Spaces:
Running
on
T4
Running
on
T4
| #SBATCH -p gpu | |
| #SBATCH --mem=32g | |
| #SBATCH --gres=gpu:rtx2080:1 | |
| #SBATCH -c 3 | |
| #SBATCH --output=example_5.out | |
| source activate mlfold | |
| folder_with_pdbs="../PDB_complexes/pdbs/" | |
| output_dir="../PDB_complexes/example_5_outputs" | |
| if [ ! -d $output_dir ] | |
| then | |
| mkdir -p $output_dir | |
| fi | |
| path_for_parsed_chains=$output_dir"/parsed_pdbs.jsonl" | |
| path_for_assigned_chains=$output_dir"/assigned_pdbs.jsonl" | |
| path_for_fixed_positions=$output_dir"/fixed_pdbs.jsonl" | |
| path_for_tied_positions=$output_dir"/tied_pdbs.jsonl" | |
| chains_to_design="A C" | |
| fixed_positions="9 10 11 12 13 14 15 16 17 18 19 20 21 22 23, 10 11 18 19 20 22" | |
| tied_positions="1 2 3 4 5 6 7 8, 1 2 3 4 5 6 7 8" #two list must match in length; residue 1 in chain A and C will be sampled togther; | |
| python ../helper_scripts/parse_multiple_chains.py --input_path=$folder_with_pdbs --output_path=$path_for_parsed_chains | |
| python ../helper_scripts/assign_fixed_chains.py --input_path=$path_for_parsed_chains --output_path=$path_for_assigned_chains --chain_list "$chains_to_design" | |
| python ../helper_scripts/make_fixed_positions_dict.py --input_path=$path_for_parsed_chains --output_path=$path_for_fixed_positions --chain_list "$chains_to_design" --position_list "$fixed_positions" | |
| python ../helper_scripts/make_tied_positions_dict.py --input_path=$path_for_parsed_chains --output_path=$path_for_tied_positions --chain_list "$chains_to_design" --position_list "$tied_positions" | |
| python ../protein_mpnn_run.py \ | |
| --jsonl_path $path_for_parsed_chains \ | |
| --chain_id_jsonl $path_for_assigned_chains \ | |
| --fixed_positions_jsonl $path_for_fixed_positions \ | |
| --tied_positions_jsonl $path_for_tied_positions \ | |
| --out_folder $output_dir \ | |
| --num_seq_per_target 2 \ | |
| --sampling_temp "0.1" \ | |
| --batch_size 1 | |