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40e5504 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 | #!/usr/bin/env bash
set -euo pipefail
# Run this script inside an already prepared GPU environment/node.
# It does not request a compute node.
cd /public/home/scnb9biwet/jiangqq/GPSite-main
GPU_ID="${1:-0}"
INPUT_FASTA="${2:-./conf/example/demo.fa}"
OUT_DIR="${3:-./results/}"
PROTTRANS_DIR="/path/to/prot_t5_xl_uniref50"
ESMFOLD_HUB_DIR="/path/to/weight"
ESMFOLD_WEIGHT="${ESMFOLD_HUB_DIR}/checkpoints/esmfold_3B_v1.pt"
ESM2_WEIGHT="${ESMFOLD_HUB_DIR}/checkpoints/esm2_t36_3B_UR50D.pt"
if [ ! -d "${PROTTRANS_DIR}" ]; then
echo "ERROR: ProtTrans directory not found: ${PROTTRANS_DIR}" >&2
exit 1
fi
if [ ! -f "${ESMFOLD_WEIGHT}" ]; then
echo "ERROR: ESMFold weight not found: ${ESMFOLD_WEIGHT}" >&2
exit 1
fi
if [ ! -f "${ESM2_WEIGHT}" ]; then
echo "ERROR: ESM2 weight not found: ${ESM2_WEIGHT}" >&2
exit 1
fi
if [ ! -f "${INPUT_FASTA}" ]; then
echo "ERROR: input FASTA not found: ${INPUT_FASTA}" >&2
exit 1
fi
chmod +x ./scripts/feature_extraction/mkdssp
export PROTTRANS_PATH="${PROTTRANS_DIR}"
export ESMFOLD_HUB_DIR="${ESMFOLD_HUB_DIR}"
echo "Using GPU: ${GPU_ID}"
echo "Input FASTA: ${INPUT_FASTA}"
echo "Output directory: ${OUT_DIR}"
echo "ProtTrans: ${PROTTRANS_DIR}"
echo "ESMFold hub dir: ${ESMFOLD_HUB_DIR}"
python ./scripts/predict.py \
-i "${INPUT_FASTA}" \
-o "${OUT_DIR}" \
--gpu "${GPU_ID}"
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