class BondSetSelectorTests(BondSetSelectorBaseTests):
def setUp(self):
self.mols = Read('Data/stringSel.pdb')
for m in self.mols:
m.buildBondsByDistance()
self.bonds = self.mols.chains.residues.atoms.bonds[0]
self.stringSel = BondSetSelector()
def tearDown(self):
"""
clean-up
"""
del(self.bonds)
del(self.mols)
def test_select_with_empty_string(self):
"""
test result with empty string returns all bonds
"""
result, msg = self.stringSel.select(self.bonds, "")
self.assertEquals(result, self.bonds)
def test_select_end(self):
"""
test select with '$' returns last item
"""
result, msg = self.stringSel.select(self.bonds, "$")
self.assertEquals(result[-1], self.bonds[-1])
def test_select_with_valid_index(self):
"""
test string with valid_index returns set with 1 item
"""
selString = "0"
result, msg = self.stringSel.select(self.bonds, selString)
self.assertEquals(len(result), 1)
self.assertEquals(result[0], self.bonds[0])
def test_select_with_invalid_index_returns_empty_set(self):
"""
test string with invalid_index returns empty set
"""
selString = "400"
result, msg = self.stringSel.select(self.bonds, selString)
self.assertEqual(result.__class__, self.bonds.__class__)
self.assertEqual(len(result), 0)
self.assertEqual(msg[0], selString)
def test_select_with_valid_range(self):
"""
test string with valid_range returns set with 2 items
"""
selString = "0-1"
result, msg = self.stringSel.select(self.bonds, selString)
self.assertEquals(len(result), 2)
def test_select_with_invalid_range(self):
"""
test string with invalid_range returns set with 0 items
"""
selString = "400-623"
result, msg = self.stringSel.select(self.bonds, selString)
self.assertEquals(len(result), 0)
def test_select_with_valid_lambda_exp(self):
"""
test string with valid_lambda_exp returns set with items
<this regex is intended to select all bonds involving NE2>
"""
selString = "lambda x: x.atom1.name=='NE2' or x.atom2.name=='NE2'"
result, msg = self.stringSel.select(self.bonds, selString)
#print "result=", result
self.assertEquals(len(result), 1)
def test_no_select_with_valid_regex_2(self):
"""
bondSelector does not support regex
test string with valid_regex returns set with 0 items
"""
selString = "[1-2]"
result, msg = self.stringSel.select(self.bonds, selString)
self.assertEquals(len(result), 0)
def test_select_valid_set(self):
"""
test string with valid set name returns 1 set
"""
these_sets = Sets()
key = 'first'
these_sets.add(key, self.bonds[1:])
selString = key
result, msg = self.stringSel.select(self.bonds, selString,
sets=these_sets)
#print "result=", result
self.assertEquals(len(result), 23)
self.assertEquals(result, self.bonds[1:])
def setUp(self):
self.mols = Read('Data/stringSel.pdb')
for m in self.mols:
m.buildBondsByDistance()
self.bonds = self.mols.chains.residues.atoms.bonds[0]
self.stringSel = BondSetSelector()
def test_constructor(self):
"""
instantiate an BondSetSelector
"""
stringSel = BondSetSelector()
self.assertEquals(stringSel.__class__, BondSetSelector)
