Skip to content

DOCUMENTATION_INDEX.md

Latest commit

 

History

History
291 lines (221 loc) · 8.99 KB

DOCUMENTATION_INDEX.md

File metadata and controls

291 lines (221 loc) · 8.99 KB

📚 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:

  1. README.md - Main project documentation
  2. ARCHITECTURE.md - System architecture & design
  3. IMPLEMENTATION_SUMMARY.md - Technical implementation details

Additional Resources:

  1. MODEL_CARD.md - HuggingFace model card
  2. PROJECT_OVERVIEW.md - Project goals & features
  3. CONTRIBUTING.md - How to contribute
  4. CHANGELOG.md - Version history
  5. LICENSE - GNU GPL v3 license

Examples & Guides:

  1. examples/README.md - Example files & file format guide
  2. examples/basic_docking.sh - Shell script example
  3. examples/python_api_example.py - Python API example

📖 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

🎯 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

🔍 Find What You Need

Installation & Setup

Running Docking Jobs

File Preparation

Technical Details

Troubleshooting

🗂️ 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?

Technical Issues?

Still Stuck?

🔄 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 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 for details.

🎓 Learn More

External Resources:

Related Projects:

🧬 Ready to start docking?

Begin with → START_HERE.md

This index is automatically generated and maintained. For suggestions, contact andrew@bleunomics.com