class AtomSetSelectorTests(AtomSetSelectorBaseTests):
def setUp(self):
self.mols = Read('Data/stringSel.pdb')
new_mols = Read("Data/1crn.pdb")
self.mols +=new_mols
self.atoms = self.mols.chains.residues.atoms
self.stringSel = AtomSetSelector()
def tearDown(self):
"""
clean-up
"""
del(self.atoms)
del(self.mols)
def test_select_with_empty_string(self):
"""
test result with empty string returns all atoms
"""
result, msg = self.stringSel.select(self.atoms, "")
self.assertEquals(result, self.atoms)
def test_select_end(self):
"""
test select with '$' returns last item
"""
result, msg = self.stringSel.select(self.atoms, "$")
self.assertEquals(result, self.atoms[-1:])
def test_select_with_valid_index(self):
"""
test string with valid_index returns set with 1 item
"""
selString = "1"
result, msg = self.stringSel.select(self.atoms, selString)
self.assertEquals(len(result), 1)
def test_select_with_invalid_index_returns_empty_set(self):
"""
test string with invalid_index returns empty set
"""
selString = "777"
result, msg = self.stringSel.select(self.atoms, selString)
self.assertEqual(result.__class__, self.atoms.__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 = "1-2"
result, msg = self.stringSel.select(self.atoms, selString)
#FIX THIS
self.assertEquals(len(result), 2)
def test_select_with_invalid_range(self):
"""
test string with invalid_range returns set with 0 items
"""
selString = "649-713"
result, msg = self.stringSel.select(self.atoms, selString)
self.assertEquals(len(result), 0)
def test_select_with_valid_regex(self):
"""
test string with valid_regex returns set with 1 items
<this regex is intended to match anything in range A-Z
followed by anything>
"""
selString = "CA"
result, msg = self.stringSel.select(self.atoms, selString)
#print "result=", result
self.assertEquals(len(result), 49)
def test_select_valid_set(self):
"""
test string with valid set name returns 1 set
"""
these_sets = Sets()
new_set = self.atoms[:10]
key = 'first_atoms'
these_sets.add(key, new_set)
selString = key
result, msg = self.stringSel.select(self.atoms, selString,
sets=these_sets)
self.assertEquals(len(result), len(new_set))
self.assertEquals(result, new_set)
