-
Notifications
You must be signed in to change notification settings - Fork 42
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Cannot get valid molecule from running sample.py for a long time #4
Comments
Hi, can you provide the index of the failed test data? |
Thank you for your prompt reply. I used the default index=0, I tried index=1, but the situation is same. |
I further check downstream, it failed at "Chem.SanitizeMol(rd_mol,Chem.SANITIZE_ALL^Chem.SANITIZE_KEKULIZE)" |
Thank you for your information. I am looking into it. |
Hi, I am having the exact same issue - is this simply because the model takes a long time to sample valid molecules. I am getting 25 valid molecules after about 12 hours. 6590 were discounted either because they were duplicates or invalid. |
Thanks in advance and also great paper ! Learnt a lot from it. |
Hi, I am meeting the similar issue. |
Can you try another random seed? Btw, please check out our latest work on SBDD (accepted to ICML 2022) here: https://github.com/pengxingang/Pocket2Mol |
Thanks for your reply. |
What's the version of RDKit and OpenBabel in your environment ? |
RDkit==2022.03.3, and OpenBabel==3.1.1 |
Thanks! |
I will read it carefully.You and your team are very helpful for me. |
I thought it was caused by the the openbabel under windows |
I read your paper which looks great.
I tried to run according to the instruction, sample.py, using the sample.yml and the two model ckpts downloaded from google drive. I waited for a long time (like half an hour) , and it still cannot produce a valid molecule, it shows [Pool] Queue 300 | Finished 0 | Failed 55.
I tried to debug, I found that most generated graph does not pass the if statement "if data_next.status == STATUS_FINISHED:".
Even for those few that can pass the if statement, it failed during "rdmol = reconstruct_from_generated(data_next)", which throws exception shown as "Ignoring, because reconstruction error encountered."
The text was updated successfully, but these errors were encountered: