error running README example

[XZhang-ML]

Hey, I would like to try the drfp feature but after pip installed it:

pip install drfp

and run the example from README:

from drfp import DrfpEncoder

rxn_smiles = [
    "CO.O[C@@H]1CCNC1.[C-]#[N+]CC(=O)OC>>[C-]#[N+]CC(=O)N1CC[C@@H](O)C1",
    "CCOC(=O)C(CC)c1cccnc1.Cl.O>>CCC(C(=O)O)c1cccnc1",
]

fps = DrfpEncoder.encode(rxn_smiles)

I ran into the numpy error shown below:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/xxx/Library/Caches/pypoetry/virtualenvs/py3.10/lib/python3.10/site-packages/drfp/fingerprint.py", line 342, in encode
    hashed_diff, smiles_diff = DrfpEncoder.internal_encode(
  File "/Users/xxx/Library/Caches/pypoetry/virtualenvs/py3.10/lib/python3.10/site-packages/drfp/fingerprint.py", line 243, in internal_encode
    return DrfpEncoder.hash(list(s)), list(s)
  File "/Users/xxx/Library/Caches/pypoetry/virtualenvs/py3.10/lib/python3.10/site-packages/drfp/fingerprint.py", line 261, in hash
    return np.array(hash_values, dtype=np.int32)
OverflowError: Python integer 2325499645 out of bounds for int32

Here is my pkg versions:

>>> import numpy
>>> numpy.__version__
'2.2.3'
>>> import rdkit
>>> rdkit.__version__
'2024.09.5'
>>> import drfp
>>> drfp.__version__
'0.3.6'

Would really appreciate your help here!

[masun]

I have the same problem. Could you solve it?

[masun]

Solved

import importlib
import drfp
import numpy as np
from hashlib import blake2b

##Monkey patch the hash function
def patched_hash(shingling):
    hash_values = []
    for t in shingling:
        # Modified to use np.int64
        hash_values.append(int(blake2b(t, digest_size=4).hexdigest(), 16))
    return np.array(hash_values, dtype=np.int64)

drfp.DrfpEncoder.hash = patched_hash  # Replace the original hash function

##Rest of your code using drfp.DrfpEncoder.encode ...
rxn_smiles = [
    "CO.O[C@@H]1CCNC1.[C-]#[N+]CC(=O)OC>>[C-]#[N+]CC(=O)N1CC[C@@H](O)C1",
    "CCOC(=O)C(CC)c1cccnc1.Cl.O>>CCC(C(=O)O)c1cccnc1"
]

fps = drfp.DrfpEncoder.encode(rxn_smiles, n_folded_length=2048)