def test_read_mol(self):
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files', "molecules")
for fname in ("methane.log", "c60.xyz", "ethane.gjf"):
filename = os.path.join(test_dir, fname)
mol = read_mol(filename)
self.assertIsInstance(mol, Molecule)
for ext in [".xyz", ".json", ".gjf"]:
fn = "smartio_mol_test" + ext
write_mol(mol, fn)
back = read_mol(fn)
self.assertEqual(back, mol)
os.remove(fn)
def test_read_mol(self):
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files', "molecules")
for fname in ("methane.log", "c60.xyz", "ethane.gjf"):
filename = os.path.join(test_dir, fname)
mol = read_mol(filename)
self.assertIsInstance(mol, Molecule)
for ext in [".xyz", ".json", ".gjf"]:
fn = "smartio_mol_test" + ext
write_mol(mol, fn)
back = read_mol(fn)
self.assertEqual(back, mol)
os.remove(fn)
def test_read_mol_babel(self):
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files', "molecules")
for fname in ("ethane.mol", ):
filename = os.path.join(test_dir, fname)
mol = read_mol(filename)
self.assertIsInstance(mol, Molecule)
def test_read_mol_babel(self):
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files', "molecules")
for fname in ("ethane.mol", ):
filename = os.path.join(test_dir, fname)
mol = read_mol(filename)
self.assertIsInstance(mol, Molecule)
def test_get_meta_from_structure(self):
mol = read_mol(os.path.join(test_dir, "thiophene1.xyz"))
meta = get_meta_from_structure(mol)
json.dumps(meta, indent=4, sort_keys=True)
meta_ref_text = '''
{
"anonymized_formula": "AB3C3D5",
"chemsystem": "C-Cl-H-S",
"elements": ["C", "Cl", "H", "S"],
"formula": "H3 C5 S1 Cl3",
"inchi": "InChI=1S/C5H3Cl3S/c6-5(7,8)4-1-2-9-3-4/h1-3H",
"is_valid": true,
"known_bonds": [[0, 1], [1, 2], [1, 10], [1, 11], [2, 3], [2, 5], [3, 4],
[3, 9], [5, 6], [5, 7], [7, 8], [7, 9]],
"nelements": 4,
"nsites": 12,
"reduced_cell_formula": "H3C5SCl3",
"reduced_cell_formula_abc": "C5 Cl3 H3 S1"
}'''
meta_ref = json.loads(meta_ref_text)
self.assertEqual(meta, meta_ref)