def test_inchi():
smiles = "CC(=O)Oc1ccccc1C(=O)O"
mol = dm.to_mol(smiles)
inchi = dm.to_inchi(mol)
assert inchi == "InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)"
inchikey = dm.to_inchikey(mol)
assert inchikey == "BSYNRYMUTXBXSQ-UHFFFAOYSA-N"
new_mol = dm.from_inchi(inchi)
assert dm.to_smiles(new_mol) == smiles
assert dm.to_inchi(None) is None
assert dm.to_inchikey(None) is None
assert dm.from_inchi(None) is None
def _preprocess(i, row):
# print('hello')
mol = dm.to_mol(str(row[smiles_column]), ordered=True)
mol = dm.fix_mol(mol)
mol = dm.sanitize_mol(mol, sanifix=True, charge_neutral=False)
mol = dm.standardize_mol(mol, disconnect_metals=False, normalize=True, reionize=True, uncharge=False, stereo=True)
fingerprint_function = rdMolDescriptors.GetMorganFingerprintAsBitVect
pars = { "radius": 2,
"nBits": 8192,
"invariants": [],
"fromAtoms": [],
"useChirality": True,
"useBondTypes": True,
"useFeatures": False,
}
fp = fingerprint_function(mol, **pars)
row["standard_smiles"] = dm.standardize_smiles(dm.to_smiles(mol))
row["selfies"] = dm.to_selfies(mol)
row["inchi"] = dm.to_inchi(mol)
row["inchikey"] = dm.to_inchikey(mol)
row["onbits_fp"] =list(fp.GetOnBits())
return row
def _preprocess(i, row):
# print('hello')
try:
mol = dm.to_mol(str(row[smiles_column]), ordered=True)
mol = dm.fix_mol(mol)
mol = dm.sanitize_mol(mol, sanifix=True, charge_neutral=False)
mol = dm.standardize_mol(mol,
disconnect_metals=False,
normalize=True,
reionize=True,
uncharge=False,
stereo=True)
opts = StereoEnumerationOptions(unique=True,
maxIsomers=20,
rand=0xf00d)
isomers = EnumerateStereoisomers(mol, options=opts)
enum_smiles = sorted(
Chem.MolToSmiles(y, isomericSmiles=True) for y in isomers)
smiles_list = []
for count, smi in enumerate(enum_smiles):
smiles_string = smi
smiles_list.append(smiles_string)
# fingerprint_function = rdMolDescriptors.GetMorganFingerprintAsBitVect
# pars = { "radius": 2,
# "nBits": 8192,
# "invariants": [],
# "fromAtoms": [],
# "useChirality": False,
# "useBondTypes": True,
# "useFeatures": False,
# }
# fp = fingerprint_function(mol, **pars)
row["standard_smiles"] = dm.standardize_smiles(dm.to_smiles(mol))
row["selfies"] = dm.to_selfies(mol)
row["inchi"] = dm.to_inchi(mol)
row["inchikey"] = dm.to_inchikey(mol)
row["enumerated_smiles"] = smiles_list
# row["onbits_fp"] =list(fp.GetOnBits())
return row
except ValueError:
row["standard_smiles"] = 'dropped'
row["selfies"] = 'dropped'
row["inchi"] = 'dropped'
row["inchikey"] = 'dropped'
row["enumerated_smiles"] = list('dropped')
return row