#!/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=$output_dir"/bias_pdbs.jsonl"
#Adding global polar amino acid bias (Doug Tischer)
AA_list="D E H K N Q R S T W Y"
bias_list="1.39 1.39 1.39 1.39 1.39 1.39 1.39 1.39 1.39 1.39 1.39"
python "${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"