pandamap-color 2.1

Versatile visualization tool for protein-ligand interactions with customizable color schemes

PandaMap-Color: A versatile tool for protein-ligand interaction visualization with customizable color schemes.

Overview

PandaMap-Color is a powerful Python package for visualizing protein-ligand interactions in 2D with customizable color schemes. Generate publication-quality interaction diagrams directly from PDB files with minimal configuration.

Key Features

• Stunning Visualizations: Create detailed, publication-ready 2D diagrams of protein-ligand interactions
• Multiple Color Schemes: Choose from several pre-defined color schemes (Default, Colorblind-friendly, Monochrome, Dark mode, Publication-ready)
• Customizable Appearance: Easily modify colors and styling to match your publication or presentation needs
• Automatic Interaction Detection: Identifies hydrogen bonds, π-π stacking, hydrophobic interactions, and more
• Intuitive Representation: Clearly shows interaction types between protein residues and ligands
• Command Line Interface: Simple to use in scripts or from the terminal

Installation

pip install pandamap-color

Quick Start

PandaMapColor: Visualize protein-ligand interactions from PDB files with
customizable styling and coloring options.

pandamap-color -h

usage: pandamap-color [-h] [--output OUTPUT] [--ligand LIGAND] [--dpi DPI] [--title TITLE]
                      [--color-scheme {default,colorblind,monochrome,dark,publication}] [--custom-colors CUSTOM_COLORS]
                      [--simple-styling] [--no-color-by-type] [--jitter JITTER] [--h-bond-cutoff H_BOND_CUTOFF]
                      [--pi-stack-cutoff PI_STACK_CUTOFF] [--hydrophobic-cutoff HYDROPHOBIC_CUTOFF]
                      [--figsize FIGSIZE FIGSIZE] [--generate-report] [--report-file REPORT_FILE] [--use-dssp]
                      [--show-directionality] [--ionic-cutoff IONIC_CUTOFF] [--halogen-cutoff HALOGEN_CUTOFF]
                      pdb_file

PandaMap-Color: Visualize protein-ligand interactions from PDB files with customizable styling and coloring options.

positional arguments:
  pdb_file              Path to PDB file with protein-ligand complex

options:
  -h, --help            show this help message and exit
  --output OUTPUT, -o OUTPUT
                        Output image file path
  --ligand LIGAND, -l LIGAND
                        Specific ligand residue name to analyze
  --dpi DPI             Image resolution (default: 300 dpi)
  --title TITLE, -t TITLE
                        Custom title for the visualization
  --color-scheme {default,colorblind,monochrome,dark,publication}, -c {default,colorblind,monochrome,dark,publication}
                        Color scheme to use (default: default)
  --custom-colors CUSTOM_COLORS
                        Path to JSON file with custom color scheme
  --simple-styling      Use simple styling instead of enhanced effects
  --no-color-by-type    Disable coloring residues by amino acid type
  --jitter JITTER       Amount of positional randomization (0.0-1.0) for more natural look
  --h-bond-cutoff H_BOND_CUTOFF
                        Distance cutoff for hydrogen bonds in Angstroms
  --pi-stack-cutoff PI_STACK_CUTOFF
                        Distance cutoff for pi-stacking interactions in Angstroms
  --hydrophobic-cutoff HYDROPHOBIC_CUTOFF
                        Distance cutoff for hydrophobic interactions in Angstroms
  --figsize FIGSIZE FIGSIZE
                        Figure size in inches (width height)
  --generate-report     Generate a detailed interaction report
  --report-file REPORT_FILE
                        Path for the interaction report (default: <pdb_name>_interactions_report.txt)
  --use-dssp            Use DSSP for solvent accessibility calculation if available
  --show-directionality
                        Show interaction directionality with arrows
  --ionic-cutoff IONIC_CUTOFF
                        Distance cutoff for ionic interactions in Angstroms
  --halogen-cutoff HALOGEN_CUTOFF
                        Distance cutoff for halogen bonds in Angstroms

Command Line Usage

# Basic usage
pandamap-color path/to/complex.pdb -o output_image.png

# Specify ligand residue name (if multiple ligands in file)
pandamap-color path/to/complex.pdb --ligand LIG -o output_image.png

# Change color scheme
pandamap-color path/to/complex.pdb --color-scheme publication -o output_image.png
pandamap-color path/to/complex.pdb --color-scheme monochrome -o output_image.png
pandamap-color path/to/complex.pdb --color-scheme colorblind -o output_image.png
pandamap-color path/to/complex.pdb --color-scheme dark -o output_image.png

#Jitter
pandamap-color path/to/complex.pdb --jitter 0.3 --color-scheme publication -o output_image.png

#Report file
pandamap-color path/to/complex.pdb  --color-scheme publication -o output_image.png --generate-report

============================================================================= PandaMap-Color Interaction Report

Ligand: PFL:D:601 Name: PFL Type: LIGAND File: complex.pdb

---

Interacting Chains: D, C Interacting Residues: 13 Solvent Accessible Residues: 6

---

Interaction Summary: Hydrogen Bonds: 1 Hydrophobic Interactions: 4 π-π Stacking: 1 Carbon-π Interactions: 1 Donor-π Interactions: 1 Amide-π Interactions: 2 Alkyl-π Interactions: 7

---

Hydrogen Bonds:

1. ILE228D -- 2.75Å -- PFL

---

Hydrophobic Interactions:

1. MET286C -- 3.89Å -- PFL
2. LEU285C -- 3.95Å -- PFL
3. PHE289C (Solvent accessible) -- 3.61Å -- PFL
4. MET236D (Solvent accessible) -- 3.55Å -- PFL

---

π-π Stacking:

1. PHE289C (Solvent accessible) -- 3.61Å -- PFL

---

Carbon-π Interactions:

1. PHE289C (Solvent accessible) -- 3.61Å -- PFL

---

Donor-π Interactions:

1. ASP282C (Solvent accessible) -- 3.75Å -- PFL

---

Amide-π Interactions:

1. ASN265C (Solvent accessible) -- 3.69Å -- PFL
2. GLN229D (Solvent accessible) -- 3.35Å -- PFL

---

Alkyl-π Interactions:

1. MET286C -- 3.89Å -- PFL
2. ILE228D -- 4.06Å -- PFL
3. LEU232D -- 4.01Å -- PFL
4. PRO233D -- 4.03Å -- PFL
5. LEU285C -- 3.95Å -- PFL
6. MET261C -- 5.02Å -- PFL
7. MET236D (Solvent accessible) -- 3.55Å -- PFL

=============================================================================

# Help
pandamap-color --help

Python API Usage

from pandamap_color import PandaMapColor

# Create a mapper instance
mapper = PandaMapColor(
    pdb_file="path/to/complex.pdb",
    ligand_resname="LIG",  # Optional: specify ligand residue name
    color_scheme="default",
    use_enhanced_styling=True
)

# Detect interactions
mapper.detect_interactions()

# Identify solvent-accessible residues
mapper.estimate_solvent_accessibility()

# Generate visualization
mapper.visualize(output_file="interaction_diagram.png")

Examples

Monochrome Mode

Dark Style

Default Style

Colorblind-Friendly Style

Publication Mode

No Color By Type Mode

No Color By Type Mode

Available Color Schemes

PandaMap-Color comes with multiple built-in color schemes:

• default: Standard vibrant colors
• colorblind: Colorblind-friendly palette
• monochrome: Grayscale for simple publications
• dark: Dark background for presentations
• publication: Clean style for scientific publications

Custom Color Schemes

You can define custom color schemes using JSON:

import json
from pandamap_color import PandaMapColor

# Define a custom color scheme
custom_colors = {
    "element_colors": {
        "C": "#333333",
        "N": "#3060F0",
        "O": "#FF2010",
        # Add more elements...
    },
    "interaction_styles": {
        "hydrogen_bonds": {
            "color": "#2E8B57",
            "linestyle": "-",
            # More styling options...
        },
        # More interaction types...
    }
}

# Save to a file (optional)
with open("my_colors.json", "w") as f:
    json.dump(custom_colors, f, indent=2)

# Use with the mapper
mapper = PandaMapColor(
    pdb_file="path/to/complex.pdb",
    color_scheme=custom_colors  # Pass the dictionary directly
)

# Or load from file
mapper = PandaMapColor(
    pdb_file="path/to/complex.pdb",
    color_scheme="my_colors.json"  # Or path to JSON file
)

Documentation

For detailed documentation, see:

• Usage Guide
• Color Scheme Reference
• API Reference

Package Structure

PandaMap-Color is organized into modular components:

• pandamap.py: Main PandaMapColor class for protein-ligand interaction analysis
• visualization.py: Visualization functionality for creating beautiful diagrams
• ligand.py: Ligand structure representation and 2D projection
• colorschemes.py: Pre-defined color schemes and customization utilities
• cli.py: Command-line interface
• utils.py: Utility functions and helper classes

Requirements

• Python 3.7+
• NumPy
• Matplotlib
• BioPython

Citing PandaMap-Color

If you use PandaMap-Color in your research, please cite:

Pritam Kumar Panda. (2025). PandaMap-Color: A versatile tool for protein-ligand interaction visualization with customizable color schemes.

License

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

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

1. Fork the repository
2. Create your feature branch (git checkout -b feature/amazing-feature)
3. Commit your changes (git commit -m 'Add some amazing feature')
4. Push to the branch (git push origin feature/amazing-feature)
5. Open a Pull Request