DOCUMENTATION_INDEX.md

# 📚 Docking@HOME Documentation Index

Welcome to Docking@HOME - A distributed platform for molecular docking with GPU acceleration!

## 🚀 Quick Navigation

### For New Users:
1. **[START_HERE.md](START_HERE.md)** ⭐ **START HERE!** - Your first steps
2. **[GETTING_STARTED.md](GETTING_STARTED.md)** - Comprehensive quick start guide
3. **[QUICKSTART.md](QUICKSTART.md)** - Quick reference guide

### Core Documentation:
4. **[README.md](README.md)** - Main project documentation
5. **[ARCHITECTURE.md](ARCHITECTURE.md)** - System architecture & design
6. **[IMPLEMENTATION_SUMMARY.md](IMPLEMENTATION_SUMMARY.md)** - Technical implementation details

### Additional Resources:
7. **[MODEL_CARD.md](MODEL_CARD.md)** - HuggingFace model card
8. **[PROJECT_OVERVIEW.md](PROJECT_OVERVIEW.md)** - Project goals & features
9. **[CONTRIBUTING.md](CONTRIBUTING.md)** - How to contribute
10. **[CHANGELOG.md](CHANGELOG.md)** - Version history
11. **[LICENSE](LICENSE)** - GNU GPL v3 license

### Examples & Guides:
12. **[examples/README.md](examples/README.md)** - Example files & file format guide
13. **[examples/basic_docking.sh](examples/basic_docking.sh)** - Shell script example
14. **[examples/python_api_example.py](examples/python_api_example.py)** - Python API example

---

## 📖 Documentation by Topic

### Getting Started

| Document | Purpose | Time to Read |
|----------|---------|--------------|
| [START_HERE.md](START_HERE.md) | First-time setup | 5 min |
| [GETTING_STARTED.md](GETTING_STARTED.md) | Detailed walkthrough | 15 min |
| [QUICKSTART.md](QUICKSTART.md) | Quick reference | 3 min |

### Understanding the System

| Document | Purpose | Level |
|----------|---------|-------|
| [ARCHITECTURE.md](ARCHITECTURE.md) | System design & diagrams | Intermediate |
| [IMPLEMENTATION_SUMMARY.md](IMPLEMENTATION_SUMMARY.md) | Technical details | Advanced |
| [PROJECT_OVERVIEW.md](PROJECT_OVERVIEW.md) | High-level overview | Beginner |

### Using the Platform

| Document | Purpose | Audience |
|----------|---------|----------|
| [README.md](README.md) | Main documentation | All users |
| [examples/README.md](examples/README.md) | File formats & examples | Scientists |
| [MODEL_CARD.md](MODEL_CARD.md) | ML model info | Researchers |

### Development

| Document | Purpose | Audience |
|----------|---------|----------|
| [CONTRIBUTING.md](CONTRIBUTING.md) | Contribution guide | Developers |
| [CHANGELOG.md](CHANGELOG.md) | Version history | Developers |
| [LICENSE](LICENSE) | Legal terms | Everyone |

---

## 🎯 Documentation by User Type

### I'm a Biologist/Chemist:
→ Start with [START_HERE.md](START_HERE.md)  
→ Learn from [examples/README.md](examples/README.md)  
→ Use the GUI (see [GETTING_STARTED.md](GETTING_STARTED.md))

### I'm a Computational Scientist:
→ Read [ARCHITECTURE.md](ARCHITECTURE.md)  
→ Check [IMPLEMENTATION_SUMMARY.md](IMPLEMENTATION_SUMMARY.md)  
→ Use Python API (see [examples/python_api_example.py](examples/python_api_example.py))

### I'm a Developer:
→ Review [ARCHITECTURE.md](ARCHITECTURE.md)  
→ Study [IMPLEMENTATION_SUMMARY.md](IMPLEMENTATION_SUMMARY.md)  
→ See [CONTRIBUTING.md](CONTRIBUTING.md)

### I'm a System Administrator:
→ Read [README.md](README.md) installation section  
→ Review [ARCHITECTURE.md](ARCHITECTURE.md) deployment options  
→ Check [IMPLEMENTATION_SUMMARY.md](IMPLEMENTATION_SUMMARY.md) for requirements

---

## 🔍 Find What You Need

### Installation & Setup
- First-time installation → [START_HERE.md](START_HERE.md)
- Detailed setup → [GETTING_STARTED.md](GETTING_STARTED.md)
- System requirements → [README.md](README.md#prerequisites)

### Running Docking Jobs
- Web GUI → [GETTING_STARTED.md](GETTING_STARTED.md#using-the-web-gui)
- Command line → [QUICKSTART.md](QUICKSTART.md#cli-commands)
- Python API → [examples/python_api_example.py](examples/python_api_example.py)

### File Preparation
- PDBQT format → [examples/README.md](examples/README.md#file-format-details)
- Converting files → [examples/README.md](examples/README.md#converting-your-own-files)
- Example files → [examples/](examples/)

### Technical Details
- Architecture → [ARCHITECTURE.md](ARCHITECTURE.md)
- Implementation → [IMPLEMENTATION_SUMMARY.md](IMPLEMENTATION_SUMMARY.md)
- API documentation → [IMPLEMENTATION_SUMMARY.md](IMPLEMENTATION_SUMMARY.md#api-endpoints)

### Troubleshooting
- Common issues → [START_HERE.md](START_HERE.md#-troubleshooting)
- Performance tips → [GETTING_STARTED.md](GETTING_STARTED.md#performance-tips)
- Support contacts → All docs have support info at bottom

---

## 🗂️ File Organization

```
Docking@HOME/
│
├── 📄 Documentation (YOU ARE HERE!)
│   ├── START_HERE.md ⭐ Start here!
│   ├── GETTING_STARTED.md
│   ├── QUICKSTART.md
│   ├── README.md
│   ├── ARCHITECTURE.md
│   ├── IMPLEMENTATION_SUMMARY.md
│   ├── MODEL_CARD.md
│   ├── PROJECT_OVERVIEW.md
│   ├── CONTRIBUTING.md
│   ├── CHANGELOG.md
│   └── LICENSE
│
├── 🚀 Launchers
│   ├── start.py (Python launcher)
│   ├── START_WINDOWS.bat (Windows)
│   └── start.sh (Linux/Mac)
│
├── 🐍 Python Package
│   └── python/docking_at_home/
│       ├── __init__.py
│       ├── gui.py (Web interface)
│       ├── server.py (AutoDock integration)
│       └── cli.py (Command-line tools)
│
├── 💻 Source Code
│   ├── src/ (C++/CUDA code)
│   ├── include/ (Headers)
│   └── external/ (Dependencies)
│
├── 🧬 Examples
│   └── examples/
│       ├── README.md
│       ├── example_ligand.pdbqt
│       ├── example_receptor.pdbqt
│       ├── basic_docking.sh
│       └── python_api_example.py
│
├── ⚙️ Configuration
│   ├── requirements.txt
│   ├── setup.py
│   ├── pyproject.toml
│   ├── package.json
│   └── CMakeLists.txt
│
└── 📊 Output Directories
    ├── uploads/ (User files)
    └── results/ (Docking results)
```

---

## 📝 Documentation Standards

All our documentation follows these principles:

✅ **Clear** - Easy to understand  
✅ **Complete** - No missing steps  
✅ **Current** - Up to date  
✅ **Tested** - All examples work  
✅ **Accessible** - For all skill levels

---

## 🆘 Getting Help

### Quick Questions?
- Check [START_HERE.md](START_HERE.md#-troubleshooting)
- See [GETTING_STARTED.md](GETTING_STARTED.md#troubleshooting)

### Technical Issues?
- Review [IMPLEMENTATION_SUMMARY.md](IMPLEMENTATION_SUMMARY.md#-known-limitations)
- Check [ARCHITECTURE.md](ARCHITECTURE.md) for system design

### Still Stuck?
- 📧 Email: [email protected]
- 🤗 Discussions: https://huggingface.co/OpenPeerAI/DockingAtHOME/discussions
- 💬 HuggingFace Community

---

## 🔄 Documentation Updates

This documentation is actively maintained. Last updated: 2025

### Recent Changes:
- ✅ Complete AutoDock integration implemented
- ✅ Web GUI with real-time updates
- ✅ Simulation mode for testing
- ✅ GPU acceleration support
- ✅ Comprehensive guides added

### Upcoming:
- [ ] Video tutorials
- [ ] API reference (auto-generated)
- [ ] More examples
- [ ] Docker guide
- [ ] Cloud deployment guide

---

## 📊 Documentation Metrics

| Metric | Value |
|--------|-------|
| Total documents | 15+ |
| Total pages | 100+ |
| Code examples | 20+ |
| Diagrams | 5+ |
| Installation guides | 3 |
| Languages covered | Python, C++, CUDA, JS |

---

## 🌟 Contribution

Help us improve the documentation!

- Found a typo? → Open an issue
- Missing info? → Suggest additions
- Have examples? → Submit a PR

See [CONTRIBUTING.md](CONTRIBUTING.md) for details.

---

## 👥 Authors

Documentation by:
- **OpenPeer AI** - AI/ML documentation
- **Riemann Computing Inc.** - Technical architecture
- **Bleunomics** - Scientific documentation
- **Andrew Magdy Kamal** - Overall coordination

---

## 📜 License

All documentation is licensed under GNU GPL v3.0 (same as code).

See [LICENSE](LICENSE) for details.

---

## 🎓 Learn More

### External Resources:
- AutoDock: https://autodock.scripps.edu/
- CUDA Programming: https://docs.nvidia.com/cuda/
- FastAPI: https://fastapi.tiangolo.com/
- Molecular Docking: https://en.wikipedia.org/wiki/Docking_(molecular)

### Related Projects:
- BOINC: https://boinc.berkeley.edu/
- CUDPP: https://cudpp.github.io/
- The Decentralized Internet SDK: https://github.com/Lonero-Team/Decentralized-Internet/
- Cloud Agents: https://huggingface.co/OpenPeerAI/Cloud-Agents

---

**🧬 Ready to start docking?**

Begin with → [START_HERE.md](START_HERE.md)

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*This index is automatically generated and maintained. For suggestions, contact [email protected]*