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_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_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), ])