Dynamic Dock

A molecular docking platform that enables protein-ligand docking analysis and molecular dynamics preparation.

Features

• PDB structure loading (via PDB ID or file upload)
• Co-crystallized ligand analysis and visualization
• Active site identification
• Molecular docking using AutoDock Vina
• Results download and molecular dynamics preparation

Project Structure

dynamic_dock/
├── frontend/           # React frontend application
├── backend/           # Python FastAPI backend
├── vina/              # AutoDock Vina executable
└── README.md         # This file

System Requirements

• Operating System: macOS, Linux, or Windows (with WSL2)
• Python: 3.8 or higher
• Node.js: 16.x or higher
• npm: 8.x or higher
• Memory: Minimum 4GB RAM (8GB recommended)
• Storage: At least 2GB free space

Prerequisites Installation

1. Install Python 3.8+

macOS (using Homebrew):

brew install python@3.9

Ubuntu/Debian:

sudo apt update
sudo apt install python3.9 python3.9-pip python3.9-venv

Windows: Download and install from python.org

2. Install Node.js 16+

macOS (using Homebrew):

brew install node

Ubuntu/Debian:

curl -fsSL https://deb.nodesource.com/setup_18.x | sudo -E bash -
sudo apt-get install -y nodejs

Windows: Download and install from nodejs.org

3. Install Poetry (Python Dependency Manager)

curl -sSL https://install.python-poetry.org | python3 -

Add Poetry to your PATH (restart terminal after):

export PATH="$HOME/.local/bin:$PATH"

Installation Guide

Step 1: Clone the Repository

git clone https://github.com/your-username/Dynamic_Dock.git
cd Dynamic_Dock/Dynamic_Dock

Step 2: Backend Setup

Option A: Using Poetry (Recommended)

1. Navigate to the backend directory:

cd backend

2. Install Python dependencies using Poetry:

poetry install

3. Activate the virtual environment:

poetry shell

4. Verify installation:

poetry run python -c "import rdkit, biopython; print('Dependencies installed successfully')"

Option B: Using pip (Alternative)

1. Navigate to the backend directory:

cd backend

2. Create and activate a virtual environment:

python3 -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate

3. Install dependencies using pip:

pip install -r requirements.txt

⚠️ Note: Some dependencies like RDKit may be difficult to install with pip on certain systems. If you encounter issues, especially with RDKit, consider using conda:

conda install -c conda-forge rdkit biopython numpy
pip install fastapi uvicorn python-multipart pydantic python-dotenv requests starlette typing-extensions

4. Verify installation:

python -c "import rdkit, biopython; print('Dependencies installed successfully')"

Step 3: Frontend Setup

1. Navigate to the frontend directory (from the root directory):

cd ../frontend

2. Install Node.js dependencies:

npm install

3. Verify installation:

npm --version
node --version

Step 4: AutoDock Vina Setup

The project includes a pre-compiled AutoDock Vina executable in the vina/ directory.

For macOS users: The executable vina/autodock_vina_1_1_2_mac_catalina_64bit/ is already included.

For Linux/Windows users: Download the appropriate version from AutoDock Vina and place it in the vina/ directory.

Make the executable executable (Linux/macOS):

chmod +x vina/vina

Running the Application

Option 1: Using the Root Script (Recommended)

From the root directory (Dynamic_Dock/):

npm start

This will start both the frontend and backend simultaneously.

Option 2: Manual Startup

Using Poetry: Terminal 1 - Start Backend:

cd backend
poetry shell
poetry run uvicorn app.main:app --host 0.0.0.0 --port 8000 --reload

Terminal 2 - Start Frontend:

cd frontend
npm start

Using pip: Terminal 1 - Start Backend:

cd backend
source venv/bin/activate  # On Windows: venv\Scripts\activate
uvicorn app.main:app --host 0.0.0.0 --port 8000 --reload

Terminal 2 - Start Frontend:

cd frontend
npm start

Accessing the Application

• Frontend: http://localhost:3000
• Backend API: http://localhost:8000
• API Documentation: http://localhost:8000/docs

Troubleshooting

Common Issues

1. Poetry not found:

   • Ensure Poetry is installed and in your PATH
   • Restart your terminal after installation

2. RDKit installation fails:

   • RDKit requires conda on some systems. Consider using Miniconda:

   conda install -c conda-forge rdkit

   • Or use the pip alternative mentioned in Step 2

3. Port already in use:

   • Kill processes using ports 3000 or 8000:

   lsof -ti:3000 | xargs kill -9
   lsof -ti:8000 | xargs kill -9

4. Permission denied on Vina executable:

   chmod +x vina/vina

5. Node.js version incompatible:

   • Use nvm to manage Node.js versions:

   nvm install 18
   nvm use 18

Verification Commands

Check Python dependencies:

Using Poetry:

cd backend
poetry run python -c "import fastapi, uvicorn, biopython, rdkit; print('All dependencies OK')"

Using pip:

cd backend
source venv/bin/activate  # On Windows: venv\Scripts\activate
python -c "import fastapi, uvicorn, biopython, rdkit; print('All dependencies OK')"

Check Node.js dependencies:

cd frontend
npm list --depth=0

Development

Running Tests

Backend tests:

Using Poetry:

cd backend
poetry run pytest

Using pip:

cd backend
source venv/bin/activate  # On Windows: venv\Scripts\activate
pytest

Frontend tests:

cd frontend
npm test

Code Formatting

Backend:

Using Poetry:

cd backend
poetry run black .
poetry run isort .

Using pip:

cd backend
source venv/bin/activate  # On Windows: venv\Scripts\activate
black .
isort .

Frontend:

cd frontend
npm run lint

Contributing

1. Fork the repository
2. Create a feature branch: git checkout -b feature-name
3. Make your changes and test thoroughly
4. Submit a pull request

License

MIT

Support

For issues and questions:

• Create an issue on GitHub
• Check the troubleshooting section above
• Ensure all prerequisites are properly installed