def test_sample_has_correct_shape(self):
mapper = mapping.PeakMapper("test", n_peaks=3, atom_names=["N", "H"])
state = mapper.get_initial_state()
trial_state = mapper.sample(state)
self.assertEqual(trial_state.shape[0], 3)
def test_extract_value_should_fail_with_map_name_mismatch(self):
mapper = mapping.PeakMapper("test", n_peaks=10, atom_names=["N", "H"])
m = mapping.PeakMapping(map_name="fail", peak_id=0, atom_name="H")
state = mapper.get_initial_state()
with self.assertRaises(KeyError):
mapper.extract_value(m, state)
def test_atom_groups_length_should_match(self):
mapper = mapping.PeakMapper("test", n_peaks=10, atom_names=["N", "H"])
mapper.add_atom_group(N=AtomIndex(0), H=AtomIndex(1))
mapper.add_atom_group(N=AtomIndex(2), H=AtomIndex(3))
mapper.add_atom_group(N=AtomIndex(4), H=AtomIndex(5))
self.assertEqual(mapper.n_atom_groups, 3)
def test_extract_value_should_return_not_mapped(self):
mapper = mapping.PeakMapper("test", n_peaks=3, atom_names=["N", "H"])
mapper.add_atom_group(N=AtomIndex(0), H=AtomIndex(1))
state = mapper.get_initial_state()
val1 = mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=0, atom_name="N"),
state)
val2 = mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=0, atom_name="H"),
state)
val3 = mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=1, atom_name="N"),
state)
val4 = mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=1, atom_name="H"),
state)
val5 = mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=2, atom_name="N"),
state)
val6 = mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=2, atom_name="H"),
state)
# We have 3 peaks, but only one atom group, so only one peak will
# map to something. With the default initialization, this will be
# the first peak.
self.assertEqual(val1, 0)
self.assertEqual(val2, 1)
self.assertIsInstance(val3, mapping.NotMapped)
self.assertIsInstance(val4, mapping.NotMapped)
self.assertIsInstance(val5, mapping.NotMapped)
self.assertIsInstance(val6, mapping.NotMapped)
def test_initial_state_should_have_correct_size(self):
mapper1 = mapping.PeakMapper("test", n_peaks=3, atom_names=["N", "H"])
mapper1.add_atom_group(N=AtomIndex(0), H=AtomIndex(1))
# mapper1 has 3 peaks, but 1 atom_group
# Initial state should have the size of max of these two,
# so it should be 3
self.assertEqual(mapper1.get_initial_state().shape[0], 3)
mapper2 = mapping.PeakMapper("test", n_peaks=1, atom_names=["N", "H"])
mapper2.add_atom_group(N=AtomIndex(0), H=AtomIndex(1))
mapper2.add_atom_group(N=AtomIndex(2), H=AtomIndex(3))
mapper2.add_atom_group(N=AtomIndex(4), H=AtomIndex(5))
# mapper2 has 1 peak, but 3 atom_group
# Initial state should have the size of max of these two,
# so it should be 3
self.assertEqual(mapper2.get_initial_state().shape[0], 3)
def test_get_atom_mapping_should_raise_with_bad_peak_id(self):
mapper = mapping.PeakMapper("test", n_peaks=10, atom_names=["N", "H"])
with self.assertRaises(KeyError):
# no peak_id 10
mapper.get_mapping(peak_id=10, atom_name="H")
with self.assertRaises(KeyError):
# peak_id -1 is bad
mapper.get_mapping(peak_id=-1, atom_name="H")
def test_extract_value_should_raise_with_illegal_peak_id(self):
mapper = mapping.PeakMapper("test", n_peaks=1, atom_names=["N", "H"])
mapper.add_atom_group(N=AtomIndex(0), H=AtomIndex(1))
mapper.add_atom_group(N=AtomIndex(2), H=AtomIndex(3))
mapper.add_atom_group(N=AtomIndex(4), H=AtomIndex(5))
state = mapper.get_initial_state()
with self.assertRaises(KeyError):
mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=1, atom_name="H"),
state)
def test_extract_value_should_give_correct_indices_with_equal_length(self):
mapper = mapping.PeakMapper("test", n_peaks=3, atom_names=["N", "H"])
mapper.add_atom_group(N=AtomIndex(0), H=AtomIndex(1))
mapper.add_atom_group(N=AtomIndex(2), H=AtomIndex(3))
mapper.add_atom_group(N=AtomIndex(4), H=AtomIndex(5))
state = mapper.get_initial_state()
self.assertEqual(
mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=0, atom_name="N"),
state),
0,
)
self.assertEqual(
mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=0, atom_name="H"),
state),
1,
)
self.assertEqual(
mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=1, atom_name="N"),
state),
2,
)
self.assertEqual(
mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=1, atom_name="H"),
state),
3,
)
self.assertEqual(
mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=2, atom_name="N"),
state),
4,
)
self.assertEqual(
mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=2, atom_name="H"),
state),
5,
)
def test_should_raise_with_negative_n_peeaks(self):
with self.assertRaises(ValueError):
mapping.PeakMapper("test", n_peaks=-1, atom_names=["N", "H"])
def test_get_atom_mapping_should_have_correct_atom_name(self):
mapper = mapping.PeakMapper("test", n_peaks=10, atom_names=["N", "H"])
m = mapper.get_mapping(peak_id=0, atom_name="N")
self.assertEqual(m.atom_name, "N")
def test_get_atom_mapping_should_raise_with_name(self):
mapper = mapping.PeakMapper("test", n_peaks=10, atom_names=["N", "H"])
with self.assertRaises(KeyError):
# no name Q
mapper.get_mapping(peak_id=0, atom_name="Q")
def test_should_raise_with_non_atom_index(self):
mapper = mapping.PeakMapper("test", n_peaks=10, atom_names=["N", "H"])
with self.assertRaises(ValueError):
mapper.add_atom_group(N=0, H=AtomIndex(1))
def test_add_atom_group_should_fail_with_mismatch(self):
mapper = mapping.PeakMapper("test", n_peaks=10, atom_names=["N", "H"])
with self.assertRaises(KeyError):
# no Q
mapper.add_atom_group(N=AtomIndex(0), Q=AtomIndex(1))
