AlphaFold3 Dash App

A user-friendly web interface for submitting AlphaFold3 jobs to a Slurm-powered compute cluster. Built with Dash and Bootstrap, this app lets researchers with minimal computational background define protein, ligand, and ion entities, generate the necessary JSON input, and submit jobs.

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🚀 Features

• Intuitive UI: Add and configure entities (protein, ligand, ion) through dynamic cards.
• JSON Generation: One-click generation and pretty-printing of the input.json for AlphaFold3.
• Downloadable Inputs: Download your JSON input named after your job if you need it.
• SLURM Submission: Automatically render and submit a Singularity-based Slurm script on longleaf.
• Job Tracking: View a Job History table with timestamps and download result archives (.zip).

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🛠️ Installation

1. Clone the repository

   git clone https://github.com/molecularmodelinglab/AF3_dashapp.git
   cd AF3_dashapp

2. Create a virtual environment

   python3 -m venv venv
   source venv/bin/activate

3. Install dependencies

   pip install -r requirements.txt

4. Run the app

   python app.py

   Then open your browser to http://localhost:8050.

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📂 Project Structure

├── app.py                 # Entry point, wires layout + callbacks
├── layout.py              # Defines Dash layout and custom components
├── callbacks.py           # Dash callback registrations
├── helpers.py             # File I/O, Slurm script rendering, job-directory logic
├── submission.py          # AF3Submission model: validate & JSON serialization
├── assets/
│   └── style.css          # Custom CSS for button effects, layout tweaks
├── templates/
│   └── submit_template.sh # Slurm + Singularity submission script template
├── jobs/                  # (git-ignored) Per-job directories with inputs & results
├── tests/                 # pytest suite for submission & helper modules
└── requirements.txt       # Python dependencies

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📝 Usage Guide

1. Submit Job

   • Enter a Job Name and your Email for notifications.
   • Click Add Entity to include proteins, ligands, or ions. Specify sequences or SMILES/CCD codes and bonded atom pairs.
   • Click Generate JSON to preview the input.json.
   • Click Download JSON to save the file if you need to.
   • Finally, click Submit Job to render and dispatch the Slurm script. You’ll see a confirmation with your Slurm Job ID.

2. Job History

   • Switch to the Job History tab.
   • A table lists all completed runs with their timestamps.
   • Click Download in any row to fetch the <jobname>_<timestamp>.zip archive of AlphaFold3 outputs.

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✅ Testing

We use pytest for unit tests of both the core AF3Submission model and the helper utilities.

# from the repo root
pytest

All tests live under tests/ and rely on built-in fixtures like tmp_path and monkeypatch for isolation.

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🤝 Contributing

Contributions, bug reports, and feature requests are welcome! Please:

1. Fork the repo
2. Create a feature branch (git checkout -b feature/your-idea)
3. Commit your changes (git commit -am 'Add new feature')
4. Push to the branch (git push origin feature/your-idea)
5. Open a Pull Request

Please ensure new code is covered by tests and follows the existing style (run black . and flake8).

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📜 License

This project is licensed under the MIT License.