Error in the decoding phase

[grassogianvito]

Hello,
I'm trying to convert the dataset available on Huggingface and decode it in SMILES code, but I get several errors. Do you have any information about this?

Best regards,

Gianvito

[maclandrol]

Hello @grassogianvito , We have been informed, that there might be some issues with the huggingface dataset (predate these two commits that patch it #23, #25).

I would recommend reprocessing the full dataset ZINC dataset if you can. Otherwise, I will update it during the week.

Are you errors related to samples that could not be decoded into valid molecular graphs ?

[grassogianvito]

Hello @maclandrol, thanks for your prompt answer. You can find below an example of code and error.

safe_notation = "CC6.N63.C3(C5C4.c15cnn2c1.C2C.c14ccc(Cl)cc1Cl"

try:
smi = safe.decode(safe_notation, canonical=True)
except safe.DecoderError:
pass

---

ArgumentError Traceback (most recent call last)
File ~/miniconda3/envs/CPPfeatures/lib/python3.10/site-packages/safe/converter.py:434, in decode(safe_str, as_mol, canonical, fix, remove_added_hs, remove_dummies, ignore_errors)
433 try:
--> 434 decoded = safe_obj.decoder(
435 safe_str,
436 as_mol=as_mol,
437 canonical=canonical,
438 fix=fix,
439 remove_dummies=remove_dummies,
440 remove_added_hs=remove_added_hs,
441 )
443 except Exception as e:

File ~/miniconda3/envs/CPPfeatures/lib/python3.10/site-packages/safe/converter.py:187, in SAFEConverter.decoder(self, inp, as_mol, canonical, fix, remove_dummies, remove_added_hs)
186 if canonical:
--> 187 out = dm.standardize_smiles(out)
188 return out

File ~/miniconda3/envs/CPPfeatures/lib/python3.10/site-packages/datamol/mol.py:409, in standardize_smiles(smiles)
398 r"""
399 Apply smile standardization procedure. This is a convenient function wrapped arrounf RDKit
400 smiles standardizer and tautomeric canonicalization.
(...)
406 standard_smiles: the standardized smiles
407 """
--> 409 smiles = rdMolStandardize.StandardizeSmiles(smiles)
410 return smiles

ArgumentError: Python argument types in
rdkit.Chem.MolStandardize.rdMolStandardize.StandardizeSmiles(NoneType)
did not match C++ signature:
StandardizeSmiles(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator> smiles)

The above exception was the direct cause of the following exception:

SAFEDecodeError Traceback (most recent call last)
Cell In[8], line 11
10 try:
---> 11 smi = safe.decode(safe_notation, canonical=True) # CC(C)Cc1ccc(C(C)C(=O)O)cc1
12 except safe.DecoderError:

File ~/miniconda3/envs/CPPfeatures/lib/python3.10/site-packages/safe/converter.py:446, in decode(safe_str, as_mol, canonical, fix, remove_added_hs, remove_dummies, ignore_errors)
445 return None
--> 446 raise SAFEDecodeError(f"Failed to decode {safe_str}") from e
447 return decoded

SAFEDecodeError: Failed to decode CC6.N63.C3(C5C4.c15cnn2c1.C2C.c14ccc(Cl)cc1Cl

During handling of the above exception, another exception occurred:

AttributeError Traceback (most recent call last)
Cell In[8], line 12
10 try:
11 smi = safe.decode(safe_notation, canonical=True) # CC(C)Cc1ccc(C(C)C(=O)O)cc1
---> 12 except safe.DecoderError:
13 pass

AttributeError: module 'safe' has no attribute 'DecoderError'