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