Installation¶

Requirements¶

Python 3.12 or higher
pip or uv package manager

Install from PyPI¶

pipuv

pip install phoenix-chem

uv pip install phoenix-chem

Development Installation¶

For contributing or development:

# Clone the repository
git clone https://github.com/Ameyanagi/phoenix-chem.git
cd phoenix-chem

# Create virtual environment
uv venv --python 3.12
source .venv/bin/activate  # Linux/macOS
# or: .venv\Scripts\activate  # Windows

# Install with dev dependencies
uv pip install -e ".[dev]"

# Install pre-commit hooks
pre-commit install

Dependencies¶

PHOENIX automatically installs these dependencies:

Package	Purpose
`rdkit`	Molecular parsing, SMILES handling
`pgradd`	Benson Group Additivity estimation
`chemicals`	Thermodynamic reference data
`scipy`	Linear programming for decomposition
`numpy`	Numerical operations
`pandas`	Data handling for batch results
`pydantic`	Data validation

Verify Installation¶

import phoenix
print(phoenix.__version__)

# Quick test
from phoenix import Compound
ethanol = Compound.from_smiles("CCO")
print(f"Ethanol: {ethanol.formula}, MW = {ethanol.molecular_weight:.2f}")

Troubleshooting¶

RDKit Installation Issues¶

RDKit requires specific system libraries. If installation fails:

Linux (Ubuntu/Debian)macOSWindows

sudo apt-get install libboost-all-dev
pip install rdkit

brew install boost
pip install rdkit

Use conda for easiest installation:

conda install -c conda-forge rdkit
pip install phoenix-chem

pgradd Issues¶

The pgradd library (Benson GA) may have issues on some systems:

# Try installing with specific version
pip install pgradd>=2.9.13

If pgradd fails, PHOENIX falls back to the chemicals library for thermodynamic data.

Optional Dependencies¶

For documentation development:

pip install phoenix-chem[docs]

For all optional features:

pip install phoenix-chem[all]