Ramachandran graph plotting tool- Ramachandran Plot Generator

Overview The Ramachandran Plot Generator is a graphical tool for analyzing the backbone dihedral angles (Φ, Ψ) of a protein structure from a PDB file. It generates a high-resolution Ramachandran plot with a density heatmap and scatter points, visually distinguishing most favorable, favorable, allowed, and disallowed regions with percentage calculations.

The tool features a colorful GUI for ease of use and produces a comprehensive report file detailing the classifications of dihedral angles.

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Features

• Upload PDB Files: Easily select and analyze protein structure files.
• Ramachandran Plot Visualization:
  • Uses Seaborn to generate a cool-warm gradient heatmap.
  • Scatter points for individual residues.
  • Displays percentages for each region (Most Favorable, Favorable, Allowed, Disallowed).
  • Phi (Φ) and Psi (Ψ) labels are clearly represented.
• Report Generation:
  • Saves a CSV file listing each residue's dihedral angles and classification.
  • Summary file with region percentages.
• Professional GUI:
  • Colorful fonts and stylish buttons.
  • Easy-to-use interface with PDB file upload functionality.

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Installation Prerequisites Ensure you have Python 3.x installed along with the following dependencies:

pip install numpy matplotlib seaborn pandas biopython tkinter

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Usage Running the Tool To launch the graphical interface, execute the script:

python ramachandran_plot.py

Steps to Use:

1. Click "Upload PDB File".
2. Select a .pdb file from your computer.
3. The tool processes the file and generates:
   • A Ramachandran plot (saved as ramachandran_plot.png).
   • A detailed CSV report (ramachandran_report.csv).
   • A summary CSV file (ramachandran_summary.csv) with region percentages.
4. The visual representation of the plot is displayed with distinct colors for each region.

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Output Files

1. ramachandran_plot.png – The high-resolution Ramachandran plot.
2. ramachandran_report.csv – Detailed report of dihedral angles and classifications.
3. ramachandran_summary.csv – Summary with region percentages.

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Example Output Ramachandran Plot The generated Ramachandran plot will include:

• Heatmap background (cool-warm gradient).
• Scatter points categorized into:
  • Most Favorable (Lime)
  • Favorable (Gold)
  • Allowed (Dodgerblue)
  • Disallowed (Red)
• Region percentages displayed outside the plot area.

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License This project is open-source and available under the MIT License.

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For suggestions or bug reports, feel free to open an issue on GitHub!

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Contact For any queries, contact Mukesh Nitin at drmukeshnitin@gmail.com or raise an issue on GitHub.

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