def test_pchemblimp():
files = glob.glob('tests/test_mols/test_pchembl/*.sdf')
mols = []
for file in files:
molid = file.split('/')[-1].split('.')[0]
test_mol = aemol(molid)
test_mol.from_file_pyb(file, ftype='sdf')
test_mol.from_pybel(test_mol.pybmol)
pmol = dataframe_prep.prep_mol_ic50(
test_mol, 'tests/test_mols/test_pchembl/test_ic50.tsv', 'ic50')
mols.append(pmol)
atom_df = dataframe_write.make_atom_df(mols)
pair_df = dataframe_write.make_pair_df(mols)
assert np.array_equal(
atom_df.loc[(
atom_df['molecule_name'] == "CHEMBL460962")]['ic50'].to_numpy(),
np.full(len(atom_df.loc[(atom_df['molecule_name'] == "CHEMBL460962"
)]['typeint'].to_numpy()),
8.92,
dtype=np.float64))
assert np.array_equal(
atom_df.loc[(
atom_df['molecule_name'] == "CHEMBL2179015")]['ic50'].to_numpy(),
np.full(len(atom_df.loc[(atom_df['molecule_name'] == "CHEMBL2179015"
)]['typeint'].to_numpy()),
7.54,
dtype=np.float64))
def test_getcouplingtypes():
test_mol = aemol(0)
test_mol.from_file_pyb('tests/test_mols/qm9_9.nmredata.sdf', ftype='sdf')
test_mol.from_pybel(test_mol.pybmol)
nmr.nmr_ops.get_coupling_types(test_mol)
assert test_mol.pair_properties['nmr_types'] == [
['0JCC', '1JCC', '2JCC', '1JCH', '1JCH', '1JCH', '3JCH'],
['1JCC', '0JCC', '1JCC', '2JCH', '2JCH', '2JCH', '2JCH'],
['2JCC', '1JCC', '0JCC', '3JCH', '3JCH', '3JCH', '1JCH'],
['1JCH', '2JCH', '3JCH', '0JHH', '2JHH', '2JHH', '4JHH'],
['1JCH', '2JCH', '3JCH', '2JHH', '0JHH', '2JHH', '4JHH'],
['1JCH', '2JCH', '3JCH', '2JHH', '2JHH', '0JHH', '4JHH'],
['3JCH', '2JCH', '1JCH', '4JHH', '4JHH', '4JHH', '0JHH']
]
def test_prep_mol():
test_mol = aemol(0)
test_mol.from_file_pyb('tests/test_mols/qm9_8.nmredata.sdf', ftype='sdf')
test_mol.from_pybel(test_mol.pybmol)
test_mol = dataframe_prep.prep_mol_nmr(
test_mol,
nmr_file='tests/test_mols/qm9_8.nmredata.sdf',
nmr_type='nmredata')
assert np.array_equal(
test_mol.atom_properties['shift'],
np.asarray([
46.06039042, 327.955, 3.76051871, 3.76014554, 3.59063345,
-0.6359735
]))
assert test_mol.pair_properties['nmr_types'] == [
['0JCC', '1JOC', '1JCH', '1JCH', '1JCH', '2JCH'],
['1JOC', '0JOO', '2JOH', '2JOH', '2JOH', '1JOH'],
['1JCH', '2JOH', '0JHH', '2JHH', '2JHH', '3JHH'],
['1JCH', '2JOH', '2JHH', '0JHH', '2JHH', '3JHH'],
['1JCH', '2JOH', '2JHH', '2JHH', '0JHH', '3JHH'],
['2JCH', '1JOH', '3JHH', '3JHH', '3JHH', '0JHH']
]
assert np.array_equal(
test_mol.pair_properties['coupling'],
np.asarray([[0., 0., 87.6326, 87.6253, 90.0888, -1.36995],
[0., 0., 0., 0., 0., 0.],
[87.6326, 0., 0., -6.48291, -10.6098, 1.43077],
[87.6253, 0., -6.48291, 0., -10.6153, 1.45233],
[90.0888, 0., -10.6098, -10.6153, 0., 13.7865],
[-1.36995, 0., 1.43077, 1.45233, 13.7865, 0.]]))
assert np.array_equal(
test_mol.structure['xyz'],
np.asarray([[0.6607, -0.0193, 0.], [-0.748, 0.1217, 0.],
[1.035, -0.5428, 0.8925], [1.0348, -0.5448, -0.8914],
[1.0819, 0.9897, -0.0012], [-1.1318, -0.7597, 0.]]))
assert np.array_equal(test_mol.structure['types'],
np.asarray([6, 8, 1, 1, 1, 1]))
assert np.array_equal(
test_mol.structure['conn'],
np.asarray([[0, 1, 1, 1, 1, 0], [1, 0, 0, 0, 0, 1], [1, 0, 0, 0, 0, 0],
[1, 0, 0, 0, 0, 0], [1, 0, 0, 0, 0, 0], [0, 1, 0, 0, 0,
0]]))
assert np.array_equal(
test_mol.structure['path_len'],
np.asarray([[0, 1, 1, 1, 1, 2], [1, 0, 2, 2, 2, 1], [1, 2, 0, 2, 2, 3],
[1, 2, 2, 0, 2, 3], [1, 2, 2, 2, 0, 3], [2, 1, 3, 3, 3,
0]]))
def test_getpchembl():
files = glob.glob('tests/test_mols/test_pchembl/*.sdf')
mols = []
for file in files:
molid = file.split('/')[-1].split('.')[0]
test_mol = aemol(molid)
test_mol.from_file_pyb(file, ftype='sdf')
test_mol.from_pybel(test_mol.pybmol)
test_mol.prop_fromfile('tests/test_mols/test_pchembl/test_ic50.tsv',
prop='ic50',
format='tsv')
mols.append(test_mol)
assert mols[0].info['molid'] == "CHEMBL460962"
assert mols[0].mol_properties['ic50'] == 8.92
assert mols[1].info['molid'] == "CHEMBL2179452"
assert mols[1].mol_properties['ic50'] == 7.55
def test_dataframe_write():
files = glob.glob("tests/test_mols/qm9_*.nmredata.sdf")
mols = []
for file in files:
f = int(file.split('_')[-1].split('.')[0])
test_mol = aemol(f)
test_mol.from_file_pyb(file, ftype='sdf')
test_mol.from_pybel(test_mol.pybmol)
test_mol = dataframe_prep.prep_mol_nmr(test_mol,
nmr_file=file,
nmr_type='nmredata')
mols.append(test_mol)
atom_df = dataframe_write.make_atom_df(mols)
pair_df = dataframe_write.make_pair_df(mols)
assert np.all(
pair_df.loc[(pair_df.path_len == 0)]['coupling'].to_numpy() == 0)
assert np.all([
x[2] == x[3]
for x in pair_df.loc[(pair_df.path_len == 0)]['nmr_types'].to_list()
])
assert pair_df['path_len'].to_list() == [
int(x[0]) for x in pair_df['nmr_types'].to_list()
]
mol_atoms = atom_df.loc[atom_df.molecule_name == 8]
mol_pairs = pair_df.loc[pair_df.molecule_name == 8]
assert np.array_equal(
mol_atoms['shift'].to_numpy(),
np.asarray([
46.06039042, 327.955, 3.76051871, 3.76014554, 3.59063345,
-0.6359735
]))
assert mol_pairs['nmr_types'].to_list() == [
'0JCC', '1JOC', '1JCH', '1JCH', '1JCH', '2JCH', '1JOC', '0JOO', '2JOH',
'2JOH', '2JOH', '1JOH', '1JCH', '2JOH', '0JHH', '2JHH', '2JHH', '3JHH',
'1JCH', '2JOH', '2JHH', '0JHH', '2JHH', '3JHH', '1JCH', '2JOH', '2JHH',
'2JHH', '0JHH', '3JHH', '2JCH', '1JOH', '3JHH', '3JHH', '3JHH', '0JHH'
]
assert np.array_equal(
mol_pairs['coupling'],
np.asarray([[0., 0., 87.6326, 87.6253, 90.0888, -1.36995],
[0., 0., 0., 0., 0., 0.],
[87.6326, 0., 0., -6.48291, -10.6098, 1.43077],
[87.6253, 0., -6.48291, 0., -10.6153, 1.45233],
[90.0888, 0., -10.6098, -10.6153, 0., 13.7865],
[-1.36995, 0., 1.43077, 1.45233, 13.7865, 0.]]).flatten())
assert np.array_equal(
np.asarray([mol_atoms['x'], mol_atoms['y'],
mol_atoms['z']]).transpose(),
np.asarray([[0.6607, -0.0193, 0.], [-0.748, 0.1217, 0.],
[1.035, -0.5428, 0.8925], [1.0348, -0.5448, -0.8914],
[1.0819, 0.9897, -0.0012], [-1.1318, -0.7597, 0.]]))
assert np.array_equal(mol_atoms['typeint'].to_numpy(),
np.asarray([6, 8, 1, 1, 1, 1]))
assert np.array_equal([list(x) for x in mol_atoms['conn'].to_numpy()],
np.asarray([[0, 1, 1, 1, 1, 0], [1, 0, 0, 0, 0, 1],
[1, 0, 0, 0, 0, 0], [1, 0, 0, 0, 0, 0],
[1, 0, 0, 0, 0, 0], [0, 1, 0, 0, 0, 0]]))
assert np.array_equal(
mol_pairs['path_len'].to_numpy(),
np.asarray([[0, 1, 1, 1, 1, 2], [1, 0, 2, 2, 2, 1], [1, 2, 0, 2, 2, 3],
[1, 2, 2, 0, 2, 3], [1, 2, 2, 2, 0, 3], [2, 1, 3, 3, 3,
0]]).flatten())