def test_count_by_time_weight(self, universe_AWA_AWWA):
'''
This test tests if modyfing the analysis_func allows the weight to be changed
in count_by_type().
:return:
'''
wb = WaterBridgeAnalysis(universe_AWA_AWWA,
'protein and (resid 1 or resid 5)',
'protein and (resid 4 or resid 8)',
order=2)
wb.run(verbose=False)
def analysis(current, output, u):
sele1_index, sele1_heavy_index, atom2, heavy_atom2, dist, angle = current[
0]
atom1, heavy_atom1, sele2_index, sele2_heavy_index, dist, angle = current[
-1]
sele1 = u.atoms[sele1_index]
sele2 = u.atoms[sele2_index]
(s1_resname, s1_resid, s1_name) = (sele1.resname, sele1.resid,
sele1.name)
(s2_resname, s2_resid, s2_name) = (sele2.resname, sele2.resid,
sele2.name)
key = (s1_resname, s1_resid, s2_resname, s2_resid)
output[key] += len(current) - 1
assert_equal(wb.count_by_time(analysis_func=analysis), [
(0, 3),
])
def test_empty_selection(self, universe_DA):
'''Test the case when selection yields empty result'''
wb = WaterBridgeAnalysis(universe_DA,
'protein and (resid 9)',
'protein and (resid 10)',
order=0)
wb.run()
assert wb._network == [{}]
def test_count_by_type_single_link(self, universe_DWA):
'''
This test tests the simplest water bridge to see if count_by_type() works.
'''
wb = WaterBridgeAnalysis(universe_DWA, 'protein and (resid 1)',
'protein and (resid 4)')
wb.run(verbose=False)
assert_equal(wb.count_by_type(),
[(1, 4, 'ALA', 1, 'H', 'ALA', 4, 'O', 1.)])
def test_accepter_donor(self, universe_AD):
'''Test zeroth order acceptor to donor hydrogen bonding'''
wb = WaterBridgeAnalysis(universe_AD,
'protein and (resid 1)',
'protein and (resid 4)',
order=0)
wb.run(verbose=False)
network = wb._network[0]
assert_equal(list(network.keys())[0][:4], (0, None, 1, 2))
def test_same_selection(self, universe_DWA):
'''
This test tests that if the selection 1 and selection 2 are both protein.
However, the protein only forms one hydrogen bond with the water.
This entry won't be included.
'''
wb = WaterBridgeAnalysis(universe_DWA, 'protein and resid 1',
'protein and resid 1')
wb.run(verbose=False)
assert_equal(wb._network[0], defaultdict(dict))
def test_donor_accepter_pbc(self, universe_DA_PBC):
'''Test zeroth order donor to acceptor hydrogen bonding in PBC conditions'''
wb = WaterBridgeAnalysis(universe_DA_PBC,
'protein and (resid 1)',
'protein and (resid 4)',
order=0,
pbc=True)
wb.run(verbose=False)
network = wb._network[0]
assert_equal(list(network.keys())[0][:4], (1, 0, 2, None))
def test_donor_water_donor(self, universe_DWD):
'''Test case where the hydrogen bond donor from selection 1 form
water bridge with hydrogen bond donor from selection 2'''
wb = WaterBridgeAnalysis(universe_DWD, 'protein and (resid 1)',
'protein and (resid 4)')
wb.run(verbose=False)
network = wb._network[0]
assert_equal(list(network.keys())[0][:4], (1, 0, 2, None))
second = network[list(network.keys())[0]]
assert_equal(list(second.keys())[0][:4], (2, None, 3, 4))
assert_equal(second[list(second.keys())[0]], None)
def test_acceptor_water_accepter(self, universe_AWA):
'''Test case where the hydrogen bond acceptor from selection 1 form
water bridge with hydrogen bond acceptor from selection 2'''
wb = WaterBridgeAnalysis(universe_AWA, 'protein and (resid 1)',
'protein and (resid 4)')
wb.run(verbose=False)
network = wb._network[0]
assert_equal(list(network.keys())[0][:4], (0, None, 2, 1))
second = network[list(network.keys())[0]]
assert_equal(list(second.keys())[0][:4], (3, 1, 4, None))
assert_equal(second[list(second.keys())[0]], None)
def test_donor_accepter(self, universe_DA):
'''Test zeroth order donor to acceptor hydrogen bonding'''
wb = WaterBridgeAnalysis(universe_DA,
'protein and (resid 1)',
'protein and (resid 4)',
order=0,
update_selection=True,
debug=True)
wb.run(verbose=False)
network = wb._network[0]
assert_equal(list(network.keys())[0][:4], (1, 0, 2, None))
def test_count_by_type_multiple_link(self, universe_AWA_AWWA):
'''
This test tests if count_by_type() can give the correct result for more than 1 links.
'''
wb = WaterBridgeAnalysis(universe_AWA_AWWA,
'protein and (resid 1 or resid 5)',
'protein and (resid 4 or resid 8)',
order=2)
wb.run(verbose=False)
assert_equal(sorted(wb.count_by_type()),
[[0, 4, 'ALA', 1, 'O', 'ALA', 4, 'O', 1.0],
[5, 11, 'ALA', 5, 'O', 'ALA', 8, 'O', 1.0]])
def test_acceptor_22water_accepter(self, universe_branch):
'''Test case where the hydrogen bond acceptor from selection 1 form a second order
water bridge with hydrogen bond acceptor from selection 2
and the last water is linked to two residues in selection 2'''
wb = WaterBridgeAnalysis(universe_branch,
'protein and (resid 1)',
'protein and (resid 4 or resid 5)',
order=2)
wb.run(verbose=False)
network = wb._network[0]
assert_equal(list(network.keys())[0][:4], (0, None, 2, 1))
second = network[list(network.keys())[0]]
assert_equal(list(second.keys())[0][:4], (3, 1, 4, None))
third = second[list(second.keys())[0]]
assert_equal([(5, 4, 7, None), (6, 4, 8, None)],
sorted([key[:4] for key in list(third.keys())]))
def test_count_by_time_empty(self, universe_AWA_AWWA):
'''
See if count_by_time() can handle zero well.
:return:
'''
wb = WaterBridgeAnalysis(universe_AWA_AWWA,
'protein and (resid 1 or resid 5)',
'protein and (resid 4 or resid 8)',
order=2)
wb.run(verbose=False)
def analysis(current, output, u):
pass
assert_equal(wb.count_by_time(analysis_func=analysis), [
(0, 0),
])
def test_timeseries_hba(self, universe_branch):
'''Test if the time series data is correctly generated in hydrogen bond analysis format'''
wb = WaterBridgeAnalysis(universe_branch,
'protein and (resid 1)',
'protein and (resid 4 or resid 5)',
order=2)
wb.output_format = 'donor_acceptor'
wb.run(verbose=False)
timeseries = sorted(wb.timeseries[0])
assert_equal(timeseries[0][:4],
(2, 0, ('SOL', 2, 'HW1'), ('ALA', 1, 'O')))
assert_equal(timeseries[1][:4],
(3, 4, ('SOL', 2, 'HW2'), ('SOL', 3, 'OW')))
assert_equal(timeseries[2][:4],
(5, 7, ('SOL', 3, 'HW1'), ('ALA', 4, 'O')))
assert_equal(timeseries[3][:4],
(6, 8, ('SOL', 3, 'HW2'), ('ALA', 5, 'O')))
def wb_multiframe():
'''A water bridge object with multipley frames'''
grofile = '''Test gro file
13
1ALA O 1 0.000 0.000 0.000
1ALA H 2 0.000 0.000 0.000
2SOL OW 3 0.300 0.000 0.000
2SOL HW1 4 0.200 0.000 0.000
2SOL HW2 5 0.400 0.000 0.000
3SOL OW 6 0.600 0.000 0.000
3SOL HW1 7 0.700 0.000 0.000
4SOL OW 8 0.900 0.000 0.000
4SOL HW1 9 1.000 0.000 0.000
5SOL OW 10 1.200 0.000 0.000
5SOL HW1 11 1.300 0.000 0.000
6ALA H 12 1.400 0.000 0.000
6ALA O 13 1.400 0.000 0.000
10.0 10.0 10.0'''
u = MDAnalysis.Universe(StringIO(grofile), format='gro')
wb = WaterBridgeAnalysis(u,
'protein and (resid 1)',
'protein and (resid 4)',
order=4)
# Build an dummy WaterBridgeAnalysis object for testing
wb._network = []
wb._network.append({(1, 0, 12, None, 2.0, 180.0): None})
wb._network.append({(0, None, 12, 13, 2.0, 180.0): None})
wb._network.append({
(1, 0, 3, None, 2.0, 180.0): {
(4, 2, 12, None, 2.0, 180.0): None
}
})
wb._network.append({
(0, None, 3, 2, 2.0, 180.0): {
(4, 2, 5, None, 2.0, 180.0): {
(5, None, 11, 12, 2.0, 180.0): None
}
}
})
wb.timesteps = range(len(wb._network))
return wb
def test_selection_type_error(self, universe_DA):
'''Test the case when the wrong selection1_type is given'''
try:
wb = WaterBridgeAnalysis(universe_DA,
'protein and (resid 1)',
'protein and (resid 4)',
order=0,
selection1_type='aaa')
except ValueError:
pass
else:
raise pytest.fail("selection_type aaa should rasie error")
def test_nodata(self, universe_DA):
'''Test if the funtions can run when there is no data.
This is achieved by not runing the run() first.'''
wb = WaterBridgeAnalysis(universe_DA,
'protein and (resid 1)',
'protein and (resid 4)',
order=0)
wb.generate_table()
assert_equal(wb.timesteps_by_type(), None)
assert_equal(wb.count_by_time(), None)
assert_equal(wb.count_by_type(), None)
def test_acceptor_12water_accepter(self, universe_AWA_AWWA):
'''Test of independent first order and second can be recognised correctely'''
wb = WaterBridgeAnalysis(universe_AWA_AWWA,
'protein and (resid 1 or resid 5)',
'protein and (resid 4 or resid 8)',
order=1)
wb.run(verbose=False)
network = wb._network[0]
assert_equal(list(network.keys())[0][:4], (0, None, 2, 1))
second = network[list(network.keys())[0]]
assert_equal(list(second.keys())[0][:4], (3, 1, 4, None))
assert_equal(second[list(second.keys())[0]], None)
network = wb._network[0]
wb = WaterBridgeAnalysis(universe_AWA_AWWA,
'protein and (resid 1 or resid 5)',
'protein and (resid 4 or resid 8)',
order=2)
wb.run(verbose=False)
network = wb._network[0]
assert_equal([(0, None, 2, 1), (5, None, 7, 6)],
sorted([key[:4] for key in list(network.keys())]))
def test_empty(self, universe_empty):
'''Test case where no water bridge exists'''
wb = WaterBridgeAnalysis(universe_empty, 'protein', 'protein')
wb.run(verbose=False)
assert_equal(wb._network[0], defaultdict(dict))
def test_loop(self, universe_loop):
'''Test if loop can be handled correctly'''
wb = WaterBridgeAnalysis(universe_loop, 'protein and (resid 1)',
'protein and (resid 1 or resid 4)')
wb.run()
assert_equal(len(wb._network[0].keys()), 2)
def test_acceptor_2water_accepter(self, universe_AWWA):
'''Test case where the hydrogen bond acceptor from selection 1 form second order
water bridge with hydrogen bond acceptor from selection 2'''
# test first order
wb = WaterBridgeAnalysis(universe_AWWA, 'protein and (resid 1)',
'protein and (resid 4)')
wb.run(verbose=False)
assert_equal(wb._network[0], defaultdict(dict))
# test second order
wb = WaterBridgeAnalysis(universe_AWWA,
'protein and (resid 1)',
'protein and (resid 4)',
order=2)
wb.run(verbose=False)
network = wb._network[0]
assert_equal(list(network.keys())[0][:4], (0, None, 2, 1))
second = network[list(network.keys())[0]]
assert_equal(list(second.keys())[0][:4], (3, 1, 4, None))
third = second[list(second.keys())[0]]
assert_equal(list(third.keys())[0][:4], (5, 4, 6, None))
assert_equal(third[list(third.keys())[0]], None)
# test third order
wb = WaterBridgeAnalysis(universe_AWWA,
'protein and (resid 1)',
'protein and (resid 4)',
order=3)
wb.run(verbose=False)
network = wb._network[0]
assert_equal(list(network.keys())[0][:4], (0, None, 2, 1))
second = network[list(network.keys())[0]]
assert_equal(list(second.keys())[0][:4], (3, 1, 4, None))
third = second[list(second.keys())[0]]
assert_equal(list(third.keys())[0][:4], (5, 4, 6, None))
assert_equal(third[list(third.keys())[0]], None)
def test_acceptor_4water_accepter(self, universe_AWWWWA):
'''Test case where the hydrogen bond acceptor from selection 1 form fourth order
water bridge with hydrogen bond acceptor from selection 2'''
wb = WaterBridgeAnalysis(universe_AWWWWA,
'protein and (resid 1)',
'protein and (resid 6)',
order=3)
wb.run(verbose=False)
assert_equal(wb._network[0], defaultdict(dict))
wb = WaterBridgeAnalysis(universe_AWWWWA,
'protein and (resid 1)',
'protein and (resid 6)',
order=4)
wb.run(verbose=False)
network = wb._network[0]
assert_equal(list(network.keys())[0][:4], (0, None, 2, 1))
second = network[list(network.keys())[0]]
assert_equal(list(second.keys())[0][:4], (3, 1, 4, None))
third = second[list(second.keys())[0]]
assert_equal(list(third.keys())[0][:4], (5, 4, 6, None))
fourth = third[list(third.keys())[0]]
assert_equal(list(fourth.keys())[0][:4], (7, 6, 8, None))
fifth = fourth[list(fourth.keys())[0]]
assert_equal(list(fifth.keys())[0][:4], (9, 8, 10, None))
assert_equal(fifth[list(fifth.keys())[0]], None)
wb = WaterBridgeAnalysis(universe_AWWWWA,
'protein and (resid 1)',
'protein and (resid 6)',
order=5)
wb.run(verbose=False)
network = wb._network[0]
assert_equal(list(network.keys())[0][:4], (0, None, 2, 1))
second = network[list(network.keys())[0]]
assert_equal(list(second.keys())[0][:4], (3, 1, 4, None))
third = second[list(second.keys())[0]]
assert_equal(list(third.keys())[0][:4], (5, 4, 6, None))
fourth = third[list(third.keys())[0]]
assert_equal(list(fourth.keys())[0][:4], (7, 6, 8, None))
fifth = fourth[list(fourth.keys())[0]]
assert_equal(list(fifth.keys())[0][:4], (9, 8, 10, None))
assert_equal(fifth[list(fifth.keys())[0]], None)