Installation

PDBFixer is distributed as the pdbfixer-neoralab package for Python 3.11 and newer. You can install it from PyPI, uv, or conda-forge, or work directly from a cloned repository.

Prerequisites

• Python 3.11+
• A C++ toolchain and OpenMM runtime dependencies as required by your platform (see the OpenMM installation guide).
• Optional: Git, if installing from source.

Install from PyPI

pip install pdbfixer-neoralab

Install with uv

uv pip install pdbfixer-neoralab

Install from conda-forge

conda install -c conda-forge pdbfixer

Install from source

git clone https://github.com/neoralab/pdbfixer.git
cd pdbfixer
python -m venv .venv
source .venv/bin/activate  # On Windows use: .venv\\Scripts\\activate
pip install -e .

The source install respects optional extras. For development and testing, install with tests enabled:

pip install -e ".[tests]"

Documentation dependencies

To build or serve the MkDocs site locally, install the documentation extra defined in pyproject.toml:

pip install -e ".[docs]"

Then run mkdocs serve from the repository root and open the printed local URL.