| #!/bin/bash |
|
|
| SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" |
| PROJECT_ROOT="$(cd "${SCRIPT_DIR}/../.." && pwd)" |
| ONESCIENCE_ROOT="${ONESCIENCE_ROOT:-$(cd "${PROJECT_ROOT}/.." && pwd)}" |
| export PYTHONPATH="${PROJECT_ROOT}/model:${ONESCIENCE_ROOT}/src:${PYTHONPATH:-}" |
|
|
| folder_with_pdbs="${PROJECT_ROOT}/data/inputs/PDB_monomers/pdbs/" |
|
|
| output_dir="${PROJECT_ROOT}/outputs/example_8_outputs" |
| if [ ! -d "$output_dir" ] |
| then |
| mkdir -p "$output_dir" |
| fi |
|
|
| path_for_bias=$output_dir"/bias_pdbs.jsonl" |
| |
| AA_list="D E H K N Q R S T W Y" |
| bias_list="1.39 1.39 1.39 1.39 1.39 1.39 1.39 1.39 1.39 1.39 1.39" |
| python "${PROJECT_ROOT}/scripts/helper_scripts/make_bias_AA.py" --output_path="$path_for_bias" --AA_list="$AA_list" --bias_list="$bias_list" |
|
|
| path_for_parsed_chains=$output_dir"/parsed_pdbs.jsonl" |
| python "${PROJECT_ROOT}/scripts/helper_scripts/parse_multiple_chains.py" --input_path="$folder_with_pdbs" --output_path="$path_for_parsed_chains" |
|
|
| python "${PROJECT_ROOT}/scripts/inference.py" \ |
| --jsonl_path "$path_for_parsed_chains" \ |
| --out_folder "$output_dir" \ |
| --bias_AA_jsonl "$path_for_bias" \ |
| --num_seq_per_target 2 \ |
| --sampling_temp "0.1" \ |
| --seed 37 \ |
| --batch_size 1 \ |
| --path_to_model_weights "${PROJECT_ROOT}/weight/vanilla_model_weights" |
|
|
