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| #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 | |