def test_check_read_lipids_topH_failure(self):
"""Test check_read_lipids_topH() with a file in a wrong format."""
bad_file = "Berger_wrongformat.json"
with pytest.raises(ValueError) as err:
lipids.read_lipids_topH([PATH_ROOT_DATA / bad_file])
assert f"{bad_file} is in a bad format: keyword 'resname' is missing." in str(
err.value)
def setup_class(self):
"""Initialize attributes."""
# Create correct lipid topology dict
lipids_tops = lipids.read_lipids_topH(
[lipids.PATH_JSON / "Berger_POPC.json"])
dic_lipid = lipids_tops["Berger_POPC"]
self.args["dic_lipid"] = dic_lipid
def setup_class(self):
"""Initialize all data."""
lipids_tops = lipids.read_lipids_topH(
[lipids.PATH_JSON / "Berger_POPC.json"])
# Input parameters
self.pdb = self.PATH_DATA / "10POPC.pdb"
self.defop = self.PATH_DATA / "OP_def_BergerPOPC.def"
self.dic_lipid = lipids_tops["Berger_POPC"]
self.begin = 0
self.end = 1
# attributes
self.universe_woH = mda.Universe(str(self.pdb))
self.dic_atname2genericname = init_dics.make_dic_atname2genericname(
self.defop)
self.dic_OP, self.dic_corresp_numres_index_dic_OP = init_dics.init_dic_OP(
self.universe_woH, self.dic_atname2genericname,
self.dic_lipid['resname'])
self.dic_Cname2Hnames = init_dics.make_dic_Cname2Hnames(self.dic_OP)
# Compute the order parameter
core.fast_build_all_Hs_calc_OP(self.universe_woH, self.begin, self.end,
self.dic_OP, self.dic_lipid,
self.dic_Cname2Hnames)
def test_fail_main_coord_topology_mismatch(self):
"""Test when coord file and topology doesn't match."""
args = self.args.copy()
lipids_tops = lipids.read_lipids_topH(
[lipids.PATH_JSON / "CHARMM36_POPC.json"])
dic_lipid = lipids_tops["CHARMM36_POPC"]
args["dic_lipid"] = dic_lipid
with pytest.raises(BuildHError) as err:
UI.main(**args)
assert "The topology chosen does not match the structure provided" in str(
err.value)
def inputs():
"""Define some input parameters for the tests."""
# Input parameters
path_data = PATH_ROOT_DATA / "Berger_POPC"
pdb = path_data / "10POPC.pdb"
defop = path_data / "OP_def_BergerPOPC.def"
lipids_tops = lipids.read_lipids_topH(
[lipids.PATH_JSON / "Berger_POPC.json"])
dic_lipid = lipids_tops["Berger_POPC"]
universe_woH = mda.Universe(str(pdb))
dic_atname2genericname = init_dics.make_dic_atname2genericname(defop)
return {
'universe': universe_woH,
'defop': defop,
'dic_lipid': dic_lipid,
'dic_atname2genericname': dic_atname2genericname
}
def setup_class(self):
"""Initialize attributes."""
lipids_tops = lipids.read_lipids_topH(
[lipids.PATH_JSON / "Berger_POPC.json"])
# Input parameters
self.pdb = self.PATH_DATA / "2POPC.pdb"
self.defop = self.PATH_DATA / "OP_def_BergerPOPC.def"
self.dic_lipid = lipids_tops["Berger_POPC"]
# attributes
self.universe_woH = mda.Universe(str(self.pdb))
self.dic_atname2genericname = init_dics.make_dic_atname2genericname(
self.defop)
self.dic_OP, self.dic_corresp_numres_index_dic_OP = init_dics.init_dic_OP(
self.universe_woH, self.dic_atname2genericname,
self.dic_lipid['resname'])
self.dic_Cname2Hnames = init_dics.make_dic_Cname2Hnames(self.dic_OP)
def test_check_read_lipids_topH_success(self):
"""Test check_read_lipids_topH() with correct files."""
lipids_tops = lipids.read_lipids_topH(self.path_files)
# key : key of the outer dict
# values : number of atoms in each dict
reference = {
'Berger_POPC': 41,
'Berger_PLA': 41,
'Berger_POP': 41,
'CHARMM36_POPC': 41
}
assert len(lipids_tops) == 4
assert lipids_tops.keys() == set(
['Berger_POPC', 'Berger_PLA', 'Berger_POP', 'CHARMM36_POPC'])
# Test if each dic contains the right number of atoms
for name in lipids_tops.keys():
assert len(lipids_tops[name]) == reference[name]