README.md

---
license: artistic-2.0
tags:
- chemistry
- biology
- medical
- gpt2
---
# DrugGPT
A generative drug design model based on GPT2.
<img src="https://img.shields.io/badge/license-Artistic%20License%202.0-green"><img src="https://img.shields.io/badge/python-3.7-blue"><img src="https://img.shields.io/github/stars/LIYUESEN/druggpt?style=social">
## Deployment
1. Clone
    ```shell
    git clone https://github.com/LIYUESEN/druggpt.git
    cd druggpt
    ```
   Or you can visit our [GitHub repo](https://github.com/LIYUESEN/druggpt) and click *Code>Download ZIP* to download this repo.
2. Create virtual environment
    ```shell
    conda create -n druggpt python=3.7
    conda activate druggpt
    ```
3. Download python dependencies
    ```shell
    pip install datasets transformers scipy scikit-learn
    pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu117
    conda install -c openbabel openbabel
    ```
## Example usage
Run the script with the desired arguments, such as the protein sequence, ligand prompt, number of molecules to generate, and output directory.  
- If you want to input a protein FASTA file
    ```shell
    python drug_generator.py -f bcl2.fasta -n 50
    ```
- If you want to input the amino acid sequence of the protein
    ```shell
    python drug_generator.py -p MAKQPSDVSSECDREGRQLQPAERPPQLRPGAPTSLQTEPQGNPEGNHGGEGDSCPHGSPQGPLAPPASPGPFATRSPLFIFMRRSSLLSRSSSGYFSFDTDRSPAPMSCDKSTQTPSPPCQAFNHYLSAMASMRQAEPADMRPEIWIAQELRRIGDEFNAYYARRVFLNNYQAAEDHPRMVILRLLRYIVRLVWRMH -n 50
    ```
    
- If you want to provide a prompt for the ligand  
    ```shell
    python drug_generator.py -f bcl2.fasta -l COc1ccc(cc1)C(=O) -n 50
    ```
## License
[Artistic License 2.0](https://opensource.org/license/artistic-license-2-0-php/)