Installation

Installation#

Via PyPI#

The simplest way to install shepherd-score is via pip:

pip install shepherd-score

Install xTB#

xTB will need to be installed manually since there are no PyPI bindings. This can be done in a conda environment, but since this approach has been reported to lead to conflicts, we suggest installing from source and adding it to PATH.

Optional Dependencies#

JAX Support#

For faster scoring and alignment using JAX:

pip install "shepherd-score[jax]"

Docking Evaluation Tools#

Include docking evaluation tools:

pip install "shepherd-score[docking]"

Note

Installing shepherd-score[docking] will automatically install the Python bindings for Autodock Vina. However, a manual installation of the executable of Autodock Vina v1.2.5 is required and can be found at: https://vina.scripps.edu/downloads/

All Dependencies#

Install everything:

pip install "shepherd-score[all]"

Local Development#

For local development:

git clone https://github.com/coleygroup/shepherd-score.git
cd shepherd-score
pip install -e ".[all]"

Requirements#

This package works where PyTorch, Open3D, RDKit, and xTB can be installed for Python >=3.9. If you are coming from the ShEPhERD repository, you can use the same environment.

Core dependencies (installed automatically):

  • python>=3.9

  • numpy

  • torch>=1.12

  • open3d>=0.18

  • rdkit>=2023.03

  • pandas>=2.0

  • scipy>=1.10

Note

If using torch<=2.4, ensure that mkl==2024.0 with conda since there is a known issue that prevents importing torch.