Overview

Key Features

Installation

pip install pandamap-color

Quick Start

PandaMapColor: Visualize protein-ligand interactions from PDB files withcustomizable styling and coloring options.pandamap-color -husage: 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_filePandaMap-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 complexoptions:  -h, --help            show thishelp message andexit  --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 titlefor 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 acidtype  --jitter JITTER       Amount of positional randomization (0.0-1.0)for more natural look  --h-bond-cutoff H_BOND_CUTOFF                        Distance cutoffforhydrogen bondsin Angstroms  --pi-stack-cutoff PI_STACK_CUTOFF                        Distance cutoffforpi-stacking interactionsin Angstroms  --hydrophobic-cutoff HYDROPHOBIC_CUTOFF                        Distance cutoffforhydrophobic interactionsin Angstroms  --figsize FIGSIZE FIGSIZE                        Figure sizein inches (width height)  --generate-report     Generate a detailed interaction report  --report-file REPORT_FILE                        Pathfor the interaction report (default:<pdb_name>_interactions_report.txt)  --use-dssp            Use DSSPfor solvent accessibility calculationif available  --show-directionality                        Show interaction directionality with arrows  --ionic-cutoff IONIC_CUTOFF                        Distance cutoffforionic interactionsin Angstroms  --halogen-cutoff HALOGEN_CUTOFF                        Distance cutoffforhalogen bondsin Angstroms

Command Line Usage

# Basic usagepandamap-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 schemepandamap-color path/to/complex.pdb --color-scheme publication -o output_image.pngpandamap-color path/to/complex.pdb --color-scheme monochrome -o output_image.pngpandamap-color path/to/complex.pdb --color-scheme colorblind -o output_image.pngpandamap-color path/to/complex.pdb --color-scheme dark -o output_image.png#Jitterpandamap-color path/to/complex.pdb --jitter 0.3 --color-scheme publication -o output_image.png#Report filepandamap-color path/to/complex.pdb  --color-scheme publication -o output_image.png --generate-report

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

# Helppandamap-color --help

Python API Usage

frompandamap_colorimportPandaMapColor# Create a mapper instancemapper=PandaMapColor(pdb_file="path/to/complex.pdb",ligand_resname="LIG",# Optional: specify ligand residue namecolor_scheme="default",use_enhanced_styling=True)# Detect interactionsmapper.detect_interactions()# Identify solvent-accessible residuesmapper.estimate_solvent_accessibility()# Generate visualizationmapper.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

Custom Color Schemes

importjsonfrompandamap_colorimportPandaMapColor# Define a custom color schemecustom_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)withopen("my_colors.json","w")asf:json.dump(custom_colors,f,indent=2)# Use with the mappermapper=PandaMapColor(pdb_file="path/to/complex.pdb",color_scheme=custom_colors# Pass the dictionary directly)# Or load from filemapper=PandaMapColor(pdb_file="path/to/complex.pdb",color_scheme="my_colors.json"# Or path to JSON file)

Documentation

Package Structure

Requirements

Citing PandaMap-Color

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

License

Contributing