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! - Your first steps
2. GETTING_STARTED.md - Comprehensive quick start guide
3. QUICKSTART.md - Quick reference guide

Core Documentation:

4. README.md - Main project documentation
5. ARCHITECTURE.md - System architecture & design
6. IMPLEMENTATION_SUMMARY.md - Technical implementation details

Additional Resources:

7. MODEL_CARD.md - HuggingFace model card
8. PROJECT_OVERVIEW.md - Project goals & features
9. CONTRIBUTING.md - How to contribute
10. CHANGELOG.md - Version history
11. LICENSE - GNU GPL v3 license

Examples & Guides:

12. examples/README.md - Example files & file format guide
13. examples/basic_docking.sh - Shell script example
14. examples/python_api_example.py - Python API example

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📖 Documentation by Topic

Getting Started

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

Understanding the System

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

Using the Platform

Document	Purpose	Audience
README.md	Main documentation	All users
examples/README.md	File formats & examples	Scientists
MODEL_CARD.md	ML model info	Researchers

Development

Document	Purpose	Audience
CONTRIBUTING.md	Contribution guide	Developers
CHANGELOG.md	Version history	Developers
LICENSE	Legal terms	Everyone

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🎯 Documentation by User Type

I'm a Biologist/Chemist:

→ Start with START_HERE.md
→ Learn from examples/README.md
→ Use the GUI (see GETTING_STARTED.md)

I'm a Computational Scientist:

→ Read ARCHITECTURE.md
→ Check IMPLEMENTATION_SUMMARY.md
→ Use Python API (see examples/python_api_example.py)

I'm a Developer:

→ Review ARCHITECTURE.md
→ Study IMPLEMENTATION_SUMMARY.md
→ See CONTRIBUTING.md

I'm a System Administrator:

→ Read README.md installation section
→ Review ARCHITECTURE.md deployment options
→ Check IMPLEMENTATION_SUMMARY.md for requirements

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🔍 Find What You Need

Installation & Setup

• First-time installation → START_HERE.md
• Detailed setup → GETTING_STARTED.md
• System requirements → README.md

Running Docking Jobs

• Web GUI → GETTING_STARTED.md
• Command line → QUICKSTART.md
• Python API → examples/python_api_example.py

File Preparation

• PDBQT format → examples/README.md
• Converting files → examples/README.md
• Example files → examples/

Technical Details

• Architecture → ARCHITECTURE.md
• Implementation → IMPLEMENTATION_SUMMARY.md
• API documentation → IMPLEMENTATION_SUMMARY.md

Troubleshooting

• Common issues → START_HERE.md
• Performance tips → GETTING_STARTED.md
• Support contacts → All docs have support info at bottom

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🗂️ 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)

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📝 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

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🆘 Getting Help

Quick Questions?

• Check START_HERE.md
• See GETTING_STARTED.md

Technical Issues?

• Review IMPLEMENTATION_SUMMARY.md
• Check ARCHITECTURE.md for system design

Still Stuck?

• 📧 Email: [email protected]
• 🤗 Discussions: https://huggingface.co/OpenPeerAI/DockingAtHOME/discussions
• 💬 HuggingFace Community

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🔄 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

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📊 Documentation Metrics

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

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🌟 Contribution

Help us improve the documentation!

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

See CONTRIBUTING.md for details.

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👥 Authors

Documentation by:

• OpenPeer AI - AI/ML documentation
• Riemann Computing Inc. - Technical architecture
• Bleunomics - Scientific documentation
• Andrew Magdy Kamal - Overall coordination

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📜 License

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

See LICENSE for details.

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🎓 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

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🧬 Ready to start docking?

Begin with → START_HERE.md

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