def test_mmtf(self):
path = '../../../resources/files/'
pdb = mmtfReader.read_mmtf_files(path)
self.assertEqual(4, pdb.count())
tmp_path = tempfile.mkdtemp()
print(tmp_path)
mmtfWriter.write_mmtf_files(tmp_path, pdb)
pdb = mmtfReader.read_mmtf_files(tmp_path)
self.assertEqual(4, pdb.count())
def test_1J6T_models(self):
print('test_1J6T_modelS')
path = '../../../resources/files/'
pdb = mmtfReader.read_mmtf_files(path)
pdb = pdb.filter(lambda t: t[0] == '1J6T')
structure = pdb.values().first()
models = structure.get_models()
self.assertEqual(3, len(models))
def test_4HHB_pandas(self):
print('test_4HHB_structure')
path = '../../../resources/files/'
pdb = mmtfReader.read_mmtf_files(path)
pdb = pdb.filter(lambda t: t[0] == '4HHB')
structure = pdb.values().first()
df = structure.to_pandas()
self.assertEqual((4779, 13), df.shape)
def test_1J6T_chains_first_model(self):
print('test_1J6T_chains_first_model')
path = '../../../resources/files/'
pdb = mmtfReader.read_mmtf_files(path, first_model=True)
pdb = pdb.filter(lambda t: t[0] == '1J6T')
structure = pdb.values().first()
chains = structure.get_chains()
self.assertEqual(2, len(chains))
def test_4HHB_chains(self):
print('test_4HHB_chains')
path = '../../../resources/files/'
pdb = mmtfReader.read_mmtf_files(path)
pdb = pdb.filter(lambda t: t[0] == '4HHB')
structure = pdb.values().first()
chains = structure.get_chains()
self.assertEqual(4, len(chains))
def test_4hhb(self):
path = '../../../resources/files/'
pdb = mmtfReader.read_mmtf_files(path)
pdb = pdb.filter(lambda t: t[0] == '4HHB')
structure = pdb.values().first()
self.assertEqual('1.0.0', structure.mmtf_version)
self.assertEqual('UNKNOWN', structure.mmtf_producer)
self.assertEqual(
np.testing.assert_allclose(
[63.150, 83.590, 53.800, 90.00, 99.34, 90.00],
structure.unit_cell,
atol=0.001), None)
self.assertEqual(structure.space_group, 'P 1 21 1')
self.assertEqual(4779, structure.num_atoms)
self.assertEqual(801, structure.num_groups)
self.assertEqual(14, structure.num_chains)
self.assertEqual(1, structure.num_models)
self.assertEqual(
np.testing.assert_allclose([6.204, 6.913, 8.504],
structure.x_coord_list[0:3],
atol=0.001), None)
self.assertEqual(
np.testing.assert_allclose([16.869, 17.759, 17.378],
structure.y_coord_list[0:3],
atol=0.001), None)
self.assertEqual(
np.testing.assert_allclose([4.854, 4.607, 4.797],
structure.z_coord_list[0:3],
atol=0.001), None)
self.assertEqual(
np.testing.assert_allclose([49.05, 43.14, 24.80],
structure.b_factor_list[0:3],
atol=0.01), None)
self.assertEqual(
np.testing.assert_allclose([1.0, 1.0, 1.0],
structure.occupancy_list[0:3],
atol=0.01), None)
self.assertListEqual([1, 2, 3], structure.atom_id_list[0:3].tolist())
self.assertListEqual(['', '', ''],
structure.alt_loc_list[0:3].tolist())
self.assertListEqual(['A', 'A', 'A'],
structure.chain_names[0:3].tolist())
self.assertListEqual(['A', 'A', 'A'],
structure.chain_ids[0:3].tolist())
self.assertListEqual(['1', '1', '1'],
structure.group_numbers[0:3].tolist())
self.assertListEqual(['VAL', 'VAL', 'VAL'],
structure.group_names[0:3].tolist())
self.assertListEqual(['N', 'CA', 'C'],
structure.atom_names[0:3].tolist())
self.assertListEqual(['N', 'C', 'C'], structure.elements[0:3].tolist())
self.assertListEqual(['L-PEPTIDE LINKING', 'L-PEPTIDE LINKING'],
structure.chem_comp_types[0:2].tolist())
self.assertListEqual([True, True, True],
structure.polymer[0:3].tolist())
self.assertListEqual([0, 0, 0], structure.entity_indices[0:3].tolist())
self.assertListEqual([0, 0, 0],
structure.sequence_positions[0:3].tolist())
def test_4HHB_pandas_add_cols(self):
print('test_4HHB_structure')
path = '../../../resources/files/'
pdb = mmtfReader.read_mmtf_files(path)
pdb = pdb.filter(lambda t: t[0] == '4HHB')
structure = pdb.values().first()
df = structure.to_pandas(
add_cols=['sequence_position', 'chem_comp_type'])
self.assertEqual((4779, 15), df.shape)
def test_1J6T_model_first_model(self):
print('test_1J6T_model_first_model')
path = '../../../resources/files/'
pdb = mmtfReader.read_mmtf_files(path, first_model=True)
pdb = pdb.filter(lambda t: t[0] == '1J6T')
structure = pdb.values().first()
model = structure.get_model(0)
self.assertEqual(3555, model.num_atoms)
self.assertEqual(144 + 85, model.num_groups)
self.assertEqual(2, model.num_chains)
self.assertEqual(1, model.num_models)
def test_4HHB_polychains(self):
print('test_4HHB_polychains')
path = '../../../resources/files/'
pdb = mmtfReader.read_mmtf_files(path)
pdb = pdb.filter(lambda t: t[0] == '4HHB')
structure = pdb.values().first()
chain = MmtfSubstructure(structure,
'A+B',
chain_names=['A', 'B'],
entity_types=['polymer'])
self.assertEqual(1069 + 1123, chain.num_atoms)
self.assertEqual(141 + 146, chain.num_groups)
self.assertEqual(1 + 1, chain.num_chains)
self.assertEqual(1, chain.num_models)
def test_1J6T_model_chains(self):
print('test_1J6T_model_chains')
path = '../../../resources/files/'
pdb = mmtfReader.read_mmtf_files(path)
pdb = pdb.filter(lambda t: t[0] == '1J6T')
structure = pdb.values().first()
model = structure.get_model(0)
self.assertEqual(3555, model.num_atoms)
self.assertEqual(144 + 85, model.num_groups)
self.assertEqual(2, model.num_chains)
self.assertEqual(1, model.num_models)
chain = model.get_chain('A')
self.assertEqual(2266, chain.num_atoms)
self.assertEqual(144, chain.num_groups)
self.assertEqual(1, chain.num_chains)
self.assertEqual(1, chain.num_models)
model = structure.get_model(1)
self.assertEqual(3559, model.num_atoms)
self.assertEqual(144 + 85 + 1, model.num_groups)
self.assertEqual(3, model.num_chains)
self.assertEqual(1, model.num_models)
chain = model.get_chain('A')
self.assertEqual(2266, chain.num_atoms)
self.assertEqual(144, chain.num_groups)
self.assertEqual(1, chain.num_chains)
self.assertEqual(1, chain.num_models)
chain = model.get_chain('B')
self.assertEqual(1289, chain.num_atoms)
self.assertEqual(85, chain.num_groups)
self.assertEqual(1, chain.num_chains)
self.assertEqual(1, chain.num_models)
model = structure.get_model(2)
self.assertEqual(3559, model.num_atoms)
self.assertEqual(144 + 85 + 1, model.num_groups)
self.assertEqual(3, model.num_chains)
self.assertEqual(1, model.num_models)
chain = model.get_chain('A')
self.assertEqual(2266, chain.num_atoms)
self.assertEqual(144, chain.num_groups)
self.assertEqual(1, chain.num_chains)
self.assertEqual(1, chain.num_models)
chain = model.get_chain('B')
self.assertEqual(1289, chain.num_atoms)
self.assertEqual(85, chain.num_groups)
self.assertEqual(1, chain.num_chains)
self.assertEqual(1, chain.num_models)
def test_1J6T_structure_first_model(self):
print('test_1J6T_structure')
path = '../../../resources/files/'
pdb = mmtfReader.read_mmtf_files(path, first_model=True)
pdb = pdb.filter(lambda t: t[0] == '1J6T')
structure = pdb.values().first()
# Check entity info
self.assertEqual(2, len(structure.entity_list))
ids = structure.entities_to_pandas()['chain_ids'].tolist()
self.assertEqual(
2, len(ids)
) # first model has only two entities (2nd, 3rd model have 3: +PO4)
self.assertListEqual(['A'], ids[0])
self.assertListEqual(['B'], ids[1])
self.assertEqual(3555, structure.num_atoms)
self.assertEqual(144 + 85, structure.num_groups)
self.assertEqual(2, structure.num_chains)
self.assertEqual(1, structure.num_models)
def test_4HHB_group_numbers(self):
print('test_4HHB_chain_ids')
path = '../../../resources/files/'
pdb = mmtfReader.read_mmtf_files(path)
pdb = pdb.filter(lambda t: t[0] == '4HHB')
structure = pdb.values().first()
chain = MmtfSubstructure(structure,
'HEM',
chain_names=['A'],
group_numbers=['1', '10'])
self.assertEqual(43, chain.num_atoms)
self.assertEqual(1, chain.num_groups)
self.assertEqual(1, chain.num_chains)
self.assertEqual(1, chain.num_models)
chain = MmtfSubstructure(structure, 'HEM', group_names=['HEM'])
self.assertEqual(43 * 4, chain.num_atoms)
self.assertEqual(1 * 4, chain.num_groups)
self.assertEqual(1 * 4, chain.num_chains)
self.assertEqual(1, chain.num_models)
def test_1J6T_structure(self):
print('test_1J6T_structure')
path = '../../../resources/files/'
pdb = mmtfReader.read_mmtf_files(path)
pdb = pdb.filter(lambda t: t[0] == '1J6T')
structure = pdb.values().first()
# Check entity info
#self.assertEqual(3, len(structure.entity_list))
self.assertEqual(2, len(structure.entity_list)
) # MMTF file only contains entities for first model
ids = structure.entities_to_pandas()['chain_ids'].tolist()
self.assertEqual(2, len(ids))
self.assertListEqual(['A'], ids[0])
self.assertListEqual(['B'], ids[1])
# self.assertListEqual(['C'], ids[2]) # PO3 missing in MMTF, present in model 2 and 3
self.assertEqual(3555 + 3559 + 3559, structure.num_atoms)
self.assertEqual(144 + 85 + 144 + 1 + 85 + 144 + 85 + 1,
structure.num_groups)
self.assertEqual(2 + 3 + 3, structure.num_chains)
self.assertEqual(3, structure.num_models)
def test_4HHB_structure(self):
print('test_4HHB_structure')
path = '../../../resources/files/'
pdb = mmtfReader.read_mmtf_files(path)
pdb = pdb.filter(lambda t: t[0] == '4HHB')
structure = pdb.values().first()
# Check metadata
self.assertEqual('1.0.0', structure.mmtf_version)
self.assertEqual('UNKNOWN', structure.mmtf_producer)
self.assertEqual(
np.testing.assert_allclose(
[63.150, 83.590, 53.800, 90.00, 99.34, 90.00],
structure.unit_cell,
atol=0.001), None)
self.assertEqual(structure.space_group, 'P 1 21 1')
self.assertEqual(4779, structure.num_atoms)
self.assertEqual(801, structure.num_groups)
self.assertEqual(14, structure.num_chains)
self.assertEqual(1, structure.num_models)
# Check entity info
ids = structure.entities_to_pandas()['chain_ids'].tolist()
self.assertEqual(5, len(ids))
self.assertListEqual(['A', 'C'], ids[0]) # Hemoglobin alpha
self.assertListEqual(['B', 'D'], ids[1]) # Hemoglobin beta
self.assertListEqual(['E', 'G', 'H', 'J'], ids[2]) # Heme
self.assertListEqual(['F', 'I'], ids[3]) # PO4
self.assertListEqual(['K', 'L', 'M', 'N'], ids[4]) # HOH
# Check atom info
self.assertEqual(
np.testing.assert_allclose([6.204, 6.913, 8.504],
structure.x_coord_list[0:3],
atol=0.001), None)
self.assertEqual(
np.testing.assert_allclose([16.869, 17.759, 17.378],
structure.y_coord_list[0:3],
atol=0.001), None)
self.assertEqual(
np.testing.assert_allclose([4.854, 4.607, 4.797],
structure.z_coord_list[0:3],
atol=0.001), None)
self.assertEqual(
np.testing.assert_allclose([49.05, 43.14, 24.80],
structure.b_factor_list[0:3],
atol=0.01), None)
self.assertEqual(
np.testing.assert_allclose([1.0, 1.0, 1.0],
structure.occupancy_list[0:3],
atol=0.01), None)
self.assertListEqual([1, 2, 3], structure.atom_id_list[0:3].tolist())
self.assertListEqual(['', '', ''],
structure.alt_loc_list[0:3].tolist())
self.assertListEqual(['A', 'A', 'A'],
structure.chain_names[0:3].tolist())
self.assertListEqual(['A', 'A', 'A'],
structure.chain_ids[0:3].tolist())
self.assertListEqual(['1', '1', '1'],
structure.group_numbers[0:3].tolist())
self.assertListEqual(['VAL', 'VAL', 'VAL'],
structure.group_names[0:3].tolist())
self.assertListEqual(['N', 'CA', 'C'],
structure.atom_names[0:3].tolist())
self.assertListEqual(['N', 'C', 'C'], structure.elements[0:3].tolist())
self.assertListEqual(['L-PEPTIDE LINKING', 'L-PEPTIDE LINKING'],
structure.chem_comp_types[0:2].tolist())
self.assertListEqual([True, True, True],
structure.polymer[0:3].tolist())
self.assertListEqual(
[0, 0, 0],
structure.entity_indices[0:3].tolist()) # hemoglobin alpha
self.assertListEqual(
[1, 1, 1],
structure.entity_indices[1069:1072].tolist()) # hemoglobin beta
self.assertListEqual(
[4, 4, 4], structure.entity_indices[4776:4779].tolist()) # water
self.assertListEqual([0, 0, 0],
structure.sequence_positions[0:3].tolist())
def test_mmtf(self):
path = '../../../resources/files/'
pdb = mmtfReader.read_mmtf_files(path)
self.assertEqual(4, pdb.count())
def test_4HHB_chain(self):
print('test_4HHB_chain')
path = '../../../resources/files/'
pdb = mmtfReader.read_mmtf_files(path)
pdb = pdb.filter(lambda t: t[0] == '4HHB')
structure = pdb.values().first()
chain = structure.get_chain('A')
self.assertEqual(1069, chain.num_atoms)
self.assertEqual(141, chain.num_groups)
self.assertEqual(1, chain.num_chains)
self.assertEqual(1, chain.num_models)
self.assertEqual(
np.testing.assert_allclose([6.204, 6.913, 8.504],
chain.x_coord_list[0:3],
atol=0.001), None)
self.assertEqual(
np.testing.assert_allclose([16.869, 17.759, 17.378],
chain.y_coord_list[0:3],
atol=0.001), None)
self.assertEqual(
np.testing.assert_allclose([4.854, 4.607, 4.797],
chain.z_coord_list[0:3],
atol=0.001), None)
self.assertEqual(
np.testing.assert_allclose([49.05, 43.14, 24.80],
chain.b_factor_list[0:3],
atol=0.01), None)
self.assertEqual(
np.testing.assert_allclose([1.0, 1.0, 1.0],
chain.occupancy_list[0:3],
atol=0.01), None)
self.assertListEqual([1, 2, 3], chain.atom_id_list[0:3].tolist())
self.assertListEqual(['', '', ''], chain.alt_loc_list[0:3].tolist())
self.assertListEqual(['A', 'A', 'A'], chain.chain_names[0:3].tolist())
self.assertListEqual(['A', 'A', 'A'], chain.chain_ids[0:3].tolist())
self.assertListEqual(['1', '1', '1'],
chain.group_numbers[0:3].tolist())
self.assertListEqual(['VAL', 'VAL', 'VAL'],
chain.group_names[0:3].tolist())
self.assertListEqual(['N', 'CA', 'C'], chain.atom_names[0:3].tolist())
self.assertListEqual(['N', 'C', 'C'], chain.elements[0:3].tolist())
self.assertListEqual(['L-PEPTIDE LINKING', 'L-PEPTIDE LINKING'],
chain.chem_comp_types[0:2].tolist())
self.assertListEqual([True, True, True], chain.polymer[0:3].tolist())
self.assertListEqual([0, 0, 0], chain.entity_indices[0:3].tolist())
self.assertListEqual([0, 0, 0], chain.sequence_positions[0:3].tolist())
chain = structure.get_chain('B')
self.assertEqual(1123, chain.num_atoms)
self.assertEqual(146, chain.num_groups)
self.assertEqual(1, chain.num_chains)
self.assertEqual(1, chain.num_models)
self.assertEqual(
np.testing.assert_allclose([9.223, 8.694, 9.668],
chain.x_coord_list[0:3],
atol=0.001), None)
self.assertEqual(
np.testing.assert_allclose([-20.614, -20.026, -21.068],
chain.y_coord_list[0:3],
atol=0.001), None)
self.assertEqual(
np.testing.assert_allclose([1.365, -0.123, -1.645],
chain.z_coord_list[0:3],
atol=0.001), None)
self.assertEqual(
np.testing.assert_allclose([46.08, 70.96, 69.74],
chain.b_factor_list[0:3],
atol=0.01), None)
self.assertEqual(
np.testing.assert_allclose([1.0, 1.0, 1.0],
chain.occupancy_list[0:3],
atol=0.01), None)
self.assertListEqual([1070, 1071, 1072],
chain.atom_id_list[0:3].tolist())
self.assertListEqual(['', '', ''], chain.alt_loc_list[0:3].tolist())
self.assertListEqual(['B', 'B', 'B'], chain.chain_names[0:3].tolist())
self.assertListEqual(['B', 'B', 'B'], chain.chain_ids[0:3].tolist())
self.assertListEqual(['1', '1', '1'],
chain.group_numbers[0:3].tolist())
self.assertListEqual(['VAL', 'VAL', 'VAL'],
chain.group_names[0:3].tolist())
self.assertListEqual(['N', 'CA', 'C'], chain.atom_names[0:3].tolist())
self.assertListEqual(['N', 'C', 'C'], chain.elements[0:3].tolist())
self.assertListEqual(['L-PEPTIDE LINKING', 'L-PEPTIDE LINKING'],
chain.chem_comp_types[0:2].tolist())
self.assertListEqual([True, True, True], chain.polymer[0:3].tolist())
self.assertListEqual([1, 1, 1], chain.entity_indices[0:3].tolist())
self.assertListEqual([0, 0, 0], chain.sequence_positions[0:3].tolist())
def test_mmtf(self):
path = './resources/files/'
pdb = mmtfReader.read_mmtf_files(path, self.sc)
self.assertTrue(pdb.count() == 3)
