class TestWholeMLMoverPublicAPI(TestMoverBaseClassPublicAPI):
def setUp(self):
self.stat_source_real = StatStorage("test/fess/data/real.stats")
cg = ftmc.CoarseGrainRNA.from_dotbracket(
dotbracket_str=
"((((((((((......))))).....(((((......)))))....(((((......))))))))))"
)
self.sm = SpatialModel(cg)
self.sm.sample_stats(self.stat_source_real)
self.sm.new_traverse_and_build()
self.mover = fbmov.WholeMLMover(self.stat_source_real)
def test_whole_ml_mover_moves_whole_ml(self):
for i in range(RAND_REPETITIONS):
sm = copy.deepcopy(self.sm)
stats_old = copy.deepcopy(sm.elem_defs)
self.mover.move(sm)
changed = set()
for elem in sm.elem_defs:
if sm.elem_defs[elem].pdb_name != stats_old[elem].pdb_name:
changed.add(elem)
if any(elem[0] == "m" for elem in changed):
self.assertEqual(
len(changed),
3,
msg="Changed is {}, should be 3 ml segments".format(
changed))
else:
self.assertEqual(len(changed), 1)
class TestMoverBaseClassPublicAPI(unittest.TestCase):
def setUp(self):
self.stat_source_real = StatStorage("test/fess/data/real.stats")
self.stat_source_limited = StatStorage("test/fess/data/test1.stats")
cg1 = ftmc.CoarseGrainRNA.from_dotbracket(
dotbracket_str="(((((.....(((((......)))))..)))))")
self.sm = SpatialModel(cg1)
self.sm.sample_stats(self.stat_source_limited)
self.sm.new_traverse_and_build()
self.mover = fbmov.Mover(self.stat_source_real)
def test_move_changes_sm(self):
coords_old = copy.deepcopy(self.sm.bg.coords)
log.info(self.mover.move(self.sm))
self.assertNotEqual(
self.sm.bg.coords,
coords_old,
msg="At least one coordinate should have changed significantly.")
def test_move_and_reset(self):
for i in range(10):
coords_old = copy.deepcopy(self.sm.bg.coords)
log.info(self.mover.move(self.sm))
self.mover.revert(self.sm)
self.assertEqual(self.sm.bg.coords, coords_old)
def setUp(self):
self.stat_source_real = StatStorage("test/fess/data/real.stats")
self.stat_source_limited = StatStorage("test/fess/data/test1.stats")
cg1 = ftmc.CoarseGrainRNA.from_dotbracket(
dotbracket_str="(((((.....(((((......)))))..)))))")
self.sm = SpatialModel(cg1)
self.sm.sample_stats(self.stat_source_limited)
self.sm.new_traverse_and_build()
self.mover = fbmov.Mover(self.stat_source_real)
def test_iter_moves_many(self):
cg = ftmc.CoarseGrainRNA.from_dotbracket(
dotbracket_str="(((((.....)))))", seq="GGCGCAAAAAGCGCC")
self.sm = SpatialModel(cg)
mov = fbmov.ExhaustiveMover("s0",
"h0",
stat_source=self.stat_source_limited,
sm=self.sm)
move_list = list(mov._iter_moves(self.sm))
self.assertEqual([x[0] for x in move_list], ["s0", "h0", "h0"])
self.assertEqual([x[1].pdb_name for x in move_list],
["test:s_0", "test:h_1", "test:h_2"])
class TestMSTchangingMoverPublicAPI(TestMoverBaseClassPublicAPI):
def setUp(self):
self.stat_source_real = StatStorage("test/fess/data/real.stats")
self.stat_source_limited = StatStorage("test/fess/data/test1.stats")
cg1 = ftmc.CoarseGrainRNA.from_dotbracket(
dotbracket_str="((((......))((......))))")
self.sm = SpatialModel(cg1)
self.sm.sample_stats(self.stat_source_real)
self.sm.new_traverse_and_build()
self.mover = fbmov.Mover(self.stat_source_real)
self.mover = fbmov.MSTchangingMover(self.stat_source_real)
def test_change_and_reset_m(self):
assert "m1" in self.sm.bg.mst
initial_coords = copy.deepcopy(self.sm.bg.coords)
old_get_elem = self.mover._get_elem
self.mover._get_elem = lambda *args: "m1"
log.info(self.mover.move(self.sm))
self.assertNotEqual(
self.sm.bg.coords,
initial_coords,
msg="At least one coordinate should have changed significantly.")
self.mover.revert(self.sm)
self.assertEqual(self.sm.bg.coords, initial_coords)
self.mover._get_elem = old_get_elem
def test_mst_is_changed_and_resetted(self):
assert "m1" in self.sm.bg.mst
initial_mst = copy.deepcopy(self.sm.bg.mst)
old_get_elem = self.mover._get_elem
self.mover._get_elem = lambda *args: "m1"
log.info(self.mover.move(self.sm))
self.assertNotEqual(self.sm.bg.mst,
initial_mst,
msg="The MST should have changed.")
self.mover.revert(self.sm)
self.assertEqual(self.sm.bg.mst, initial_mst)
self.mover._get_elem = old_get_elem
class TestMoverBaseClassPrivateMembers(unittest.TestCase):
longMessage = True
def setUp(self):
self.stat_source_real = StatStorage("test/fess/data/real.stats")
self.stat_source_limited = StatStorage("test/fess/data/test1.stats")
cg = ftmc.CoarseGrainRNA.from_dotbracket(
dotbracket_str="(((((......)))))", seq="GGCGCAAAAAAGCGCC")
self.sm = SpatialModel(cg)
self.sm.sample_stats(self.stat_source_limited)
self.sm.new_traverse_and_build()
self.mover_realstats = fbmov.Mover(self.stat_source_real)
self.mover_limitedstats = fbmov.Mover(self.stat_source_limited)
def test_get_elem_and_stat_real_stats(self):
elems = Counter()
for i in range(RAND_REPETITIONS):
elem, new_stat = self.mover_realstats._get_elem_and_stat(self.sm)
elems[elem] += 1
self.assertIn(elem, ["s0", "h0"],
msg="Only elements from SpatialModel can be picked")
if elem == "s0":
self.assertIsInstance(new_stat, ftmstat.StemStat)
else:
self.assertIsInstance(new_stat, ftmstat.LoopStat)
print(list(elems.items()))
c, p = chisquare(list(elems.values()))
self.assertGreater(
p,
0.05,
msg=" We do not sample all elements uniformely with a p-value "
"below 0.2. We sampled with the following frequencies {}. (You might consider repeating "
"the test if the frequencies look ok)".format(elems.most_common()))
def test_get_elem_and_stat_limited_stats(self):
elems = Counter()
for i in range(RAND_REPETITIONS):
elem, new_stat = self.mover_limitedstats._get_elem_and_stat(
self.sm)
elems[elem] += 1
self.assertIn(elem, ["s0", "h0"],
msg="Only elements from SpatialModel can be picked")
if elem == "s0":
self.assertEqual(new_stat.pdb_name, "test:s_0")
else:
self.assertEqual(new_stat.pdb_name, "test:h_0")
print(list(elems.items()))
c, p = chisquare(list(elems.values()))
self.assertGreater(
p,
0.05,
msg=" We do not sample all elements uniformely with a p-value "
"below 0.2. We sampled with the following frequencies {}. (You might consider repeating "
"the test if the frequencies look ok)".format(elems.most_common()))
def test_move(self):
stat = ftmstat.StemStat("stem new:s_0 5 10.388 2.43294047108")
oldstat = self.sm.elem_defs["s0"]
self.mover_realstats._prev_stats = {}
movestring = self.mover_realstats._move(self.sm, "s0", stat)
self.assertEqual(self.sm.elem_defs["s0"], stat)
self.assertEqual(self.mover_realstats._prev_stats["s0"], oldstat)
self.assertEqual(movestring, "s0:test:s_0->new:s_0;")
def setUp(self):
self.stat_source = StatStorage("test/fess/data/test1.stats")
cg = ftmc.CoarseGrainRNA.from_dotbracket(
dotbracket_str="(((((......)))))")
self.sm = SpatialModel(cg)