def test_from_file(self, filepath, compute2d):
"""
Test if input produces an RDKit molecule.
"""
rmol = Rdkit.from_file(filepath, compute2d)
self._rdkit_format_tests(rmol)
def to_rdkit(self,
structure_klifs_id_or_filepath,
entity="complex",
extension="mol2",
compute2d=True): # pylint: disable=W0221
filepath = self._to_filepath(structure_klifs_id_or_filepath, entity,
extension)
rdkit_mol = Rdkit.from_file(filepath, compute2d)
return rdkit_mol
def test_from_mol2_file(self, mol2_file):
"""
Test loading mol2 files as RDKit molecule.
Parameters
----------
mol2_file : pathlib.Path or str
Path to mol2 file.
"""
rmol = Rdkit._from_mol2_file(mol2_file)
self._rdkit_format_tests(rmol)
def test_from_text(self, filepath, format, compute2d):
"""
Test if input produces an RDKit molecule.
Note: Use file as test function input; file content will be read as string,
which is the input for the class method to be tested here!
"""
# Let's load a file's content as string (text) to simulate example input data
with open(filepath, "r") as f:
text = f.read()
rmol = Rdkit.from_text(text, format, compute2d)
self._rdkit_format_tests(rmol)
def test_from_mol2_text(self, mol2_file):
"""
Test loading mol2 file contents (text) as RDKit molecule.
Parameters
----------
mol2_file : pathlib.Path or str
Path to mol2 file.
"""
# Let's load a file's content as string (text) to simulate example input data
with open(mol2_file, "r") as f:
mol2_text = f.read()
rmol = Rdkit._from_mol2_text(mol2_text)
self._rdkit_format_tests(rmol)
def to_rdkit(self, structure_klifs_id, entity="complex", extension="mol2", compute2d=True):
text = self.to_text(structure_klifs_id, entity, extension)
rdkit_mol = Rdkit.from_text(text, extension, compute2d)
return rdkit_mol