how can I address the error which calls “SMILES Pass Error”

Question

When I run the python script, it shows the problem "SMILES Pass Error"image image2 image3. Codes show as below.

def convert_vocab_to_smiles_fn(smi_vocab_coding_padded,
                               token_EOS=SmilesVocab.smi_vocab.index('<EOS>')):
  index_eos = np.where(smi_vocab_coding_padded == token_EOS)[0]
  f_counter = 0
  if index_eos.size == 0:
    f_counter += 1
    return None, ''.join(
      [SmilesVocab.smi_vocab[x] for x in smi_vocab_coding_padded])
  elif index_eos[0] == 0:
    f_counter += 1
    return False, ''.join(
      [SmilesVocab.smi_vocab[x] for x in smi_vocab_coding_padded])
  else:
    int_encoding = smi_vocab_coding_padded[:index_eos[0]]
    smiles_encoding = ''.join(
      [SmilesVocab.smi_vocab[x] for x in int_encoding])

    try:
      rdkit_mol_encoding = rdkit_chem.MolFromSmiles(smiles_encoding)
    except:
      rdkit_mol_encoding = None
  return smiles_encoding, rdkit_mol_encoding

I search the solution on the Internet, but I find nothing

Please edit your answer and insert the code of "the python script". Please also copy and paste the full error traceback to give us more insights. — Tarquinius, Apr 24 '23 at 06:59
Don't insert a picture, instead insert it as text and format it as code. — Tarquinius, Apr 24 '23 at 12:07
As you can see in the error messages, you have SMILES that are completely broken. They are only parts of complete SMILES. And by the way, you should include code not as an image but as formatted text in the question. — rapelpy, Apr 24 '23 at 19:15

score 1 · Answer 1 · answered Apr 25 '23 at 20:53

I don't understand how you build smiles_encoding, but it gives you corupted SMILES.

Here is an example where only the first SMILES is correct.

from rdkit import Chem

s = ['c1ccccc1', '-c1ccccc1c', 'c1c(cccc1', 'c1cccc']

mol = []

for smiles_encoding in s:
    try:
        rdkit_mol_encoding = Chem.MolFromSmiles(smiles_encoding)
        mol.append(rdkit_mol_encoding)
    except:
        rdkit_mol_encoding = None

print(mol)

Output:

[<rdkit.Chem.rdchem.Mol object at 0x00000175DDA89F20>, None, None, None]


[22:43:58] SMILES Parse Error: syntax error while parsing: -c1ccccc1c
[22:43:58] SMILES Parse Error: Failed parsing SMILES '-c1ccccc1c' for input: '-c1ccccc1c'
[22:43:58] SMILES Parse Error: extra open parentheses for input: 'c1c(cccc1'
[22:43:58] SMILES Parse Error: unclosed ring for input: 'c1cccc'

Either your creation of SMILES is not good or you are working with corrupted SMILES.

how can I address the error which calls “SMILES Pass Error”

1 Answers1