Source code for "Generating Highly Designable Proteins with Geometric Algebra Flow Matching" (https://arxiv.org/abs/2411.05238)
If you use this code, please cite:
@inproceedings{wagnerseute2024gafl,
title={Generating Highly Designable Proteins with Geometric Algebra Flow Matching},
author={Wagner, Simon and Seute, Leif and Viliuga, Vsevolod and Wolf, Nicolas and Gr{\"a}ter, Frauke and St{\"u}hmer, Jan},
booktitle={Thirty-eighth Conference on Neural Information Processing Systems},
year={2024}
}
This repository is based on FrameFlow (https://github.com/microsoft/protein-frame-flow).
The datasets and weights of the models reported in the paper will be made available in the future
conda env create -f environment.yaml
conda activate gafl
bash install_gatr.sh # Apply patches to gatr
# Install package:
pip install -e .Geometric Algebra Transformer (gatr) in version 1.2.0 requires the xformers package that resulted in conflicting package dependencies. We therefore require to install gatr from source and apply patches to remove the dependency on xformers. Please note that gatr is distributed under its own license, which you can find in LICENSE.
To install gatr with the required patches please run
conda activate gafl
bash install_gatr.sh
After installing the requirements from environment.yaml and applying the patches to gatr, you can install the gafl package by running
pip install -e .To sample backbone structures using the model (without the re-folding procedure, which is implemented e.g. in FrameDiff), run
python experiments/inference.py inference.ckpt_path=<path/to/ckpt>The weights of the models reported in the paper will be made available in the future
To train the model on the scope dataset, paste the path to your metadata csv file in configs/data/default.yaml and run
python experiments/train.py model=gaflFor training on pdb, set paths to the metadata csv file and to the cluster-defining file (as in FrameDiff) in configs/data/pdb.yaml and run
python experiments/train.py model=gafl data=pdbThe datasets reported in the paper will be made available in the future