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Refactor waterorientation to standard API #38

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Refactor waterorientation to standard API #38

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b2b0132
Refactor waterorientation to standard API
robinzyb Jun 29, 2024
a4926be
compilance with PEP8
robinzyb Jun 29, 2024
235f690
autopep8 enable non-whitespace changes
robinzyb Jun 29, 2024
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129 changes: 84 additions & 45 deletions waterdynamics/tests/test_waterdynamics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,31 +43,48 @@ def universe():

def test_WaterOrientationalRelaxation(universe):
wor = waterdynamics.WaterOrientationalRelaxation(
universe, SELECTION1, 0, 5, 2, order=2)
wor.run()
assert_almost_equal(wor.timeseries[1][2], 0.35887,
universe.atoms, ["name OH2", "name OH2 ", "name H1 or name H2"], 2, 1.2, update_selections=False, order=1)
wor.run(start=0, stop=4)
assert_almost_equal(wor.results["correlation"][2], 0.7148607552,
decimal=5)


def test_WaterOrientationalRelaxation_zeroMolecules(universe):
wor_zero = waterdynamics.WaterOrientationalRelaxation(
universe, SELECTION2, 0, 5, 2, order=2)
wor_zero.run()
assert_almost_equal(wor_zero.timeseries[1], (0.0, 0.0, 0.0))

def test_WaterOrientationalRelaxation_order_1(universe):
def test_WaterOrientationalRelaxationRegion(universe):
wor = waterdynamics.WaterOrientationalRelaxation(
universe, SELECTION1, 0, 5, 2, order=1)
wor.run()
assert_almost_equal(wor.timeseries[1][2], 0.71486,
universe.atoms, ["name OH2", "name OH2 and prop z <5 ", "name H1 or name H2"], 2, 1.2, order=1)
wor.run(start=0, stop=4)
assert_almost_equal(wor.results["correlation"][2], 0.810989,
decimal=5)


def test_WaterOrientationalRelaxation_order_1_zeroMolecules(universe):
wor_zero = waterdynamics.WaterOrientationalRelaxation(
universe, SELECTION2, 0, 5, 2, order=1)
wor_zero.run()
assert_almost_equal(wor_zero.timeseries[1], (0.0, 0.0, 0.0))
# def test_WaterOrientationalRelaxationDeprecated(universe):
# wor = waterdynamics.WaterOrientationalRelaxation(
# universe, SELECTION1, 0, 5, 2, order=2)
# wor.run()
# assert_almost_equal(wor.timeseries[1][2], 0.35887,
# decimal=5)


# def test_WaterOrientationalRelaxation_zeroMoleculesDeprecated(universe):
# wor_zero = waterdynamics.WaterOrientationalRelaxation(
# universe, SELECTION2, 0, 5, 2, order=2)
# wor_zero.run()
# assert_almost_equal(wor_zero.timeseries[1], (0.0, 0.0, 0.0))

# def test_WaterOrientationalRelaxation_order_1Deprecated(universe):
# wor = waterdynamics.WaterOrientationalRelaxation(
# universe, SELECTION1, 0, 5, 2, order=1)
# wor.run()
# print(wor.timeseries)
# assert_almost_equal(wor.timeseries[1][2], 0.71486,
# decimal=5)


# def test_WaterOrientationalRelaxation_order_1_zeroMoleculesDeprecated(universe):
# wor_zero = waterdynamics.WaterOrientationalRelaxation(
# universe, SELECTION2, 0, 5, 2, order=1)
# wor_zero.run()
# assert_almost_equal(wor_zero.timeseries[1], (0.0, 0.0, 0.0))


def test_AngularDistribution(universe):
Expand Down Expand Up @@ -99,7 +116,8 @@ def test_SurvivalProbability_intermittency1and2(universe):
"""
with patch.object(universe, 'select_atoms') as select_atoms_mock:
ids = [(9, 8), (), (8,), (9,), (8,), (), (9, 8), (), (8,), (9, 8)]
select_atoms_mock.side_effect = lambda selection: Mock(ids=ids.pop()) # atom IDs fed set by set
select_atoms_mock.side_effect = lambda selection: Mock(
ids=ids.pop()) # atom IDs fed set by set
sp = waterdynamics.SurvivalProbability(universe, "")
sp.run(tau_max=3, stop=10, verbose=True, intermittency=2)
assert all(x == {9, 8} for x in sp._intermittent_selected_ids)
Expand All @@ -113,7 +131,8 @@ def test_SurvivalProbability_intermittency2lacking(universe):
"""
with patch.object(universe, 'select_atoms') as select_atoms_mock:
ids = [(9,), (), (), (), (9,), (), (), (), (9,)]
select_atoms_mock.side_effect = lambda selection: Mock(ids=ids.pop()) # atom IDs fed set by set
select_atoms_mock.side_effect = lambda selection: Mock(
ids=ids.pop()) # atom IDs fed set by set
sp = waterdynamics.SurvivalProbability(universe, "")
sp.run(tau_max=3, stop=9, verbose=True, intermittency=2)
assert_almost_equal(sp.sp_timeseries, [1, 0, 0, 0])
Expand All @@ -125,8 +144,10 @@ def test_SurvivalProbability_intermittency1_step5_noSkipping(universe):
No frames should be skipped.
"""
with patch.object(universe, 'select_atoms') as select_atoms_mock:
ids = [(2, 3), (3,), (2, 3), (3,), (2,), (3,), (2, 3), (3,), (2, 3), (2, 3)]
select_atoms_mock.side_effect = lambda selection: Mock(ids=ids.pop()) # atom IDs fed set by set
ids = [(2, 3), (3,), (2, 3), (3,), (2,),
(3,), (2, 3), (3,), (2, 3), (2, 3)]
select_atoms_mock.side_effect = lambda selection: Mock(
ids=ids.pop()) # atom IDs fed set by set
sp = waterdynamics.SurvivalProbability(universe, "")
sp.run(tau_max=2, stop=10, verbose=True, intermittency=1, step=5)
assert all((x == {2, 3} for x in sp._intermittent_selected_ids))
Expand All @@ -141,7 +162,8 @@ def test_SurvivalProbability_intermittency1_step5_Skipping(universe):
with patch.object(universe, 'select_atoms') as select_atoms_mock:
ids = [(1,), (), (1,), (), (1,), (), (1,), (), (1,), (1,)]
beforepopsing = len(ids) - 2
select_atoms_mock.side_effect = lambda selection: Mock(ids=ids.pop()) # atom IDs fed set by set
select_atoms_mock.side_effect = lambda selection: Mock(
ids=ids.pop()) # atom IDs fed set by set
sp = waterdynamics.SurvivalProbability(universe, "")
sp.run(tau_max=1, stop=10, verbose=True, intermittency=1, step=5)
assert all((x == {1} for x in sp._intermittent_selected_ids))
Expand All @@ -151,44 +173,50 @@ def test_SurvivalProbability_intermittency1_step5_Skipping(universe):

def test_intermittency_none():
# No changes asked - returns the same data
input_ids = [{1}, {1}, {1}, set(), set(), {1}, {1}, {1}, set(), set(), {1}, set(), set(), {1}]
input_ids = [{1}, {1}, {1}, set(), set(), {1}, {1}, {1}, set(),
set(), {1}, set(), set(), {1}]
corrected = correct_intermittency(input_ids, intermittency=0)
assert all(x == y for x,y in zip(input_ids, corrected))
assert all(x == y for x, y in zip(input_ids, corrected))


def test_intermittency_1and2():
# The maximum gap in the dataset is 2, so the IDs are always present after correction
input_ids = [{9, 8}, set(), {8, }, {9, }, {8, }, set(), {9, 8}, set(), {8, }, {9, 8, }]
input_ids = [{9, 8}, set(), {8, }, {9, }, {8, }, set(),
{9, 8}, set(), {8, }, {9, 8, }]
corrected = correct_intermittency(input_ids, intermittency=2)
assert all((x == {9, 8} for x in corrected))


def test_intermittency_2tooShort():
#The IDs are abscent for too long/
input_ids = [{9,}, {}, {}, {}, {9,}, {}, {}, {}, {9,}]
# The IDs are abscent for too long/
input_ids = [{9, }, {}, {}, {}, {9, }, {}, {}, {}, {9, }]
corrected = correct_intermittency(input_ids, intermittency=2)
assert all(x == y for x, y in zip(input_ids, corrected))


def test_intermittency_setsOfSets():
# Verificaiton for the case of hydrogen bonds (sets of sets)
input_ids = [{frozenset({1,2}), frozenset({3, 4})},set(), set(),
input_ids = [{frozenset({1, 2}), frozenset({3, 4})}, set(), set(),
{frozenset({1, 2}), frozenset({3, 4})}, set(), set(),
{frozenset({1, 2}), frozenset({3, 4})}, set(), set(),
{frozenset({1, 2}), frozenset({3, 4})}]
corrected = correct_intermittency(input_ids, intermittency=2)
assert all((x == {frozenset({1, 2}), frozenset({3, 4})} for x in corrected))
assert all((x == {frozenset({1, 2}), frozenset({3, 4})}
for x in corrected))


def test_autocorrelation_alwaysPresent():
input = [{1, 2}, {1, 2}, {1, 2}, {1, 2}, {1, 2}, {1, 2}, {1, 2}]
tau_timeseries, sp_timeseries, sp_timeseries_data = autocorrelation(input, tau_max=3)
tau_timeseries, sp_timeseries, sp_timeseries_data = autocorrelation(
input, tau_max=3)
assert all(np.equal(sp_timeseries, 1))


def test_autocorrelation_definedTaus():
input_ids = [{9, 8, 7}, {8, 7, 6}, {7, 6, 5}, {6, 5, 4}, {5, 4, 3}, {4, 3, 2}, {3, 2, 1}]
tau_timeseries, sp_timeseries, sp_timeseries_data = autocorrelation(input_ids, tau_max=3)
input_ids = [{9, 8, 7}, {8, 7, 6}, {7, 6, 5}, {
6, 5, 4}, {5, 4, 3}, {4, 3, 2}, {3, 2, 1}]
tau_timeseries, sp_timeseries, sp_timeseries_data = autocorrelation(
input_ids, tau_max=3)
assert_almost_equal(sp_timeseries, [1, 2/3., 1/3., 0])


Expand All @@ -197,7 +225,8 @@ def test_autocorrelation_intermittency1_windowJump_intermittencyAll():
Step leads to skipping frames if (tau_max + 1) + (intermittency * 2) < step.
No frames should be skipped so intermittency should be applied to all.
"""
input_ids = [{2, 3}, {3,}, {2, 3}, {3,}, {2,}, {3,}, {2, 3}, {3,}, {2, 3}, {2, 3}]
input_ids = [{2, 3}, {3, }, {2, 3}, {3, }, {
2, }, {3, }, {2, 3}, {3, }, {2, 3}, {2, 3}]
corrected = correct_intermittency(input_ids, intermittency=1)
tau_timeseries, sp_timeseries, sp_timeseries_data = autocorrelation(corrected, tau_max=2,
window_step=5)
Expand All @@ -206,21 +235,26 @@ def test_autocorrelation_intermittency1_windowJump_intermittencyAll():


def test_autocorrelation_windowBigJump():
#The empty sets are ignored (no intermittency)
input_ids = [{1}, {1}, {1}, set(), set(), {1}, {1}, {1}, set(), set(), {1}, {1}, {1}]
tau_timeseries, sp_timeseries, sp_timeseries_data = autocorrelation(input_ids, tau_max=2, window_step=5)
# The empty sets are ignored (no intermittency)
input_ids = [{1}, {1}, {1}, set(), set(), {1}, {1}, {1},
set(), set(), {1}, {1}, {1}]
tau_timeseries, sp_timeseries, sp_timeseries_data = autocorrelation(
input_ids, tau_max=2, window_step=5)
assert_almost_equal(sp_timeseries, [1, 1, 1])


def test_autocorrelation_windowBigJump_absence():
# In the last frame the molecules are absent
input_ids = [{1}, {1}, {1}, set(), set(), {1}, {1}, {1}, set(), set(), {1}, set(), set()]
tau_timeseries, sp_timeseries, sp_timeseries_data = autocorrelation(input_ids, tau_max=2, window_step=5)
input_ids = [{1}, {1}, {1}, set(), set(), {1}, {1}, {1},
set(), set(), {1}, set(), set()]
tau_timeseries, sp_timeseries, sp_timeseries_data = autocorrelation(
input_ids, tau_max=2, window_step=5)
assert_almost_equal(sp_timeseries, [1, 2/3., 2/3.])


def test_autocorrelation_intermittency1_many():
input_ids = [{1}, set(), {1}, set(), {1}, set(), {1}, set(), {1}, set(), {1}, set(), {1}, set(), {1}]
input_ids = [{1}, set(), {1}, set(), {1}, set(), {1}, set(), {
1}, set(), {1}, set(), {1}, set(), {1}]
corrected = correct_intermittency(input_ids, intermittency=1)
tau_timeseries, sp_timeseries, sp_timeseries_data = autocorrelation(corrected, tau_max=14,
window_step=5)
Expand All @@ -229,7 +263,8 @@ def test_autocorrelation_intermittency1_many():

def test_autocorrelation_intermittency2_windowBigJump():
# The intermittency corrects the last frame
input_ids = [{1}, {1}, {1}, set(), set(), {1}, {1}, {1}, set(), set(), {1}, set(), set(), {1}]
input_ids = [{1}, {1}, {1}, set(), set(), {1}, {1}, {1}, set(),
set(), {1}, set(), set(), {1}]
corrected = correct_intermittency(input_ids, intermittency=2)
tau_timeseries, sp_timeseries, sp_timeseries_data = autocorrelation(corrected, tau_max=2,
window_step=5)
Expand All @@ -238,17 +273,21 @@ def test_autocorrelation_intermittency2_windowBigJump():

def test_SurvivalProbability_t0tf(universe):
with patch.object(universe, 'select_atoms') as select_atoms_mock:
ids = [(0, ), (0, ), (7, 6, 5), (6, 5, 4), (5, 4, 3), (4, 3, 2), (3, 2, 1), (0, )]
select_atoms_mock.side_effect = lambda selection: Mock(ids=ids.pop(2)) # atom IDs fed set by set
ids = [(0, ), (0, ), (7, 6, 5), (6, 5, 4),
(5, 4, 3), (4, 3, 2), (3, 2, 1), (0, )]
select_atoms_mock.side_effect = lambda selection: Mock(
ids=ids.pop(2)) # atom IDs fed set by set
sp = waterdynamics.SurvivalProbability(universe, "")
sp.run(tau_max=3, start=2, stop=7)
assert_almost_equal(sp.sp_timeseries, [1, 2 / 3.0, 1 / 3.0, 0])


def test_SurvivalProbability_definedTaus(universe):
with patch.object(universe, 'select_atoms') as select_atoms_mock:
ids = [(9, 8, 7), (8, 7, 6), (7, 6, 5), (6, 5, 4), (5, 4, 3), (4, 3, 2), (3, 2, 1)]
select_atoms_mock.side_effect = lambda selection: Mock(ids=ids.pop()) # atom IDs fed set by set
ids = [(9, 8, 7), (8, 7, 6), (7, 6, 5), (6, 5, 4),
(5, 4, 3), (4, 3, 2), (3, 2, 1)]
select_atoms_mock.side_effect = lambda selection: Mock(
ids=ids.pop()) # atom IDs fed set by set
sp = waterdynamics.SurvivalProbability(universe, "")
sp.run(tau_max=3, start=0, stop=7, verbose=True)
assert_almost_equal(sp.sp_timeseries, [1, 2 / 3.0, 1 / 3.0, 0])
Expand Down
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