errors when run examples/intro_to_chemvae.ipynb about chemical_vae HOT 4 OPEN

Hi this error is due to not decoding any molecules and so since you try to plot the resulting molecules (None) you get an error.

The non-decoding could be due to the z vector, or the smiles or the number of decoding attempts.
What z-vector/molecule are you trying to decode?

from chemical_vae.

Thank you! I also found this reason, because I found this on my command line,

[10:45:10] SMILES Parse Error: syntax error for input: 'CC1ccc(c1cc@NH2)N[3H]2(CCO)C'
[10:45:10] SMILES Parse Error: syntax error for input: 'Ccccccc(=O)[NHOH+]3CCC@=O- C'
[10:45:10] SMILES Parse Error: syntax error for input: 'CCc1cN(=O=N+2(C[OC[NCO)n21)'
[10:45:10] SMILES Parse Error: syntax error for input: 'Cc1C(=(=C@)[C@H]1Nc1)1 ='

I selected a few SMILES randomly from the csv file, what I used here is CC(=O)c1c(O)cccc1COc1ccccc1 and CCCN(CC)c1cc[nH+]c(C(=O)[O-])c1 . I also try to find the middle of the z-vector of the two SMILES, but the output is OC(C1cc(c(O)cccccc(F)F)c1c1 , this is obviously an invalid SMILES , so what should I do to get more valid SMILES output. Thanks!

from chemical_vae.

What do you mean by middle of the z-vector of two smiles?

To get more valid smiles, you should increase the number of decoding attempts (how many are you using?) or slightly increase the noise radius (how much are you using?).

from chemical_vae.

HI !I don't know middle of the z-vector. But, Isn't Z-vector Z-distance?
Z-distance is three -dimensional distance (euclidian metric of three material property values) ,right?

from chemical_vae.