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504d922 | 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 | #!/usr/bin/env bash
#SBATCH --job-name=prepare_500k_dataset
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=80
#SBATCH --mem=0
#SBATCH --time=48:00:00
set -euo pipefail
source ~/.bashrc
conda activate portable-rdock-pipeline
export PDB_ID=${PDB_ID:-1IEP}
export RECEPTOR_CHAIN=${RECEPTOR_CHAIN:-A}
export REF_LIGAND=${REF_LIGAND:-STI}
export REF_CHAIN=${REF_CHAIN:-A}
export DATASET_DIR=${DATASET_DIR:-$SCRATCH/plgproma/data/rdock_${PDB_ID}_pubchem_500k}
python scripts/prepare_pdb_ligand_dataset.py \
--pdb-id "$PDB_ID" \
--receptor-chain "$RECEPTOR_CHAIN" \
--reference-ligand-resname "$REF_LIGAND" \
--reference-ligand-chain "$REF_CHAIN" \
--n-ligands 500000 \
--ligand-source pubchem_similarity \
--pubchem-threshold-ladder 99,95,90,85,80,75,70,65,60,55,50,45,40,35,30 \
--allow-partial-ligand-set \
--ligand-batch-size 100 \
--ligand-jobs 60 \
--ligand-cpu-fraction 0.85 \
--out "$DATASET_DIR" \
--force | tee "${DATASET_DIR}.prepare.log"
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