ProteinMPNN/examples/submit_example_6.sh

#!/bin/bash
#SBATCH -p gpu
#SBATCH --mem=32g
#SBATCH --gres=gpu:rtx2080:1
#SBATCH -c 3
#SBATCH --output=example_6.out

source activate mlfold

folder_with_pdbs="../inputs/PDB_homooligomers/pdbs/"

output_dir="../outputs/example_6_outputs"
if [ ! -d $output_dir ]
then
    mkdir -p $output_dir
fi


path_for_parsed_chains=$output_dir"/parsed_pdbs.jsonl"
path_for_tied_positions=$output_dir"/tied_pdbs.jsonl"
path_for_designed_sequences=$output_dir"/temp_0.1"

python ../helper_scripts/parse_multiple_chains.py --input_path=$folder_with_pdbs --output_path=$path_for_parsed_chains

python ../helper_scripts/make_tied_positions_dict.py --input_path=$path_for_parsed_chains --output_path=$path_for_tied_positions --homooligomer 1

python ../protein_mpnn_run.py \
        --jsonl_path $path_for_parsed_chains \
        --tied_positions_jsonl $path_for_tied_positions \
        --out_folder $output_dir \
        --num_seq_per_target 2 \
        --sampling_temp "0.2" \
        --seed 37 \
        --batch_size 1