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Installation

We support two installation modes:

  • core installation allows you to build and benchmark your own models or search algorithms
  • full installation also allows you to perform end-to-end search using the supported models

There are also two installation sources:

  • pip, which provides the most recent released version
  • GitHub, which provides the latest changes but may be less stable and may not be backward-compatible with the latest released version
conda env create -f environment.yml
conda activate syntheseus

pip install syntheseus

conda env create -f environment_full.yml
conda activate syntheseus-full

pip install "syntheseus[all]"

conda env create -f environment.yml
conda activate syntheseus

pip install -e .

conda env create -f environment_full.yml
conda activate syntheseus-full

pip install -e ".[all]"

Note

Make sure you are viewing the version of the docs matching your syntheseus installation. Select the x.y.z version you installed if you used pip (go here for the latest one), or dev if you installed syntheseus directly from GitHub.

Core installation includes only minimal dependencies (no ML libraries), while full installation includes all supported models and also dependencies for visualization/development.

Instructions above assume you already cloned the repository via

git clone https://github.com/microsoft/syntheseus.git
cd syntheseus

Note that environment_full.yml pins the CUDA version (to 11.3) for reproducibility. If you want to use a different one, make sure to edit the environment file accordingly.

Setting up GLN

We also support GLN, but it requires a specialized environment and is thus not installed via pip. See here for a Docker environment necessary for running GLN.

Reducing the number of dependencies

To keep the environment smaller, you can replace the all option with a comma-separated subset of {chemformer,local-retro,megan,mhn-react,retro-knn,root-aligned,viz,dev} (viz and dev correspond to visualization and development dependencies, respectively). For example, pip install -e ".[local-retro,root-aligned]" installs only LocalRetro and RootAligned. If installing a subset of models, you can also delete the lines in environment_full.yml marked with names of models you do not wish to use.

If you only want to use a very specific part of syntheseus, you could also install it without dependencies:

pip install -e .  --no-dependencies

You then would need to manually install a subset of dependencies that are required for a particular functionality you want to access. See pyproject.toml for a list of dependencies tied to the search and reaction_prediction subpackages.