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| #SBATCH -p gpu | |
| #SBATCH --mem=32g | |
| #SBATCH --gres=gpu:rtx2080:1 | |
| #SBATCH -c 3 | |
| #SBATCH --output=example_4_non_fixed.out | |
| source activate mlfold | |
| folder_with_pdbs="../inputs/PDB_complexes/pdbs/" | |
| output_dir="../outputs/example_4_non_fixed_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" | |
| chains_to_design="A C" | |
| #The first amino acid in the chain corresponds to 1 and not PDB residues index for now. | |
| design_only_positions="1 2 3 4 5 6 7 8 9 10, 3 4 5 6 7 8" #design only these residues; use flag --specify_non_fixed | |
| 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 "$design_only_positions" --specify_non_fixed | |
| 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 \ | |
| --out_folder $output_dir \ | |
| --num_seq_per_target 2 \ | |
| --sampling_temp "0.1" \ | |
| --seed 37 \ | |
| --batch_size 1 | |