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 setup_method(self):
"""Reset some attributes.
self.dic_op needs to be reinitialized
since it is modified by some of the functions tested.
"""
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'])
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 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_make_dic_Cname2Hnames(inputs):
"""Test for make_dic_Cname2Hnames().
Parameters
----------
inputs : function
Callback which generates input data.
"""
dic_OP, _ = init_dics.init_dic_OP(inputs['universe'],
inputs['dic_atname2genericname'],
inputs['dic_lipid']['resname'])
dic = init_dics.make_dic_Cname2Hnames(dic_OP)
# Number of Carbons with attached hydrogens
assert len(dic) == 40
assert dic['C1'] == ('H11', 'H12', 'H13')
assert dic['C13'] == ('H131', )
assert dic['C49'] == ('H491', 'H492')
assert dic['CA2'] == ('HA21', 'HA22', 'HA23')
def test_init_dic_OP(inputs):
"""Test for init_dic_OP().
Parameters
----------
inputs : function
Callback which generates input data.
"""
dic_OP, dic_corresp_numres_index_dic_OP = init_dics.init_dic_OP(
inputs['universe'], inputs['dic_atname2genericname'],
inputs['dic_lipid']['resname'])
# Number of Order parmeters
assert len(dic_OP) == 82
for key in [('C1', 'H11'), ('C44', 'H442'), ('C17', 'H171'),
('CA1', 'HA11')]:
assert key in dic_OP.keys()
# Number of lipid molecules
assert len(dic_OP[('C37', 'H371')]) == 10
# Number of lipid molecules
assert len(dic_corresp_numres_index_dic_OP) == 10
assert dic_corresp_numres_index_dic_OP[2] == 0
assert dic_corresp_numres_index_dic_OP[11] == 9