def test_structured_chains_joined_with_unstructured_are_joined(self):
chains = [
IfeChain(internal=10, pdb='1S72', model=1, chain='A', length=50),
IfeChain(internal=10, pdb='1S72', model=1, chain='B', length=50),
IfeChain(internal=0, pdb='1S72', model=1, chain='C', length=10)
]
interactions = {
'A': {
'B': 30,
'C': 5
},
'B': {
'A': 30,
'C': 5
},
'C': {
'A': 5,
'B': 5
}
}
ans = {
'1S72|1|A': ['1S72|1|A+1S72|1|B'],
'1S72|1|B': ['1S72|1|A+1S72|1|B'],
'1S72|1|C': ['1S72|1|A+1S72|1|B'],
}
val = self.grouping(chains, interactions)
self.assertEquals(ans, val)
def test_structured_chains_joined_only_by_unstructureds_arent_joined(self):
chains = [
IfeChain(internal=10, pdb='1S72', model=1, chain='A', length=50),
IfeChain(internal=10, pdb='1S72', model=1, chain='B', length=50),
IfeChain(internal=0, pdb='1S72', model=1, chain='C', length=10),
IfeChain(internal=0, pdb='1S72', model=1, chain='D', length=10)
]
interactions = {
'A': {
'B': 1,
'C': 5
},
'B': {
'A': 1,
'C': 5
},
'C': {
'A': 5,
'B': 5,
'D': 10
},
'D': {
'A': 0,
'B': 0,
'C': 10
}
}
val = self.grouping(chains, interactions)
ans = {
'1S72|1|A': ['1S72|1|A'],
'1S72|1|B': ['1S72|1|B'],
'1S72|1|C': ['1S72|1|A', '1S72|1|B'],
'1S72|1|D': ['1S72|1|A', '1S72|1|B'],
}
self.assertEquals(ans, val)
def test_structured_chains_joined_only_by_unstructured_arent_joined(self):
chains = [
IfeChain(internal=10, pdb='1S72', model=1, chain='A', length=50),
IfeChain(internal=10, pdb='1S72', model=1, chain='B', length=50),
IfeChain(internal=0, pdb='1S72', model=1, chain='C', length=10)
]
interactions = {
'A': {
'B': 1,
'C': 5
},
'B': {
'A': 1,
'C': 5
},
'C': {
'A': 5,
'B': 5
}
}
assert self.grouping(chains, interactions) == {
'1S72|1|A': ['1S72|1|A'],
'1S72|1|B': ['1S72|1|B'],
'1S72|1|C': ['1S72|1|A', '1S72|1|B']
}
def test_compares_using_length(self):
ife1 = IfeChain(pdb='0111', chain='A', length=10, internal=50)
ife2 = IfeChain(pdb='0111', chain='C', length=50, internal=50)
self.assertTrue(ife1 < ife2)
self.assertTrue(ife1 <= ife2)
self.assertFalse(ife1 == ife2)
self.assertTrue(ife2 > ife1)
def test_sorts_by_full_length(self):
val1 = IfeChain(pdb='01GG', chain='A', internal=0, length=10,
full_length=10, db_id=1)
val2 = IfeChain(pdb='01GG', chain='A', internal=0, length=10,
full_length=12, db_id=1)
self.assertTrue(val1 < val2)
self.assertTrue(val2 > val1)
def test_puts_non_interactions_unstructured_chains_seperately(self):
chains = [
IfeChain(internal=0, pdb='1S72', model=1, chain='A', length=10),
IfeChain(internal=0, pdb='1S72', model=1, chain='B', length=10)
]
ans = {'1S72|1|A': ['1S72|1|A'], '1S72|1|B': ['1S72|1|B']}
self.assertEquals(ans, self.grouping(chains, {}))
def test_it_sorts_by_chain_and_internal(self):
ife1 = IfeChain(pdb='0111', chain='A', internal=5)
ife2 = IfeChain(pdb='0111', chain='D', internal=6)
self.assertTrue(ife1 < ife2)
self.assertTrue(ife1 <= ife2)
self.assertTrue(ife2 > ife1)
self.assertTrue(ife2 >= ife1)
self.assertTrue(ife2 != ife1)
def test_will_put_structured_but_interacting_chains_seperatly(self):
chains = [
IfeChain(internal=10, pdb='1S72', model=1, chain='A', length=50),
IfeChain(internal=10, pdb='1S72', model=1, chain='B', length=50)
]
interactions = {'A': {'B': 3}, 'B': {'A': 3}}
val = self.grouping(chains, interactions)
ans = {'1S72|1|A': ['1S72|1|A'], '1S72|1|B': ['1S72|1|B']}
self.assertEquals(ans, val)
def test_will_join_unstructured_chains_on_interactions(self):
chains = [
IfeChain(internal=0, pdb='1S72', model=1, chain='A', length=10),
IfeChain(internal=0, pdb='1S72', model=1, chain='B', length=10)
]
interactions = {'A': {'B': 10}, 'B': {'A': 10}}
val = self.grouping(chains, interactions)
ans = {
'1S72|1|A': ['1S72|1|A+1S72|1|B'],
'1S72|1|B': ['1S72|1|A+1S72|1|B']
}
self.assertEquals(ans, val)
def setUp(self):
super(PartitingInteractionsTest, self).setUp()
inters = {
'A': {
'A': 0,
'B': 3,
'C': 2,
'D': 0
},
'B': {
'A': 3,
'B': 0,
'C': 0,
'D': 4
},
'C': {
'A': 2,
'B': 0,
'C': 0,
'D': 0
},
'D': {
'A': 0,
'B': 4,
'C': 0,
'D': 0
}
}
ifes = [
IfeChain(chain='A', internal=10),
IfeChain(chain='B', internal=0),
IfeChain(chain='C', internal=10),
IfeChain(chain='D', internal=0),
]
self.same, self.rest = self.loader.parition_interactions(ifes, inters)
def test_sorts_by_chain(self):
val1 = IfeChain(chain='A')
val2 = IfeChain(chain='B')
self.assertTrue(val1 > val2)
self.assertTrue(val2 < val1)
def test_can_load_correct_with_sym_ops(self):
ifes = [IfeChain(pdb='1A34', chain='B'),
IfeChain('1A34', chain='C')]
val = self.loader.cross_chain_interactions(ifes, sym_op='P_1')
ans = {'B': {'B': 0, 'C': 9}, 'C': {'B': 9, 'C': 0}}
self.assertEquals(ans, val)
def test_can_load_yeast_ribo_interactions(self):
ifes = [IfeChain(pdb='4V7R', chain='D1'),
IfeChain(pdb='4V7R', chain='D3')]
val = self.loader.cross_chain_interactions(ifes)
ans = {'D1': {'D1': 0, 'D3': 16}, 'D3': {'D1': 16, 'D3': 0}}
self.assertEquals(ans, val)
def test_loads_interactions_symmetrically(self):
ifes = [IfeChain(pdb='2MKN', chain='C'),
IfeChain(pdb='2MKN', chain='B')]
val = self.loader.cross_chain_interactions(ifes)
ans = {'C': {'C': 0, 'B': 19}, 'B': {'B': 0, 'C': 19}}
self.assertEquals(ans, val)
def test_knows_if_two_chains_are_not_equal(self):
val1 = IfeChain(internal=4)
val2 = IfeChain(chain='G', internal=4)
self.assertNotEquals(val1, val2)
def test_duplicate_additions_do_nothing(self):
val = IfeGroup(IfeChain(pdb='0111', chain='A', internal=4, model=4),
IfeChain(pdb='0111', chain='C', internal=0, model=4))
val.add(IfeChain(pdb='0111', chain='A', internal=4, model=4))
self.assertEquals('0111|4|A+0111|4|C', val.id)
def test_has_an_id(self):
val = IfeGroup(IfeChain(pdb='0111', chain='A', internal=5, model=10),
IfeChain(pdb='0111', chain='C', internal=0, model=10))
self.assertEquals('0111|10|A', val.id)
def test_knows_if_structured_if_has_no_structured_chain(self):
val = IfeGroup(IfeChain(chain='A', internal=4),
IfeChain(chain='B', internal=0))
self.assertFalse(val.is_structured)
def test_knows_if_chain_is_not_structured(self):
val = IfeChain(internal=4)
self.assertFalse(val.is_structured)
def test_dispatches_model_to_integral(self):
val = IfeGroup(IfeChain(pdb='0111', chain='A', internal=100,
full_length=5, model=2),
IfeChain(pdb='0111', chain='B', internal=10,
full_length=5, model=10))
self.assertEquals(2, val.model)
def test_dispatches_bps_to_integral(self):
val = IfeGroup(IfeChain(pdb='0111', chain='A', internal=100,
full_length=5, bps=120),
IfeChain(pdb='0111', chain='B', internal=10,
full_length=5, bps=12))
self.assertEquals(120, val.bps)
def test_dispatches_pdb_to_integral(self):
val = IfeGroup(IfeChain(pdb='0111', chain='A', internal=4,
full_length=5))
self.assertEquals('0111', val.pdb)
def test_it_is_bigger_than_none(self):
val = IfeChain(pdb='01GG', chain='A', internal=0, length=10,
full_length=10, db_id=1)
self.assertTrue(val > None)
self.assertTrue(None < val)
def test_uses_name_to_tiebreak_integral_chain(self):
val = IfeGroup(IfeChain(pdb='0111', chain='C', length=10, internal=0,
model=3),
IfeChain(pdb='0111', chain='A', length=10, internal=0,
model=3))
self.assertEquals('0111|3|A', val.integral.id)
def test_getattr_complains_if_missing_key(self):
val = IfeGroup(IfeChain(pdb='0111', chain='A', internal=4,
full_length=5))
self.assertRaises(AttributeError, lambda: val.bob)
def test_if_no_structured_in_id_uses_all(self):
val = IfeGroup(IfeChain(pdb='0111', chain='A', internal=2, model=1),
IfeChain(pdb='0111', chain='C', internal=0, model=2),
IfeChain(pdb='0111', chain='D', internal=2, model=3))
self.assertEquals('0111|1|A+0111|3|D+0111|2|C', val.id)
def test_knows_how_many_chains_in_it(self):
val = IfeGroup(IfeChain(chain='A', internal=4),
IfeChain(chain='B', internal=0))
self.assertEquals(2, len(val))
def test_uses_most_bp_chain_as_integral(self):
val = IfeGroup(IfeChain(pdb='0111', chain='A', internal=4, model=1),
IfeChain(pdb='0111', chain='C', internal=0, model=1))
self.assertEquals('0111|1|A', val.integral.id)
def test_uses_structured_only_in_id(self):
val = IfeGroup(IfeChain(pdb='0111', chain='A', internal=5, model=10),
IfeChain(pdb='0111', chain='C', internal=0, model=0),
IfeChain(pdb='0111', chain='D', internal=6, model=10))
self.assertEquals('0111|10|D+0111|10|A', val.id)
def test_uses_length_as_tiebreak(self):
val = IfeGroup(IfeChain(pdb='0111', chain='A', length=10, internal=50,
model=10),
IfeChain(pdb='0111', chain='C', length=50, internal=50,
model=10))
self.assertEquals('0111|10|C', val.integral.id)