Why "--homooligomer 1" is used in the submit_example_6.sh of ProteinMPNN for homo-dimer and homo-trimer proteins?

[lanselibai]

The submit_example_6.sh of ProteinMPNN designs homo-dimer and homo-trimer proteins
https://github.com/dauparas/ProteinMPNN/blob/main/examples/submit_example_6.sh

What is the meaning of --homooligomer 1?

Similarly, "--homo_oligomer 1" is used in the LigandMPNN. What is the meaning of "1" here?
https://github.com/dauparas/LigandMPNN?tab=readme-ov-file

python run.py \
        --model_type "ligand_mpnn" \
        --seed 111 \
        --pdb_path "./inputs/4GYT.pdb" \
        --out_folder "./outputs/homooligomer" \
        --homo_oligomer 1 \
        --number_of_batches 2

[roccomoretti]

Given that it's specific to ProteinMPNN/LigandMPNN instead of the Rosetta package per se, it's best to open such discussion questions on one of those repos.

That said, it's very common (in Rosetta as well) to represent true/false values as 1/0. Many programming languages and tools make parsing 0 & 1 into true and false easier than parsing strings like "true" and "false".

--homo_oligomer 1 should be read like --homo_oligomer true (though actually putting true may or may not work.)

[lanselibai]

Thank you very much! So I think, whatever the homooligomer is dimer, trimer, the software will consider all the chains as identical if --homo_oligomer 1 is used.

Where are the dedicated repos for Protein/LigandMPNN?