Protein 3D Structure Analysis Suite

A comprehensive tool for analyzing protein structures from the PDB with 3D visualization, feature engineering, and machine learning classification.

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📂 Repository Structure & Purpose

src/ - Core Application Code

• Purpose: Contains Python source code for the analysis pipeline
• Audience: Developers
• Key File: main.py (Central script)

notebooks/ - Interactive Interface

• Purpose: Jupyter Notebook for end-users
• Audience: Researchers/Students
• Key File: demo.ipynb (Ready-to-run demo)

screenshots/ (Optional) - Visual Examples

• Purpose: Documentation assets
• Audience: Maintainers

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Audience Guide

User Type	Primary Folder	Activities
Biologists/Researchers	notebooks/	Run interface, view 3D visualizations
Developers	src/	Modify core logic, add features
Educators	Both folders	Teach using demo, experiment with code

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Installation

git clone https://github.com/tabasaleemm/protein-3d-analysis-tool.git
cd protein-3d-analysis-tool
pip install -r requirements.txt
pip install biopython  # If not already installed

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Usage Workflow

End-User Flow

graph TD
    A[Open notebooks/demo.ipynb] --> B[Run create_interface]
    B --> C[Input PDB ID]
    C --> D[View Interactive Report]

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Developer Flow

graph TD
    A[Edit src/main.py] --> B[Test Changes]
    B --> C[Update Requirements]
    C --> D[Commit to Repository]

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Example Interface (Optional)

Add screenshots to screenshots/ folder:

mkdir screenshots
# Add your PNG files here

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Repository Structure

protein-3d-analysis-tool/
├── notebooks/
│   └── demo.ipynb       # Interactive demo notebook
├── screenshots/       
│   ├── input.png
│   ├── style-dropdown.png
│   └── report.png
├── src/
│   └── main.py          # Core analysis logic
├── README.md            
├── requirements.txt     # Python dependencies 
└── setup.py