def test_two_dimensional_pdb_file(self):
hypercubic_setting.HypercubicSetting(beta=1.0,
dimension=2,
system_length=1.0)
# Ignore warnings in logger
logging.getLogger(
"jellyfysh.input_output_handler.input_handler.pdb_input_handler"
).setLevel(logging.ERROR)
electric_charge_values = ChargeValues([-1.0], "electric_charge")
# This file also contains positions outside the system box which should be corrected for periodic boundaries
pdb_input_handler = PdbInputHandler("pdb_test_files/atom_test_2D.pdb",
[electric_charge_values])
state = pdb_input_handler.read()
self.assertEqual(len(state), 2)
atom_one = state[0]
self.assertIsNone(atom_one.parent)
self.assertEqual(atom_one.weight, 1.0)
self.assertEqual(atom_one.value.charge, {"electric_charge": -1.0})
self.assertEqual(len(atom_one.value.position), 2)
# MDAnalysis only uses c floats (not doubles) -> reduce precision
self.assertAlmostEqual(atom_one.value.position[0], 0.983, places=6)
self.assertAlmostEqual(atom_one.value.position[1], 0.032, places=6)
self.assertEqual(len(atom_one.children), 0)
atom_two = state[1]
self.assertIsNone(atom_two.parent)
self.assertEqual(atom_two.weight, 1.0)
self.assertEqual(atom_two.value.charge, {"electric_charge": -1.0})
self.assertEqual(len(atom_two.value.position), 2)
# MDAnalysis only uses c floats (not doubles) -> reduce precision
self.assertAlmostEqual(atom_two.value.position[0], 0.618, places=6)
self.assertAlmostEqual(atom_two.value.position[1], 0.697, places=6)
self.assertEqual(len(atom_two.children), 0)
def test_pdb_file_atom_origin_l2(self):
# Origin of system box in pdb file at [-L/2, -L/2, -L/2]
hypercubic_setting.HypercubicSetting(beta=1.0,
dimension=3,
system_length=1.0)
electric_charge_values = ChargeValues([1.0], "electric_charge")
# This file also contains positions outside the system box which should be corrected for periodic boundaries
with warnings.catch_warnings():
# Ignore warnings of MDAnalysis
warnings.simplefilter("ignore", UserWarning)
pdb_input_handler = PdbInputHandler(
"pdb_test_files/atom_test_origin_l2.pdb",
[electric_charge_values])
state = pdb_input_handler.read()
self.assertEqual(len(state), 4)
atom_one = state[0]
self.assertIsNone(atom_one.parent)
self.assertEqual(atom_one.weight, 1.0)
self.assertEqual(atom_one.value.charge, {"electric_charge": 1.0})
self.assertEqual(len(atom_one.value.position), 3)
# MDAnalysis only uses c floats (not doubles) -> reduce precision
self.assertAlmostEqual(atom_one.value.position[0], 0.983, places=6)
self.assertAlmostEqual(atom_one.value.position[1], 0.032, places=6)
self.assertAlmostEqual(atom_one.value.position[2], 0.714, places=6)
self.assertEqual(len(atom_one.children), 0)
atom_two = state[1]
self.assertIsNone(atom_two.parent)
self.assertEqual(atom_two.weight, 1.0)
self.assertEqual(atom_two.value.charge, {"electric_charge": 1.0})
self.assertEqual(len(atom_two.value.position), 3)
# MDAnalysis only uses c floats (not doubles) -> reduce precision
self.assertAlmostEqual(atom_two.value.position[0], 0.618, places=6)
self.assertAlmostEqual(atom_two.value.position[1], 0.697, places=6)
self.assertAlmostEqual(atom_two.value.position[2], 0.848, places=6)
self.assertEqual(len(atom_two.children), 0)
atom_three = state[2]
self.assertIsNone(atom_three.parent)
self.assertEqual(atom_three.weight, 1.0)
self.assertEqual(atom_three.value.charge, {"electric_charge": 1.0})
self.assertEqual(len(atom_three.value.position), 3)
# MDAnalysis only uses c floats (not doubles) -> reduce precision
self.assertAlmostEqual(atom_three.value.position[0], 0.312, places=6)
self.assertAlmostEqual(atom_three.value.position[1], 0.806, places=6)
self.assertAlmostEqual(atom_three.value.position[2], 0.642, places=6)
self.assertEqual(len(atom_three.children), 0)
atom_four = state[3]
self.assertIsNone(atom_four.parent)
self.assertEqual(atom_four.weight, 1.0)
self.assertEqual(atom_four.value.charge, {"electric_charge": 1.0})
self.assertEqual(len(atom_four.value.position), 3)
# MDAnalysis only uses c floats (not doubles) -> reduce precision
self.assertAlmostEqual(atom_four.value.position[0], 0.012, places=6)
self.assertAlmostEqual(atom_four.value.position[1], 0.923, places=6)
self.assertAlmostEqual(atom_four.value.position[2], 0.100, places=6)
self.assertEqual(len(atom_four.children), 0)
def test_two_dimensional_pdb_file_contains_three_dimensional_position_raises_error(
self):
hypercubic_setting.HypercubicSetting(beta=1.0,
dimension=2,
system_length=1.0)
# Ignore warnings in logger
logging.getLogger(
"jellyfysh.input_output_handler.input_handler.pdb_input_handler"
).setLevel(logging.ERROR)
pdb_input_handler = PdbInputHandler(
"pdb_test_files/atom_test_2D_wrong_positions.pdb")
with self.assertRaises(AssertionError):
pdb_input_handler.read()
def test_non_equal_composite_point_objects_raises_error(self):
hypercubic_setting.HypercubicSetting(beta=1.0,
dimension=3,
system_length=10.261)
with self.assertRaises(ConfigurationError):
PdbInputHandler(
"pdb_test_files/test_non_equal_composite_point_objects.pdb")
def test_not_matching_system_lengths_raises_error(self):
# PDB file has system_length=10.261
hypercubic_setting.HypercubicSetting(beta=1.0,
dimension=3,
system_length=10.26)
with self.assertRaises(ConfigurationError):
PdbInputHandler("pdb_test_files/water_test_origin_0.pdb")
def test_no_charge_for_every_point_mass_raises_error(self):
hypercubic_setting.HypercubicSetting(beta=1.0,
dimension=3,
system_length=10.261)
# Only specify two charges although three are required
electric_charge_values = ChargeValues([0.41, -0.82], "electric_charge")
with self.assertRaises(ConfigurationError):
PdbInputHandler("pdb_test_files/water_test_origin_0.pdb",
[electric_charge_values])
def test_repeated_charge_name_raises_error(self):
hypercubic_setting.HypercubicSetting(beta=1.0,
dimension=3,
system_length=10.261)
# Create two charge values with the same name
electric_charge_values = ChargeValues([0.41, -0.82, 0.41],
"electric_charge")
oxygen_indicator_charge = ChargeValues([0.0, 1.0, 0.0],
"electric_charge")
with self.assertRaises(ConfigurationError):
PdbInputHandler("pdb_test_files/water_test_origin_0.pdb",
[electric_charge_values, oxygen_indicator_charge])
def test_wrong_file_suffix_raises_error(self):
hypercubic_setting.HypercubicSetting(beta=1.0,
dimension=3,
system_length=10.261)
with self.assertRaises(ConfigurationError):
PdbInputHandler("pdb_test_files/water_test_origin_0.wrong_ending")
def test_dimension_to_high_raises_error(self):
hypercubic_setting.HypercubicSetting(beta=1.0,
dimension=4,
system_length=10.261)
with self.assertRaises(ConfigurationError):
PdbInputHandler("pdb_test_files/water_test_origin_0.pdb")
def test_non_existing_file_raises_error(self):
hypercubic_setting.HypercubicSetting(beta=1.0,
dimension=3,
system_length=10.261)
with self.assertRaises(FileNotFoundError):
PdbInputHandler("not_existing.pdb")
def test_pdb_file_water_origin_zero(self):
# Origin of system box in pdb file at [0.0, 0.0, 0.0]
hypercubic_setting.HypercubicSetting(beta=1.0,
dimension=3,
system_length=10.261)
electric_charge_values = ChargeValues([0.41, -0.82, 0.41],
"electric_charge")
oxygen_indicator_charge = ChargeValues([0.0, 1.0, 0.0],
"oxygen_indicator")
pdb_input_handler = PdbInputHandler(
"pdb_test_files/water_test_origin_0.pdb",
[electric_charge_values, oxygen_indicator_charge])
state = pdb_input_handler.read()
self.assertEqual(len(state), 4)
water_one = state[0]
self.assertIsNone(water_one.parent)
self.assertEqual(water_one.weight, 1.0)
self.assertIsNone(water_one.value.charge)
self.assertEqual(len(water_one.value.position), 3)
# MDAnalysis only uses c floats (not doubles) -> reduce precision
self.assertAlmostEqual(water_one.value.position[0],
8.43866666666667,
places=6)
self.assertAlmostEqual(water_one.value.position[1],
5.736333333333333,
places=6)
self.assertAlmostEqual(water_one.value.position[2],
1.384333333333333,
places=6)
self.assertEqual(len(water_one.children), 3)
h_one = water_one.children[0]
self.assertIs(h_one.parent, water_one)
self.assertEqual(h_one.weight, 1.0 / 3.0)
self.assertEqual(h_one.value.charge, {
"electric_charge": 0.41,
"oxygen_indicator": 0.0
})
self.assertEqual(len(h_one.value.position), 3)
self.assertAlmostEqual(h_one.value.position[0], 7.859, places=6)
self.assertAlmostEqual(h_one.value.position[1], 5.311, places=6)
self.assertAlmostEqual(h_one.value.position[2], 0.879, places=6)
self.assertEqual(len(h_one.children), 0)
o_one = water_one.children[1]
self.assertIs(o_one.parent, water_one)
self.assertEqual(o_one.weight, 1.0 / 3.0)
self.assertEqual(o_one.value.charge, {
"electric_charge": -0.82,
"oxygen_indicator": 1.0
})
self.assertEqual(len(o_one.value.position), 3)
self.assertAlmostEqual(o_one.value.position[0], 8.663, places=6)
self.assertAlmostEqual(o_one.value.position[1], 5.863, places=6)
self.assertAlmostEqual(o_one.value.position[2], 1.139, places=6)
self.assertEqual(len(o_one.children), 0)
h_two = water_one.children[2]
self.assertIs(h_two.parent, water_one)
self.assertEqual(h_two.weight, 1.0 / 3.0)
self.assertEqual(h_two.value.charge, {
"electric_charge": 0.41,
"oxygen_indicator": 0.0
})
self.assertEqual(len(h_two.value.position), 3)
self.assertAlmostEqual(h_two.value.position[0], 8.794, places=6)
self.assertAlmostEqual(h_two.value.position[1], 6.035, places=6)
self.assertAlmostEqual(h_two.value.position[2], 2.135, places=6)
self.assertEqual(len(h_two.children), 0)
water_two = state[1]
self.assertIsNone(water_two.parent)
self.assertEqual(water_two.weight, 1.0)
self.assertIsNone(water_two.value.charge)
self.assertEqual(len(water_two.value.position), 3)
self.assertAlmostEqual(water_two.value.position[0], 10.119, places=6)
self.assertAlmostEqual(water_two.value.position[1],
1.288666666666666,
places=6)
self.assertAlmostEqual(water_two.value.position[2],
10.17866666666667,
places=6)
self.assertEqual(len(water_two.children), 3)
h_one = water_two.children[0]
self.assertIs(h_one.parent, water_two)
self.assertEqual(h_one.weight, 1.0 / 3.0)
self.assertEqual(h_one.value.charge, {
"electric_charge": 0.41,
"oxygen_indicator": 0.0
})
self.assertEqual(len(h_one.value.position), 3)
self.assertAlmostEqual(h_one.value.position[0], 9.969, places=6)
self.assertAlmostEqual(h_one.value.position[1], 1.519, places=6)
self.assertAlmostEqual(h_one.value.position[2], 9.446, places=6)
self.assertEqual(len(h_one.children), 0)
o_one = water_two.children[1]
self.assertIs(o_one.parent, water_two)
self.assertEqual(o_one.weight, 1.0 / 3.0)
self.assertEqual(o_one.value.charge, {
"electric_charge": -0.82,
"oxygen_indicator": 1.0
})
self.assertEqual(len(o_one.value.position), 3)
self.assertAlmostEqual(o_one.value.position[0], 10.068, places=6)
self.assertAlmostEqual(o_one.value.position[1], 1.315, places=6)
self.assertAlmostEqual(o_one.value.position[2], 0.160, places=6)
self.assertEqual(len(o_one.children), 0)
h_two = water_two.children[2]
self.assertIs(h_two.parent, water_two)
self.assertEqual(h_two.weight, 1.0 / 3.0)
self.assertEqual(h_two.value.charge, {
"electric_charge": 0.41,
"oxygen_indicator": 0.0
})
self.assertEqual(len(h_two.value.position), 3)
self.assertAlmostEqual(h_two.value.position[0], 0.059, places=6)
self.assertAlmostEqual(h_two.value.position[1], 1.032, places=6)
self.assertAlmostEqual(h_two.value.position[2], 0.408, places=6)
self.assertEqual(len(h_two.children), 0)
water_three = state[2]
self.assertIsNone(water_three.parent)
self.assertEqual(water_three.weight, 1.0)
self.assertIsNone(water_three.value.charge)
self.assertEqual(len(water_three.value.position), 3)
self.assertAlmostEqual(water_three.value.position[0], 2.045, places=6)
self.assertAlmostEqual(water_three.value.position[1],
0.3630000000000001,
places=6)
self.assertAlmostEqual(water_three.value.position[2],
0.5586666666666666,
places=6)
self.assertEqual(len(water_three.children), 3)
h_one = water_three.children[0]
self.assertIs(h_one.parent, water_three)
self.assertEqual(h_one.weight, 1.0 / 3.0)
self.assertEqual(h_one.value.charge, {
"electric_charge": 0.41,
"oxygen_indicator": 0.0
})
self.assertEqual(len(h_one.value.position), 3)
self.assertAlmostEqual(h_one.value.position[0], 2.429, places=6)
self.assertAlmostEqual(h_one.value.position[1], 10.081, places=6)
self.assertAlmostEqual(h_one.value.position[2], 0.100, places=6)
self.assertEqual(len(h_one.children), 0)
o_one = water_three.children[1]
self.assertIs(o_one.parent, water_three)
self.assertEqual(o_one.weight, 1.0 / 3.0)
self.assertEqual(o_one.value.charge, {
"electric_charge": -0.82,
"oxygen_indicator": 1.0
})
self.assertEqual(len(o_one.value.position), 3)
self.assertAlmostEqual(o_one.value.position[0], 1.747, places=6)
self.assertAlmostEqual(o_one.value.position[1], 0.149, places=6)
self.assertAlmostEqual(o_one.value.position[2], 0.744, places=6)
self.assertEqual(len(o_one.children), 0)
h_two = water_three.children[2]
self.assertIs(h_two.parent, water_three)
self.assertEqual(h_two.weight, 1.0 / 3.0)
self.assertEqual(h_two.value.charge, {
"electric_charge": 0.41,
"oxygen_indicator": 0.0
})
self.assertEqual(len(h_two.value.position), 3)
self.assertAlmostEqual(h_two.value.position[0], 1.959, places=6)
self.assertAlmostEqual(h_two.value.position[1], 1.120, places=6)
self.assertAlmostEqual(h_two.value.position[2], 0.832, places=6)
self.assertEqual(len(h_two.children), 0)
water_four = state[3]
self.assertIsNone(water_four.parent)
self.assertEqual(water_four.weight, 1.0)
self.assertIsNone(water_four.value.charge)
self.assertEqual(len(water_four.value.position), 3)
self.assertAlmostEqual(water_four.value.position[0], 4.568, places=6)
self.assertAlmostEqual(water_four.value.position[1],
9.38066666666667,
places=6)
self.assertAlmostEqual(water_four.value.position[2],
10.03266666666667,
places=6)
self.assertEqual(len(water_four.children), 3)
h_one = water_four.children[0]
self.assertIs(h_one.parent, water_four)
self.assertEqual(h_one.weight, 1.0 / 3.0)
self.assertEqual(h_one.value.charge, {
"electric_charge": 0.41,
"oxygen_indicator": 0.0
})
self.assertEqual(len(h_one.value.position), 3)
self.assertAlmostEqual(h_one.value.position[0], 4.283, places=6)
self.assertAlmostEqual(h_one.value.position[1], 8.790, places=6)
self.assertAlmostEqual(h_one.value.position[2], 0.340, places=6)
self.assertEqual(len(h_one.children), 0)
o_one = water_four.children[1]
self.assertIs(o_one.parent, water_four)
self.assertEqual(o_one.weight, 1.0 / 3.0)
self.assertEqual(o_one.value.charge, {
"electric_charge": -0.82,
"oxygen_indicator": 1.0
})
self.assertEqual(len(o_one.value.position), 3)
self.assertAlmostEqual(o_one.value.position[0], 4.247, places=6)
self.assertAlmostEqual(o_one.value.position[1], 9.615, places=6)
self.assertAlmostEqual(o_one.value.position[2], 9.967, places=6)
self.assertEqual(len(o_one.children), 0)
h_two = water_four.children[2]
self.assertIs(h_two.parent, water_four)
self.assertEqual(h_two.weight, 1.0 / 3.0)
self.assertEqual(h_two.value.charge, {
"electric_charge": 0.41,
"oxygen_indicator": 0.0
})
self.assertEqual(len(h_two.value.position), 3)
self.assertAlmostEqual(h_two.value.position[0], 5.174, places=6)
self.assertAlmostEqual(h_two.value.position[1], 9.737, places=6)
self.assertAlmostEqual(h_two.value.position[2], 9.530, places=6)
self.assertEqual(len(h_two.children), 0)