#!/usr/bin/env bash
set -euo pipefail

ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/../../.." && pwd)"
export PYTHONPATH="${ROOT_DIR}/model:${PYTHONPATH:-}"

FASTA_DIR="${ROOT_DIR}/data/demo/monomer/fasta_dir"
OUTPUT_DIR="${ROOT_DIR}/outputs/demo_monomer"
PRECOMPUTED_ALIGNMENT_DIR="${ROOT_DIR}/data/demo/monomer/alignments"
TEMPLATE_MMCIF_DIR="${TEMPLATE_MMCIF_DIR:-${ROOT_DIR}/data/databases/pdb_mmcif/mmcif_files}"
CHECKPOINT_PATH="${CHECKPOINT_PATH:-${ROOT_DIR}/weight/openfold.pt}"

python "${ROOT_DIR}/scripts/inference.py" "${FASTA_DIR}" "${TEMPLATE_MMCIF_DIR}" \
  --output_dir "${OUTPUT_DIR}" \
  --config_preset model_1_ptm \
  --model_device "${MODEL_DEVICE:-cuda:0}" \
  --data_random_seed 42 \
  --use_precomputed_alignments "${PRECOMPUTED_ALIGNMENT_DIR}" \
  --openfold_checkpoint_path "${CHECKPOINT_PATH}" \
  --skip_relaxation