def test_reconstruct_Hs_first_frame(self):
"""Test for build_system_hydrogens()."""
dic_lipids_with_indexes = core.make_dic_lipids_with_indexes(self.universe_woH,
self.dic_lipid,
self.dic_OP)
new_df_atoms = core.build_system_hydrogens(self.universe_woH, self.dic_lipid,
self.dic_Cname2Hnames, dic_lipids_with_indexes)
assert new_df_atoms.shape == (1340, 7)
# Test random atoms
col_series=["atnum", "atname","resname", "resnum","x", "y", "z"]
ref_atom = pd.Series([1, "C1", "POPC", 2, 34.41999816, 46.93999862, 26.30999946],
index=col_series)
pd.testing.assert_series_equal(new_df_atoms.loc[0], ref_atom, check_names=False)
ref_atom = pd.Series([2, "H11", "POPC", 2, 35.06161421, 47.69320272, 26.76728762],
index=col_series)
pd.testing.assert_series_equal(new_df_atoms.loc[1], ref_atom, check_names=False)
ref_atom = pd.Series([259, "H501", "POPC", 3, 74.16520229, 36.21701104, 35.03256486],
index=col_series)
pd.testing.assert_series_equal(new_df_atoms.loc[258], ref_atom, check_names=False)
ref_atom = pd.Series([1339, "HA22", "POPC", 11, 27.72946942, 16.74704078, 40.53260384],
index=col_series)
pd.testing.assert_series_equal(new_df_atoms.loc[1338], ref_atom, check_names=False)
def test_reconstruct_Hs(self):
"""Test for build_all_Hs_calc_OP().
The results should be indentical to the test_fast_build_all_Hs_calc_OP() test.
"""
dic_lipids_with_indexes = core.make_dic_lipids_with_indexes(
self.universe_woH, self.dic_lipid, self.dic_OP)
pdb_wH = self.PATH_DATA / "10POPC_wH.pdb"
universe_wH = mda.Universe(str(pdb_wH))
ts = self.universe_woH.trajectory[0]
core.build_all_Hs_calc_OP(self.universe_woH, ts, self.dic_lipid,
self.dic_Cname2Hnames, universe_wH,
self.dic_OP,
self.dic_corresp_numres_index_dic_OP,
dic_lipids_with_indexes)
# Check statistics
assert_almost_equal(np.mean(self.dic_OP[('C21', 'H212')]), -0.22229490)
assert_almost_equal(np.mean(self.dic_OP[('CA2', 'HA23')]), 0.22305829)
# Check few particular cases
# Use of a loop to check key and value separately.
# The values need to be assert with float desired precision.
for (key), value in self.ref_OP.items():
assert key in self.dic_OP.keys()
assert_almost_equal(value, self.dic_OP[key])
def test_make_dic_lipids_with_indexes(self):
"""Test for make_dic_lipids_with_indexes()."""
dic_lipids_with_indexes = core.make_dic_lipids_with_indexes(self.universe_woH,
self.dic_lipid,
self.dic_OP)
assert dic_lipids_with_indexes['C1'] == ['CH3', 'N4', 'C5', 0, 3, 4]
assert dic_lipids_with_indexes['C5'] == ['CH2', 'N4', 'C6', 4, 3, 5]
assert dic_lipids_with_indexes['C13'] == ['CH', 'C12', 'C32', 'O14', 12, 11, 31, 13]
assert dic_lipids_with_indexes['C24'] == ['CHdoublebond', 'C23', 'C25', 23, 22, 24]
assert dic_lipids_with_indexes['C50'] == ['CH3', 'C49', 'C48', 49, 48, 47]
