Setting Up OpenFold

In this guide, we will OpenFold and its dependencies.

Pre-requisites

This package is currently supported for CUDA 12 and Pytorch 2. All dependencies are listed in the environment.yml.

At this time, only Linux systems are supported.

Instructions

Installation:

  1. Clone the repository, e.g. git clone https://github.com/aqlaboratory/openfold.git

  2. From the openfold repo:

    • Create a Mamba environment, e.g. mamba env create -n openfold_env -f environment.yml Mamba is recommended as the dependencies required by OpenFold are quite large and mamba can speed up the process.

    • Activate the environment, e.g conda activate openfold_env

  3. Run the setup script to configure kernels and folding resources.

    scripts/install_third_party_dependencies.sh

  4. Prepend the conda environment to the $LD_LIBRARY_PATH and $LIBRARY_PATH., e.g.

    export LIBRARY_PATH=$CONDA_PREFIX/lib:$LIBRARY_PATH
export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH

    You may optionally set this as a conda environment variable according to the conda docs to activate each time the environment is used.

  5. Download parameters. We recommend using a destination as openfold/resources as our unittests will look for the weights there.

    • For AlphaFold2 weights, use

      ./scripts/download_alphafold_params.sh

    • For OpenFold weights, use :

      ./scripts/download_openfold_params.sh

    • For OpenFold SoloSeq weights, use:

      ./scripts/download_openfold_soloseq_params.sh

Checking your build with unit tests:

To test your installation, you can run OpenFold unit tests. Make sure that the OpenFold and AlphaFold parameters have been downloaded, and that they are located (or symlinked) in the directory openfold/resources

Run with the following script:

scripts/run_unit_tests.sh

The script is a thin wrapper around Python’s unittest suite, and recognizes unittest arguments. E.g., to run a specific test verbosely:

scripts/run_unit_tests.sh -v tests.test_model

Alphafold Comparison tests: Certain tests perform equivalence comparisons with the AlphaFold implementation. Instructions to run this level of tests requires an environment with both AlphaFold 2.0.1 and OpenFold installed, and is not covered in this guide. These tests are skipped by default if no installation of AlphaFold is found.

Environment specific modifications

MPI

To use OpenFold with MPI support, you will need to add the package mpi4py. This can be done with pip in your OpenFold environment, e.g. $ pip install mpi4py.

cuEquivariance

cuEquivariance can be installed from pip: $ pip install cuequivariance_ops_torch_cu13 cuequivariance_torch (on CUDA13) or $ pip install cuequivariance_ops_torch_cu12 cuequivariance_torch (on CUDA12)

Install OpenFold parameters without aws

If you don’t have access to aws on your system, you can use a different download source:

  • HuggingFace (requires git-lts): scripts/download_openfold_params_huggingface.sh

  • Google Drive: scripts/download_openfold_params_gdrive.sh

Docker setup

A Dockerfile is provided to build an OpenFold Docker image. Additional notes for setting up a docker container for OpenFold and running inference can be found here.