README.md

metadata

license: artistic-2.0

Install

conda create -n druggpt python=3.7
conda activate druggpt

pip install datasets
pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu117
pip install transformers
pip install scipy scikit-learn
conda install -c openbabel openbabel

How to use

1. Download the drug_generator.py file and bcl2.fasta.
2. Activate the druggpt environment using conda activate druggpt.
3. Navigate to the directory containing the drug_generator.py file using cd path/to/directory.
4. Run the script with the desired arguments, such as the protein sequence, ligand prompt, number of molecules to generate, and output directory.

Example usage:

## If you want to input a protein FASTA file,  
python drug_generator.py -f bcl2.fasta -n 50

## If you want to input the amino acid sequence of the protein,  
python drug_generator.py -p MAKQPSDVSSECDREGRQLQPAERPPQLRPGAPTSLQTEPQGNPEGNHGGEGDSCPHGSPQGPLAPPASPGPFATRSPLFIFMRRSSLLSRSSSGYFSFDTDRSPAPMSCDKSTQTPSPPCQAFNHYLSAMASMRQAEPADMRPEIWIAQELRRIGDEFNAYYARRVFLNNYQAAEDHPRMVILRLLRYIVRLVWRMH -n 50

## If you want to provide a prompt for the ligand  
python drug_generator.py -f bcl2.fasta -l COc1ccc(cc1)C(=O) -n 50