Official containers for RosettaCommons ProteinMPNN protocol
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This image is built from the ProteinMPNNrepository
ProteinMPNN is fully open-source under an MIT License whose full text can be found here.
Please note that this image is not compatible with systems using the ARM architecture.
docker run -it --rm \
-v /path/to/your/input_dir:/input \
-v /path/to/your/output_dir:/output \
rosettacommons/proteinmpnn \
--pdb_path /input/3HTN.pdb \
--pdb_path_chains "A B" \
--out_folder /output
Please see below for an example of running a helper scripts from ProteinMPNN.
docker run -it --rm \
--entrypoint python \
-v /path/to/your/input_dir:/input \
-v /path/to/your/output_dir:/output \
rosettacommons/proteinmpnn \
/app/proteinmpnn/helper_scripts/parse_multiple_chains.py \
--input_path=/input/PDB_monomers/pdbs/ \
--output_path=/output/parsed_pdbs.jsonl
The instructions below use Apptainer, but the same commands will work with Singularity.
To run the image using Apptainer you need to pull it using
apptainer pull proteinmpnn.sif docker://rosettacommons/proteinmpnn
Then you can use it very similarly to the Docker example above:
apptainer run --nv \
proteinmpnn.sif \
--pdb_path /path/to/your/input_dir/1BC8.pdb \
--pdb_path_chains "A B" \
--out_folder /path/to/your/output_dir"
Please see the below example for running one of the helper scripts from ProteinMPNN with apptainer.
apptainer exec \
proteinmpnn.sif \
python /app/proteinmpnn/helper_scripts/parse_multiple_chains.py \
--input_path=/path/to/your/input_dir/PDB_monomers/pdbs/ \
--output_path=./parsed_pdbs.jsonl
Please contact us with any questions, feedback, or issues you have concerning these containers here.
Content type
Image
Digest
sha256:de4960fed…
Size
2.9 GB
Last updated
about 1 year ago
docker pull rosettacommons/proteinmpnn