def test_fixmol():
sm = "C.Cl.CC.[H][N:1]1(C)=CC(O)=CC2CCCCC12"
mol = Chem.MolFromSmiles(sm, sanitize=False)
# mol.UpdatePropertyCache(False)
# Chem.Kekulize(mol)
res = dm.fix_mol(mol, n_iter=1) # copy by default
# should still be invalid in term of valence for nitrogen
assert not dm.incorrect_valence(res)
res2 = dm.fix_mol(mol, n_iter=2)
# not expecting difference between res2 and res3
assert Chem.MolToSmiles(res) == Chem.MolToSmiles(res2)
# only largest expected_here
res_largest = dm.fix_mol(mol, largest_only=True)
dm.fix_mol(mol, remove_singleton=True, largest_only=True)
assert len(Chem.rdmolops.GetMolFrags(res_largest)) == 1
expected_largest_fix = dm.standardize_smiles("OC1=CC2CCCCC2[N:1]=C1")
assert dm.standardize_smiles(
Chem.MolToSmiles(res_largest)) == expected_largest_fix
res_no_singleton = dm.fix_mol(mol, n_iter=2, remove_singleton=True)
assert len(Chem.rdmolops.GetMolFrags(res_largest)) == 1
assert len(Chem.rdmolops.GetMolFrags(res_no_singleton)) == 2
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 test_standardize_mol():
sm = "[Na]OC1=CC2CCCCC2N=C1"
sm_standard = dm.to_smiles(dm.standardize_smiles(sm))
standard_mol = dm.standardize_mol(dm.to_mol(sm),
disconnect_metals=True,
uncharge=True)
mol_standard = dm.to_smiles(Chem.MolToSmiles(standard_mol))
assert sm_standard == mol_standard
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
def test_standardize_smiles_tautomer():
smiles = "C1=CC=CN=C1"
std_smiles = dm.standardize_smiles(smiles, tautomer=True)
assert "c1ccncc1" == std_smiles
def _preprocess(i, row):
'''Takes a smiles string and generates a clean rdkit mol with datamol. The stereoisomers
are then enumerated while holding defined stereochemistry. Morgan fingerprints are then
generated using RDkit with and without stereochemistry. The try/except logic deals with
RDkit mol failures on conversion of an invalid smiles string. Smarts are added for later
searching.'''
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)
# enum_dm_smiles = sorted(dm.standardize_smiles(dm.to_smiles(x)) for x in isomers)
smiles_list = []
achiral_fp_lis = []
chiral_fp_lis = []
# standard_smiles_list = []
for count, smi in enumerate(enum_smiles):
smiles_string = smi
mol = dm.to_mol(smi, 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, }
pars2 = { "radius": 2,
"nBits": 8192,
"invariants": [],
"fromAtoms": [],
"useChirality": False,
"useBondTypes": True,
"useFeatures": False, }
fp = fingerprint_function(mol, **pars)
fp1 = fingerprint_function(mol, **pars2)
smiles_list.append(dm.standardize_smiles(smiles_string))
achiral_fp_lis.append(list(fp1.GetOnBits()))
chiral_fp_lis.append(list(fp.GetOnBits()))
row["standard_smiles"] = dm.standardize_smiles(dm.to_smiles(mol))
row["smarts"] = dm.to_smarts(mol)
row["selfies"] = dm.to_selfies(mol)
row["enumerated_smiles"] = smiles_list
row["achiral_fp"] = achiral_fp_lis
row["chiral_fp"] = chiral_fp_lis
# row["dm_enumerated_smiles"] = enum_dm_smiles_lis
# row["onbits_fp"] =list(fp.GetOnBits())
return row
except ValueError:
# row["standard_smiles"] = 'dropped'
# row["selfies"] = 'dropped'
# row["inchi"] = 'dropped'
# row["inchikey"] = 'dropped'
row["standard_smiles"] = 'dropped'
row["smarts"] = 'dropped'
row["selfies"] = 'dropped'
row["enumerated_smiles"] = list('dropped')
row["achiral_fp"] = list('dropped')
row["chiral_fp"] = list('dropped')
# row["dm_enumerated_smiles"] = 'dropped'
return row