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Installation

Requirements

plotlyMol requires Python 3.9 or higher.

Install from Source

Currently, plotlyMol is best installed from source:

# Clone the repository
git clone https://github.com/The-Schultz-Lab/plotlyMol.git
cd plotlyMol

# Create a virtual environment (recommended)
python -m venv .venv

# Activate the virtual environment
# On Windows:
.venv\Scripts\activate
# On macOS/Linux:
source .venv/bin/activate

# Install the package
pip install -e .

Dependencies

plotlyMol automatically installs the following dependencies:

Core Runtime Dependencies

  • plotly (≥5.0.0) - Interactive 3D plotting
  • numpy (≥1.20.0) - Numerical arrays and operations
  • rdkit (≥2022.3.1) - Cheminformatics toolkit
  • kaleido (≥0.2.1) - Static image export

Optional Dependencies

For development and testing:

pip install -r requirements.txt

This includes: - pytest - Testing framework - black - Code formatting - ruff - Fast linting - mypy - Type checking - dash + dash-bootstrap-components - GUI application

Verify Installation

Test that plotlyMol is correctly installed:

from plotlymol3d import draw_3D_rep

# Create a simple molecule
fig = draw_3D_rep(smiles="CCO")
print("plotlyMol is installed correctly!")

Troubleshooting

RDKit Installation Issues

RDKit can be challenging to install on some systems. If you encounter issues:

Using conda (recommended for RDKit): 

conda create -n plotlymol python=3.11
conda activate plotlymol
conda install -c conda-forge rdkit
pip install plotly numpy kaleido
pip install -e .

Using pip on Windows: - Ensure you have Visual C++ Build Tools installed - Or use pre-built wheels from conda-forge

Kaleido Issues

If static image export fails: 

pip install --upgrade kaleido

Import Errors

If you get ModuleNotFoundError: 1. Ensure the virtual environment is activated 2. Try reinstalling: pip install -e . 3. Check that you're importing from plotlymol3d (with "3d")

Platform-Specific Notes

Windows: - Use py -m venv .venv if python command not found - May need Visual C++ Build Tools for some dependencies

macOS (Apple Silicon): - Some packages may require Rosetta 2 - Consider using conda for better ARM64 support

Linux: - May need to install system libraries: sudo apt-get install build-essential

Next Steps

Once installed, check out the Quick Start guide to start visualizing molecules!