Update README.md

README.md

@@ -1,31 +1,45 @@
 ---
 license: artistic-2.0
+tags:
+- chemistry
+- biology
+- medical
+- gpt2
 ---
-# Install
-    
+# 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">
+## Deployment
+1. Clone
+    ```shell
+    git lfs install
+    git clone https://huggingface.co/liyuesen/druggpt
+    ```
+2. Create virtual environment
+    ```shell
     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
+    ```
+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
-
-# 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,  
+    ```
+## 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,  
+    ```
+- 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  
-    python drug_generator.py -f bcl2.fasta -l COc1ccc(cc1)C(=O) -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/)