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_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_water_network(self):
'''
This test tests if the internal water object is generated correctly.
:return:
'''
grofile = '''Test gro file
5
1ALA N 1 0.000 0.000 0.000
1ALA H 2 0.100 0.000 0.000
2SOL OW 3 0.300 0.000 0.000
2SOL HW2 4 0.400 0.000 0.000
4ALA O 5 0.600 0.000 0.000
1.0 1.0 1.0'''
u = MDAnalysis.Universe(StringIO(grofile), format='gro')
wb = WaterBridgeAnalysis(u, 'protein and (resid 1)',
'protein and (resid 4)')
wb.run(verbose=False)
water_network = wb._water_network[0]
assert_equal(list(water_network.keys()), [('SOL', 2)])
values = list(water_network.values())
assert_equal(
list(values[0][0])[0][:4],
(1, 2, ('ALA', 1, 'H'), ('SOL', 2, 'OW')))
assert_equal(
list(values[0][1])[0][:4],
(3, 4, ('SOL', 2, 'HW2'), ('ALA', 4, 'O')))
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_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_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_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_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_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_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_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 test_empty(self):
'''Test case where no water bridge exists'''
grofile = '''Test gro file
5
1ALA N 1 0.000 0.000 0.000
1ALA H 2 0.100 0.000 0.000
2SOL OW 3 3.000 0.000 0.000
4ALA H 4 0.500 0.000 0.000
4ALA N 5 0.600 0.000 0.000
1.0 1.0 1.0'''
u = MDAnalysis.Universe(StringIO(grofile), format='gro')
wb = WaterBridgeAnalysis(u, 'protein', 'protein')
wb.run(verbose=False)
assert_equal(wb._timeseries, [[]])
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_empty(self):
'''Test case where no water bridge exists'''
grofile = '''Test gro file
5
1ALA N 1 0.000 0.000 0.000
1ALA H 2 0.100 0.000 0.000
2SOL OW 3 3.000 0.000 0.000
4ALA H 4 0.500 0.000 0.000
4ALA N 5 0.600 0.000 0.000
1.0 1.0 1.0'''
u = MDAnalysis.Universe(StringIO(grofile), format='gro')
wb = WaterBridgeAnalysis(u, 'protein', 'protein')
wb.run(verbose=False)
assert_equal(wb._timeseries, [[]])
def test_same_selection(self):
'''
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.
:return:
'''
grofile = '''Test gro file
3
1ALA N 1 0.000 0.000 0.000
1ALA H 2 0.100 0.000 0.000
2SOL OW 3 0.300 0.000 0.000
1.0 1.0 1.0'''
u = MDAnalysis.Universe(StringIO(grofile), format='gro')
wb = WaterBridgeAnalysis(u, 'protein', 'protein')
wb.run(verbose=False)
assert_equal(wb._timeseries, [[]])
def test_same_selection(self):
'''
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.
:return:
'''
grofile = '''Test gro file
3
1ALA N 1 0.000 0.000 0.000
1ALA H 2 0.100 0.000 0.000
2SOL OW 3 0.300 0.000 0.000
1.0 1.0 1.0'''
u = MDAnalysis.Universe(StringIO(grofile), format='gro')
wb = WaterBridgeAnalysis(u, 'protein', 'protein')
wb.run(verbose=False)
assert_equal(wb._timeseries, [[]])
def test_count_by_type_single_link(self):
'''
This test tests the simplest water bridge to see if count_by_type() works.
:return:
'''
grofile = '''Test gro file
5
1ALA N 1 0.000 0.000 0.000
1ALA H 2 0.100 0.000 0.000
2SOL OW 3 0.300 0.000 0.000
2SOL HW2 4 0.400 0.000 0.000
4ALA O 5 0.600 0.000 0.000
1.0 1.0 1.0'''
u = MDAnalysis.Universe(StringIO(grofile), format='gro')
wb = WaterBridgeAnalysis(u, 'protein and (resid 1)', 'protein and (resid 4)')
wb.run(verbose=False)
assert_equal(wb.count_by_type().tolist(), [(1, 4, 'ALA', 1, 'H', 'ALA', 4, 'O', 1.)])
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_acceptor_water_accepter(self):
'''Test case where the hydrogen bond acceptor from selection 1 form
water bridge with hydrogen bond acceptor from selection 2'''
grofile = '''Test gro file
5
1ALA O 1 0.000 0.000 0.000
2SOL OW 2 0.300 0.000 0.000
2SOL HW1 3 0.200 0.000 0.000
2SOL HW2 4 0.400 0.000 0.000
4ALA O 5 0.600 0.000 0.000
1.0 1.0 1.0'''
u = MDAnalysis.Universe(StringIO(grofile), format='gro')
wb = WaterBridgeAnalysis(u, 'protein and (resid 1)', 'protein and (resid 4)')
wb.run(verbose=False)
timeseries = wb._timeseries
assert_equal(timeseries[0][0][:4], (2, 0, ('SOL', 2, 'HW1'), ('ALA', 1, 'O')))
assert_equal(timeseries[0][1][:4], (3, 4, ('SOL', 2, 'HW2'), ('ALA', 4, 'O')))
def test_donor_water_donor(self):
'''Test case where the hydrogen bond donor from selection 1 form
water bridge with hydrogen bond donor from selection 2'''
grofile = '''Test gro file
5
1ALA N 1 0.000 0.000 0.000
1ALA H 2 0.100 0.000 0.000
2SOL OW 3 0.300 0.000 0.000
4ALA H 4 0.500 0.000 0.000
4ALA N 5 0.600 0.000 0.000
1.0 1.0 1.0'''
u = MDAnalysis.Universe(StringIO(grofile), format='gro')
wb = WaterBridgeAnalysis(u, 'protein and (resid 1)', 'protein and (resid 4)')
wb.run(verbose=False)
timeseries = wb._timeseries
assert_equal(timeseries[0][0][:4], (1, 2, ('ALA', 1, 'H'), ('SOL', 2, 'OW')))
assert_equal(timeseries[0][1][:4], (3, 2, ('ALA', 4, 'H'), ('SOL', 2, 'OW')))
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_count_by_type_single_link(self):
'''
This test tests the simplest water bridge to see if count_by_type() works.
:return:
'''
grofile = '''Test gro file
5
1ALA N 1 0.000 0.000 0.000
1ALA H 2 0.100 0.000 0.000
2SOL OW 3 0.300 0.000 0.000
2SOL HW2 4 0.400 0.000 0.000
4ALA O 5 0.600 0.000 0.000
1.0 1.0 1.0'''
u = MDAnalysis.Universe(StringIO(grofile), format='gro')
wb = WaterBridgeAnalysis(u, 'protein and (resid 1)',
'protein and (resid 4)')
wb.run(verbose=False)
assert_equal(wb.count_by_type().tolist(),
[(1, 4, 'ALA', 1, 'H', 'ALA', 4, 'O', 1.)])
def test_acceptor_water_accepter(self):
'''Test case where the hydrogen bond acceptor from selection 1 form
water bridge with hydrogen bond acceptor from selection 2'''
grofile = '''Test gro file
5
1ALA O 1 0.000 0.000 0.000
2SOL OW 2 0.300 0.000 0.000
2SOL HW1 3 0.200 0.000 0.000
2SOL HW2 4 0.400 0.000 0.000
4ALA O 5 0.600 0.000 0.000
1.0 1.0 1.0'''
u = MDAnalysis.Universe(StringIO(grofile), format='gro')
wb = WaterBridgeAnalysis(u, 'protein and (resid 1)',
'protein and (resid 4)')
wb.run(verbose=False)
timeseries = wb._timeseries
assert_equal(timeseries[0][0][:4],
(2, 0, ('SOL', 2, 'HW1'), ('ALA', 1, 'O')))
assert_equal(timeseries[0][1][:4],
(3, 4, ('SOL', 2, 'HW2'), ('ALA', 4, 'O')))
def test_donor_water_donor(self):
'''Test case where the hydrogen bond donor from selection 1 form
water bridge with hydrogen bond donor from selection 2'''
grofile = '''Test gro file
5
1ALA N 1 0.000 0.000 0.000
1ALA H 2 0.100 0.000 0.000
2SOL OW 3 0.300 0.000 0.000
4ALA H 4 0.500 0.000 0.000
4ALA N 5 0.600 0.000 0.000
1.0 1.0 1.0'''
u = MDAnalysis.Universe(StringIO(grofile), format='gro')
wb = WaterBridgeAnalysis(u, 'protein and (resid 1)',
'protein and (resid 4)')
wb.run(verbose=False)
timeseries = wb._timeseries
assert_equal(timeseries[0][0][:4],
(1, 2, ('ALA', 1, 'H'), ('SOL', 2, 'OW')))
assert_equal(timeseries[0][1][:4],
(3, 2, ('ALA', 4, 'H'), ('SOL', 2, 'OW')))
def test_water_network(self):
'''
This test tests if the internal water object is generated correctly.
:return:
'''
grofile = '''Test gro file
5
1ALA N 1 0.000 0.000 0.000
1ALA H 2 0.100 0.000 0.000
2SOL OW 3 0.300 0.000 0.000
2SOL HW2 4 0.400 0.000 0.000
4ALA O 5 0.600 0.000 0.000
1.0 1.0 1.0'''
u = MDAnalysis.Universe(StringIO(grofile), format='gro')
wb = WaterBridgeAnalysis(u, 'protein and (resid 1)', 'protein and (resid 4)')
wb.run(verbose=False)
water_network = wb._water_network[0]
assert_equal(list(water_network.keys()), [('SOL', 2)])
values = list(water_network.values())
assert_equal(list(values[0][0])[0][:4], (1, 2, ('ALA', 1, 'H'), ('SOL', 2, 'OW')))
assert_equal(list(values[0][1])[0][:4], (3, 4, ('SOL', 2, 'HW2'), ('ALA', 4, 'O')))
def test_acceptor_3water_accepter(self, universe_AWWWA):
'''Test case where the hydrogen bond acceptor from selection 1 form third order
water bridge with hydrogen bond acceptor from selection 2'''
wb = WaterBridgeAnalysis(universe_AWWWA, 'protein and (resid 1)',
'protein and (resid 5)', order=2)
wb.run(verbose=False)
assert_equal(wb._network[0], defaultdict(dict))
wb = WaterBridgeAnalysis(universe_AWWWA, 'protein and (resid 1)',
'protein and (resid 5)', 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))
fourth = third[list(third.keys())[0]]
assert_equal(list(fourth.keys())[0][:4], (7, 6, 8, None))
assert_equal(fourth[list(fourth.keys())[0]], None)
wb = WaterBridgeAnalysis(universe_AWWWA, 'protein and (resid 1)',
'protein and (resid 5)', 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))
assert_equal(fourth[list(fourth.keys())[0]], None)
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_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_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)
