def setUp(self):
self.atom_numbers = [1000, 1001]
self.atom_names = ["ABCD", "A2"]
self.residue_numbers = [999, 1000]
self.residue_names = ["XYZ", "R2"]
self.coords = np.zeros((2, 3))
self.coords[0, :] = 1.0
self.coords[1, :] = 2.0
self.writer = PDBWriter(self.atom_numbers, self.atom_names,
self.residue_numbers, self.residue_names)
def setUp(self):
self.atom_numbers = [1000, 1001]
self.atom_names = ['ABCD', 'A2']
self.residue_numbers = [999, 1000]
self.residue_names = ['XYZ', 'R2']
self.coords = np.zeros((2, 3))
self.coords[0, :] = 1.0
self.coords[1, :] = 2.0
self.writer = PDBWriter(self.atom_numbers, self.atom_names,
self.residue_numbers, self.residue_names)
def get_pdb_writer(self):
return PDBWriter(
range(1,
len(self._atom_names) + 1),
self._atom_names,
self._residue_numbers,
self._residue_names,
)
def setUp(self):
self.atom_numbers = [1000, 1001]
self.atom_names = ['ABCD', 'A2']
self.residue_numbers = [999, 1000]
self.residue_names = ['XYZ', 'R2']
self.coords = np.zeros((2, 3))
self.coords[0, :] = 1.0
self.coords[1, :] = 2.0
self.writer = PDBWriter(self.atom_numbers, self.atom_names, self.residue_numbers, self.residue_names)
class TestPDBWriter(unittest.TestCase):
def setUp(self):
self.atom_numbers = [1000, 1001]
self.atom_names = ['ABCD', 'A2']
self.residue_numbers = [999, 1000]
self.residue_names = ['XYZ', 'R2']
self.coords = np.zeros((2, 3))
self.coords[0, :] = 1.0
self.coords[1, :] = 2.0
self.writer = PDBWriter(self.atom_numbers, self.atom_names, self.residue_numbers, self.residue_names)
def test_should_raise_with_wrong_number_of_atom_names(self):
with self.assertRaises(AssertionError):
PDBWriter(self.atom_numbers, ['CA'], self.residue_numbers, self.residue_names)
def test_should_raise_with_wrong_number_of_residue_numbers(self):
with self.assertRaises(AssertionError):
PDBWriter(self.atom_numbers, self.atom_names, [1], self.residue_names)
def test_should_raise_with_wrong_number_of_residue_names(self):
with self.assertRaises(AssertionError):
PDBWriter(self.atom_numbers, self.atom_names, self.residue_numbers, ['R1'])
def test_should_raise_with_bad_coordinate_size(self):
with self.assertRaises(AssertionError):
self.writer.get_pdb_string(np.zeros((3, 3)), 1)
def test_output_should_have_six_lines(self):
result = self.writer.get_pdb_string(self.coords, 1)
lines = result.splitlines()
self.assertEqual(len(lines), 6)
def test_header_should_have_correct_stage(self):
result = self.writer.get_pdb_string(self.coords, 1)
lines = result.splitlines()
self.assertIn('REMARK', lines[0])
self.assertIn('stage 1', lines[0])
def test_atom_line_should_have_correct_format(self):
result = self.writer.get_pdb_string(self.coords, 1)
lines = result.splitlines()
result = lines[1]
expected_result = 'ATOM 1000 ABCD XYZ 999 1.000 1.000 1.000'
print expected_result
print lines[1]
self.assertEqual(result, expected_result)
def test_other_atom_line_should_have_correct_format(self):
result = self.writer.get_pdb_string(self.coords, 1)
lines = result.splitlines()
result = lines[2]
expected_result = 'ATOM 1001 A2 R2 1000 2.000 2.000 2.000'
print expected_result
print lines[2]
self.assertEqual(result, expected_result)
class TestPDBWriter(unittest.TestCase):
def setUp(self):
self.atom_numbers = [1000, 1001]
self.atom_names = ["ABCD", "A2"]
self.residue_numbers = [999, 1000]
self.residue_names = ["XYZ", "R2"]
self.coords = np.zeros((2, 3))
self.coords[0, :] = 1.0
self.coords[1, :] = 2.0
self.writer = PDBWriter(self.atom_numbers, self.atom_names,
self.residue_numbers, self.residue_names)
def test_should_raise_with_wrong_number_of_atom_names(self):
with self.assertRaises(AssertionError):
PDBWriter(self.atom_numbers, ["CA"], self.residue_numbers,
self.residue_names)
def test_should_raise_with_wrong_number_of_residue_numbers(self):
with self.assertRaises(AssertionError):
PDBWriter(self.atom_numbers, self.atom_names, [1],
self.residue_names)
def test_should_raise_with_wrong_number_of_residue_names(self):
with self.assertRaises(AssertionError):
PDBWriter(self.atom_numbers, self.atom_names, self.residue_numbers,
["R1"])
def test_should_raise_with_bad_coordinate_size(self):
with self.assertRaises(AssertionError):
self.writer.get_pdb_string(np.zeros((3, 3)), 1)
def test_output_should_have_six_lines(self):
result = self.writer.get_pdb_string(self.coords, 1)
lines = result.splitlines()
self.assertEqual(len(lines), 6)
def test_header_should_have_correct_stage(self):
result = self.writer.get_pdb_string(self.coords, 1)
lines = result.splitlines()
self.assertIn("REMARK", lines[0])
self.assertIn("stage 1", lines[0])
def test_atom_line_should_have_correct_format(self):
result = self.writer.get_pdb_string(self.coords, 1)
lines = result.splitlines()
result = lines[1]
expected_result = "ATOM 1000 ABCD XYZ 999 1.000 1.000 1.000"
self.assertEqual(result, expected_result)
def test_other_atom_line_should_have_correct_format(self):
result = self.writer.get_pdb_string(self.coords, 1)
lines = result.splitlines()
result = lines[2]
expected_result = "ATOM 1001 A2 R2 1000 2.000 2.000 2.000"
self.assertEqual(result, expected_result)
def test_should_raise_with_wrong_number_of_residue_names(self):
with self.assertRaises(AssertionError):
PDBWriter(self.atom_numbers, self.atom_names, self.residue_numbers,
["R1"])
