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plotlyMol

Interactive 3D Molecular Visualization

Tests Lint License: MIT

Interactive 3D molecular visualizations with Plotly

plotlyMol is a Python package for creating beautiful, interactive 3D molecular visualizations using Plotly. It supports multiple input formats including SMILES, XYZ, MOL/SDF, PDB files, and Gaussian cube files for orbital visualization.

Key Features

  • Multiple Visualization Modes: Ball-and-stick, stick-only, and van der Waals (VDW) representations
  • Flexible Input Formats: SMILES strings, XYZ, MOL/SDF, PDB, and Gaussian cube files
  • SMILES-to-3D: Automatic 3D coordinate generation from SMILES via RDKit
  • Orbital Visualization: Isosurface rendering from quantum chemistry cube files
  • Bond Order Display: Visual differentiation of single, double, triple, and aromatic bonds
  • Interactive GUI: Dash-based web interface for easy exploration
  • Export Options: Save as interactive HTML or static PNG images

Quick Example

from plotlymol3d import draw_3D_rep

# Visualize a molecule from SMILES
fig = draw_3D_rep(smiles="CCO", mode="ball+stick")
fig.show()

# Or from an XYZ file
fig = draw_3D_rep(xyzfile="molecule.xyz", mode="ball+stick")
fig.show()

  • Ball and Stick

    Classic molecular representation with atoms as spheres and bonds as cylinders

  • Stick Model

    Simplified view with small atoms and prominent bonds

  • Van der Waals

    Space-filling representation showing atomic volumes

  • Orbital Visualization

    Render molecular orbitals from quantum chemistry calculations

Why plotlyMol?

Built on Powerful Tools

  • Plotly: Industry-leading interactive plotting library
  • RDKit: Comprehensive cheminformatics toolkit
  • NumPy: Efficient numerical operations

Modern Architecture

  • Uses Plotly's Mesh3d traces for smooth, performant 3D rendering
  • Fibonacci sphere algorithm for uniform atom tessellation
  • Customizable lighting and materials
  • Half-bond coloring for clear heteroatom visualization

Easy to Use

  • Simple API with sensible defaults
  • Comprehensive documentation and examples
  • Interactive GUI for visual exploration
  • Well-tested and CI/CD pipeline

Get Started

Ready to visualize molecules? Check out the Installation guide and Quick Start tutorial!

Community & Support

Citation

If you use plotlyMol in your research, please cite:

@software{plotlymol2026,
  title = {plotlyMol: Interactive 3D Molecular Visualizations},
  author = {Schultz, Jonathan and Lear, Benjamin},
  year = {2026},
  url = {https://github.com/The-Schultz-Lab/plotlyMol}
}