def test_reading():
""" Test reading molecule files to ChemDataFrame """
df = opd.read_sdf(input_fname)
# Check dimensions
assert len(df) == 100
assert len(df.columns) == 15
df = opd.read_sdf(input_fname, smiles_column='smi_col')
assert 'smi_col' in df.columns
df = opd.read_sdf(input_fname,
molecule_column=None,
molecule_name_column=None,
usecols=['name'])
assert 'mol' not in df.columns
assert 'mol_name' not in df.columns
assert len(df.columns) == 1
df = opd.read_sdf(input_fname, usecols=['name', 'uniprot_id', 'act'])
assert len(df.columns) == 5 # 3 from use_cols + 1 'mol' + 1 'mol_name'
assert 'uniprot_id' in df.columns
assert 'smi_col' not in df.columns
# Chunk reading
chunks = []
for chunk in opd.read_sdf(input_fname, chunksize=10):
assert len(chunk) == 10
chunks.append(chunk)
assert len(chunks) == 10
df = pd.concat(chunks)
# Check dimensions
assert len(df) == 100
def test_reading():
""" Test reading molecule files to ChemDataFrame """
df = opd.read_sdf(input_fname)
# Check dimensions
assert_equal(len(df), 100)
assert_equal(len(df.columns), 15)
df = opd.read_sdf(input_fname, smiles_column='smi_col')
assert_in('smi_col', df.columns)
df = opd.read_sdf(input_fname,
molecule_column=None,
molecule_name_column=None,
usecols=['name'])
assert_not_in('mol', df.columns)
assert_not_in('mol_name', df.columns)
assert_equal(len(df.columns), 1)
df = opd.read_sdf(input_fname, usecols=['name', 'uniprot_id', 'act'])
assert_equal(len(df.columns),
5) # 3 from use_cols + 1 'mol' + 1 'mol_name'
assert_in('uniprot_id', df.columns)
assert_not_in('smi_col', df.columns)
# Chunk reading
chunks = []
for chunk in opd.read_sdf(input_fname, chunksize=10):
assert_equal(len(chunk), 10)
chunks.append(chunk)
assert_equal(len(chunks), 10)
df = pd.concat(chunks)
# Check dimensions
assert_equal(len(df), 100)
def test_reading():
""" Test reading molecule files to ChemDataFrame """
df = opd.read_sdf(input_fname)
# Check dimensions
assert len(df) == 100
assert len(df.columns) == 15
df = opd.read_sdf(input_fname, smiles_column='smi_col')
assert 'smi_col' in df.columns
df = opd.read_sdf(input_fname,
molecule_column=None,
molecule_name_column=None,
usecols=['name'])
assert 'mol' not in df.columns
assert 'mol_name' not in df.columns
assert len(df.columns) == 1
df = opd.read_sdf(input_fname,
usecols=['name', 'uniprot_id', 'act'])
assert len(df.columns) == 5 # 3 from use_cols + 1 'mol' + 1 'mol_name'
assert 'uniprot_id' in df.columns
assert 'smi_col' not in df.columns
# Chunk reading
chunks = []
for chunk in opd.read_sdf(input_fname, chunksize=10):
assert len(chunk) == 10
chunks.append(chunk)
assert len(chunks) == 10
df = pd.concat(chunks)
# Check dimensions
assert len(df) == 100
def test_sdf():
"""Writing ChemDataFrame to SDF molecular files"""
df = opd.read_sdf(os.path.join(test_data_dir, 'data/dude/xiap/actives_docked.sdf'))
with NamedTemporaryFile(suffix='.sdf') as f:
df.to_sdf(f.name)
df2 = opd.read_sdf(f.name)
assert_array_equal(df.columns, df2.columns)
with NamedTemporaryFile(suffix='.sdf') as f:
df.to_sdf(f.name, columns=['name', 'uniprot_id', 'act'])
df2 = opd.read_sdf(f.name)
assert_equal(len(df2.columns), 5)
def test_sdf():
"""Writing ChemDataFrame to SDF molecular files"""
df = opd.read_sdf(input_fname)
with NamedTemporaryFile(suffix='.sdf') as f:
df.to_sdf(f.name)
df2 = opd.read_sdf(f.name)
assert_array_equal(df.columns.sort_values(), df2.columns.sort_values())
with NamedTemporaryFile(suffix='.sdf') as f:
df.to_sdf(f.name, columns=['name', 'uniprot_id', 'act'])
df2 = opd.read_sdf(f.name)
assert len(df2.columns) == 5
def test_sdf():
"""Writing ChemDataFrame to SDF molecular files"""
df = opd.read_sdf(input_fname)
with NamedTemporaryFile(suffix='.sdf') as f:
df.to_sdf(f.name)
df2 = opd.read_sdf(f.name)
assert_array_equal(df.columns, df2.columns)
with NamedTemporaryFile(suffix='.sdf') as f:
df.to_sdf(f.name, columns=['name', 'uniprot_id', 'act'])
df2 = opd.read_sdf(f.name)
assert len(df2.columns) == 5
def test_csv():
df = opd.read_sdf(
input_fname,
columns=['mol', 'name', 'chembl_id', 'dude_smiles', 'act'])
df['act'] = df['act'].astype(float)
df['name'] = df['name'].astype(int)
with NamedTemporaryFile(suffix='.csv', mode='w+') as f:
for str_buff in (f, f.name):
df.to_csv(str_buff, index=False)
f.seek(0)
df2 = opd.read_csv(f.name,
smiles_to_molecule='mol',
molecule_column='mol')
assert df.shape == df2.shape
assert df.columns.tolist() == df2.columns.tolist()
assert df.dtypes.tolist() == df2.dtypes.tolist()
with NamedTemporaryFile(suffix='.csv', mode='w+') as f:
for str_buff in (f, f.name):
df.to_csv(str_buff, index=False, columns=['name', 'act'])
f.seek(0)
df2 = pd.read_csv(f.name)
assert df[['name', 'act']].shape == df2.shape
assert df[['name', 'act']].columns.tolist() == df2.columns.tolist()
assert df[['name', 'act']].dtypes.tolist() == df2.dtypes.tolist()
def test_chemseries_writers():
df = opd.read_sdf(
input_fname,
columns=['mol', 'name', 'chembl_id', 'dude_smiles', 'act'])
mols = df['mol']
# SMILES
with NamedTemporaryFile(suffix='.ism', mode='w') as f:
mols.to_smiles(f)
for mol in oddt.toolkit.readfile('smi', f.name):
assert isinstance(mol, oddt.toolkit.Molecule)
# SDF
with NamedTemporaryFile(suffix='.sdf', mode='w') as f:
mols.to_sdf(f)
for mol in oddt.toolkit.readfile('sdf', f.name):
assert isinstance(mol, oddt.toolkit.Molecule)
# mol2
if oddt.toolkit.backend == 'ob':
with NamedTemporaryFile(suffix='.mol2', mode='w') as f:
mols.to_mol2(f)
for mol in oddt.toolkit.readfile('mol2', f.name):
assert isinstance(mol, oddt.toolkit.Molecule)
def test_reading():
""" Test reading molecule files to ChemDataFrame """
df = opd.read_sdf(
os.path.join(test_data_dir, 'data/dude/xiap/actives_docked.sdf'))
# Check dimensions
assert_equal(len(df), 100)
assert_equal(len(df.columns), 15)
df = opd.read_sdf(os.path.join(test_data_dir,
'data/dude/xiap/actives_docked.sdf'),
smiles_column='smi_col')
assert_in('smi_col', df.columns)
df = opd.read_sdf(os.path.join(test_data_dir,
'data/dude/xiap/actives_docked.sdf'),
molecule_column=None,
molecule_name_column=None,
usecols=['name'])
assert_not_in('mol', df.columns)
assert_not_in('mol_name', df.columns)
assert_equal(len(df.columns), 1)
df = opd.read_sdf(os.path.join(test_data_dir,
'data/dude/xiap/actives_docked.sdf'),
usecols=['name', 'uniprot_id', 'act'])
assert_equal(len(df.columns),
5) # 3 from use_cols + 1 'mol' + 1 'mol_name'
assert_in('uniprot_id', df.columns)
assert_not_in('smi_col', df.columns)
# Chunk reading
chunks = []
for chunk in opd.read_sdf(os.path.join(
test_data_dir, 'data/dude/xiap/actives_docked.sdf'),
chunksize=10):
assert_equal(len(chunk), 10)
chunks.append(chunk)
assert_equal(len(chunks), 10)
df = pd.concat(chunks)
# Check dimensions
assert_equal(len(df), 100)
def test_excel():
# just check if it doesn't fail
df = opd.read_sdf(input_fname,
columns=['mol', 'name', 'chembl_id', 'dude_smiles', 'act'])
df = df.head(10) # it's slow so use first 10 mols
df['act'] = df['act'].astype(float)
df['name'] = df['name'].astype(int)
with NamedTemporaryFile(suffix='.xls', mode='w') as f:
df.to_excel(f.name, index=False)
writer = pd.ExcelWriter(f.name, engine='xlsxwriter')
df.to_excel(writer, index=False)
def test_substruct_sim_search():
df = opd.read_sdf(os.path.join(test_data_dir, 'data/dude/xiap/actives_docked.sdf')).head(10)
query = oddt.toolkit.readstring('smi', 'C(=O)(N1C[C@H](C[C@H]1C(=O)N[C@@H]1CCCc2c1cccc2)Oc1ccccc1)[C@@H](NC(=O)[C@H](C)NC)C1CCCCC1')
ge_answear = [True, True, True, False, True, False, False, False, False, False]
assert_equal((df.mol >= query).tolist(), ge_answear)
le_answear = [True, True, True, True, True, True, False, False, False, True]
assert_equal((df.mol <= query).tolist(), le_answear)
sim = df.mol.calcfp() | query.calcfp()
assert_equal(sim.dtype, 'float64')
def test_csv():
df = opd.read_sdf(os.path.join(test_data_dir, 'data/dude/xiap/actives_docked.sdf'),
columns=['mol', 'name', 'chembl_id', 'dude_smiles', 'act'])
df['act'] = df['act'].astype(float)
df['name'] = df['name'].astype(int)
with NamedTemporaryFile(suffix='.csv', mode='w+') as f:
df.to_csv(f, index=False)
f.seek(0)
df2 = opd.read_csv(f, smiles_to_molecule='mol', molecule_column='mol')
assert_equal(df.shape, df2.shape)
assert_equal(df.columns.tolist(), df2.columns.tolist())
assert_equal(df.dtypes.tolist(), df2.dtypes.tolist())
def test_ipython():
"""iPython Notebook molecule rendering in SVG"""
df = opd.read_sdf(os.path.join(test_data_dir, 'data/dude/xiap/actives_docked.sdf'))
# mock ipython
oddt.toolkit.ipython_notebook = True
# png
oddt.toolkit.image_backend = 'png'
html = df.head(1).to_html()
assert_in('<img src="data:image/png;base64,', html)
# svg
oddt.toolkit.image_backend = 'svg'
html = df.head(1).to_html()
assert_in('<svg', html)
oddt.toolkit.ipython_notebook = False
def test_ipython():
"""iPython Notebook molecule rendering in SVG"""
df = opd.read_sdf(input_fname)
# mock ipython
oddt.toolkit.ipython_notebook = True
# png
oddt.toolkit.image_backend = 'png'
html = df.head(1).to_html()
assert '<img src="data:image/png;base64,' in html
# svg
oddt.toolkit.image_backend = 'svg'
html = df.head(1).to_html()
assert '<svg' in html
oddt.toolkit.ipython_notebook = False
def test_ipython():
"""iPython Notebook molecule rendering in SVG"""
df = opd.read_sdf(input_fname)
# mock ipython
oddt.toolkit.ipython_notebook = True
# png
oddt.toolkit.image_backend = 'png'
html = df.head(1).to_html()
assert '<img src="data:image/png;base64,' in html
# svg
oddt.toolkit.image_backend = 'svg'
html = df.head(1).to_html()
assert '<svg' in html
oddt.toolkit.ipython_notebook = False
def test_substruct_sim_search():
df = opd.read_sdf(input_fname).head(10)
query = oddt.toolkit.readstring('smi', 'C(=O)(N1C[C@H](C[C@H]1C(=O)N[C@@H]1CCCc2c1cccc2)Oc1ccccc1)[C@@H](NC(=O)[C@H](C)NC)C1CCCCC1')
ge_answear = [True, True, True, False, True, False, False, False, False, False]
assert (df.mol >= query).tolist() == ge_answear
assert (query <= df.mol).tolist() == ge_answear
le_answear = [True, True, True, True, True, True, False, False, False, True]
assert (df.mol <= query).tolist() == le_answear
assert (query >= df.mol).tolist() == le_answear
sim = df.mol.calcfp() | query.calcfp()
assert sim.dtype == 'float64'
def test_mol2():
"""Writing and reading of mol2 fils to/from ChemDataFrame"""
if (oddt.toolkit.backend == 'ob' and oddt.toolkit.__version__ >= '2.4.0'):
df = opd.read_sdf(input_fname)
with NamedTemporaryFile(suffix='.mol2') as f:
df.to_mol2(f.name)
df2 = opd.read_mol2(f.name)
assert_equal(df.shape, df2.shape)
chunks = []
for chunk in opd.read_mol2(f.name, chunksize=10):
assert_equal(len(chunk), 10)
chunks.append(chunk)
df3 = pd.concat(chunks)
assert_equal(df.shape, df3.shape)
with NamedTemporaryFile(suffix='.mol2') as f:
df.to_mol2(f.name, columns=['name', 'uniprot_id', 'act'])
df2 = opd.read_mol2(f.name)
assert_equal(len(df2.columns), 5)
def test_mol2():
"""Writing and reading of mol2 fils to/from ChemDataFrame"""
if (oddt.toolkit.backend == 'ob' and oddt.toolkit.__version__ >= '2.4.0'):
df = opd.read_sdf(input_fname)
with NamedTemporaryFile(suffix='.mol2') as f:
df.to_mol2(f.name)
df2 = opd.read_mol2(f.name)
assert df.shape == df2.shape
chunks = []
for chunk in opd.read_mol2(f.name, chunksize=10):
assert len(chunk) == 10
chunks.append(chunk)
df3 = pd.concat(chunks)
assert df.shape == df3.shape
with NamedTemporaryFile(suffix='.mol2') as f:
df.to_mol2(f.name, columns=['name', 'uniprot_id', 'act'])
df2 = opd.read_mol2(f.name)
assert len(df2.columns) == 5
def test_mol2():
"""Writing and reading of mol2 fils to/from ChemDataFrame"""
if oddt.toolkit.backend == 'ob':
df = opd.read_sdf(input_fname)
with NamedTemporaryFile(suffix='.mol2') as f:
df.to_mol2(f.name)
df2 = opd.read_mol2(f.name)
assert df.shape == df2.shape
chunks = []
for chunk in opd.read_mol2(f.name, chunksize=10):
assert len(chunk) == 10
chunks.append(chunk)
df3 = pd.concat(chunks)
assert df.shape == df3.shape
with NamedTemporaryFile(suffix='.mol2') as f:
df.to_mol2(f.name, columns=['name', 'uniprot_id', 'act'])
df2 = opd.read_mol2(f.name)
assert len(df2.columns) == 5
def test_mol2():
"""Writing and reading of mol2 fils to/from ChemDataFrame"""
if oddt.toolkit.backend == 'ob': # RDKit does not support mol2 writing yet
df = opd.read_sdf(
os.path.join(test_data_dir, 'data/dude/xiap/actives_docked.sdf'))
with NamedTemporaryFile(suffix='.mol2') as f:
df.to_mol2(f.name)
df2 = opd.read_mol2(f.name)
assert_equal(df.shape, df2.shape)
chunks = []
for chunk in opd.read_mol2(f.name, chunksize=10):
assert_equal(len(chunk), 10)
chunks.append(chunk)
df3 = pd.concat(chunks)
assert_equal(df.shape, df3.shape)
with NamedTemporaryFile(suffix='.mol2') as f:
df.to_mol2(f.name, columns=['name', 'uniprot_id', 'act'])
df2 = opd.read_mol2(f.name)
assert_equal(len(df2.columns), 5)
def test_classes():
""" Test oddt.pandas classes behavior """
df = opd.read_sdf(input_fname)
# Check classes inheritance
assert isinstance(df, opd.ChemDataFrame)
assert isinstance(df, pd.DataFrame)
assert isinstance(df['mol'], opd.ChemSeries)
assert isinstance(df['mol'], pd.Series)
assert isinstance(df, pd.DataFrame)
# Check custom metadata
assert hasattr(df, '_molecule_column')
assert hasattr(df[['mol']], '_molecule_column')
assert df._molecule_column == df[['mol']]._molecule_column
# Check if slicing perserve classes
assert isinstance(df.head(1), opd.ChemDataFrame)
assert isinstance(df['mol'].head(1), opd.ChemSeries)
def test_classes():
""" Test oddt.pandas classes behavior """
df = opd.read_sdf(input_fname)
# Check classes inheritance
assert isinstance(df, opd.ChemDataFrame)
assert isinstance(df, pd.DataFrame)
assert isinstance(df['mol'], opd.ChemSeries)
assert isinstance(df['mol'], pd.Series)
assert isinstance(df, pd.DataFrame)
# Check custom metadata
assert hasattr(df, '_molecule_column')
assert hasattr(df[['mol']], '_molecule_column')
assert df._molecule_column == df[['mol']]._molecule_column
# Check if slicing perserve classes
assert isinstance(df.head(1), opd.ChemDataFrame)
assert isinstance(df['mol'].head(1), opd.ChemSeries)
def test_classes():
""" Test oddt.pandas classes behavior """
df = opd.read_sdf(os.path.join(test_data_dir, 'data/dude/xiap/actives_docked.sdf'))
# Check classes inheritance
assert_true(isinstance(df, opd.ChemDataFrame))
assert_true(isinstance(df, pd.DataFrame))
assert_true(isinstance(df['mol'], opd.ChemSeries))
assert_true(isinstance(df['mol'], pd.Series))
assert_true(isinstance(df, pd.DataFrame))
# Check custom metadata
assert_true(hasattr(df, '_molecule_column'))
assert_true(hasattr(df[['mol']], '_molecule_column'))
assert_equal(df._molecule_column, df[['mol']]._molecule_column)
# Check if slicing perserve classes
assert_true(isinstance(df.head(1), opd.ChemDataFrame))
assert_true(isinstance(df['mol'].head(1), opd.ChemSeries))
def test_csv():
df = opd.read_sdf(input_fname,
columns=['mol', 'name', 'chembl_id', 'dude_smiles', 'act'])
df['act'] = df['act'].astype(float)
df['name'] = df['name'].astype(int)
with NamedTemporaryFile(suffix='.csv', mode='w+') as f:
for str_buff in (f, f.name):
df.to_csv(str_buff, index=False)
f.seek(0)
df2 = opd.read_csv(f.name, smiles_to_molecule='mol',
molecule_column='mol')
assert df.shape == df2.shape
assert df.columns.tolist() == df2.columns.tolist()
assert df.dtypes.tolist() == df2.dtypes.tolist()
with NamedTemporaryFile(suffix='.csv', mode='w+') as f:
for str_buff in (f, f.name):
df.to_csv(str_buff, index=False, columns=['name', 'act'])
f.seek(0)
df2 = pd.read_csv(f.name)
assert df[['name', 'act']].shape == df2.shape
assert df[['name', 'act']].columns.tolist() == df2.columns.tolist()
assert df[['name', 'act']].dtypes.tolist() == df2.dtypes.tolist()
def test_chemseries_writers():
df = opd.read_sdf(input_fname,
columns=['mol', 'name', 'chembl_id', 'dude_smiles', 'act'])
mols = df['mol']
# SMILES
with NamedTemporaryFile(suffix='.ism', mode='w') as f:
mols.to_smiles(f)
for mol in oddt.toolkit.readfile('smi', f.name):
assert isinstance(mol, oddt.toolkit.Molecule)
# SDF
with NamedTemporaryFile(suffix='.sdf', mode='w') as f:
mols.to_sdf(f)
for mol in oddt.toolkit.readfile('sdf', f.name):
assert isinstance(mol, oddt.toolkit.Molecule)
# mol2
if oddt.toolkit.backend == 'ob':
with NamedTemporaryFile(suffix='.mol2', mode='w') as f:
mols.to_mol2(f)
for mol in oddt.toolkit.readfile('mol2', f.name):
assert isinstance(mol, oddt.toolkit.Molecule)
