Open manavsingh415 opened 3 years ago
Did you find a solution to this?
Because they explicitly mention in the README that the token length limit is 128, I decided to use SmilesVectorizer
from molvecgen
. I removed all SMILES for which the token vector has a length larger than the limit.
Suppose your data frame is called data
in the example below.
remove = []
TOKEN_LENGTH_LIMIT = 128
for index, row in tqdm(data.iterrows(), total=len(data)):
mol = Chem.MolFromSmiles(row.SMILES)
sm_en = SmilesVectorizer(canonical=True, augment=False)
sm_en.fit([mol], extra_chars=["\\"])
if sm_en.maxlength > TOKEN_LENGTH_LIMIT:
remove.append(index)
print(
f"There are {len(remove)} smiles with a token length larger than {TOKEN_LENGTH_LIMIT}"
)
data.drop(remove, inplace=True)
data.to_csv("preprocessed.csv", index=False, header=False)
And now it worked.
The other way will be that if too many molecules are discarded because they have a token length larger than 128, you retrain the autoencoder again.
Good luck.
Hi. When trying to create 512 dimensional vector representations of some new molecules (that the encoder may not have seen during training), I get the following error
Traceback (most recent call last): File "encode.py", line 56, in
encode(**args)
File "encode.py", line 35, in encode
latent = model.transform(model.vectorize(mols_in))
File "/content/latent-gan/ddc_pub/ddc_v3.py", line 1042, in vectorize
return self.smilesvec1.transform(mols_test)
File "/content/latent-gan/molvecgen/vectorizers.py", line 145, in transform
one_hot[i,j+offset,charidx] = 1
IndexError: index -201 is out of bounds for axis 1 with size 138
I am using the pretrained chembl encoder. Any ideas about how to resolve? Thanks