def setUp(self):
"""
Set up tests.
"""
super(TestPBSA, self).setUp()
# get charges and radii
antechamber = amber_utils.Antechamber()
self.charges, self.radii = antechamber.get_charges_and_radii(self.mol)
def calculate_esp(self, mol):
"""
Calculate electrostatic potential grid.
Procedure
---------
1. Prepare molecule by adding hydrogens and canonicalizing the
orientation and alignment.
2. Calculate charges and radii with Antechamber.
3. Calculate electrostatic potential grids with PBSA.
PBSA requires PQR input, which is similar to PDB with charge and
radius information added. Neither Antechamber nor PBSA take piped
input, so we have to use a lot of temporary files and directories.
Parameters
----------
mol : RDMol
Molecule.
"""
# the molecule must have at least one conformer
if mol.GetNumConformers() < 1:
name = ''
if mol.HasProp('_Name'):
name = mol.GetProp('_Name')
raise AssertionError(
"Molecule '{}' has zero conformers.".format(name))
# calculate charges and radii
antechamber = amber_utils.Antechamber()
charges, radii = antechamber.get_charges_and_radii(mol)
# get ESP grid for each conformer
grids = []
pbsa = amber_utils.PBSA(self.size, self.resolution, self.nb_cutoff,
self.ionic_strength)
for i, conf in enumerate(mol.GetConformers()):
try:
grid, center = pbsa.get_esp_grid(mol, charges, radii,
conf_id=conf.GetId())
assert center == (0, 0, 0) # should be centered on the origin
grids.append(grid)
except subprocess.CalledProcessError as e:
print e
if mol.HasProp('_Name'):
name = mol.GetProp('_Name')
else:
name = Chem.MolToSmiles(mol, isomericSmiles=True)
warnings.warn(
"Conformer {} of molecule '{}' failed ".format(i, name) +
"ESP calculation.".format(name))
grids.append(None)
grids = np.asarray(grids)
return grids
def test_antechamber_charges_and_radii(self):
"""
Test Antechamber charges and radii.
"""
antechamber = amber_utils.Antechamber()
charges, radii = antechamber.get_charges_and_radii(self.mol)
assert charges.size == 21 # 21 atoms: C_9H_8O_4
assert np.allclose(charges.sum(), 0) # neutral molecule
assert radii.size == 21 # 12 atoms
assert np.count_nonzero(radii > 0) # no zero radii