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_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_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_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)