def test_ob_round_trip(self):
"""Test conversion to and from OBMol"""
for mol in self.test_mols:
ob_mol = to_ob_mol(mol)
new_mol = from_ob_mol(Molecule(), ob_mol)
self.assertTrue(mol.is_isomorphic(new_mol) or self.test_Hbond_free_mol.is_isomorphic(new_mol))
self.assertEqual(mol.get_element_count(), new_mol.get_element_count())
def xyz_to_mol(xyz):
if isinstance(xyz, dict):
string = xyz_to_xyz_file_format(xyz)
elif isinstance(xyz, str):
if not xyz[0].isdigit():
atom_num = len(xyz.splitlines())
string = f'{atom_num}\n\n' + xyz
else:
string = xyz
elif os.path.isfile(xyz):
string = xyz_to_xyz_file_format(parse_xyz_from_file(xyz))
else:
raise ValueError(f'Invalid xyz input, got: {xyz}')
molecule = pybel.readstring('xyz', string)
mol = Molecule()
from_ob_mol(mol, molecule.OBMol)
return mol
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()
# In OpenBabel 3+ the function obmol.AssignSpinMultiplicity(True) does nothing.
# We could write our own method here and call obatom.SetSpinMultiplicity on
# each atom, but instead we will leave them blank for now and fix them
# in the from_ob_mol() method.
if mol is None:
mol = mm.Molecule()
output = from_ob_mol(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 = to_ob_mol(input_object)
output = ob_conversion.WriteString(obmol).strip()
else:
raise ValueError('Unexpected input format. Should be a Molecule or a string.')
return output
def toRMGmol(OBMol):
rmg_mol = from_ob_mol(rmgpy.molecule.molecule.Molecule(), OBMol)
return rmg_mol