def atom_pair_fp(self):
df = pd.read_csv(self.csv_path)
smiles_list = df['Smiles'].tolist()
fingerprints = []
not_found = []
for i in tqdm(range(len(smiles_list))):
try:
mol = Chem.MolFromSmiles(smiles_list[i])
fp = Pairs.GetAtomPairFingerprintAsIntVect(mol)
fp._sumCache = fp.GetTotalVal(
) #Bit vector here will be huge, which is why taking TotalVal()
# bits = fp.ToBitString()
# bits_array = (np.fromstring(fp.ToBitString(),'u1') - ord('0'))
fingerprints.append(fp._sumCache)
print('fing', fingerprints)
except:
fingerprints.append(np.nan)
not_found.append(i)
pass
df.drop(not_found, axis=0, inplace=True)
print('Number of FPs not found: {}'.format(len(not_found)))
df.reset_index(drop=True, inplace=True)
labelencoder = LabelEncoder()
Y = labelencoder.fit_transform(df['Label'].values)
Y = Y.reshape(Y.shape[0], 1)
print('Output shape: {}'.format(Y.shape))
fp_array = (np.asarray((fingerprints), dtype=object))
X = np.delete(fp_array, not_found, axis=0)
X = np.vstack(X).astype(np.float32)
print('Typeof X', type(X))
print(X)
print('Input shape: {}'.format(X.shape))
final_array = np.concatenate((X, Y), axis=1)
# Removing rows, from final_array, where duplicate FPs are present
final_array_slice = final_array[:, 0:(final_array.shape[1] - 1)]
_, unq_row_indices = np.unique(final_array_slice,
return_index=True,
axis=0)
final_array_unique = final_array[unq_row_indices]
print(
'Number of Duplicate FPs: {}'.format(final_array.shape[0] -
final_array_unique.shape[0]))
print('Final Numpy array shape: {}'.format(final_array_unique.shape))
print('Type of final array: {}'.format(type(final_array_unique)))
final_numpy_array = np.asarray((final_array_unique), dtype=np.float32)
return final_numpy_array
def atom(SMILES):
ms = [Chem.MolFromSmiles(i) for i in SMILES]
fp = [Pairs.GetAtomPairFingerprintAsIntVect(x) for x in ms]
return fp
def BuildAtomPairFP(mol):
from rdkit.Chem.AtomPairs import Pairs
fp = Pairs.GetAtomPairFingerprintAsIntVect(mol)
fp._sumCache = fp.GetTotalVal()
return fp
def Calc_AtomPairs_Int(self): #type error
pairFps_int = [Pairs.GetAtomPairFingerprintAsIntVect(x) for x in self.sd]
return pairFps_int
