def get_smiles(molecule):
"""
Get the RDKit canonical, isomeric SMILES of `molecule`.
Parameters
----------
molecule : :class:`.Molecule`
The molecule whose SMILES is required.
Returns
-------
:class:`str`
The SMILES.
"""
rdkit_mol = molecule.with_canonical_atom_ordering().to_rdkit_mol()
rdkit.SanitizeMol(rdkit_mol)
rdkit.AssignStereochemistryFrom3D(rdkit_mol)
rdkit_mol = rdkit.RemoveHs(rdkit_mol)
return rdkit.MolToSmiles(
mol=rdkit_mol,
isomericSmiles=True,
canonical=True,
)
def generate_inchi_and_xyz(mol_string: str,
special_cases: bool = True) -> Tuple[str, str]:
"""Generate the XYZ coordinates and InChI string for a molecule using
a standard procedure.
We use the following deterministic procedure:
1. Generates 3D coordinates with RDKit. Use a set random number seed
2. Assign yet-undetermined stereochemistry based on the 3D geometry
3. Generate an InCHi string for the molecules
We then have post-processing steps for common mistakes in generating geometries:
1. Ensuring cyclopropenyl groups are planar
Args:
mol_string: SMILES or InChI string
special_cases: Whether to perform the post-processing
Returns:
- InChI string for the molecule
- XYZ coordinates for the molecule
"""
with _generate_lock:
# Generate 3D coordinates for the molecule
mol = parse_from_molecule_string(mol_string)
mol = Chem.AddHs(mol)
AllChem.EmbedMolecule(mol, randomSeed=1)
AllChem.MMFFOptimizeMolecule(mol)
# Generate an InChI string with stereochemistry information
AllChem.AssignStereochemistryFrom3D(mol)
inchi = Chem.MolToInchi(mol)
# Save geometry as 3D coordinates
xyz = f"{mol.GetNumAtoms()}\n"
xyz += inchi + "\n"
conf = mol.GetConformer()
for i, a in enumerate(mol.GetAtoms()):
s = a.GetSymbol()
c = conf.GetAtomPosition(i)
xyz += f"{s} {c[0]} {c[1]} {c[2]}\n"
# Special cases for odd kinds of molecules
if special_cases:
fix_cyclopropenyl(xyz, mol_string)
return inchi, xyz
