Joshua Meyers

Hi @C0921, thanks for your interest in DeeplyTough, could you post the output you get when running the script? Cheers, J.

Hey @C0921, apologies for the slow reply. The ProSPECCTs dataset had moved, I have updated the url. Can you confirm this now works for you? Thanks for highlighting the issue....

Hello @vinbl, thanks for raising an issue! Yep, DeeplyTough could be exactly what you're looking for. Apologies for the delay. Obtaining the descriptors for each pocket is relatively straightforward, there...

Hey @LivC182, thanks for your interest in our code! Yes isomericSmiles is set to `False` although this name can be somewhat misleading since it only affects stereoisomers (see [rdkit doc](https://rdkit.org/docs/source/rdkit.Chem.rdmolfiles.html#rdkit.Chem.rdmolfiles.MolToSmiles))....

Yes this is true. In the GuacaMol v1 SMILES training dataset, there are in fact 45 occurrences of the SMILES you give as an example (as substrings of larger molecules)....

Hey @L40S38, thanks for opening a ticket. It seems this is due to the RCSB PDBs cluster file moving. See https://www.rcsb.org/news/feature/6205750d8f40f9265109d39f (in fact its discontinued and changed, so this may...

Hey Marc, Sorry that was a lazy report! Here is some simplified code and an example image. I have not included a dataset, any should recreate the issue. If you...

Hey, thanks for your interest in our code. The version needed is specified in the dockerfile provided: https://github.com/BenevolentAI/DeeplyTough/blob/7536c5bb7d4e1e7e5d4f6cfacd1a437db03596e9/Dockerfile#L47 I recommend you use the dockerfile, or the prebuilt image on dockerhub...

Hey @raghavchandra123 thanks for your interest in our work. The pretrained models are already available in this repo. Please follow the readme, I recommend using the docker image on DockerHub....

Hey @shahik, sounds like an interesting project. GuacaMol is a benchmark suite for comparing small molecule generators, while the baseline methods we provide can be tweaked in the direction of...