RNAfold to RNArtist

A powerful, modern GUI application for RNA/DNA structure prediction and visualization.
Combines the scientific accuracy of ViennaRNA with the artistic rendering of RNArtistCore.

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📋 Table of Contents

• Key Features
• Getting Started
  • Run the Executable (No Install)
  • Run from Source
• How to Use the App
• Command Line Interface (CLI)
• Benchmarking
• Project Structure
• Technical Details
• License
• Acknowledgements

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✨ Key Features

Feature	Description
🖥️ Modern GUI	Sleek, dark-mode interface built with CustomTkinter.
⚡ Direct Engine	Runs the folding engine directly in Python memory (no fragile subprocess calls).
🎨 Visualization	Real-time Colormap Previews (Sequential, Diverging, RNA Analysis). Output to SVG, PNG.
🧪 Scientific Accuracy	Aligned with RNAfold Web Server defaults (T=37°C, dangles=2, noLP=1).
📂 Project Management	Organize outputs by sequence name. Automatic export of probability data and Vienna files.
🔄 Portable Config	Configuration files are resolved relative to engine location for maximum portability.

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🚀 Getting Started

Option A: Executable (Windows) [Recommended]

The easiest way to use the app. No Python installation required.

Requirements: Java 8+ (for RNArtistCore visualization)

1. Go to the Releases section of this repository.
2. Download RNAfold_to_RNArtist_Windows_v1.0.0.zip.
3. Extract the zip file to a folder of your choice.
4. Double-click RNAfold_to_RNArtist.exe.
5. The app will launch instantly.

Option B: Run from Source (Developers)

If you want to modify the code or run it on Linux/macOS.

Prerequisites:

• Python 3.9+
• Java (JRE 8+) (Required for the RNArtist visualization core)
• ViennaRNA Python bindings installed

Install Dependencies:

pip install -r RNAfold_App/requirements.txt

Launch:

cd RNAfold_App
python app.py

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🎮 How to Use the App

1. Input: Select a .fasta file (single or multiple sequences) or paste a sequence directly.
2. Configure:
   • Constraints: Apply hard constraints using dot-bracket notation.
   • Parameters: Adjust temperature, salt, or algorithm options (MFE vs Partition Function).
   • Visuals: Pick a colormap (e.g., coolwarm, viridis, plasma) and see a live preview.
3. Run: Click the green RUN ENGINE button at the bottom.
4. Results: Check the outputs/ folder for your generated structures and data.

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💻 Command Line Interface (CLI)

For power users who need to process hundreds of files in batches, we preserve the robust CLI version.

• Script: Legacy_Versions/RNAfold_to_RNArtist_CLI.py
• Documentation: Read CLI Docs

Usage:

python RNAfold_to_RNArtist_CLI.py <input_file_or_folder> [max_workers]

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📊 Benchmarking

The Dev_Tools/ folder contains benchmark scripts with real RNA sequences from Rfam:

File	Sequences	Purpose
benchmark_single.fasta	1	Quick single-sequence test
benchmark_10seq.fasta	10	Multithread parallel test

Run benchmarks:

cd Dev_Tools
python benchmark_profiling.py single   # Quick test
python benchmark_profiling.py multi    # Full parallel test

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📂 Project Structure

RNAfold_to_RNArtist/
├── RNAfold_App/                 # MAIN APPLICATION
│   ├── app.py                   # GUI Entry point
│   ├── RNAfold_to_RNArtist_engine.py # Core Logic
│   ├── app_gui/                 # GUI components (tabs, widgets)
│   ├── bin/                     # RNArtistCore JAR
│   ├── config.yaml              # Configuration file
│   └── colormaps.yaml           # Visual styling configs
├── Legacy_Versions/             # CLI TOOLS
│   └── RNAfold_to_RNArtist_CLI.py
├── Dev_Tools/                   # DEVELOPMENT & BENCHMARKING
│   ├── benchmark_profiling.py
│   ├── benchmark_single.fasta
│   └── benchmark_10seq.fasta
├── Tests/                       # QUALITY ASSURANCE
│   └── run_tests.py
└── docs/                        # DOCUMENTATION

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🔧 Technical Details

• Engine: Pure Python integration with the ViennaRNA Python interface (SWIG bindings).
• Visualization: Generates .kts (Kotlin Script) files rendered by the embedded RNArtistCore.jar.
• Packaging: Built with PyInstaller in "One-Directory" mode for fast startup.
• Configuration: YAML-based config with portable path resolution.

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📄 License

This project is licensed under the MIT License - see the LICENSE file for details.

Copyright (c) 2025 Vikram Sen (@sen-vikram)

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👏 Acknowledgements

• Original Concept & Code: Vikram Sen
• AI Assistance: Code architecture and GUI development assisted by AI coding agents.
• Core Technologies:
  • ViennaRNA Package (Folding Engine)
  • RNArtistCore (Visualization)
  • Matplotlib (Colormap support)
  • CustomTkinter (UI Framework)