README.md

# 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