def test_atom_ordering(self):
all_dists = bond_length_distribution.AllAtomPairLengthDistributions()
all_dists.add(ATOM_N, ATOM_O, BOND_SINGLE,
bond_length_distribution.FixedWindow(1, 2, None))
self.assertEqual(
all_dists.pdf_length_given_type(ATOM_N, ATOM_O, BOND_SINGLE, 1.5),
1)
self.assertEqual(
all_dists.pdf_length_given_type(ATOM_O, ATOM_N, BOND_SINGLE, 1.5),
1)
self.assertEqual(
all_dists.pdf_length_given_type(ATOM_N, ATOM_O, BOND_SINGLE, 999),
0)
self.assertEqual(
all_dists.pdf_length_given_type(ATOM_O, ATOM_N, BOND_SINGLE, 999),
0)
# Make sure subsequent additions work as well
all_dists.add(ATOM_N, ATOM_O, BOND_DOUBLE,
bond_length_distribution.FixedWindow(2, 3, None))
self.assertEqual(
all_dists.pdf_length_given_type(ATOM_N, ATOM_O, BOND_DOUBLE, 2.5),
1)
self.assertEqual(
all_dists.pdf_length_given_type(ATOM_O, ATOM_N, BOND_DOUBLE, 2.5),
1)
def setUp(self):
super().setUp()
self.dists = bond_length_distribution.AtomPairLengthDistributions()
self.dists.add(BOND_SINGLE,
bond_length_distribution.FixedWindow(1.2, 1.8, None))
self.dists.add(BOND_DOUBLE,
bond_length_distribution.FixedWindow(1.0, 1.4, None))
def test_probability_bond_types(self):
all_dists = bond_length_distribution.AllAtomPairLengthDistributions()
all_dists.add(ATOM_N, ATOM_O, BOND_SINGLE,
bond_length_distribution.FixedWindow(1, 4, None))
all_dists.add(ATOM_N, ATOM_O, BOND_DOUBLE,
bond_length_distribution.FixedWindow(1, 2, None))
got = all_dists.probability_of_bond_types(ATOM_N, ATOM_O, 1.5)
self.assertLen(got, 2)
self.assertAlmostEqual(got[BOND_SINGLE], 0.25)
self.assertAlmostEqual(got[BOND_DOUBLE], 0.75)
def test_simple(self):
dist = bond_length_distribution.Mixture()
dist.add(bond_length_distribution.FixedWindow(0.5, 1.5, None), 75)
dist.add(bond_length_distribution.FixedWindow(1, 2, None), 25)
self.assertAlmostEqual(dist.pdf(0.25), 0)
self.assertAlmostEqual(dist.pdf(0.75), .75)
self.assertAlmostEqual(dist.pdf(1.25), 1)
self.assertAlmostEqual(dist.pdf(1.75), .25)
self.assertAlmostEqual(dist.pdf(2.25), 0)
self.assertEqual(dist.min(), 0.5)
self.assertEqual(dist.max(), 2)
def test_simple(self):
dist = bond_length_distribution.FixedWindow(3, 5, None)
self.assertAlmostEqual(dist.pdf(2.9), 0.0)
self.assertAlmostEqual(dist.pdf(5.1), 0.0)
self.assertAlmostEqual(dist.pdf(3.456), 0.5)
self.assertEqual(dist.min(), 3)
self.assertEqual(dist.max(), 5)
def get_smu_dists(self):
bld = bond_length_distribution.AllAtomPairLengthDistributions()
# This is set up to make the O=C length of 1.25 a much better fit than
# the [O-]-C bond
bld.add(dataset_pb2.BondTopology.ATOM_O, dataset_pb2.BondTopology.ATOM_C,
dataset_pb2.BondTopology.BondType.BOND_SINGLE,
triangular_distribution(1.2, 1.6, 1.8))
bld.add(dataset_pb2.BondTopology.ATOM_O, dataset_pb2.BondTopology.ATOM_C,
dataset_pb2.BondTopology.BondType.BOND_DOUBLE,
triangular_distribution(1.2, 1.25, 1.3))
bld.add(dataset_pb2.BondTopology.ATOM_C, dataset_pb2.BondTopology.ATOM_N,
dataset_pb2.BondTopology.BondType.BOND_DOUBLE,
bond_length_distribution.FixedWindow(1.1, 1.3, None))
bld.add(dataset_pb2.BondTopology.ATOM_C, dataset_pb2.BondTopology.ATOM_N,
dataset_pb2.BondTopology.BondType.BOND_TRIPLE,
bond_length_distribution.FixedWindow(1.2, 1.4, None))
return bld
def test_missing_types(self):
all_dists = bond_length_distribution.AllAtomPairLengthDistributions()
all_dists.add(ATOM_N, ATOM_O, BOND_SINGLE,
bond_length_distribution.FixedWindow(1, 2, None))
with self.assertRaises(KeyError):
all_dists.probability_of_bond_types(ATOM_C, ATOM_C, 1.0)
with self.assertRaises(KeyError):
all_dists.pdf_length_given_type(ATOM_C, ATOM_C, BOND_SINGLE, 1.0)
def test_right_tail(self):
dist = bond_length_distribution.FixedWindow(3, 5, right_tail_mass=0.8)
# 0.2 of the mass is in the window, divded by 2 (size of the window)
self.assertAlmostEqual(dist.pdf(3.456), 0.1)
self.assertAlmostEqual(dist.pdf(5), 0.1)
# Test slightly above the maximum to make sure we got the left side of the
# right tail correct.
self.assertAlmostEqual(dist.pdf(5.00000001), 0.1)
self.assertAlmostEqual(dist.pdf(6), 0.08824969)
self.assertEqual(dist.min(), 3)
self.assertEqual(dist.max(), np.inf)
def test_bad_values(self):
with self.assertRaises(ValueError):
bond_length_distribution.FixedWindow(-1, 1, None)
with self.assertRaises(ValueError):
bond_length_distribution.FixedWindow(-2, -1, None)
with self.assertRaises(ValueError):
bond_length_distribution.FixedWindow(10, 8, None)
with self.assertRaises(ValueError):
bond_length_distribution.FixedWindow(np.inf, 1, None)
with self.assertRaises(ValueError):
bond_length_distribution.FixedWindow(np.nan, 1, None)
with self.assertRaises(ValueError):
bond_length_distribution.FixedWindow(1, np.inf, None)
with self.assertRaises(ValueError):
bond_length_distribution.FixedWindow(1, np.nan, None)
with self.assertRaises(ValueError):
bond_length_distribution.FixedWindow(1, 2, -1.0)
with self.assertRaises(ValueError):
bond_length_distribution.FixedWindow(1, 2, 2)
with self.assertRaises(ValueError):
bond_length_distribution.FixedWindow(1, 2, np.inf)
def test_bad_weight(self):
dist = bond_length_distribution.Mixture()
with self.assertRaises(ValueError):
dist.add(bond_length_distribution.FixedWindow(1, 2, None), 0)
with self.assertRaises(ValueError):
dist.add(bond_length_distribution.FixedWindow(1, 2, None), 0)