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 parse_stats_file(file_handle):
stats = {
"stem": defaultdict(list),
"angle": defaultdict(list),
"loop": defaultdict(list),
"3prime": defaultdict(list),
"5prime": defaultdict(list)
}
for line in file_handle:
line = line.strip()
if "#" in line:
line = line.split('#')[0]
if not line:
continue
if line.startswith("stem"):
stem_stat = ftmstats.StemStat(line)
stats["stem"][stem_stat.bp_length].append(stem_stat)
elif line.startswith("angle") or line.startswith(
"open") or line.startswith("pseudo"):
angle_stat = ftmstats.AngleStat()
try:
angle_stat.parse_line(line)
except Exception as e:
with log_to_exception(log, e):
log.error(
"Could not parse file due to error parsing line '{}'".
format(line))
raise
if len(angle_stat.define) > 0 and angle_stat.define[
0] == 1: #An angle at the beginning of a structure
#I guess this should never happen, if the stats do not stem from faulty bulge graphs.
log.error(
"Ignoring angle stat {} because it is at the beginning of a structure."
" Does the stat come from a faulty BulgeGraph?".format(
angle_stat.pdb_name))
continue
angle_stat.ang_type = patch_angtype(angle_stat.ang_type)
log.debug(
"Reading angle_stat with dimensions %s and %s, and type %s. With define %s",
angle_stat.dim1, angle_stat.dim2, angle_stat.ang_type,
angle_stat.define)
stats["angle"][(angle_stat.dim1, angle_stat.dim2,
angle_stat.ang_type)].append(angle_stat)
# Adding the reverse does not work as intended and produces a lot of structures
# that do not fulfill the constraint energy.
# stats["angle"][(angle_stat.dim1, angle_stat.dim2, -angle_stat.ang_type)].append(angle_stat)
# Note that CoarseGrainRNA.get_stats extracts two angle stats per angle.
else:
key = line.split()[0]
if key not in ["3prime", "5prime", "loop"]:
raise ValueError(
"Illegal line in stats file: '{}'".format(line))
stat = ftmstats.LoopStat(line)
stats[key][stat.bp_length].append(stat)
return stats
def get_stem_stats(self, stem):
'''
Calculate the statistics for a stem and return them. These statistics will describe the
length of the stem as well as how much it twists.
@param stem: The name of the stem.
@return: A StemStat structure containing the above information.
'''
ss = ftms.StemStat()
ss.pdb_name = self.name
#ss.bp_length = abs(self.defines[stem][0] - self.defines[stem][1])
ss.bp_length = self.stem_length(stem)
ss.phys_length = ftuv.magnitude(self.coords[stem][0] - self.coords[stem][1])
ss.twist_angle = ftug.get_twist_angle(self.coords[stem], self.twists[stem])
ss.define = self.defines[stem]
return ss
def test_read_stats_file(self):
stats = fbstat.read_stats_file("test/fess/data/test1.stats")
log.info(stats)
self.assertEqual(len(stats["stem"]), 1)
self.assertEqual(len(stats["angle"]), 3)
self.assertEqual(len(stats["loop"]), 2)
self.assertEqual(len(stats["3prime"]), 1)
self.assertEqual(len(stats["5prime"]), 1)
self.assertEqual(stats["stem"][5], [
ftmstats.StemStat(
"stem test:s_0 5 10.388 2.43294047108 1 5 10 15 GCAUG UGCAU")
])
a_stat = ftmstats.AngleStat()
a_stat.parse_line(
"angle test:i_0 5 2 2.203691 2.099941 0.586450 17.134279 1.191397 1.274896 1"
)
self.assertEqual(stats["angle"][(5, 2, 1)], [a_stat])
a_stat.parse_line(
"angle test:m_0 4 1000 0.985166 -1.185545 -2.000463 13.701389 0.982669 0.267821 -4"
)
self.assertEqual(
stats["angle"][(
4, 1000, 6
)], # We patched ang_type to use 6 for all ml-segments. -6<=>-3, but -6<=>+4
[a_stat])
self.assertEqual(stats["loop"][6], [
ftmstats.LoopStat(
"loop test:h_0 6 15.2401560955 0.269833051418 0.731484795668")
])
self.assertEqual(stats["3prime"][4], [
ftmstats.LoopStat(
"3prime test:t_0 4 20.4034805163 1.47912394946 -0.0715301558972"
)
])
self.assertEqual(stats["5prime"][4], [
ftmstats.LoopStat(
"5prime test:f_0 4 20.4034805163 1.47912394946 -0.0715301558972"
)
])
def setUp(self):
self.example_stem_stat = ftms.StemStat(
"stem exampleStat 3 5.29399999969 1.19302425058 1 3 7 9")
self.example_hairpin_stat = ftms.LoopStat(
"loop exampleStat 3 14.8069260882 1.2124527925 1.12478051025 86 88"
)