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MPNN
- Dominant language
- Python
- Stars
- 966
- Forks
- 181
- Avg merge
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- Merged PRs (30d)
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Description
Hi
I am getting this error when trying mpnn sequence design.
Environment variable PDB_MIRROR_PATH not set. Will not be able to use function requiring this variable.
Is this something to worry about? I am using following script as suggested in #121 to run mpnn -
PDB_DIR_PATH="./renamed/"
cif_files=($PDB_DIR_PATH/*.cif)
for file in "${cif_files[@]}"; do
mpnn --model_type "protein_mpnn" \
--structure_path "$file" \
--out_directory MPNN \
--batch_size 2 \
--number_of_batches 1 \
--omit '["CYS"]' \
--is_legacy_weights "True" \
--checkpoint_path "/opt/checkpoints/solublempnn_v_48_020.pt"
done
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating the code that checks PDB_MIRROR_PATH and trace whether the shown mpnn command requires it for structure_path inputs. Confirm the expected behavior for this script and document or reproduce the required configuration so the warning's impact is clear.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- machine-learning
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100