def test_answer_letters(self):
residues = ["GLU30", "TRP32"]
input_values = (val for val in ["0.0", "4.0"])
with mock.patch('builtins.input', lambda *x: next(input_values)):
residue_and_atom.residues_from_descriptors(residues, self.by_bonds_geom2frags,
self.geom2frags.top,
)
def test_extra_dicts(self):
residues = ["GLU30", "TRP32"]
consensus_dicts = {"BW": {0: "3.50"},
"CGN": {2: "CGNt"}}
residue_and_atom.residues_from_descriptors(residues, self.by_bonds_geom2frags,
self.geom2frags.top,
additional_resnaming_dicts=consensus_dicts,
pick_this_fragment_by_default=0
)
def test_default_fragment_idx_is_none_ans_should_be_in_list(self):
input_values = (val for val in ["123"])
with mock.patch('builtins.input', lambda *x: next(input_values)):
with pytest.raises((ValueError, AssertionError)):
residue_and_atom.residues_from_descriptors("GLU30", self.by_bonds_geom2frags, self.geom2frags.top)
input_values = (val for val in ["123"])
with mock.patch('builtins.input', lambda *x: next(input_values)):
with pytest.raises((ValueError, AssertionError)):
residue_and_atom.residues_from_descriptors("30", self.by_bonds_geom2frags, self.geom2frags.top)
def test_default_fragment_idx_is_passed_special_case(self):
with pytest.raises((ValueError, AssertionError)):
residue_and_atom.residues_from_descriptors("GLU30", self.by_bonds_geom2frags,
self.geom2frags.top,
pick_this_fragment_by_default=99)
with pytest.raises((ValueError, AssertionError)):
residue_and_atom.residues_from_descriptors(30, self.by_bonds_geom2frags,
self.geom2frags.top,
pick_this_fragment_by_default=99)
def test_ambiguous_just_inform(self):
residues = ["GLU30", 30]
residxs, fragidx = residue_and_atom.residues_from_descriptors(residues,
self.by_bonds_geom2frags,
self.geom2frags.top,
just_inform=True)
self.assertListEqual(residxs,[0,8])
self.assertListEqual(fragidx,[0,4])
def test_no_ambiguous(self):
residues = ["GLU30", "GDP382", 30, 382]
residxs, fragidxs = residue_and_atom.residues_from_descriptors(residues, self.by_bonds_geom,
self.geom.top)
self.assertSequenceEqual([0,7,0,7], residxs)
# GLU30 is the 1st residue
# GDP382 is the 8th residue
self.assertSequenceEqual([0,3,0,3], fragidxs)
def test_ambiguous(self):
input_values = (val for val in ["4", "4"])
with mock.patch('builtins.input', lambda *x: next(input_values)):
residues = ["GLU30", 30]
residxs, fragidx = residue_and_atom.residues_from_descriptors(residues,
self.by_bonds_geom2frags,
self.geom2frags.top)
self.assertSequenceEqual([8, 8], residxs)
self.assertSequenceEqual([4, 4], fragidx)
input_values = (val for val in ["3", "3"])
with mock.patch('builtins.input', lambda *x: next(input_values)):
residues = ["GDP382", 382]
residxs, fragidx = residue_and_atom.residues_from_descriptors(residues,
self.by_bonds_geom2frags,
self.geom2frags.top)
self.assertSequenceEqual([7, 7], residxs)
self.assertSequenceEqual([3, 3], fragidx)
def test_default_fragment_idx_is_passed(self):
residues = ["GLU30", 30]
residxs, fragidx = residue_and_atom.residues_from_descriptors(residues, self.by_bonds_geom2frags,
self.geom2frags.top,
pick_this_fragment_by_default=4)
# Checking if residue names gives the correct corresponding residue id
# NOTE:Enter 4 for GLU30 when asked "input one fragment idx"
self.assertSequenceEqual([8, 8], residxs)
self.assertSequenceEqual([4, 4], fragidx)
def test_fragment_idx_is_none_last_answer(self):
residues = ["GLU30", 30]
input_values = (val for val in ["", ""])
with mock.patch('builtins.input', lambda *x: next(input_values)):
residxs, fragidxs = residue_and_atom.residues_from_descriptors(residues, self.by_bonds_geom2frags,
self.geom2frags.top)
# NOTE:Accepted default "" for GLU30 when asked "input one fragment idx"
self.assertSequenceEqual(residxs, [0, 0])
self.assertSequenceEqual(fragidxs, [0, 0])
def test_fragment_name(self):
residues = ["GLU30", 30]
input_values = (val for val in ["0", "0"])
with mock.patch('builtins.input', lambda *x: next(input_values)):
residxs, fragidx = residue_and_atom.residues_from_descriptors(residues, self.by_bonds_geom2frags,
self.geom2frags.top,
fragment_names=["A", "B", "C", "D",
"E", "F", "G", "H"])
# Checking if residue names gives the correct corresponding residue id
# NOTE:Enter 0 for GLU30 when asked "input one fragment idx"
self.assertSequenceEqual([0, 0], residxs)
self.assertSequenceEqual([0, 0], fragidx)
def test_idx_not_present(self):
residxs, fragidx = residue_and_atom.residues_from_descriptors(["GLU99", 99], self.by_bonds_geom2frags,
self.geom2frags.top,
pick_this_fragment_by_default=99)
self.assertSequenceEqual([None, None], residxs)
self.assertSequenceEqual([None, None], fragidx)
def test_not_in_fragment(self):
residues = ["GLU30"]
with pytest.raises(ValueError):
residue_and_atom.residues_from_descriptors(residues, [np.arange(3,5)],
self.geom.top)
def test_overlaping_frags(self):
residues = ["GLU30"]
with pytest.raises(ValueError):
residue_and_atom.residues_from_descriptors(residues, [np.arange(self.geom.n_residues),
[np.arange(self.geom.n_residues)]],
self.geom.top)