedrals
assert_array_almost_equal(dihedral(np.array((1, 0, 0)),
np.array((0, 0, 0)),
np.array((0, 1, 0)),
np.array((1, 1, 0))), 0)
assert_array_almost_equal(dihedral(np.array((1, 0, 0)),
np.array((0, 0, 0)),
np.array((0, 1, 0)),
np.array((1, 1, 1))), -45)
# Check benzene ring dihedral
assert_array_almost_equal(dihedral(mol.coords[0],
mol.coords[1],
mol.coords[2],
mol.coords[3]), 0, decimal=1)
mol = oddt.toolkit.readstring('smi', 'c1ccccc1')
mol.make3D()
mol2 = mol.clone
# Test rotation
assert_almost_equal(mol2.coords, rotate(mol2.coords, np.pi, np.pi, np.pi))
# Rotate perpendicular to ring
mol2.coords = rotate(mol2.coords, 0, 0, np.pi)
# RMSD
assert_almost_equal(rmsd(mol, mol2, method=None), 2.77, decimal=1)
# Hungarian must be close to zero (RDKit is 0.3)
assert_almost_equal(rmsd(mol, mol2, method='hungarian'), 0, decimal=0)
# pick one molecule from docked poses
mols = list(oddt.toolkit.readfile('sdf', os.path.join(test_data_dir, 'data/dude/xiap/actives_docked.sdf')))
mols = list(filter(lambda x: x.title == '312335', mols))
assert_array_almost_equal([rmsd(mols[0], mol) for mol in mols[1:]],
[4.753552, 2.501487, 2.7941732, 1.1281863, 0.74440968,
1.6256877, 4.762476, 2.7167852, 2.5504358, 1.9303833,
2.6200771, 3.1741529, 3.225431, 4.7784939, 4.8035369,
7.8962774, 2.2385094, 4.8625236, 3.2036853])
assert_array_almost_equal([rmsd(mols[0], mol, method='hungarian') for mol in mols[1:]],
[2.5984519, 1.7295024, 1.1268076, 1.0285776, 0.73529714,
1.4094033, 2.5195069, 1.7449125, 1.5116163, 1.7796179,
2.6064286, 3.1576841, 3.2135022, 3.1675091, 2.7001681,
5.1263351, 2.0836117, 3.542397, 3.1873631])
def dock(self, ligands, protein=None):
"""Automated docking procedure.
Parameters
----------
ligands: iterable of oddt.toolkit.Molecule objects
Ligands to dock
protein: oddt.toolkit.Molecule object or None
Protein object to be used. If None, then the default one
is used, else the protein is new default.
Returns
-------
ligands : array of oddt.toolkit.Molecule objects
Array of ligands (scores are stored in mol.data method)
"""
if protein:
self.set_protein(protein)
if not self.protein_file:
raise IOError("No receptor.")
if is_molecule(ligands):
ligands = [ligands]
ligand_dir = mkdtemp(dir=self.tmp_dir, prefix='ligands_')
output_array = []
for n, ligand in enumerate(ligands):
check_molecule(ligand, force_coords=True)
ligand_file = write_vina_pdbqt(ligand, ligand_dir, name_id=n)
ligand_outfile = ligand_file[:-6] + '_out.pdbqt'
try:
scores = parse_vina_docking_output(
subprocess.check_output([
self.executable, '--receptor', self.protein_file,
'--ligand', ligand_file, '--out', ligand_outfile
] + self.params + ['--cpu', str(self.n_cpu)],
stderr=subprocess.STDOUT))
except subprocess.CalledProcessError as e:
sys.stderr.write(e.output.decode('ascii'))
if self.skip_bad_mols:
continue # TODO: print some warning message
else:
raise Exception('Autodock Vina failed. Command: "%s"' %
' '.join(e.cmd))
# docked conformations may have wrong connectivity - use source ligand
if is_openbabel_molecule(ligand):
if oddt.toolkits.ob.__version__ >= '2.4.0':
# find the order of PDBQT atoms assigned by OpenBabel
with open(ligand_file) as f:
write_order = [
int(line[7:12].strip()) for line in f
if line[:4] == 'ATOM'
]
new_order = sorted(range(len(write_order)),
key=write_order.__getitem__)
new_order = [i + 1
for i in new_order] # OBMol has 1 based idx
assert len(new_order) == len(ligand.atoms)
else:
# Openbabel 2.3.2 does not support perserving atom order.
# We read back the PDBQT ligand to get "correct" bonding.
ligand = next(oddt.toolkit.readfile('pdbqt', ligand_file))
if 'REMARK' in ligand.data:
del ligand.data['REMARK']
docked_ligands = oddt.toolkit.readfile('pdbqt', ligand_outfile)
for docked_ligand, score in zip(docked_ligands, scores):
# Renumber atoms to match the input ligand
if (is_openbabel_molecule(docked_ligand)
and oddt.toolkits.ob.__version__ >= '2.4.0'):
docked_ligand.OBMol.RenumberAtoms(new_order)
# HACK: copy docked coordinates onto source ligand
# We assume that the order of atoms match between ligands
clone = ligand.clone
clone.clone_coords(docked_ligand)
clone.data.update(score)
# Calculate RMSD to the input pose
try:
clone.data['vina_rmsd_input'] = rmsd(ligand, clone)
clone.data['vina_rmsd_input_min'] = rmsd(
ligand, clone, method='min_symmetry')
except Exception:
pass
output_array.append(clone)
rmtree(ligand_dir)
return output_array
def dock(self, ligands, protein=None):
"""Automated docking procedure.
Parameters
----------
ligands: iterable of oddt.toolkit.Molecule objects
Ligands to dock
protein: oddt.toolkit.Molecule object or None
Protein object to be used. If None, then the default one
is used, else the protein is new default.
Returns
-------
ligands : array of oddt.toolkit.Molecule objects
Array of ligands (scores are stored in mol.data method)
"""
if protein:
self.set_protein(protein)
if not self.protein_file:
raise IOError("No receptor.")
if is_molecule(ligands):
ligands = [ligands]
ligand_dir = mkdtemp(dir=self.tmp_dir, prefix='ligands_')
output_array = []
for n, ligand in enumerate(ligands):
check_molecule(ligand, force_coords=True)
ligand_file = write_vina_pdbqt(ligand, ligand_dir, name_id=n)
ligand_outfile = ligand_file[:-6] + '_out.pdbqt'
try:
scores = parse_vina_docking_output(
subprocess.check_output([self.executable, '--receptor',
self.protein_file,
'--ligand', ligand_file,
'--out', ligand_outfile] +
self.params +
['--cpu', str(self.n_cpu)],
stderr=subprocess.STDOUT))
except subprocess.CalledProcessError as e:
sys.stderr.write(e.output.decode('ascii'))
if self.skip_bad_mols:
continue # TODO: print some warning message
else:
raise Exception('Autodock Vina failed. Command: "%s"' %
' '.join(e.cmd))
# docked conformations may have wrong connectivity - use source ligand
if is_openbabel_molecule(ligand):
if oddt.toolkits.ob.__version__ >= '2.4.0':
# find the order of PDBQT atoms assigned by OpenBabel
with open(ligand_file) as f:
write_order = [int(line[7:12].strip())
for line in f
if line[:4] == 'ATOM']
new_order = sorted(range(len(write_order)),
key=write_order.__getitem__)
new_order = [i + 1 for i in new_order] # OBMol has 1 based idx
assert len(new_order) == len(ligand.atoms)
else:
# Openbabel 2.3.2 does not support perserving atom order.
# We read back the PDBQT ligand to get "correct" bonding.
ligand = next(oddt.toolkit.readfile('pdbqt', ligand_file))
if 'REMARK' in ligand.data:
del ligand.data['REMARK']
docked_ligands = oddt.toolkit.readfile('pdbqt', ligand_outfile)
for docked_ligand, score in zip(docked_ligands, scores):
# Renumber atoms to match the input ligand
if (is_openbabel_molecule(docked_ligand) and
oddt.toolkits.ob.__version__ >= '2.4.0'):
docked_ligand.OBMol.RenumberAtoms(new_order)
# HACK: copy docked coordinates onto source ligand
# We assume that the order of atoms match between ligands
clone = ligand.clone
clone.clone_coords(docked_ligand)
clone.data.update(score)
# Calculate RMSD to the input pose
clone.data['vina_rmsd_input'] = rmsd(ligand, clone)
clone.data['vina_rmsd_input_min'] = rmsd(ligand, clone,
method='min_symmetry')
output_array.append(clone)
rmtree(ligand_dir)
return output_array
