def test_dump_to_sdf_file(self):
s1 = dpdata.BondOrderSystem("bond_order/methane.sdf", fmt="sdf")
s2 = deepcopy(s1)
s2.data["coords"] += 1.0
s2.to_sdf_file("bond_order/test.sdf")
nsyst = dpdata.BondOrderSystem("bond_order/test.sdf", fmt="sdf")
self.assertEqual(nsyst["coords"][0, 0, 0] - s1["coords"][0, 0, 0], 1.0)
os.remove("bond_order/test.sdf")
def test_from_mol_file(self):
syst = dpdata.BondOrderSystem("bond_order/CH3OH.mol", fmt='mol', type_map=['O','C','H'])
self.assertEqual(syst.get_nframes(), 1)
self.assertEqual(syst.get_nbonds(), 5)
self.assertEqual(syst.get_natoms(), 6)
self.assertEqual(syst['atom_names'], ['O','C','H'])
self.assertAlmostEqual(syst['coords'][0][0][0], -0.3858)
def test_formal_charge(self):
names = ["C5H5-", "CH3CC-", "CH3NC", "CH3NH3+", "CH3NO2", "OCH3+",
"gly", "arg", "oxpy", "CH3OPO3_2-", "CH3PH3+", "CH3OAsO3_2-",
"CH3SH", "CH3_2SO", "CH3_2SO2", "CH3SO3-", "BOH4-"]
charges = [-1, -1, 0, 1, 0, 1, 0, 1, 0, -2, 1, -2, 0, 0, 0, -1, -1]
mols = [dpdata.BondOrderSystem(f"bond_order/{name}.mol") for name in names]
self.assertEqual(charges, [mol.get_charge() for mol in mols])
def test_from_rdkit_mol(self):
mol = Chem.MolFromSmiles("CC")
mol = Chem.AddHs(mol)
AllChem.EmbedMultipleConfs(mol, 10)
system = dpdata.BondOrderSystem(rdkit_mol=mol)
self.assertEqual(system.get_nframes(), 10)
self.assertEqual(system.get_nbonds(), 7)
def test_sanitize_mol_origin(self):
cnt = 0
for sdf_file in glob.glob("bond_order/refined-set-ligands/origin/*sdf"):
syst = dpdata.BondOrderSystem(sdf_file, sanitize_level='high', verbose=False)
if syst.rdkit_mol is None:
cnt += 1
self.assertEqual(cnt, 0)
def test_regularize_formal_charges(self):
non_regular = Chem.MolFromMolFile("bond_order/formal_charge.mol",
removeHs=False)
regular = dpdata.BondOrderSystem("bond_order/formal_charge.mol",
fmt="mol")
self.assertFalse(non_regular)
self.assertTrue(isinstance(regular.rdkit_mol, Chem.rdchem.Mol))
def test_dump_to_deepmd_npy(self):
syst = dpdata.BondOrderSystem("bond_order/methane.sdf", fmt="sdf")
syst.to_deepmd_npy("bond_order/methane")
formal_charges = list(np.loadtxt("bond_order/methane/formal_charges.raw"))
self.assertTrue(formal_charges, [0 for _ in range(5)])
bonds = np.loadtxt("bond_order/methane/bonds.raw")
for bond_idx in range(4):
for ii in range(3):
self.assertEqual(syst['bonds'][bond_idx][ii], bonds[bond_idx][ii])
shutil.rmtree("bond_order/methane")
def test_from_sdf_file(self):
syst = dpdata.BondOrderSystem("bond_order/methane.sdf", type_map=['C','H'])
self.assertEqual(syst.get_nframes(), 4)
self.assertEqual(syst.get_nbonds(), 4)
self.assertEqual(syst.get_natoms(), 5)
self.assertEqual(syst['atom_names'], ['C','H'])
self.assertAlmostEqual(syst['coords'][0][0][0], 0.0059)
self.assertAlmostEqual(syst['coords'][1][0][0], 0.0043)
self.assertAlmostEqual(syst['coords'][2][0][0], 0.0071)
self.assertAlmostEqual(syst['coords'][3][0][0], 0.0032)
def setUp(self):
self.system = dpdata.BondOrderSystem("amber/methane.mol", fmt='mol', type_map=['H','C'])
with open('amber/sqm.in', 'r') as f:
self.sqm_in = f.read()
