def is_connected(self):
if not self._pair_table:
self._pair_table = make_pair_table(self.structure)
if not self._loop_index:
try :
# make loop index raises error when disconnected.
self._loop_index, self._exterior_loops = make_loop_index(self._pair_table)
except SecondaryStructureError as e:
return False
return True
def exterior_domains(self):
"""
Returns all domains in exterior loops.
"""
if not self._exterior_domains:
if not self._pair_table:
self._pair_table = make_pair_table(self.structure)
if not self._loop_index or self._exterior_loops:
self._loop_index, self._exterior_loops = make_loop_index(self._pair_table)
self._exterior_domains = []
self._enclosed_domains = []
for si, strand in enumerate(self._loop_index):
for di, domain in enumerate(strand):
if self._loop_index[si][di] in self._exterior_loops:
if self._pair_table[si][di] is None:
self._exterior_domains.append((si, di))
elif self._pair_table[si][di] is None:
self._enclosed_domains.append((si, di))
return self._exterior_domains
def test_make_loop_index(self):
struct = '(((...)))'
pt = utils.make_pair_table(struct)
exp1 = [[1, 2, 3, 3, 3, 3, 3, 2, 1]]
exp2 = set([0])
out1, out2 = utils.make_loop_index(pt)
self.assertEqual(out1, exp1)
self.assertSetEqual(out2, exp2)
struct = '..(((...)))..'
pt = utils.make_pair_table(struct)
exp1 = [[0, 0, 1, 2, 3, 3, 3, 3, 3, 2, 1, 0, 0]]
exp2 = set([0])
out1, out2 = utils.make_loop_index(pt)
self.assertEqual(out1, exp1)
self.assertSetEqual(out2, exp2)
struct = '.((.((...))..((...).))).'
pt = utils.make_pair_table(struct)
exp1 = [[
0, 1, 2, 2, 3, 4, 4, 4, 4, 4, 3, 2, 2, 5, 6, 6, 6, 6, 6, 5, 5, 2,
1, 0
]]
exp2 = set([0])
out1, out2 = utils.make_loop_index(pt)
self.assertEqual(out1, exp1)
self.assertSetEqual(out2, exp2)
struct = '.((.((...)).+.((...).))).'
pt = utils.make_pair_table(struct)
exp1 = [[0, 1, 2, 2, 3, 4, 4, 4, 4, 4, 3, 2],
[2, 5, 6, 6, 6, 6, 6, 5, 5, 2, 1, 0]]
exp2 = set([0, 2])
out1, out2 = utils.make_loop_index(pt)
self.assertEqual(out1, exp1)
self.assertSetEqual(out2, exp2)
struct = '.((.((...))+..((...).))).'
pt = utils.make_pair_table(struct)
exp1 = [[0, 1, 2, 2, 3, 4, 4, 4, 4, 4, 3],
[2, 2, 5, 6, 6, 6, 6, 6, 5, 5, 2, 1, 0]]
exp2 = set([0, 2])
out1, out2 = utils.make_loop_index(pt)
self.assertEqual(out1, exp1)
self.assertSetEqual(out2, exp2)
struct = '.((.((...))+((...).))).'
pt = utils.make_pair_table(struct)
exp1 = [[0, 1, 2, 2, 3, 4, 4, 4, 4, 4, 3],
[5, 6, 6, 6, 6, 6, 5, 5, 2, 1, 0]]
exp2 = set([0, 2])
out1, out2 = utils.make_loop_index(pt)
self.assertEqual(out1, exp1)
self.assertSetEqual(out2, exp2)
with self.assertRaises(SecondaryStructureError):
struct = '..+..'
pt = utils.make_pair_table(struct)
out1, out2 = utils.make_loop_index(pt)
with self.assertRaises(SecondaryStructureError):
struct = '(.)+.(..)'
pt = utils.make_pair_table(struct)
out1, out2 = utils.make_loop_index(pt)
with self.assertRaises(SecondaryStructureError):
struct = '((..((.))+.(..).+((...))))'
pt = utils.make_pair_table(struct)
out1, out2 = utils.make_loop_index(pt)
def get_loop_index(self, loc):
if not self._pair_table:
self._pair_table = make_pair_table(self.structure)
if not self._loop_index:
self._loop_index, self._exterior_loops = make_loop_index(self._pair_table)
return self._loop_index[loc[0]][loc[1]]
def loop_index(self):
""" returns the loop index of a structure. """
if not self._pair_table:
self._pair_table = make_pair_table(self.structure)
return make_loop_index(self._pair_table)