PandaMap-Color: A versatile tool for protein-ligand interaction visualization with customizable color schemes.
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.
- 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
pip install pandamap-colorPandaMapColor: 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# 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:
- ILE228D -- 2.75Å -- PFL
Hydrophobic Interactions:
- MET286C -- 3.89Å -- PFL
- LEU285C -- 3.95Å -- PFL
- PHE289C (Solvent accessible) -- 3.61Å -- PFL
- MET236D (Solvent accessible) -- 3.55Å -- PFL
π-π Stacking:
- PHE289C (Solvent accessible) -- 3.61Å -- PFL
Carbon-π Interactions:
- PHE289C (Solvent accessible) -- 3.61Å -- PFL
Donor-π Interactions:
- ASP282C (Solvent accessible) -- 3.75Å -- PFL
Amide-π Interactions:
- ASN265C (Solvent accessible) -- 3.69Å -- PFL
- GLN229D (Solvent accessible) -- 3.35Å -- PFL
Alkyl-π Interactions:
- MET286C -- 3.89Å -- PFL
- ILE228D -- 4.06Å -- PFL
- LEU232D -- 4.01Å -- PFL
- PRO233D -- 4.03Å -- PFL
- LEU285C -- 3.95Å -- PFL
- MET261C -- 5.02Å -- PFL
- MET236D (Solvent accessible) -- 3.55Å -- PFL
=============================================================================
# Help
pandamap-color --help
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")
PandaMap-Color comes with multiple built-in color schemes:
default: Standard vibrant colorscolorblind: Colorblind-friendly palettemonochrome: Grayscale for simple publicationsdark: Dark background for presentationspublication: Clean style for scientific publications
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
)For detailed documentation, see:
PandaMap-Color is organized into modular components:
- pandamap.py: Main
PandaMapColorclass 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
- Python 3.7+
- NumPy
- Matplotlib
- BioPython
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.
This project is licensed under the MIT License - see the LICENSE file for details.
Contributions are welcome! Please feel free to submit a Pull Request.
- Fork the repository
- Create your feature branch (
git checkout -b feature/amazing-feature) - Commit your changes (
git commit -m 'Add some amazing feature') - Push to the branch (
git push origin feature/amazing-feature) - Open a Pull Request