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Running
on
T4
File size: 989 Bytes
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#!/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="../PDB_homooligomers/pdbs/"
output_dir="../PDB_homooligomers/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" \
--batch_size 1
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