scripts/slurm_prepare_500k_dataset.sh

#!/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"