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Setting Up OpenFold

In this guide, we will OpenFold and its dependencies.

Pre-requisites

This package is currently supported for CUDA 11 and Pytorch 1.12. 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 $LD_LIBRARY_PATH., e.g. export LD_LIBRARY_PATH=$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. You can download all parameters to the same destination folder as the files will not overwrite each other.
    • For AlphaFold2 weights, use

      ./scripts/download_alphafold_params.sh <dest>

    • For OpenFold weights, use :

      ./scripts/download_openfold_params.sh <dest>

    • For OpenFold SoloSeq weights, use:

      ./scripts/download_openfold_soloseq_params.sh <dest>

  6. Install OpenFold:

    python setup.py install

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

CUDA 12

To use OpenFold on CUDA 12 environment rather than a CUDA 11 environment. In step 1, use the branch pl_upgrades rather than the main branch, i.e. replace the URL in step 1 with https://github.com/aqlaboratory/openfold/tree/pl_upgrades Follow the rest of the steps of Installation Guide

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.

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.