Fragment growing' implemented in code?

[shree970]

Fantastic implementation of paper, although they have one more method of fine-tuning called as 'fragment growing', where if you give one fragment as SMILE, it will generate SMILES around that fragment. Is there any direction that you can point me to?

[topazape]

@shree970

Thank you for your comment.

Yes, Fragment Growing, in the paper, is implemented in code. For example, if you want to get new 100 molecules grew from benzamidine c1c(C(=N)N)cccc1, call lstm_chem.generator.sample(num=100, start='Gc1c(C(=N)N)cccc1').

However, be careful, this benzamidine SMILES sequence is not canonical. The SMILES is changed to elongate the molecule in a specific direction. That is, N=C(N)c1ccccc1 is canonical. N=C(N)c1ccccc1CCC is valid, but that is wrong direction. So I changed SMILES to valid and correct direction. (e.g. c1c(C(=N)N)cccc1CCC)