def test__get_atomsection_raises():
"""Test if ValueError is raised if input list is not in the mol2 format."""
expect = ("Structural data could not be loaded. "
"Is the input file/text in the mol2 format?")
def run_code():
PandasMol2()._get_atomsection(["", ""])
assert_raises(ValueError, expect, run_code)
def test_split_multimol2_wrong_format():
expect = ('Wrong file format;'
'allowed file formats are .mol2 and .mol2.gz.')
def run_code():
next(split_multimol2('40_mol2_files.pdb'))
assert_raises(ValueError,
expect,
run_code)
def test_overwrite_df():
data_path = os.path.join(this_dir, 'data', '1b5e_1.mol2')
pdmol = PandasMol2().read_mol2(data_path)
def overwrite():
pdmol.df = pdmol.df[(pdmol.df['atom_type'] != 'H')]
expect = ('Please use `PandasMol2._df = ... `'
' instead\nof `PandasMol2.df = ... `'
' if you are sure that\nyou want'
' to overwrite the `df` attribute.')
assert_raises(AttributeError, expect, overwrite)
def test_overwrite_df():
data_path = os.path.join(os.path.dirname(__file__), 'data', '3eiy.pdb')
pdb = PandasPdb().read_pdb(data_path)
def overwrite():
pdb.df = 'bla'
expect = ('Please use `PandasPdb._df = ... ` instead\n'
'of `PandasPdb.df = ... ` if you are sure that\n'
'you want to overwrite the `df` attribute.')
assert_raises(AttributeError,
expect,
overwrite)
def test__read_pdb_raises():
"""Test private _read_pdb:
Test if ValueError is raised for wrong file formats."""
expect = ('Wrong file format; allowed file formats'
' are .pdb and .pdb.gz.')
def run_code_1():
PandasPdb()._read_pdb("protein.mol2")
assert_raises(ValueError, expect, run_code_1)
def run_code_2():
PandasPdb()._read_pdb("protein.mol2.gz")
assert_raises(ValueError, expect, run_code_2)