Installation

Minimum Dependencies Installation

  1. Python >= 3.10

  2. RDKit >= 2022.03.1 (for the isomer engine)

  3. PyTorch >= 2.1.0 (for the optimization engine)

If you have an environment with the above dependencies, Auto3D can be installed by

# Using pip
pip install Auto3D

# Using uv (faster)
uv pip install Auto3D

Otherwise, you can create an environment and install Auto3D. In a terminal, the following code will create an environment named auto3D with Auto3D and its minimum dependencies installed.

git clone https://github.com/isayevlab/Auto3D_pkg.git
cd Auto3D_pkg
conda env create --file installation.yml --name auto3D
conda activate auto3D
pip install Auto3D

Optional Dependencies Installation

By installing Auto3D with the above minimum dependencies, you can use Auto3D with RDKit and AIMNet2 as the isomer engine and optimization engine, respectively. Two additional optimization engines are available: ANI-2x and ANI-2xt, which can be installed by:

conda activate auto3D
conda install -c conda-forge torchani

One additional isomer engine is available: OpenEye toolkit. It’s a commercial software from OpenEye Software. It can be installed by

conda activate auto3D
conda install -c openeye openeye-toolkits

To calculate thermodynamic properties (such as Gibbs free energy, enthalpy, entropy, geometry optimization) with Auto3D, ASE needs to be installed:

conda activate auto3D
conda install -c conda-forge ase