rosettacommons/foundry repository overview

⁠Official image for Foundry⁠

This image is maintained by Rosetta Commons⁠ staff members.

Foundry houses a variety of machine learning models for protein design, see the repository README⁠ for a full list of available models. Foundry is fully open-source under a BSD-3-Clause License whose full text can be found here⁠.

This image is not compatible with systems using the ARM architecture.

For more information on Foundry or the models it contains, see the documentation here⁠.

⁠Example Syntax

⁠RFdiffusion3 Example:

docker run -it --rm \
-v "$PWD:/work" \
-w /work \
rosettacommons/foundry rfd3 \
out_dir=rfd3_out1/ \
inputs=./rfd3.json \
ckpt_path=/app/foundry/checkpoints/rfd3_latest.ckpt \

You can find more information about the options that can be listed in the JSON file and as command line arguments here⁠.

⁠MPNN Example:

docker run -it --rm \
-v "$PWD:/work" \
-w /work \
rosettacommons/foundry mpnn \
--structure_path /PATH/TO/structure.cif \
--checkpoint_path /app/foundry/checkpoints/ligandmpnn_v_32_010_25.pt \
--is_legacy_weights True \
--model_type ligand_mpnn

You can learn more about foundry's MPNN model here⁠.

⁠RoseTTAFold3 Example:

docker run -it --rm \
-v "$PWD:/work" \
-w /work \
rosettacommons/foundry rf3 fold \
inputs=/PATH/TO/structure.cif \
ckpt_path=/app/foundry/checkpoints/rf3_foundry_01_24_latest_remapped.ckpt

You can learn more about RoseTTAFold3 here⁠.

⁠Running this Image using Apptainer (or Singularity)

Run the following command to obtain the image file:

apptainer pull foundry.sif docker://rosettacommons/foundry

The syntax for using this image with Apptainer is similar to the above, simply replace the first four lines of any of the above examples with:

apptainer exec --nv
foundry.sif <model command>

⁠Tags

⁠Slim

The default image creates containers that have the weights for the various foundry models pre-installed. If you already have these weights on your system, you can use the image with the slim tag instead. The command to get the latest version of this image is:

docker pull rosettacommons/foundry:slim

To use the syntax examples with this tag, you will need to mount the directory that contains the weights on your system. Replace the first four lines of each of the example commands with:

docker run --user "$(id -u):$(id -g)" \
-v /path/to/your/weights:/weights \
-v /path/to/your/working/directory:/w \
rosettacommons/foundry:slim <model_name>

If you would like to download the weights to your system via the Foundry image, use this command:

sh -c 'docker run --user "$(id -u):$(id -g)" \
-v /path/to/where/you/want/the/weights/downloaded:/weights \
-v /path/to/your/working/directory:/w \
rrosettacommons/foundry:slim \
foundry install base-models --checkpoint-dir /weights'

If you are downloading the weights using Apptainer (or Singularity) you will need to create a local (empty) foundry.env file and bind it:

sh -c 'apptainer exec --nv \
--bind /path/to/local/foundry.env:/app/foundry/.env \
--bind -v /path/to/where/you/want/the/weights/downloaded:/weights \
foundry.sif \
foundry install base-model --checkpoint-dir /weights`

Please contact us with any questions, feedback, or issues you have concerning these containers here⁠.