manas02/fbdd

FragmentBERT: Masked Language Models are Fragment Based Drug Designers

Masked Language Models are Fragment Based Drug Designers

Download, Process and Train FragmentBERT

bash run.sh

Steps to reproduce :

• fragment_tokenizer/tokenizer.py Defines Fragment Augmentation, Encoder and Decoder.
• moses_train_test_split.py Takes in moses_dataset.csv and produces train, test moses data.
• encode_moses.py Produces failed and augmented encoded moses smiles files.
• model/tokenizer.py Creates FragmentBERT Tokenizer.
• model.py Train the model and log to WandB.

Conda

conda env create -f environment.yml
conda activate fbdd

fbdd's Issues

Help with WandB error

Running src/model/model.py...
wandb: ERROR api_key not configured (no-tty). call wandb.login(key=[your_api_key])
Traceback (most recent call last):
File "/home/martis-e/work/code-tuts/fbdd/fbdd/src/model/model.py", line 16, in
wandb.init(project="FragmentBERT")
File "/home/martis-e/miniconda3/lib/python3.11/site-packages/wandb/sdk/wandb_init.py", line 1195, in init
raise e
File "/home/martis-e/miniconda3/lib/python3.11/site-packages/wandb/sdk/wandb_init.py", line 1172, in init
wi.setup(kwargs)
File "/home/martis-e/miniconda3/lib/python3.11/site-packages/wandb/sdk/wandb_init.py", line 306, in setup
wandb_login._login(
File "/home/martis-e/miniconda3/lib/python3.11/site-packages/wandb/sdk/wandb_login.py", line 317, in _login
wlogin.prompt_api_key()
File "/home/martis-e/miniconda3/lib/python3.11/site-packages/wandb/sdk/wandb_login.py", line 247, in prompt_api_key
raise UsageError("api_key not configured (no-tty). call " + directive)
wandb.errors.UsageError: api_key not configured (no-tty). call wandb.login(key=[your_api_key])
/home/martis-e/work/code-tuts/fbdd/fbdd
Finished running src/model/model.py.

Implement Molecule and MolOps

Implement Molecule & Fragment Ops

• Create Molecule class that can perform all the basic tasks related to conversion between rdkit.Mol object to SMILES, SMARTS, BRICS, etc.
• Add type Molecules = list[Molecule].
• Create Fragment class to hold Fragment data with connectivity information.
• Add type Fragments = list[Fragment].
• Add error handling for both classes.
• Implement __hash__ & __eq__ for both classes.

User Manual/Guide missing

@Manas02
It would be great to have a user manual or guide.
Thank you
Regards
Elvis