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()
