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_make_dic_atname2genericname(inputs):
"""Test for make_dic_atname2genericname().
Parameters
----------
inputs : function
Callback which generates input data.
"""
dic = init_dics.make_dic_atname2genericname(inputs['defop'])
assert dic[('C1', 'H11')] == 'gamma1_1'
assert dic[('C32', 'H322')] == 'g1_2'
assert dic[('C39', 'H392')] == 'palmitoyl_C5b'
assert dic[('C17', 'H171')] == 'oleoyl_C2a'
assert dic[('CA2', 'HA23')] == 'oleoyl_C18c'
# Test non existent file
with pytest.raises(ValueError) as err:
init_dics.make_dic_atname2genericname("none")
assert "Can't read order parameter" in str(err.value)
def _recreate_dicts(self, def_file):
"""Recreate dicts variable from a new `def_file`.
Parameters
----------
def_file : str
path of the new definiton file.
"""
self.dic_atname2genericname = init_dics.make_dic_atname2genericname(
def_file)
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 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)