def test_ob_round_trip(self):
"""Test conversion to and from OBMol"""
for mol in self.test_mols:
ob_mol = toOBMol(mol)
new_mol = fromOBMol(Molecule(), ob_mol)
self.assertTrue(mol.isIsomorphic(new_mol))
self.assertEqual(mol.get_element_count(), new_mol.get_element_count())
def _openbabel_translator(input_object, identifier_type, mol=None):
"""
Converts between formats using OpenBabel. If input is a :class:`Molecule`,
the identifier_type is used to determine the output type. If the input is
a `str`, then the identifier_type is used to identify the input, and the
desired output is assumed to be a :class:`Molecule` object.
Args:
input_object: either molecule or string identifier
identifier_type: format of string identifier
'inchi' -> InChI
'inchikey' -> InChI Key
'smi' -> SMILES
mol: molecule object for output (optional)
"""
ob_conversion = openbabel.OBConversion()
if isinstance(input_object, str):
# We are converting from a string identifier to a Molecule
ob_conversion.SetInFormat(identifier_type)
obmol = openbabel.OBMol()
ob_conversion.ReadString(obmol, input_object)
obmol.AddHydrogens()
obmol.AssignSpinMultiplicity(True)
if mol is None:
mol = mm.Molecule()
output = fromOBMol(mol, obmol)
elif isinstance(input_object, mm.Molecule):
# We are converting from a Molecule to a string identifier
if identifier_type == 'inchi':
ob_conversion.SetOutFormat('inchi')
ob_conversion.AddOption('w')
elif identifier_type == 'inchikey':
ob_conversion.SetOutFormat('inchi')
ob_conversion.AddOption('w')
ob_conversion.AddOption('K')
elif identifier_type == 'smi':
ob_conversion.SetOutFormat('can')
# turn off isomer and stereochemistry information
ob_conversion.AddOption('i')
else:
raise ValueError(
'Unexpected identifier type {0}.'.format(identifier_type))
obmol = toOBMol(input_object)
output = ob_conversion.WriteString(obmol).strip()
else:
raise ValueError(
'Unexpected input format. Should be a Molecule or a string.')
return output
def _openbabel_translator(input_object, identifier_type, mol=None):
"""
Converts between formats using OpenBabel. If input is a :class:`Molecule`,
the identifier_type is used to determine the output type. If the input is
a `str`, then the identifier_type is used to identify the input, and the
desired output is assumed to be a :class:`Molecule` object.
Args:
input_object: either molecule or string identifier
identifier_type: format of string identifier
'inchi' -> InChI
'inchikey' -> InChI Key
'smi' -> SMILES
mol: molecule object for output (optional)
"""
ob_conversion = openbabel.OBConversion()
if isinstance(input_object, str):
# We are converting from a string identifier to a Molecule
ob_conversion.SetInFormat(identifier_type)
obmol = openbabel.OBMol()
ob_conversion.ReadString(obmol, input_object)
obmol.AddHydrogens()
obmol.AssignSpinMultiplicity(True)
if mol is None:
mol = mm.Molecule()
output = fromOBMol(mol, obmol)
elif isinstance(input_object, mm.Molecule):
# We are converting from a Molecule to a string identifier
if identifier_type == 'inchi':
ob_conversion.SetOutFormat('inchi')
ob_conversion.AddOption('w')
elif identifier_type == 'inchikey':
ob_conversion.SetOutFormat('inchi')
ob_conversion.AddOption('w')
ob_conversion.AddOption('K')
elif identifier_type == 'smi':
ob_conversion.SetOutFormat('can')
# turn off isomer and stereochemistry information
ob_conversion.AddOption('i')
else:
raise ValueError('Unexpected identifier type {0}.'.format(identifier_type))
obmol = toOBMol(input_object)
output = ob_conversion.WriteString(obmol).strip()
else:
raise ValueError('Unexpected input format. Should be a Molecule or a string.')
return output