def test_mol_read_xyz():
file = 'tests/test_store/ethane.xyz'
pmol = next(pyb.readfile('xyz', file))
mol = get_ethane_mol()
assert np.array_equal(mol.xyz, pread.mol_read_xyz(pmol))
def test_get_dummy_features():
mol = get_ethane_mol()
mols = [mol]
x, y, r = get_dummy_features(mols, targetflag='CCS')
assert x == []
assert np.array_equal(y, mol.shift[np.where(mol.types == 6)])
assert np.array_equal(r, [['ethane', 0], ['ethane', 1]])
x, y, r = get_dummy_features(mols, targetflag='HCS')
assert x == []
assert np.array_equal(y, mol.shift[np.where(mol.types == 1)])
assert np.array_equal(r, [['ethane', 2], ['ethane', 3], ['ethane', 4],
['ethane', 5], ['ethane', 6], ['ethane', 7]])
x, y, r = get_dummy_features(mols, targetflag='1JCH')
for i, index in enumerate(r):
assert y[i] == mol.coupling[index[1]][index[2]]
assert np.array_equal(
r, [['ethane', 0, 2], ['ethane', 0, 3], ['ethane', 0, 4],
['ethane', 1, 5], ['ethane', 1, 6], ['ethane', 1, 7]])
x, y, r = get_dummy_features(mols, targetflag='3JHH')
for i, index in enumerate(r):
assert y[i] == mol.coupling[index[1]][index[2]]
assert np.array_equal(
r, [['ethane', 2, 5], ['ethane', 2, 6], ['ethane', 2, 7],
['ethane', 3, 5], ['ethane', 3, 6], ['ethane', 3, 7],
['ethane', 4, 5], ['ethane', 4, 6], ['ethane', 4, 7]])
def test_mol_getatoms():
file = 'tests/test_store/ethane.xyz'
pmol = next(pyb.readfile('xyz', file))
mol = get_ethane_mol()
size = len(mol.types)
assert size == pread.mol_getatoms(pmol)
def test_mol_iswhole():
file = 'tests/test_store/ethane.xyz'
pmol = next(pyb.readfile('xyz', file))
mol = get_ethane_mol()
size = len(mol.types)
assert psplit.mol_iswhole(pmol)
def test_mol_isequal():
mol1 = get_ethane_mol()
mol2 = get_random_mol()
# Different molecules are different
assert mol_isequal(mol1, mol2) == False
# Identical molecules are identical
assert mol_isequal(mol1, mol1) == True
def test_get_coupling_lengths():
file = 'tests/test_store/ethane.xyz'
pmol = next(pyb.readfile('xyz', file))
mol = get_ethane_mol()
size = len(mol.types)
coupling_len = pbonds.get_coupling_lengths(pmol, mol.types, maxlen=4)
assert np.array_equal(coupling_len, mol.coupling_len)
def test_mol_get_bond_table():
file = 'tests/test_store/ethane.xyz'
pmol = next(pyb.readfile('xyz', file))
mol = get_ethane_mol()
size = len(mol.types)
bond_table = pbonds.mol_get_bond_table(pmol)
assert np.array_equal(bond_table, mol.conn)
def test_get_FCHL_features():
mol = get_ethane_mol()
mols = [mol]
x, y, r = get_dummy_features(mols, targetflag='CCS')
assert x == []
assert np.array_equal(y, mol.shift[np.where(mol.types == 6)])
def test_mol_read_dist():
file = 'tests/test_store/ethane.xyz'
pmol = next(pyb.readfile('xyz', file))
mol = get_ethane_mol()
size = len(mol.types)
d_array = pread.mol_read_dist(pmol)
for i in range(size):
for j in range(size):
assert d_array[i][j] == np.absolute(
np.linalg.norm(mol.xyz[i] - mol.xyz[j]))
def test_mol_splitmol():
file = 'tests/test_store/ethane.xyz'
pmol = next(pyb.readfile('xyz', file))
mol = get_ethane_mol()
size = len(mol.types)
print(psplit.mol_splitmol(pmol))
assert len(psplit.mol_splitmol(pmol)[0]) == size
assert len(psplit.mol_splitmol(pmol)[1]) == 0
assert len(psplit.mol_splitmol(pmol)) == 2
def test_mol_read_type():
file = 'tests/test_store/ethane.xyz'
pmol = next(pyb.readfile('xyz', file))
mol = get_ethane_mol()
size = len(mol.types)
type_list, type_array = pread.mol_read_type(pmol)
assert np.array_equal(mol.types, type_array)
assert np.array_equal(
np.asarray([x for x, type in enumerate(type_list) if "H" == type]),
np.where(type_array == 1)[0])
assert np.array_equal(
np.asarray([x for x, type in enumerate(type_list) if "C" == type]),
np.where(type_array == 6)[0])
def test_qml_features():
import qml
mol = get_ethane_mol()
mbtypes = [[1], [1, 1], [1, 1, 1], [1, 1, 6], [1, 1, 7], [1, 1, 8],
[1, 1, 9], [1, 6], [1, 6, 1], [1, 6, 6], [1, 6, 7], [1, 6, 8],
[1, 6, 9], [1, 7], [1, 7, 1], [1, 7, 6], [1, 7, 7], [1, 7, 8],
[1, 7, 9], [1, 8], [1, 8, 1], [1, 8, 6], [1, 8, 7], [1, 8, 8],
[1, 8, 9], [1, 9], [1, 9, 1], [1, 9, 6], [1, 9, 7], [1, 9, 8],
[1, 9, 9], [6], [6, 1], [6, 1, 1], [6, 1, 6], [6, 1, 7],
[6, 1, 8], [6, 1, 9], [6, 6], [6, 6, 1], [6, 6, 6], [6, 6, 7],
[6, 6, 8], [6, 6, 9], [6, 7], [6, 7, 1], [6, 7, 6], [6, 7, 7],
[6, 7, 8], [6, 7, 9], [6, 8], [6, 8, 1], [6, 8, 6], [6, 8, 7],
[6, 8, 8], [6, 8, 9], [6, 9], [6, 9, 1], [6, 9, 6], [6, 9, 7],
[6, 9, 8], [6, 9, 9], [7], [7, 1], [7, 1, 1], [7, 1, 6],
[7, 1, 7], [7, 1, 8], [7, 1, 9], [7, 6], [7, 6, 1], [7, 6, 6],
[7, 6, 7], [7, 6, 8], [7, 6, 9], [7, 7], [7, 7, 1], [7, 7, 6],
[7, 7, 7], [7, 7, 8], [7, 7, 9], [7, 8], [7, 8, 1], [7, 8, 6],
[7, 8, 7], [7, 8, 8], [7, 8, 9], [7, 9], [7, 9, 1], [7, 9, 6],
[7, 9, 7], [7, 9, 8], [7, 9, 9], [8], [8, 1], [8, 1, 1],
[8, 1, 6], [8, 1, 7], [8, 1, 8], [8, 1, 9], [8, 6], [8, 6, 1],
[8, 6, 6], [8, 6, 7], [8, 6, 8], [8, 6, 9], [8, 7], [8, 7, 1],
[8, 7, 6], [8, 7, 7], [8, 7, 8], [8, 7, 9], [8, 8], [8, 8, 1],
[8, 8, 6], [8, 8, 7], [8, 8, 8], [8, 8, 9], [8, 9], [8, 9, 1],
[8, 9, 6], [8, 9, 7], [8, 9, 8], [8, 9, 9], [9], [9, 1],
[9, 1, 1], [9, 1, 6], [9, 1, 7], [9, 1, 8], [9, 1, 9], [9, 6],
[9, 6, 1], [9, 6, 6], [9, 6, 7], [9, 6, 8], [9, 6, 9], [9, 7],
[9, 7, 1], [9, 7, 6], [9, 7, 7], [9, 7, 8], [9, 7, 9], [9, 8],
[9, 8, 1], [9, 8, 6], [9, 8, 7], [9, 8, 8], [9, 8, 9], [9, 9],
[9, 9, 1], [9, 9, 6], [9, 9, 7], [9, 9, 8], [9, 9, 9]]
reps = qml.representations.generate_slatm(mol.xyz, mol.types, mbtypes)
x = np.asarray(reps)
reps = qml.representations.generate_atomic_coulomb_matrix(
mol.types, mol.xyz)
x = np.asarray(reps)
reps = qml.fchl.generate_representation(mol.xyz, mol.types)
x = np.asarray(reps)
try:
reps = qml.representations.generate_acsf(mol.types, mol.xyz)
except:
print('Warning: not using qml version with ACSF rep')
def test_mol_find_all_paths():
file = 'tests/test_store/ethane.xyz'
pmol = next(pyb.readfile('xyz', file))
mol = get_ethane_mol()
size = len(mol.types)
for i in range(size):
for j in range(size):
for k in range(size):
paths = pbonds.mol_find_all_paths(pmol, i, j, k)
if i == j:
assert len(paths) == 0
else:
for path in paths:
if len(path) == 0:
continue
assert path[0] == i
assert path[-1] == j
assert len(set(path)) == len(path)
if mol.coupling_len[i][j] == k:
assert len(paths[0]) == k + 1