def test_read_multiconformer(self):
"""
Read a multiconformer SDF file.
"""
# generate conformers
engine = conformers.ConformerGenerator(max_conformers=3,
pool_multiplier=1)
ref_mol = engine.generate_conformers(self.aspirin)
assert ref_mol.GetNumConformers() > 1
# write to disk
_, filename = tempfile.mkstemp(suffix='.sdf', dir=self.temp_dir)
with open(filename, 'wb') as f:
for conf in ref_mol.GetConformers():
f.write(Chem.MolToMolBlock(ref_mol, confId=conf.GetId()))
f.write('$$$$\n') # add molecule delimiter
# compare
self.reader.open(filename)
mols = self.reader.get_mols()
mols = list(mols)
assert len(mols) == 1
# FIXME get ToBinary test to work
# assert mols[0].ToBinary() == ref_mol.ToBinary()
assert Chem.MolToMolBlock(mols[0]) == Chem.MolToMolBlock(ref_mol)
def setUp(self):
"""
Set up for tests. Writes molecules and targets to files.
"""
self.temp_dir = tempfile.mkdtemp()
smiles = [
'CC(=O)OC1=CC=CC=C1C(=O)O', 'C[C@@H](C1=CC=C(C=C1)CC(C)C)C(=O)O'
]
self.names = ['aspirin', 'ibuprofen']
engine = conformers.ConformerGenerator(max_conformers=1)
self.mols = []
self.smiles = [] # use RDKit-generated SMILES
for i in xrange(len(smiles)):
mol = Chem.MolFromSmiles(smiles[i])
mol.SetProp('_Name', self.names[i])
self.mols.append(engine.generate_conformers(mol))
self.smiles.append(
Chem.MolToSmiles(mol, isomericSmiles=True, canonical=True))
# write mols
_, self.input_filename = tempfile.mkstemp(suffix='.sdf',
dir=self.temp_dir)
writer = serial.MolWriter()
writer.open(self.input_filename)
writer.write(self.mols)
writer.close()
# write targets
self.targets = [0, 1]
_, self.targets_filename = tempfile.mkstemp(suffix='.pkl',
dir=self.temp_dir)
write_pickle(self.targets, self.targets_filename)
def test_prune_conformers(self):
"""
Test ConformerGenerator.prune_conformers.
"""
engine = conformers.ConformerGenerator(max_conformers=10)
mol = engine.embed_molecule(self.mol)
# check that there is more than one conformer
assert mol.GetNumConformers() > 1
engine.minimize_conformers(mol)
energies = engine.get_conformer_energies(mol)
pruned = engine.prune_conformers(mol)
pruned_energies = engine.get_conformer_energies(pruned)
# check that the number of conformers is not to large
assert pruned.GetNumConformers() <= engine.max_conformers
# check that the number of conformers has not increased
assert pruned.GetNumConformers() <= mol.GetNumConformers()
# check that lowest energy conformer was selected
assert np.allclose(min(energies), min(pruned_energies))
# check that pruned energies are taken from the original set
for energy in pruned_energies:
assert np.allclose(min(np.fabs(energies - energy)), 0)
# check that conformers are in order of increasing energy
sort = np.argsort(pruned_energies)
assert np.array_equal(sort, np.arange(len(pruned_energies))), sort
def test_mmff94s_minimization(self):
"""
Generate conformers and minimize with MMFF94s force field.
"""
engine = conformers.ConformerGenerator(force_field='mmff94s')
mol = engine.generate_conformers(self.mol)
assert mol.GetNumConformers() > 0
def test_assign_stereo_from_3d(self):
"""
Test --stereo-from-3d.
"""
# generate conformers for ibuprofen
engine = conformers.ConformerGenerator()
mol = engine.generate_conformers(self.mols[1])
assert mol.GetNumConformers() > 0
self.mols[1] = mol
# rewrite input file
_, self.input_filename = tempfile.mkstemp(dir=self.temp_dir,
suffix='.sdf')
with serial.MolWriter().open(self.input_filename) as writer:
writer.write(self.mols)
# check for absence of chirality using default arguments
database = self.check_output(
['-i', self.input_filename, '-o', self.output_filename])
chiral = False
for smiles in database:
if '@' in smiles:
chiral = True
assert not chiral
# check for presence of chiraliy using --stereo-from-3d
database = self.check_output([
'-i', self.input_filename, '-o', self.output_filename,
'--stereo-from-3d'
])
chiral = False
for smiles in database:
if '@' in smiles:
chiral = True
assert chiral
def setUp(self):
"""
Set up tests.
"""
smiles = 'CC(=O)OC1=CC=CC=C1C(=O)O'
mol = Chem.MolFromSmiles(smiles)
engine = conformers.ConformerGenerator(max_conformers=1)
self.mol = engine.generate_conformers(mol)
assert self.mol.GetNumConformers() > 0
def setUp(self):
"""
Set up tests.
"""
aspirin_smiles = 'CC(=O)OC1=CC=CC=C1C(=O)O aspirin'
self.mol = Chem.MolFromSmiles(aspirin_smiles.split()[0])
self.mol.SetProp('_Name', 'aspirin')
assert self.mol.GetNumConformers() == 0
self.engine = conformers.ConformerGenerator()
def setUp(self):
"""
Set up tests.
"""
smiles = ['CC(=O)OC1=CC=CC=C1C(=O)O', 'CC(C)CC1=CC=C(C=C1)C(C)C(=O)O']
mols = [Chem.MolFromSmiles(s) for s in smiles]
engine = conformers.ConformerGenerator(max_conformers=1)
self.mols = [engine.generate_conformers(mol) for mol in mols]
for mol in self.mols:
assert mol.GetNumConformers() > 0
def setUp(self):
"""
Set up tests.
"""
smiles = 'CC(=O)OC1=CC=CC=C1C(=O)O'
mol = Chem.MolFromSmiles(smiles)
engine = conformers.ConformerGenerator(max_conformers=3)
self.mols = [engine.generate_conformers(mol)]
for mol in self.mols:
assert mol.GetNumConformers() > 0
self.max_confs = max([mol.GetNumConformers() for mol in self.mols])
self.engine = ShapeGrid()
def test_get_conformer_rmsd(self):
"""
Test ConformerGenerator.get_conformer_rmsd.
"""
engine = conformers.ConformerGenerator(max_conformers=10)
mol = engine.embed_molecule(self.mol)
# check that there is more than one conformer
assert mol.GetNumConformers() > 1
rmsd = engine.get_conformer_rmsd(mol)
# check for a valid distance matrix
assert rmsd.shape[0] == rmsd.shape[1] == mol.GetNumConformers()
assert np.allclose(np.diag(rmsd), 0)
assert np.array_equal(rmsd, rmsd.T)
# check for non-zero off-diagonal values
assert np.all(rmsd[np.triu_indices_from(rmsd, k=1)] > 0), rmsd
def test_stereo_to_3d(self):
"""
Test main with --stereo-to-3d.
"""
# generate conformers for ibuprofen
engine = conformers.ConformerGenerator()
self.mols[1] = engine.generate_conformers(self.mols[1])
assert self.mols[1].GetNumConformers() > 0
# rewrite actives file with 3D coordinates
_, self.active_filename = tempfile.mkstemp(dir=self.temp_dir,
suffix='.sdf')
with serial.MolWriter().open(self.active_filename) as writer:
for mol, y in zip(self.mols, self.y):
if y:
writer.write([self.mols[1]])
# check for absence of chirality using default arguments
smiles, targets = self.check_output([
'-a', self.active_filename, '-d', self.decoy_filename, '-o',
self.output_filename
])
chiral = False
for this_smiles in smiles:
if '@' in this_smiles:
chiral = True
assert not chiral
# update reference SMILES
self.engine = SmilesGenerator(assign_stereo_from_3d=True)
self.smiles[1] = self.engine.get_smiles(self.mols[1])
# check for presence of chiraliy using --stereo-from-3d
smiles, targets = self.check_output([
'-a', self.active_filename, '-d', self.decoy_filename, '-o',
self.output_filename, '--stereo-from-3d'
])
chiral = False
for this_smiles in smiles:
if '@' in this_smiles:
chiral = True
assert chiral
def setUp(self):
"""
Set up tests.
"""
smiles = 'CC(C)Cc1ccc([C@H](C)C(=O)O)cc1'
mol = Chem.MolFromSmiles(smiles)
# generate conformers
engine = conformers.ConformerGenerator(max_conformers=3)
self.mol = engine.generate_conformers(mol)
# ionize the oxygen manually
ionized_mol = Chem.Mol(self.mol) # create a copy
found = False
for atom in ionized_mol.GetAtoms():
if atom.GetAtomicNum() == 8 and atom.GetTotalDegree() == 2:
atom.SetFormalCharge(-1)
atom.SetNoImplicit(True)
found = True
assert found
self.ionized_mol = Chem.RemoveHs(ionized_mol)
self.ionizer = ob_utils.Ionizer()
def test_get_smiles_3d(self):
"""
Test SmilesGenerator.get_smiles with stereochemistry assigned from 3D
coordinates.
"""
# generate conformers for ibuprofen
engine = conformers.ConformerGenerator()
mol = engine.generate_conformers(self.mols[1])
assert mol.GetNumConformers() > 0
# check that chirality has not yet been assigned
smiles = self.engine.get_smiles(mol)
assert '@' not in smiles # check for absence of chirality marker
chiral_types = [
Chem.ChiralType.CHI_TETRAHEDRAL_CW,
Chem.ChiralType.CHI_TETRAHEDRAL_CCW
]
chiral = False
for atom in mol.GetAtoms():
if atom.GetChiralTag() in chiral_types:
chiral = True
assert not chiral
# generate SMILES
self.engine = SmilesGenerator(assign_stereo_from_3d=True)
smiles = self.engine.get_smiles(mol)
assert '@' in smiles # check for chirality marker
new = Chem.MolFromSmiles(smiles)
assert new.GetNumAtoms() == self.mols[1].GetNumAtoms()
# check that chirality was assigned to ibuprofen
chiral = False
for atom in mol.GetAtoms():
if atom.GetChiralTag() in chiral_types:
chiral = True
assert chiral
def test_read_multiple_multiconformer(self):
"""
Read a multiconformer SDF file containing multiple molecules.
"""
# generate conformers
ref_mols = []
engine = conformers.ConformerGenerator(max_conformers=3,
pool_multiplier=1)
for mol in self.ref_mols:
expanded = engine.generate_conformers(mol)
assert expanded.GetNumConformers() > 1
ref_mols.append(expanded)
# write to disk
_, filename = tempfile.mkstemp(suffix='.sdf', dir=self.temp_dir)
with open(filename, 'wb') as f:
for mol in ref_mols:
for conf in mol.GetConformers():
f.write(
Chem.MolToMolBlock(mol,
includeStereo=1,
confId=conf.GetId()))
f.write('$$$$\n') # add molecule delimiter
# compare
self.reader.open(filename)
mols = self.reader.get_mols()
mols = list(mols)
assert len(mols) == 2
for mol, ref_mol in zip(mols, ref_mols):
# FIXME get ToBinary test to work
# assert mol.ToBinary() == ref_mol.ToBinary()
assert Chem.MolToMolBlock(
mol, includeStereo=1) == Chem.MolToMolBlock(ref_mol,
includeStereo=1)