def sanitize_smiles_molvs(smiles, largest_fragment=False):
"""Sanitize a SMILES with MolVS
Parameters
----------
smiles : str
SMILES string for a molecule.
largest_fragment : bool
Whether to select only the largest covalent unit in a molecule with
multiple fragments. Default to False.
Returns
-------
str
SMILES string for the sanitized molecule.
"""
standardizer = Standardizer()
standardizer.prefer_organic = True
mol = Chem.MolFromSmiles(smiles)
if mol is None:
return smiles
try:
mol = standardizer.standardize(
mol) # standardize functional group reps
if largest_fragment:
mol = standardizer.largest_fragment(
mol) # remove product counterions/salts/etc.
mol = standardizer.uncharge(mol) # neutralize, e.g., carboxylic acids
except Exception:
pass
return Chem.MolToSmiles(mol)
opts,args = parser.parse_args()
fpred = open(opts.pred_path)
fgold = open(opts.gold_path)
feval = open(opts.pred_path + '.eval_by_smiles', 'w')
print('## Bond types in output files are doubles? {}'.format(opts.bonds_as_doubles))
idxfunc = lambda a: a.GetAtomMapNum()
bond_types = [Chem.rdchem.BondType.SINGLE, Chem.rdchem.BondType.DOUBLE, Chem.rdchem.BondType.TRIPLE,
Chem.rdchem.BondType.AROMATIC]
bond_types_as_double = {0.0: 0, 1.0: 1, 2.0: 2, 3.0: 3, 1.5: 4}
from molvs import Standardizer
standardizer = Standardizer()
standardizer.prefer_organic = True
def sanitize_smiles(smi, largest_fragment=False):
mol = Chem.MolFromSmiles(smi)
if mol is None:
return smi
try:
mol = standardizer.standardize(mol) # standardize functional group reps
if largest_fragment:
mol = standardizer.largest_fragment(mol) # remove product counterions/salts/etc.
mol = standardizer.uncharge(mol) # neutralize, e.g., carboxylic acids
except Exception:
pass
return Chem.MolToSmiles(mol)
try:
