def test_count_by_type_multiple_link(self):
'''
This test tests if count_by_type() can assemble linkage from water network.
: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)')
# Build an dummy WaterBridgeAnalysis object for testing
wb._timeseries = True
wb.timesteps = [0]
wb._water_network = [{
('SOL', 2):
[{(2, 0, ('SOL', 2, 'HW1'), ('ALA', 1, 'O'), 2.0, 179.99998),
(1, 2, ('ALA', 1, 'H'), ('SOL', 2, 'OW'), 2.0, 179.99998)},
{(3, 4, ('SOL', 2, 'HW2'), ('ALA', 4, 'O'), 2.0, 179.99998),
(3, 2, ('ALA', 4, 'H'), ('SOL', 2, 'OW'), 2.0, 179.99998)}]
}]
result = [(0, 3, 'ALA', 1, 'O', 'ALA', 4, 'H', 1.0),
(0, 4, 'ALA', 1, 'O', 'ALA', 4, 'O', 1.0),
(1, 3, 'ALA', 1, 'H', 'ALA', 4, 'H', 1.0),
(1, 4, 'ALA', 1, 'H', 'ALA', 4, 'O', 1.0)]
assert_equal(sorted(wb.count_by_type().tolist()), result)
def test_count_by_type_multiple_link(self):
'''
This test tests if count_by_type() can assemble linkage from water network.
: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)')
# Build an dummy WaterBridgeAnalysis object for testing
wb._timeseries = True
wb.timesteps = [0]
wb._water_network = [{('SOL', 2): [{(2, 0, ('SOL', 2, 'HW1'), ('ALA', 1, 'O'), 2.0, 179.99998),
(1, 2, ('ALA', 1, 'H'), ('SOL', 2, 'OW'), 2.0, 179.99998)},
{(3, 4, ('SOL', 2, 'HW2'), ('ALA', 4, 'O'), 2.0, 179.99998),
(3, 2, ('ALA', 4, 'H'), ('SOL', 2, 'OW'), 2.0, 179.99998)}]}]
result = [(0, 3, 'ALA', 1, 'O', 'ALA', 4, 'H', 1.0),
(0, 4, 'ALA', 1, 'O', 'ALA', 4, 'O', 1.0),
(1, 3, 'ALA', 1, 'H', 'ALA', 4, 'H', 1.0),
(1, 4, 'ALA', 1, 'H', 'ALA', 4, 'O', 1.0)]
assert_equal(sorted(wb.count_by_type().tolist()), result)
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_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_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_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_count_by_type_multiple_frame(self):
'''
This test tests if count_by_type() works in multiply situations.
: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)')
# Build an dummy WaterBridgeAnalysis object for testing
wb._timeseries = True
wb.timesteps = [0, 1, 2, 3, 4, 5]
wb._water_network = [# a 2 * 2 water netwrok consists of all four links
{('SOL', 2): [{(2, 0, ('SOL', 2, 'HW1'), ('ALA', 1, 'O'), 2.0, 179.99998),
(1, 2, ('ALA', 1, 'H'), ('SOL', 2, 'OW'), 2.0, 179.99998)},
{(3, 4, ('SOL', 2, 'HW2'), ('ALA', 4, 'O'), 2.0, 179.99998),
(3, 2, ('ALA', 4, 'H'), ('SOL', 2, 'OW'), 2.0, 179.99998)}]},
# a repeat
{('SOL', 2): [{(2, 0, ('SOL', 2, 'HW1'), ('ALA', 1, 'O'), 2.0, 179.99998),
(1, 2, ('ALA', 1, 'H'), ('SOL', 2, 'OW'), 2.0, 179.99998)},
{(3, 4, ('SOL', 2, 'HW2'), ('ALA', 4, 'O'), 2.0, 179.99998),
(3, 2, ('ALA', 4, 'H'), ('SOL', 2, 'OW'), 2.0, 179.99998)}]},
# single link 1
{('SOL', 2): [{(2, 0, ('SOL', 2, 'HW1'), ('ALA', 1, 'O'), 2.0, 179.99998)},
{(3, 4, ('SOL', 2, 'HW2'), ('ALA', 4, 'O'), 2.0, 179.99998)}]},
# single link 2
{('SOL', 2): [{(2, 0, ('SOL', 2, 'HW1'), ('ALA', 1, 'O'), 2.0, 179.99998)},
{(3, 1, ('ALA', 4, 'H'), ('SOL', 2, 'OW'), 2.0, 179.99998)}]},
# single link 3
{('SOL', 2): [{(1, 2, ('ALA', 1, 'H'), ('SOL', 2, 'OW'), 2.0, 179.99998)},
{(3, 4, ('SOL', 2, 'HW2'), ('ALA', 4, 'O'), 2.0, 179.99998)}]},
# single link 4
{('SOL', 2): [{(1, 2, ('ALA', 1, 'H'), ('SOL', 2, 'OW'), 2.0, 179.99998)},
{(3, 2, ('ALA', 4, 'H'), ('SOL', 2, 'OW'), 2.0, 179.99998)}]}]
result = [(0, 3, 'ALA', 1, 'O', 'ALA', 4, 'H', 0.5),
(0, 4, 'ALA', 1, 'O', 'ALA', 4, 'O', 0.5),
(1, 3, 'ALA', 1, 'H', 'ALA', 4, 'H', 0.5),
(1, 4, 'ALA', 1, 'H', 'ALA', 4, 'O', 0.5)]
assert_equal(sorted(wb.count_by_type().tolist()), result)
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_count_by_type_multiple_frame(self):
'''
This test tests if count_by_type() works in multiply situations.
: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)')
# Build an dummy WaterBridgeAnalysis object for testing
wb._timeseries = True
wb.timesteps = [0, 1, 2, 3, 4, 5]
wb._water_network = [ # a 2 * 2 water netwrok consists of all four links
{
('SOL', 2):
[{(2, 0, ('SOL', 2, 'HW1'), ('ALA', 1, 'O'), 2.0, 179.99998),
(1, 2, ('ALA', 1, 'H'), ('SOL', 2, 'OW'), 2.0, 179.99998)},
{(3, 4, ('SOL', 2, 'HW2'), ('ALA', 4, 'O'), 2.0, 179.99998),
(3, 2, ('ALA', 4, 'H'), ('SOL', 2, 'OW'), 2.0, 179.99998)}]
},
# a repeat
{
('SOL', 2):
[{(2, 0, ('SOL', 2, 'HW1'), ('ALA', 1, 'O'), 2.0, 179.99998),
(1, 2, ('ALA', 1, 'H'), ('SOL', 2, 'OW'), 2.0, 179.99998)},
{(3, 4, ('SOL', 2, 'HW2'), ('ALA', 4, 'O'), 2.0, 179.99998),
(3, 2, ('ALA', 4, 'H'), ('SOL', 2, 'OW'), 2.0, 179.99998)}]
},
# single link 1
{
('SOL', 2):
[{(2, 0, ('SOL', 2, 'HW1'), ('ALA', 1, 'O'), 2.0, 179.99998)},
{(3, 4, ('SOL', 2, 'HW2'), ('ALA', 4, 'O'), 2.0, 179.99998)}]
},
# single link 2
{
('SOL', 2):
[{(2, 0, ('SOL', 2, 'HW1'), ('ALA', 1, 'O'), 2.0, 179.99998)},
{(3, 1, ('ALA', 4, 'H'), ('SOL', 2, 'OW'), 2.0, 179.99998)}]
},
# single link 3
{
('SOL', 2):
[{(1, 2, ('ALA', 1, 'H'), ('SOL', 2, 'OW'), 2.0, 179.99998)},
{(3, 4, ('SOL', 2, 'HW2'), ('ALA', 4, 'O'), 2.0, 179.99998)}]
},
# single link 4
{
('SOL', 2):
[{(1, 2, ('ALA', 1, 'H'), ('SOL', 2, 'OW'), 2.0, 179.99998)},
{(3, 2, ('ALA', 4, 'H'), ('SOL', 2, 'OW'), 2.0, 179.99998)}]
}
]
result = [(0, 3, 'ALA', 1, 'O', 'ALA', 4, 'H', 0.5),
(0, 4, 'ALA', 1, 'O', 'ALA', 4, 'O', 0.5),
(1, 3, 'ALA', 1, 'H', 'ALA', 4, 'H', 0.5),
(1, 4, 'ALA', 1, 'H', 'ALA', 4, 'O', 0.5)]
assert_equal(sorted(wb.count_by_type().tolist()), result)
