def process(self, conformer):
bt = conformer.bond_topologies[0]
geom = conformer.optimized_geometry
bonded = utilities.bonded(bt)
natoms = len(bt.atoms)
for a1 in range(0, natoms):
atomic_number1 = smu_utils_lib.ATOM_TYPE_TO_ATOMIC_NUMBER[
bt.atoms[a1]]
for a2 in range(a1 + 1, natoms):
atomic_number2 = smu_utils_lib.ATOM_TYPE_TO_ATOMIC_NUMBER[
bt.atoms[a2]]
# Do not process H-H pairs
if atomic_number1 == 1 and atomic_number2 == 1:
continue
d = utilities.distance_between_atoms(geom, a1, a2)
if d > MAX_DIST:
continue
discretized = int(d * utilities.DISTANCE_BINS)
yield (min(atomic_number1, atomic_number2), int(bonded[a1,
a2]),
max(atomic_number1, atomic_number2), discretized), 1
def process(self, molecule):
bt = molecule.bond_topologies[0]
geom = molecule.optimized_geometry
bonded = utilities.bonded(bt)
natoms = len(bt.atoms)
if molecule.properties.errors.fate != dataset_pb2.Properties.FATE_SUCCESS:
return
for a1 in range(0, natoms):
atomic_number1 = smu_utils_lib.ATOM_TYPE_TO_ATOMIC_NUMBER[
bt.atoms[a1]]
for a2 in range(a1 + 1, natoms):
atomic_number2 = smu_utils_lib.ATOM_TYPE_TO_ATOMIC_NUMBER[
bt.atoms[a2]]
# Do not process H-H pairs
if atomic_number1 == 1 and atomic_number2 == 1:
continue
d = utilities.distance_between_atoms(geom, a1, a2)
if d > MAX_DIST:
continue
discretized = int(d * utilities.DISTANCE_BINS)
yield (min(atomic_number1, atomic_number2), int(bonded[a1,
a2]),
max(atomic_number1, atomic_number2), discretized), 1
def test_unit_z(self):
coords = zero2()
coords.atom_positions[1].z = 1.0 / smu_utils_lib.BOHR_TO_ANGSTROMS
self.assertAlmostEqual(utilities.distance_between_atoms(coords, 0, 1),
1.0)
def test_zero_distance(self):
coords = zero2()
self.assertEqual(utilities.distance_between_atoms(coords, 0, 1), 0.0)