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9d6a2a3 | 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 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 | #!/usr/bin/env bash
set -euo pipefail
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
ROOT_DIR="$(cd "${SCRIPT_DIR}/../../.." && pwd)"
cd "${ROOT_DIR}"
if [[ -n "${ROCM_PATH:-}" && -f "${ROCM_PATH}/cuda/env.sh" ]]; then
source "${ROCM_PATH}/cuda/env.sh"
fi
source "${ROOT_DIR}/env.sh"
export PYTHONPATH="${ROOT_DIR}/src:${PYTHONPATH:-}"
if [[ -n "${CONDA_PREFIX:-}" ]]; then
export LD_LIBRARY_PATH="${CONDA_PREFIX}/lib:${CONDA_PREFIX}/lib/python3.11/site-packages/torch/lib:${CONDA_PREFIX}/lib/python3.11/site-packages/fastpt/torch/lib:${LD_LIBRARY_PATH:-}"
fi
if [[ -n "${ROCM_PATH:-}" && -d "${ROCM_PATH}/opencl/lib" ]]; then
export LD_LIBRARY_PATH="${ROCM_PATH}/opencl/lib:${LD_LIBRARY_PATH:-}"
fi
TASK="${1:-all}"
GENSCORE_DIR="$(cd "${SCRIPT_DIR}/.." && pwd)"
BENCHMARK_DIR="${GENSCORE_DIR}/benchmarks"
MODEL_PATH="${MODEL_PATH:-${ONESCIENCE_DATASETS_DIR}/GenScore/trained_models/GatedGCN_ft_1.0_1.pth}"
OUT_ROOT="${OUT_ROOT:-${GENSCORE_DIR}/benchmark_outputs}"
GENSCORE_DATA_ROOT="${GENSCORE_DATA_ROOT:-${ONESCIENCE_DATASETS_DIR}/GenScore/genscore_data}"
CASF_DIR="${CASF_DIR:-${GENSCORE_DATA_ROOT}/CASF-2016}"
PDBBIND_DIR="${PDBBIND_DIR:-${GENSCORE_DATA_ROOT}/PDBbind_v2020}"
PDBBIND_NATIVE_LIGAND_DIR="${PDBBIND_NATIVE_LIGAND_DIR:-${PDBBIND_DIR}/mol2}"
PDBBIND_REFINED_SUBDIR="${PDBBIND_REFINED_SUBDIR:-refined-set}"
PDBBIND_OTHER_PL_SUBDIR="${PDBBIND_OTHER_PL_SUBDIR:-v2020-other-PL}"
CASF_PREPROCESSED_DIR="${CASF_PREPROCESSED_DIR:-${GENSCORE_DATA_ROOT}/rtmscore_s}"
CASF_TEST_PREFIX="${CASF_TEST_PREFIX:-v2020_casf}"
CASF_CORESET_FILE="${CASF_CORESET_FILE:-${CASF_PREPROCESSED_DIR}/v2020_casf_coreset.csv}"
ENCODER="${ENCODER:-gatedgcn}"
CUTOFF="${CUTOFF:-10.0}"
BATCH_SIZE="${BATCH_SIZE:-128}"
NUM_WORKERS="${NUM_WORKERS:-0}"
OUTPREFIX="${OUTPREFIX:-gatedgcn1x5}"
require_dir() {
local name="$1"
local path="$2"
if [[ ! -d "${path}" ]]; then
echo "Missing required directory ${name}: ${path}" >&2
exit 1
fi
}
require_file() {
local name="$1"
local path="$2"
if [[ ! -f "${path}" ]]; then
echo "Missing required file ${name}: ${path}" >&2
exit 1
fi
}
run_scoring_ranking() {
require_dir "CASF_PREPROCESSED_DIR" "${CASF_PREPROCESSED_DIR}"
require_file "CASF_CORESET_FILE" "${CASF_CORESET_FILE}"
require_file "MODEL_PATH" "${MODEL_PATH}"
echo "[run] CASF-2016 scoring/ranking"
python "${BENCHMARK_DIR}/casf2016_scoring_ranking.py" \
--data-dir "${CASF_PREPROCESSED_DIR}" \
--test-prefix "${CASF_TEST_PREFIX}" \
--coreset-file "${CASF_CORESET_FILE}" \
--model-path "${MODEL_PATH}" \
--encoder "${ENCODER}" \
--cutoff "${CUTOFF}" \
--batch-size "${BATCH_SIZE}" \
--num-workers "${NUM_WORKERS}" \
--outprefix "${OUTPREFIX}" \
--outdir "${OUT_ROOT}/power_ranking/examples"
echo "[done] CASF-2016 scoring/ranking"
}
run_docking() {
require_dir "CASF_DIR" "${CASF_DIR}"
require_dir "PDBBIND_DIR" "${PDBBIND_DIR}"
require_dir "PDBBIND_NATIVE_LIGAND_DIR" "${PDBBIND_NATIVE_LIGAND_DIR}"
require_dir "PDBbind refined subset" "${PDBBIND_DIR}/${PDBBIND_REFINED_SUBDIR}"
require_dir "PDBbind other-PL subset" "${PDBBIND_DIR}/${PDBBIND_OTHER_PL_SUBDIR}"
require_file "MODEL_PATH" "${MODEL_PATH}"
echo "[run] CASF-2016 docking"
python "${BENCHMARK_DIR}/casf2016_docking.py" \
--casf-dir "${CASF_DIR}" \
--pdbbind-dir "${PDBBIND_DIR}" \
--native-ligand-dir "${PDBBIND_NATIVE_LIGAND_DIR}" \
--refined-subdir "${PDBBIND_REFINED_SUBDIR}" \
--other-pl-subdir "${PDBBIND_OTHER_PL_SUBDIR}" \
--model-path "${MODEL_PATH}" \
--encoder "${ENCODER}" \
--cutoff "${CUTOFF}" \
--batch-size "${BATCH_SIZE}" \
--num-workers "${NUM_WORKERS}" \
--outprefix "${OUTPREFIX}" \
--outdir "${OUT_ROOT}/power_docking/examples/${OUTPREFIX}"
echo "[done] CASF-2016 docking"
}
run_screening() {
require_dir "CASF_DIR" "${CASF_DIR}"
require_dir "PDBBIND_DIR" "${PDBBIND_DIR}"
require_dir "PDBbind refined subset" "${PDBBIND_DIR}/${PDBBIND_REFINED_SUBDIR}"
require_dir "PDBbind other-PL subset" "${PDBBIND_DIR}/${PDBBIND_OTHER_PL_SUBDIR}"
require_file "MODEL_PATH" "${MODEL_PATH}"
echo "[run] CASF-2016 screening"
python "${BENCHMARK_DIR}/casf2016_screening.py" \
--casf-dir "${CASF_DIR}" \
--pdbbind-dir "${PDBBIND_DIR}" \
--refined-subdir "${PDBBIND_REFINED_SUBDIR}" \
--other-pl-subdir "${PDBBIND_OTHER_PL_SUBDIR}" \
--model-path "${MODEL_PATH}" \
--encoder "${ENCODER}" \
--cutoff "${CUTOFF}" \
--batch-size "${BATCH_SIZE}" \
--num-workers "${NUM_WORKERS}" \
--outprefix "${OUTPREFIX}" \
--outdir "${OUT_ROOT}/power_screening/examples/${OUTPREFIX}"
echo "[done] CASF-2016 screening"
}
case "${TASK}" in
scoring|scoring_ranking)
run_scoring_ranking
;;
docking)
run_docking
;;
screening)
run_screening
;;
all)
run_scoring_ranking
run_docking
run_screening
;;
*)
echo "Usage: $0 [scoring|docking|screening|all]" >&2
exit 1
;;
esac
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