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
self.preparator = MolPreparator()
def __init__(self, size=30., resolution=0.5, nb_cutoff=5.,
ionic_strength=150., ionize=True, pH=7.4, align=False):
self.size = float(size)
self.resolution = float(resolution)
self.nb_cutoff = float(nb_cutoff)
self.ionic_strength = float(ionic_strength)
self.preparator = MolPreparator(ionize, pH, align, add_hydrogens=True)
def __init__(self, size=81, resolution=0.5, hydrogens=False, align=False,
probe_radius=1.4, featurization='occupancy'):
self.size = size
self.resolution = resolution
self.hydrogens = hydrogens
self.preparator = MolPreparator(align=align, add_hydrogens=hydrogens)
self.probe_radius = probe_radius
self.featurization = featurization
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
self.preparator = MolPreparator()
class TestMolPreparator(unittest.TestCase):
"""
Test MolPreparator.
"""
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
self.preparator = MolPreparator()
def test_identity(self):
"""
Test MolPreparator does nothing by default.
"""
mol = self.preparator(self.mol)
assert mol.GetNumAtoms() == self.mol.GetNumAtoms()
assert mol.GetNumConformers() == self.mol.GetNumConformers()
def test_ionize(self):
"""
Test MolPreparator with ionize=True.
"""
self.preparator.set_ionize(True)
mol = self.preparator(self.mol)
mol_charge = sum([atom.GetFormalCharge() for atom in mol.GetAtoms()])
ref_charge = sum(
[atom.GetFormalCharge() for atom in self.mol.GetAtoms()])
assert mol_charge != ref_charge
def test_align(self):
"""
Test MolPreparator with align=True.
Really just make sure that coordinates are sane, since the alignment
tends to flatten molecules if there are hydrogens present.
"""
def _check_flat(this_mol):
"""
Check whether a molecule is flat.
Parameters
----------
this_mol : RDKit Mol
Molecule to check.
"""
for conf in this_mol.GetConformers():
coords = []
for atom in this_mol.GetAtoms():
coords.append(list(conf.GetAtomPosition(atom.GetIdx())))
coords = np.asarray(coords, dtype=float)
for i in xrange(coords.shape[1]):
assert not np.allclose(coords[:, i], 0)
# test without hydrogens
self.preparator.set_align(True)
mol = self.preparator(self.mol)
_check_flat(mol)
# test with hydrogens
self.preparator.set_add_hydrogens(True)
mol = self.preparator(self.mol)
_check_flat(mol)
def test_add_hydrogens(self):
"""
Test MolPreparator with add_hydrogens=True.
"""
self.preparator.set_add_hydrogens(True)
ref_mol = Chem.RemoveHs(self.mol)
mol = self.preparator(ref_mol)
assert mol.GetNumAtoms() > ref_mol.GetNumAtoms()
class TestMolPreparator(unittest.TestCase):
"""
Test MolPreparator.
"""
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
self.preparator = MolPreparator()
def test_identity(self):
"""
Test MolPreparator does nothing by default.
"""
mol = self.preparator(self.mol)
assert mol.GetNumAtoms() == self.mol.GetNumAtoms()
assert mol.GetNumConformers() == self.mol.GetNumConformers()
def test_ionize(self):
"""
Test MolPreparator with ionize=True.
"""
self.preparator.set_ionize(True)
mol = self.preparator(self.mol)
mol_charge = sum([atom.GetFormalCharge() for atom in mol.GetAtoms()])
ref_charge = sum([atom.GetFormalCharge()
for atom in self.mol.GetAtoms()])
assert mol_charge != ref_charge
def test_align(self):
"""
Test MolPreparator with align=True.
Really just make sure that coordinates are sane, since the alignment
tends to flatten molecules if there are hydrogens present.
"""
def _check_flat(this_mol):
"""
Check whether a molecule is flat.
Parameters
----------
this_mol : RDKit Mol
Molecule to check.
"""
for conf in this_mol.GetConformers():
coords = []
for atom in this_mol.GetAtoms():
coords.append(list(conf.GetAtomPosition(atom.GetIdx())))
coords = np.asarray(coords, dtype=float)
for i in xrange(coords.shape[1]):
assert not np.allclose(coords[:, i], 0)
# test without hydrogens
self.preparator.set_align(True)
mol = self.preparator(self.mol)
_check_flat(mol)
# test with hydrogens
self.preparator.set_add_hydrogens(True)
mol = self.preparator(self.mol)
_check_flat(mol)
def test_add_hydrogens(self):
"""
Test MolPreparator with add_hydrogens=True.
"""
self.preparator.set_add_hydrogens(True)
ref_mol = Chem.RemoveHs(self.mol)
mol = self.preparator(ref_mol)
assert mol.GetNumAtoms() > ref_mol.GetNumAtoms()