Installation Guide

Using the Apptainer Image

If possible, we highly recommend using the provided apptainer image which can be obtained via:

curl -O https://files.ipd.uw.edu/pub/2025_RFDpoly/SE3nv.sif

Here is an example for how to use this image to run RFDpoly:

apptainer run --nv /path/to/SE3nv.sif /path/to/RFDpoly/rf_diffusion/run_inference.py --config-name=multi_polymer \
diffuser.T=50 \
inference.ckpt_path=/path/to/train_session2024-07-08_1720455712_BFF_3.00.pt \
inference.num_designs=1 \
contigmap.contigs=[\'33\ 33\ 75\'] \
contigmap.polymer_chains=[\'dna\',\'rna\',\'protein\'] \
inference.output_prefix=/path/to/your/output/directory/basic_uncond_test01

If you see an error when attempting to run this related to a lack of an input file, try adding this option:

inference.input_pdb=/path/to/RFDpoly/rf_diffusion/test_data/DBP035.pdb

Creating a Conda Environment

Linux:

If the apptainer image is not compatible with your system or you are doing development with RFDpoly, you can create a conda or mamba environment with a provided environment.yml file:

conda env create -f /path/to/RFDpoly/rf_diffusion/environment/environment.yml
conda activate RFDpoly_env
pip install /path/to/RFDpoly/rf_diffusion/RF2-allatom/rf2aa/SE3Transformer

The last command installs a slightly modified version of se3-transformer. If installing this package does not work, you can try installing se3-transformer-pytorch instead, but we do not guarantee that your results will be exactly the same.

You can test your installation by running:

python /path/to/RFDpoly/rf_diffusion/run_inference.py \
--config-name=multi_polymer \
diffuser.T=50 \
inference.ckpt_path=/path/to/RFDpoly/weights/train_session2024-07-08_1720455712_BFF_3.00.pt \
inference.num_designs=1 \
contigmap.contigs=[\'33\ 33\ 75\'] \
contigmap.polymer_chains=[\'dna\',\'rna\',\'protein\'] \
inference.output_prefix=./basic_uncond_test01

If using the environment.yml file does not work, please create an issue. Or, if you modified the .yml file to work for your system, make a pull request to add it to the rf_diffusion/environment folder.

MacOS

If the apptainer image is not compatible with your system or you are doing development with RFDpoly, you can create a conda or mamba environment with a provided macos_environment.yml file:

conda env create -f /path/to/RFDpoly/rf_diffusion/environment/macos_environment.yml
conda activate RFDpoly_env
pip install /path/to/RFDpoly/rf_diffusion/RF2-allatom/rf2aa/SE3Transformer

The last command installs a slightly modified version of se3-transformer. If installing this package does not work, you can try installing se3-transformer-pytorch instead, but we do not guarantee that your results will be exactly the same.

You can test your installation by running:

python /path/to/RFDpoly/rf_diffusion/run_inference.py \
--config-name=multi_polymer \
diffuser.T=50 \
inference.ckpt_path=/path/to/RFDpoly/weights/train_session2024-07-08_1720455712_BFF_3.00.pt \
inference.num_designs=1 \
contigmap.contigs=[\'33\ 33\ 75\'] \
contigmap.polymer_chains=[\'dna\',\'rna\',\'protein\'] \
inference.output_prefix=./basic_uncond_test01

If using the macos_environment.yml file does not work, please create an issue. Or, if you modified the .yml file to work for your system, make a pull request to add it to the rf_diffusion/environment folder.